From 1e028c2eea21ff5f7277a21019bc8047ee84014d Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 00:35:33 +0100
Subject: [PATCH 01/89] update foramecogem: ecogem_data.f90
---
genie-ecogem/src/fortran/ecogem_data.f90 | 245 ++++++++++++++++++++---
1 file changed, 222 insertions(+), 23 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index cc795b953..96376427b 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -396,6 +396,34 @@ SUBROUTINE sub_init_plankton()
silicify(jp) = 0.0
autotrophy(jp) = 0.0
heterotrophy(jp) = 1.0
+ elseif (pft(jp).eq.'foram_bn') then
+ NO3up(jp) = 0.0
+ Nfix(jp) = 0.0
+ calcify(jp) = 0.0
+ silicify(jp) = 0.0
+ autotrophy(jp) = 0.0
+ heterotrophy(jp) = 1.0
+ elseif (pft(jp).eq.'foram_bn') then
+ NO3up(jp) = 0.0
+ Nfix(jp) = 0.0
+ calcify(jp) = 0.0
+ silicify(jp) = 0.0
+ autotrophy(jp) = 0.0
+ heterotrophy(jp) = 1.0
+ elseif (pft(jp).eq.'foram_bn') then
+ NO3up(jp) = 0.0
+ Nfix(jp) = 0.0
+ calcify(jp) = 0.0
+ silicify(jp) = 0.0
+ autotrophy(jp) = 0.0
+ heterotrophy(jp) = 1.0
+ elseif (pft(jp).eq.'foram_ss') then
+ NO3up(jp) = 0.0
+ Nfix(jp) = 0.0
+ calcify(jp) = 0.0
+ silicify(jp) = 0.0
+ autotrophy(jp) = 0.0
+ heterotrophy(jp) = 1.0
else
print*," "
print*,"! ERROR !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
@@ -407,6 +435,7 @@ SUBROUTINE sub_init_plankton()
endif
enddo
+
! initialise plankton parameters
qmin(:,:) = 0.0
qmax(:,:) = 0.0
@@ -423,6 +452,28 @@ SUBROUTINE sub_init_plankton()
biosink(:) = 0.0
mort(:) = 0.0
+ ! initialise foram parameters
+ if (ctrl_use_foramecogenie) then
+ symbiont_esd_scale(:) = 1.0
+ grazing_esd_scale(:) = 1.0
+ symbiont_auto_cost(:) = 1.0
+ symbiont_hetero_cost(:) = 1.0
+
+ ! modify for foraminifera only
+ if (pft(jp).eq.'foram_bs') then
+ grazing_esd_scale(:) = foram_grazing_scale_bs
+ elseif (pft(jp).eq.'foram_sn') then
+ symbiont_esd_scale(:) = foram_symbiont_esd_scale
+ symbiont_auto_cost(:) = foram_auto_cost_sn
+ symbiont_hetero_cost(:) = foram_hetero_cost_sn
+ elseif (pft(jp).eq.'foram_ss') then
+ symbiont_esd_scale(:) = foram_symbiont_esd_scale
+ symbiont_auto_cost(:) = foram_auto_cost_ss
+ symbiont_hetero_cost(:) = foram_hetero_cost_ss
+ grazing_esd_scale(:) = foram_grazing_scale_ss
+ endif
+ endif
+
!-----------------------------------------------------------------------------------------
! populate array like in wardetal.2018
if(ctrl_grazing_explicit.eqv..false.)then
@@ -438,6 +489,116 @@ SUBROUTINE sub_init_plankton()
! set growth costs (could do the same for autotrophy in coccolithophores) - Fanny Mar21
heterotrophy(:) = heterotrophy(:)*growthcost_factor(:)
+ ! overwrite the plankton PFT parameters
+ if(ctrl_use_foramecogenie)then
+ ! v1/v2 = (r1/r2)^3
+ auto_volume(:) = volume(:) * symbiont_esd_scale(:) ** 3
+ hetero_volume(:) = volume(:) * grazing_esd_scale(:) ** 3
+
+ ! vmax photosynthesis rate
+ vmax(iDIC,:) = vmax(iDIC,:) = (vmaxDIC_a + log10(auto_volume(:))) / (vmaxDIC_b + vmaxDIC_c * log10(auto_volume(:)) + log10(auto_volume(:))**2) &
+ & * autotrophy(:) * symbiont_auto_cost(:)
+ !-----------------------------------------------------------------------------------------
+ ! maximum photosynthetic rate
+ ! vmax(iDIC,:) = vmaxDIC_a * volume(:) ** vmaxDIC_b * autotrophy(:)
+ vmax(iDIC,:) = (vmaxDIC_a + log10(auto_volume(:))) / (vmaxDIC_b + vmaxDIC_c * log10(auto_volume(:)) + log10(auto_volume(:))**2) &
+ & * autotrophy(:)
+ !-----------------------------------------------------------------------------------------
+ if (nquota) then ! nitrogen parameters
+ qmin(iNitr,:) = qminN_a * auto_volume(:) ** qminN_b
+ qmax(iNitr,:) = qmaxN_a * auto_volume(:) ** qmaxN_b
+ if (maxval((qmin(iNitr,:)/qmax(iNitr,:))).gt.1.0) print*,"WARNING: Nitrogen Qmin > Qmax. Population inviable!"
+ if (useNO3) then ! nitrate parameters
+ vmax(iNO3,:) = vmaxNO3_a * auto_volume(:) ** vmaxNO3_b * autotrophy(:) * NO3up(:)
+ affinity(iNO3,:) = affinNO3_a * auto_volume(:) ** affinNO3_b * autotrophy(:) * NO3up(:)
+ endif
+ if (useNO2) then ! nitrite parameters
+ vmax(iNO2,:) = vmaxNO2_a * auto_volume(:) ** vmaxNO2_b * autotrophy(:)
+ affinity(iNO2,:) = affinNO2_a * auto_volume(:) ** affinNO2_b * autotrophy(:)
+ endif
+ if (useNH4) then ! ammonium parameters
+ vmax(iNH4,:) = vmaxNH4_a * auto_volume(:) ** vmaxNH4_b * autotrophy(:)
+ affinity(iNH4,:) = affinNH4_a * auto_volume(:) ** affinNH4_b * autotrophy(:)
+ endif
+ kexc(iNitr,:) = kexcN_a * volume(:) ** kexcN_b
+
+ ! mumax(iNitr,:) = vmax(iDIC,:)*vmax(iNO3,:) &
+ ! & /(vmax(iDIC,:)*Qmin(iNitr,:) + vmax(iNO3,:)*qmax(iNitr,:)/(qmax(iNitr,:)-qmin(iNitr,:)))
+ ! alpha(iNitr,:) = affinity(iNitr,:)/Qmin(iNitr,:)
+ endif
+ !-----------------------------------------------------------------------------------------
+ if (pquota) then ! phosphorus parameters
+ qmin(iPhos,:) = qminP_a * auto_volume(:) ** qminP_b
+ qmax(iPhos,:) = qmaxP_a * auto_volume(:) ** qmaxP_b
+ if (maxval((qmin(iPhos,:)/qmax(iPhos,:))).gt.1.0) print*,"WARNING: Phosphate Qmin > Qmax. Population inviable!"
+ vmax(iPO4,:) = vmaxPO4_a * auto_volume(:) ** vmaxPO4_b * autotrophy(:)
+ affinity(iPO4,:) = affinPO4_a * auto_volume(:) ** affinPO4_b * autotrophy(:)
+ kexc(iPhos,:) = kexcP_a * volume(:) ** kexcP_b
+ endif
+ !-----------------------------------------------------------------------------------------
+ if (fquota) then ! iron parameters
+ qmin(iIron,:) = qminFe_a * auto_volume(:) ** qminFe_b
+ qmax(iIron,:) = qmaxFe_a * auto_volume(:) ** qmaxFe_b
+ if (maxval((qmin(iIron,:)/qmax(iIron,:))).gt.1.0) print*,"WARNING: Iron Qmin > Qmax. Population inviable!"
+ vmax(iFe,:) = vmaxFe_a * auto_volume(:) ** vmaxFe_b * autotrophy(:)
+ affinity(iFe,:) = affinFe_a * auto_volume(:) ** affinFe_b * autotrophy(:)
+ kexc(iIron,:) = kexcFe_a * volume(:) ** kexcFe_b
+ endif
+ !-----------------------------------------------------------------------------------------
+ if (squota) then ! silicon parameters
+ qmin(iSili,:) = qminSi_a * auto_volume(:) ** qminSi_b * silicify(:)
+ qmax(iSili,:) = qmaxSi_a * auto_volume(:) ** qmaxSi_b * silicify(:)
+ if (maxval((qmin(iSili,:)/qmax(iSili,:))).gt.1.0) print*,"WARNING: Silicon Qmin > Qmax. Population inviable!"
+ vmax(iSiO2,:) = vmaxSiO2_a * auto_volume(:) ** vmaxSiO2_b * autotrophy(:) * silicify(:)
+ affinity(iSiO2,:) =affinSiO2_a * auto_volume(:) ** affinSiO2_b * autotrophy(:)
+ kexc(iSili,:) = kexcSi_a * auto_volume(:) ** kexcSi_b * silicify(:)
+ endif
+ !-----------------------------------------------------------------------------------------
+ ! other parameters
+ qcarbon(:) = qcarbon_a * auto_volume(:) ** qcarbon_b !seems not used
+ alphachl(:) = alphachl_a * auto_volume(:) ** alphachl_b
+ graz(:) = graz_a * hetero_volume(:) ** graz_b * heterotrophy(:)
+ kg(:) = kg_a * hetero_volume(:) ** kg_b * kg_scale(:)
+ pp_opt(:) =pp_opt_a_array * hetero_volume(:) ** pp_opt_b
+ pp_sig(:) =pp_sig_a_array * hetero_volume(:) ** pp_sig_b
+ respir(:) = respir_a * volume(:) ** respir_b + respir_cost(:)
+ biosink(:) = biosink_a * volume(:) ** biosink_b
+ mort(:) = (mort_a * volume(:) ** mort_b) * mort_protect(:) ! mort_protect added by Grigoratou, Dec2018 as a benefit for foram's calcification
+
+ ! grazing parameters
+ do jp=1,npmax ! grazing kernel (npred,nprey)
+ ! pad predator dependent pp_opt and pp_sig so that they vary along matrix columns
+ ! (they should be constant within each row)
+ ppopt_mat(:,jp)=pp_opt !added an optimal predator-prey length ratio for each plankton group, Grigoratou, Dec18
+ ppsig_mat(:,jp)=pp_sig !added an optimal standar deviation for predator-prey length ratio for each plankton group, Grigoratou, Dec18
+ enddo
+ pred_diam(:,1)=diameter(:) ! standard prey diameter vector
+ prey_diam(1,:)=diameter(:) ! transpose pred diameter vector
+ prdpry(:,:) =matmul(pred_diam,1.0/prey_diam)
+ gkernel(:,:) =exp(-log(prdpry(:,:)/ppopt_mat(:,:))**2 / (2*ppsig_mat(:,:)**2)) ! [jpred,jprey] populate whole array at once, then find exceptions to set to 0.0 based on type
+
+ do jpred=1,npmax
+ select case(pft(jpred))
+ case('foram','foram_bn','foram_bs','foram_sn','foram_ss')
+ do jprey=1,npmax
+ if(autotrophy(jprey).gt.0.0) gkernel(jpred,jprey)=gkernel(jpred,jprey) * herbivory(jpred)
+ if(heterotrophy(jprey).gt.0.0) gkernel(jpred,jprey)=gkernel(jpred,jprey) * carnivory(jpred)
+ ! foram dont eat foram, they are always brothers
+ if (index(pft(jprey), "foram") /= 0) gkernel(jpred, jprey)=0.0
+ end do
+ end select
+ end do
+
+ if (gkernel_cap) gkernel(:,:) =merge(gkernel(:,:),0.0,gkernel(:,:).gt.1e-2) ! set kernel<1e-2 to 0.0 (wardetal.2018)
+ gkernelT(:,:) =transpose(gkernel(:,:))
+
+ ! detrital partitioning
+ ! NOTE: fraction partitioned into DOM (a seperate and explicit array is created for 1-minus this -- the fraction into POM)
+ beta_graz(:) =beta_graz_a - (beta_graz_a-beta_graz_b) / (1.0+beta_mort_c/diameter(:))
+ beta_mort(:) =beta_mort_a - (beta_mort_a-beta_mort_b) / (1.0+beta_mort_c/diameter(:))
+ endif
+
+
!-----------------------------------------------------------------------------------------
! maximum photosynthetic rate
! vmax(iDIC,:) = vmaxDIC_a * volume(:) ** vmaxDIC_b * autotrophy(:)
@@ -529,7 +690,8 @@ SUBROUTINE sub_init_plankton()
! NOTE: fraction partitioned into DOM (a seperate and explicit array is created for 1-minus this -- the fraction into POM)
beta_graz(:) =beta_graz_a - (beta_graz_a-beta_graz_b) / (1.0+beta_mort_c/diameter(:))
beta_mort(:) =beta_mort_a - (beta_mort_a-beta_mort_b) / (1.0+beta_mort_c/diameter(:))
-
+
+
! ****************************************************************************************
! ****************************************************************************************
! Write plankton parameters to output file (opened in initialise_ecogem)
@@ -738,6 +900,14 @@ SUBROUTINE sub_init_explicit_grazing_params
real ::loc_palatability
real ::loc_growthcost_factor
+ if (ctrl_use_foramecogenie) then
+ ! make herbivory and carnivory not logical but range from 0 to 1
+ real ::loc_herbivory_real
+ real ::loc_carnivory_real
+ real ::loc_kg
+ real ::loc_respir
+ endif
+
! if setting plankton specific parameters
! check file format and determine number of lines of data
loc_filename = TRIM(par_indir_name)//"/"//TRIM(par_ecogem_grazing_file)
@@ -771,28 +941,57 @@ SUBROUTINE sub_init_explicit_grazing_params
DO n = 1,loc_n_start
READ(unit=in,fmt='(1X)')
END DO
- !read in population specifications
- DO n = 1,loc_n_elements
- READ(unit=in,FMT=*) &
- & loc_plnktn_pft, & ! COLUMN #01: plankton PFT (not used here)
- & loc_herbivory, & ! COLUMN #02: herbivory
- & loc_carnivory, & ! COLUMN #03: carnivory
- & loc_pp_opt_a, & ! COLUMN #04: pp_opt_a
- & loc_pp_sig_a, & ! COLUMN #05: pp_sig_a
- & loc_ns, & ! COLUMN #06: ns (prey switching)
- & loc_mort_protect, & ! COLUMN #07: mortality_protection
- & loc_palatability, & ! COLUMN #08: palatability - in development - Fanny Mar21
- & loc_growthcost_factor ! COLUMN #09: growth-cost factor - in development - Fanny Mar21
- herbivory(n) = loc_herbivory
- carnivory(n) = loc_carnivory
- pp_opt_a_array(n) = loc_pp_opt_a
- pp_sig_a_array(n) = loc_pp_sig_a
- ns_array(n) = loc_ns
- mort_protect(n) = loc_mort_protect
- palatability(n) = loc_palatability
- growthcost_factor(n) = loc_growthcost_factor
-
- END DO
+
+ if (ctrl_use_foramecogenie) then
+ !read in richer population specifications
+ DO n = 1,loc_n_elements
+ READ(unit=in,FMT=*) &
+ & loc_plnktn_pft, & ! COLUMN #01: plankton PFT (not used here)
+ & loc_herbivory, & ! COLUMN #02: herbivory
+ & loc_carnivory, & ! COLUMN #03: carnivory
+ & loc_pp_opt_a, & ! COLUMN #04: pp_opt_a
+ & loc_pp_sig_a, & ! COLUMN #05: pp_sig_a
+ & loc_ns, & ! COLUMN #06: ns (prey switching)
+ & loc_mort_protect, & ! COLUMN #07: mortality_protection
+ & loc_palatability, & ! COLUMN #08: palatability - in development - Fanny Mar21
+ & loc_growthcost_factor, & ! COLUMN #09: growth-cost factor - in development - Fanny Mar21
+ & loc_kg, & ! COLUMN #10: spine-derived kg modification Rui Oct21
+ & loc_respir ! COLUMN #11: increased respiration rate for the calcite building cost
+
+ herbivory(n) = loc_herbivory
+ carnivory(n) = loc_carnivory
+ pp_opt_a_array(n) = loc_pp_opt_a
+ pp_sig_a_array(n) = loc_pp_sig_a
+ ns_array(n) = loc_ns
+ mort_protect(n) = loc_mort_protect
+ palatability(n) = loc_palatability
+ growthcost_factor(n) = loc_growthcost_factor
+ kg_scale(n) = loc_kg
+ respir_cost(n) = loc_respir
+ else
+ !read in population specifications
+ DO n = 1,loc_n_elements
+ READ(unit=in,FMT=*) &
+ & loc_plnktn_pft, & ! COLUMN #01: plankton PFT (not used here)
+ & loc_herbivory, & ! COLUMN #02: herbivory
+ & loc_carnivory, & ! COLUMN #03: carnivory
+ & loc_pp_opt_a, & ! COLUMN #04: pp_opt_a
+ & loc_pp_sig_a, & ! COLUMN #05: pp_sig_a
+ & loc_ns, & ! COLUMN #06: ns (prey switching)
+ & loc_mort_protect, & ! COLUMN #07: mortality_protection
+ & loc_palatability, & ! COLUMN #08: palatability - in development - Fanny Mar21
+ & loc_growthcost_factor ! COLUMN #09: growth-cost factor - in development - Fanny Mar21
+ herbivory(n) = loc_herbivory
+ carnivory(n) = loc_carnivory
+ pp_opt_a_array(n) = loc_pp_opt_a
+ pp_sig_a_array(n) = loc_pp_sig_a
+ ns_array(n) = loc_ns
+ mort_protect(n) = loc_mort_protect
+ palatability(n) = loc_palatability
+ growthcost_factor(n) = loc_growthcost_factor
+ END DO
+ endif
+
!close file pipe
CLOSE(unit=in)
From ebf408b2ebd1cf18bdb99bbfcb9bd7387f0747f7 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 00:35:51 +0100
Subject: [PATCH 02/89] update foramecogem: ecogem.f90
---
genie-ecogem/src/fortran/ecogem.f90 | 26 ++++++++++++++++++++++++--
1 file changed, 24 insertions(+), 2 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem.f90 b/genie-ecogem/src/fortran/ecogem.f90
index c10de2d25..b9de4d4ca 100644
--- a/genie-ecogem/src/fortran/ecogem.f90
+++ b/genie-ecogem/src/fortran/ecogem.f90
@@ -323,7 +323,19 @@ subroutine ecogem( &
PAR_out = PAR_in * exp(-k_tot*layerthick) ! light leaving bottom of layer
PAR_in = PAR_out
endif
-
+
+ ! foram cannot live in environment with < 1 omega
+ ! Roy et al. 2015. Biogeosciences, 12, 2873–2889, 2015
+ if (ctrl_foram_oa .and. (omega(i,j,k) .lt. 1.0)) then
+ do jp=1,npmax
+ ! for any foram
+ if (index(pft(jp), "foram") /= 0) then
+ ! note mortality(:) is changing in place and mort(:) is fixed
+ mortality(jp) = mortality(jp) * 100
+ endif
+ enddo
+ endif
+
! ?
up_inorg(:,:) = 0.0 ! (iomax,npmax)
qreg(:,:) = 0.0 ! (iomax,npmax)
@@ -348,6 +360,16 @@ subroutine ecogem( &
call t_limitation(templocal,gamma_TP,gamma_TK)
+ ! symbiont bleaching for foraminifera
+ ! implementation: manually disable photosynthesis
+ if (ctrl_foram_bleach .and. (templocal .gt. (temp_bleach + 273.15))) then
+ do jp=1,npmax
+ if (pft(jp).eq.'foram_sn' .or. pft(jp).eq.'foram_ss') then
+ VLlimit(jp) = 0.0
+ endif
+ enddo
+ endif
+
call nutrient_uptake(qreg(:,:),loc_nuts(:),gamma_TK,up_inorg(:,:))
call photosynthesis(PAR_layer,loc_biomass,limit,VLlimit,up_inorg,gamma_TP,up_inorg(iDIC,:),chlsynth,totPP)
@@ -373,7 +395,7 @@ subroutine ecogem( &
! mortality(:) = mortality(:) * gamma_TK ! temp adjusted?
! calculate respiration
- respiration(:) = respir(:) !* (1.0 - exp(-1.0e10 * loc_biomass(iCarb,:))) ! reduce respiration at very low biomass
+ respiration(:) = respir(:) * gamma_T !* (1.0 - exp(-1.0e10 * loc_biomass(iCarb,:))) ! reduce respiration at very low biomass
! calculate assimilation efficiency based on quota status
!BAW: zoolimit should be optional Totzoolimit(:) = 0.0 !total food limitation - Maria May 2019 !!! Need to check if consistent!!!
From f0ac216dca7bafde3e515eb3cf5487459892d9e6 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 00:36:00 +0100
Subject: [PATCH 03/89] udpate foramecogem: ecogem_lib.f90
---
genie-ecogem/src/fortran/ecogem_lib.f90 | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index 3161d9d67..4dc2ddda8 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -138,8 +138,8 @@ MODULE ecogem_lib
namelist/ini_ecogem_nml/beta_graz_a,beta_graz_b,beta_graz_c,beta_mort_a,beta_mort_b,beta_mort_c
namelist/ini_ecogem_nml/par_bio_remin_POC_frac2,par_bio_remin_CaCO3_frac2
! Mixotrophy parameters
- real :: trophic_tradeoff
- namelist/ini_ecogem_nml/trophic_tradeoff
+ real :: trophic_tradeoff,foram_auto_cost_sn,foram_auto_cost_ss,foram_hetero_cost_sn,foram_hetero_cost_ss
+ namelist/ini_ecogem_nml/trophic_tradeoff,foram_auto_cost_sn,foram_auto_cost_ss,foram_hetero_cost_sn,foram_hetero_cost_ss
! Temperature dependence
real :: temp_A,temp_P,temp_K,temp_T0 !
namelist/ini_ecogem_nml/temp_A,temp_P,temp_K,temp_T0
@@ -168,6 +168,9 @@ MODULE ecogem_lib
namelist /ini_ecogem_nml/ctrl_force_T
character(LEN=127)::par_ecogem_force_T_file
namelist /ini_ecogem_nml/par_ecogem_force_T_file
+ ! RY Foram symbiont bleaching, ocean acidification killing control
+ logical::ctrl_foram_bleach, ctrl_foram_oa
+ namelist /ini_ecogem_nml/ctrl_foram_bleach, ctrl_foram_oa
! explicit grazing parameters
logical::ctrl_grazing_explicit
namelist /ini_ecogem_nml/ctrl_grazing_explicit
@@ -299,6 +302,10 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:) ::qcarbon,alphachl ! Carbon quota and Photosynthesis parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::graz,kg,pp_opt,pp_sig ! Grazing parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::respir,biosink,mort,beta_graz,beta_mort ! Other loss parameters
+ REAL ,ALLOCATABLE,DIMENSION(:) ::symbiont_auto_cost, symbiont_hetero_cost ! RY, foramecogenie symbiont cost parameter
+ REAL ,ALLOCATABLE,DIMENSION(:) ::auto_volume, hetero_volume, grazing_esd_scale, symbiont_esd_scale ! RY, foramecogenie size parameter
+ REAL ,ALLOCATABLE,DIMENSION(:) ::respir_cost,kg_scale, ! RY, foramecogenie grazing parameter
+
! Grazing kernel
REAL,ALLOCATABLE,DIMENSION(:,:)::gkernel,gkernelT
! netCDF and netCDF restart parameters
From 74bafda70047e5a595c195d573bdf2881d126d44 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 00:36:10 +0100
Subject: [PATCH 04/89] update foramecogem: init_ecogem.f90
---
.../src/fortran/initialise_ecogem.f90 | 27 +++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/genie-ecogem/src/fortran/initialise_ecogem.f90 b/genie-ecogem/src/fortran/initialise_ecogem.f90
index 35d6eed24..f342115c3 100644
--- a/genie-ecogem/src/fortran/initialise_ecogem.f90
+++ b/genie-ecogem/src/fortran/initialise_ecogem.f90
@@ -325,6 +325,33 @@ SUBROUTINE initialise_ecogem( &
if (useFe ) rsrcstrng(iFe) = 'Fe'
if (useSiO2 ) rsrcstrng(iSiO2) = 'SiO2'
+ ! foramecogenie arrays allocation
+ if (ctrl_use_foramecogenie) then
+ ALLOCATE(kg_scale(npmax),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+
+ ALLOCATE(respir_cost(npmax),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+
+ ALLOCATE(auto_volume(npmax),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+
+ ALLOCATE(hetero_volume(npmax),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+
+ ALLOCATE(grazing_esd_scale(npmax),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+
+ ALLOCATE(symbiont_esd_scale(npmax),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+
+ ALLOCATE(symbiont_auto_cost(npmax),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+
+ ALLOCATE(symbiont_hetero_cost(npmax),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+ endif
+
! ---------------------------------------------------------- !
! OPEN ASCII FILES !---------------------------------------- !
! ---------------------------------------------------------- !
From 24401a76dbb526765be09ff0c53bceb890bcf525 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 00:36:24 +0100
Subject: [PATCH 05/89] update foramecogem: definition.xml
---
genie-main/src/xml-config/xml/definition.xml | 61 ++++++++++++++++++++
1 file changed, 61 insertions(+)
diff --git a/genie-main/src/xml-config/xml/definition.xml b/genie-main/src/xml-config/xml/definition.xml
index 0157e86c1..6e3bce06b 100644
--- a/genie-main/src/xml-config/xml/definition.xml
+++ b/genie-main/src/xml-config/xml/definition.xml
@@ -8883,6 +8883,67 @@ par_bio_red_PC_alpha2 scales the offset of 6.0e-3 of Galbraith & Martiny, 2015 C
timeseries_sites.eco
timeseries locations file name
+
+
+
+
+
+
+ .FALSE.
+ enable foramecogenie
+
+
+
+ .FALSE.
+ disable foraminifera autotrophy when exceed temperature threshold
+
+
+
+ .FALSE.
+ kill foraminifera when calcite saturation state is less than 1
+
+
+
+ 40.0
+ temperature threshold of symbiont bleaching in Celsius
+
+
+
+ 1.0
+ symbiont/foraminifera host size ratio
+
+
+
+ 1.0
+ stronger "grazing volume" for symbiont-barren spinose foraminifera
+
+
+
+ 1.0
+ stronger "grazing volume" for symbiont-bearing spinose foraminifera
+
+
+
+
+ 1.0
+ Auto trade-off parameter
+
+
+
+ 1.0
+ Auto trade-off parameter
+
+
+
+ 1.0
+ Auto trade-off parameter
+
+
+
+ 1.0
+ Auto trade-off parameter
+
+
From 1b0b0575ec89db31ac4348bf4af322b80006445d Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 00:48:36 +0100
Subject: [PATCH 06/89] update foramecogem: change parameter names
---
genie-ecogem/src/fortran/ecogem.f90 | 2 +-
genie-ecogem/src/fortran/ecogem_data.f90 | 5 ++---
genie-ecogem/src/fortran/ecogem_lib.f90 | 4 ++--
genie-main/src/xml-config/xml/definition.xml | 4 ++--
4 files changed, 7 insertions(+), 8 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem.f90 b/genie-ecogem/src/fortran/ecogem.f90
index b9de4d4ca..3e5c5979e 100644
--- a/genie-ecogem/src/fortran/ecogem.f90
+++ b/genie-ecogem/src/fortran/ecogem.f90
@@ -362,7 +362,7 @@ subroutine ecogem( &
! symbiont bleaching for foraminifera
! implementation: manually disable photosynthesis
- if (ctrl_foram_bleach .and. (templocal .gt. (temp_bleach + 273.15))) then
+ if (ctrl_foramecogenie_bleach .and. (templocal .gt. (foramecogenie_bleach_temp + 273.15))) then
do jp=1,npmax
if (pft(jp).eq.'foram_sn' .or. pft(jp).eq.'foram_ss') then
VLlimit(jp) = 0.0
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 96376427b..0bae7b045 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -494,10 +494,9 @@ SUBROUTINE sub_init_plankton()
! v1/v2 = (r1/r2)^3
auto_volume(:) = volume(:) * symbiont_esd_scale(:) ** 3
hetero_volume(:) = volume(:) * grazing_esd_scale(:) ** 3
+ autotrophy(:) = autotrophy(:) * symbiont_auto_cost(:)
+ heterotrophy(:) = heterotrophy(:) * symbiont_hetero_cost(:)
- ! vmax photosynthesis rate
- vmax(iDIC,:) = vmax(iDIC,:) = (vmaxDIC_a + log10(auto_volume(:))) / (vmaxDIC_b + vmaxDIC_c * log10(auto_volume(:)) + log10(auto_volume(:))**2) &
- & * autotrophy(:) * symbiont_auto_cost(:)
!-----------------------------------------------------------------------------------------
! maximum photosynthetic rate
! vmax(iDIC,:) = vmaxDIC_a * volume(:) ** vmaxDIC_b * autotrophy(:)
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index 4dc2ddda8..7b0e9bb05 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -169,8 +169,8 @@ MODULE ecogem_lib
character(LEN=127)::par_ecogem_force_T_file
namelist /ini_ecogem_nml/par_ecogem_force_T_file
! RY Foram symbiont bleaching, ocean acidification killing control
- logical::ctrl_foram_bleach, ctrl_foram_oa
- namelist /ini_ecogem_nml/ctrl_foram_bleach, ctrl_foram_oa
+ logical::ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa, ctrl_use_foramecogenie
+ namelist /ini_ecogem_nml/ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa,ctrl_use_foramecogenie
! explicit grazing parameters
logical::ctrl_grazing_explicit
namelist /ini_ecogem_nml/ctrl_grazing_explicit
diff --git a/genie-main/src/xml-config/xml/definition.xml b/genie-main/src/xml-config/xml/definition.xml
index 6e3bce06b..8025ad087 100644
--- a/genie-main/src/xml-config/xml/definition.xml
+++ b/genie-main/src/xml-config/xml/definition.xml
@@ -8889,7 +8889,7 @@ par_bio_red_PC_alpha2 scales the offset of 6.0e-3 of Galbraith & Martiny, 2015 C
- .FALSE.
+ .FALSE.
enable foramecogenie
@@ -8903,7 +8903,7 @@ par_bio_red_PC_alpha2 scales the offset of 6.0e-3 of Galbraith & Martiny, 2015 C
kill foraminifera when calcite saturation state is less than 1
-
+
40.0
temperature threshold of symbiont bleaching in Celsius
From 3acdd1fb47c286616417909ab3e7c638ce978259 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 00:48:52 +0100
Subject: [PATCH 07/89] Add foramecogem user-configs
---
genie-userconfigs/FORAMECOGEM/8P7Z4F.eco | 49 +++++
genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo | 54 +++++
genie-userconfigs/FORAMECOGEM/makefile | 20 ++
...CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1 | 177 ++++++++++++++++
...CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1 | 183 ++++++++++++++++
...a.BASESFeTDTL_rb_foramecogem2.1.modernAMOC | 199 ++++++++++++++++++
...Q00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN | 144 +++++++++++++
...umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN | 144 +++++++++++++
...Q04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN | 144 +++++++++++++
...Q04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN | 144 +++++++++++++
...lg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg | 158 ++++++++++++++
...orlg4.BASESFeTDTL.foramecogem2.1.2100.2deg | 158 ++++++++++++++
...orlg4.BASESFeTDTL.foramecogem2.1.2100.3deg | 158 ++++++++++++++
...orlg4.BASESFeTDTL.foramecogem2.1.2100.4deg | 157 ++++++++++++++
...CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN | 155 ++++++++++++++
...rlg4.BASESFeTDTL.foramecogem2.1.historical | 159 ++++++++++++++
genie-userconfigs/FORAMECOGEM/readme.md | 113 ++++++++++
.../FORAMECOGEM/update_userconfig.py | 57 +++++
18 files changed, 2373 insertions(+)
create mode 100644 genie-userconfigs/FORAMECOGEM/8P7Z4F.eco
create mode 100644 genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
create mode 100644 genie-userconfigs/FORAMECOGEM/makefile
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1.modernAMOC
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.2deg
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.3deg
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.4deg
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical
create mode 100644 genie-userconfigs/FORAMECOGEM/readme.md
create mode 100644 genie-userconfigs/FORAMECOGEM/update_userconfig.py
diff --git a/genie-userconfigs/FORAMECOGEM/8P7Z4F.eco b/genie-userconfigs/FORAMECOGEM/8P7Z4F.eco
new file mode 100644
index 000000000..03d63ebe9
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/8P7Z4F.eco
@@ -0,0 +1,49 @@
+
+ 01 02 03
+ \/ \/ \/
+
+-START-OF-DATA-
+ Phytoplankton 0.60 1
+ Phytoplankton 1.90 1
+ Phytoplankton 6.00 1
+ Phytoplankton 19.00 1
+ Phytoplankton 60.00 1
+ Phytoplankton 190.00 1
+ Phytoplankton 600.00 1
+ Phytoplankton 1900.00 1
+ Zooplankton 1.90 1
+ Zooplankton 6.00 1
+ Zooplankton 19.00 1
+ Zooplankton 60.00 1
+ Zooplankton 190.00 1
+ Zooplankton 600.00 1
+ Zooplankton 1900.00 1
+ foram_bn 155.00 1
+ foram_bs 175.00 1
+ foram_sn 190.00 1
+ foram_ss 190.00 1
+-END-OF-DATA-
+
+ /\ /\ /\
+ 01 02 03
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #01: plankton functional type name
+COLUMN #02: plankton diameter (micrometers)
+COLUMN #03: number of randomised replicates
+
+INFO: TRACER ASSIGNMENT RULES
+-----------------------------
+Plankton functional type one of: Prochlorococcus
+ Synechococcus
+ Picoeukaryote
+ Diatom
+ Coccolithophore
+ Diazotroph
+ Zooplankton
+ Mixotroph
+
+
+
diff --git a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
new file mode 100644
index 000000000..78fa2831f
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
@@ -0,0 +1,54 @@
+
+01 02 03 04 05 06 07 08 09 10 11
+\/ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+foram_bn 1.0 0.0 10.0 4.0 1.0 0.7 0.8 1.0 1.0 0.04
+foram_bs 1.0 0.0 10.0 2.0 1.0 0.7 0.7 1.0 0.75 0.06
+foram_sn 1.0 0.0 10.0 4.0 1.0 0.7 0.8 1.0 1.0 0.04
+foram_ss 0.0 1.0 10.0 2.0 1.0 0.7 0.7 1.0 0.8 0.06
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 01 02 03 04 05 06 07 08 09 10 11
+
+DATA FORMAT AND ORDER
+---------------------
+COLUMN #01: functional type (dummy argument, the order MUST same as .eco file)
+COLUMN #02: herbivory (graze on phytoplankton only - if heterotrophy > 0.0)
+COLUMN #03: carnivory (graze on zooplankton only - if heterotrophy > 0.0)
+COLUMN #04: pp_opt_a (optimal predator:prey ratio)
+COLUMN #05: pp_sig_a (width of grazing kernel)
+COLUMN #06: ns (prey-switching - 2.0 = active, 1.0 = passive)
+COLUMN #07: mortality protection (e.g., 0.7 is equivalent to 30% reduced mortality rate)
+COLUMN #08: palatability (grazing protection)
+COLUMN #09: growth-cost factor (e.g., a 10% cost is equivalent to a 0.9 growth-cost factor)
+COLUMN #10: half-saturation constant (affinity) of grazing rate
+COLUMN #11: extra respiration rate for building calcite spine and test
+
+INFO: TRACER ASSIGNMENT RULES
+-----------------------------
+Plankton functional type one of: Prochlorococcus
+ Synechococcus
+ Picoeukaryote
+ Diatom
+ Coccolithophore
+ Diazotroph
+ Zooplankton
+ Mixotroph
+ Foram
diff --git a/genie-userconfigs/FORAMECOGEM/makefile b/genie-userconfigs/FORAMECOGEM/makefile
new file mode 100644
index 000000000..c7154b9f3
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/makefile
@@ -0,0 +1,20 @@
+CONFIG_DIR := $(CURDIR)
+HOME_DIR := $(HOME)
+
+.PHONY: update_userconfig update_grazing_file update_size_file update_foramecogem
+
+update_grazing_file:
+ cp $(CONFIG_DIR)/FORAMECOGEM.zoo $(HOME_DIR)/cgenie.muffin/genie-ecogem/data/input
+ @echo "Update done!"
+
+update_size_file:
+ cp $(CONFIG_DIR)/8P7Z4F.eco $(HOME_DIR)/cgenie.muffin/genie-ecogem/data/input
+ @echo "Update done!"
+
+update_userconfig:
+ @echo "Running Python script to update user-config files..."
+ @python3 update_userconfig.py $(CONFIG_DIR)
+ @echo "Update done!"
+
+update_foramecogem: update_grazing_file update_size_file update_userconfig
+ @echo "All updates completed successfully!"
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1
new file mode 100644
index 000000000..7c7b6f6c8
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1
@@ -0,0 +1,177 @@
+# *******************************************************************
+# *** muffin.CB.GIteiiaa.BASESFeTDTL.1p2tau.SPIN ********************
+# *******************************************************************
+#
+# *** CLIMATE *******************************************************
+#
+# (climate responding to changing pCO2)
+ea_36=y
+#
+# *** BIOLOGICAL NEW PRODUCTION *************************************
+#
+# biological scheme ID string
+# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
+bg_par_bio_prodopt="NONE"
+#
+# *** ORGANIC MATTER EXPORT RATIOS **********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** INORGANIC MATTER EXPORT RATIOS ********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** REMINERALIZATION **********************************************
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+# *** optional changes to align with PALEO recommendations **********
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# *** IRON CYCLING **************************************************
+#
+# iron tracer scheme
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility [Albani tuning]
+bg_par_det_Fe_sol=0.002441
+# modifier of the scavenging rate of dissolved Fe [Albani tuning]
+bg_par_scav_Fe_sf_POC=0.2250
+# exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# *** ECOGEM ********************************************************
+#
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+################## Phosphorus ############################
+eg_usePO4 =.true.
+eg_pquota =.true.
+######################## Iron ############################
+eg_useFe =.true.
+eg_fquota =.true.
+################# Chlorophyll ############################
+eg_chlquota =.true.
+################# d13C ###################################
+eg_useDIC_13C =.true.
+# Tuned parameters
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns=2
+eg_respir_a=0
+# DOM parameters
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+# ???
+eg_nsubtime=25
+eg_n_keco=1
+# exponent for modifier of CaCO3:POC export ratio
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+#
+# *** DATA SAVING ***************************************************
+#
+# BASIC + biology + tracer + proxy diagnostics
+bg_par_data_save_level=7
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+#
+# *** FORCINGS ******************************************************
+#
+# specify forcings
+bg_par_forcing_name="GIteiiaa.RpCO2_Rp13CO2.Fsal_SUR.Albani.0ka"
+bg_par_atm_force_scale_val_3=275.0E-06
+bg_par_atm_force_scale_val_4=-6.35
+#
+# *** MISC **********************************************************
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# *** optional changes to align with PALEO recommendations **********
+
+# set mixed layer to be only diagnosed (for ECOGEM)
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+
+# (no preformed)
+bg_ctrl_bio_preformed=.false.
+# add ventillation tracers
+bg_ctrl_force_ocn_age1=.true.
+# add brine rejection SH limit
+bg_par_misc_brinerejection_jmax=19
+# wind-stress
+go_13=1.3
+ea_11=1.3
+#
+# *** TUNING ********************************************************
+#
+# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
+bg_par_misc_brinerejection_frac=0.2
+# parameter: bg_par_ocn_force_scale_val_2 -- default value (1) modified by factor: 0.20
+bg_par_ocn_force_scale_val_2=0.20
+#
+# *** INITIAL CONDITIONS ********************************************
+#
+# N/A
+#
+# *******************************************************************
+# *** END ***********************************************************
+# *******************************************************************
+#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1
new file mode 100644
index 000000000..ffafa57b3
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1
@@ -0,0 +1,183 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# [Dealt with ECOGEM]
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# [Dealt with ECOGEM]
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002441
+# modifier of the scavenging rate of dissolved Fe [Albani tuning]
+bg_par_scav_Fe_sf_POC=0.2250
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="GIteiiva.RpCO2_Rp13CO2.Fsal_SUR.Albani.21ka"
+bg_par_atm_force_scale_val_3=193.0E-06
+bg_par_atm_force_scale_val_4=-6.46
+# Orbital parameters
+ea_par_orbit_osce=0.018994 # eccentricity
+ea_par_orbit_oscsob=0.389911 # sine of obliquity
+ea_par_orbit_oscgam=114.42 # longitude of perihelion (degrees)
+#
+#
+# *** TUNING ********************************************************
+#
+# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
+bg_par_misc_brinerejection_frac=0.2
+# parameter: bg_par_ocn_force_scale_val_2 -- default value (1) modified by factor: 0.05
+bg_par_ocn_force_scale_val_2=0.05
+#
+# *** INITIAL CONDITIONS ********************************************
+#
+# modern DIC (2.244E-03) + 1%
+bg_ocn_init_3=0.002275818239634
+# modern 13C DIC
+bg_ocn_init_4=0.4
+# modern ALK (2.363E-03) + 1%
+bg_ocn_init_12=0.002396505570523
+# modern PO4 (2.159E-06) + 1%
+bg_ocn_init_8=2.189613003283920e-06
+# modern SAL + 0.33 PSU
+go_saln0=35.23
+#
+# --- MISC ----------------------------------------------------------
+#
+# (no preformed)
+bg_ctrl_bio_preformed=.false.
+# add ventillation tracers
+bg_ctrl_force_ocn_age1=.true.
+# add brine rejection SH limit
+bg_par_misc_brinerejection_jmax=19
+# wind-stress
+go_13=1.3
+ea_11=1.3
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1.modernAMOC
new file mode 100644
index 000000000..3b5d3e950
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1.modernAMOC
@@ -0,0 +1,199 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# [Dealt with ECOGEM]
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# [Dealt with ECOGEM]
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002441
+# modifier of the scavenging rate of dissolved Fe [Albani tuning]
+bg_par_scav_Fe_sf_POC=0.2250
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="GIteiiva.RpCO2_Rp13CO2.Fsal_SUR.Albani.21ka"
+bg_par_atm_force_scale_val_3=193.0E-06
+bg_par_atm_force_scale_val_4=-6.46
+# Orbital parameters
+ea_par_orbit_osce=0.018994 # eccentricity
+ea_par_orbit_oscsob=0.389911 # sine of obliquity
+ea_par_orbit_oscgam=114.42 # longitude of perihelion (degrees)
+#
+#
+# *** TUNING ********************************************************
+#
+# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
+bg_par_misc_brinerejection_frac=0.2
+# saltier Atlantic and a mdoern-like AMOC
+bg_par_ocn_force_scale_val_2=0.3
+#
+# *** INITIAL CONDITIONS ********************************************
+#
+# modern DIC (2.244E-03) + 1%
+bg_ocn_init_3=0.002275818239634
+# modern 13C DIC
+bg_ocn_init_4=0.4
+# modern ALK (2.363E-03) + 1%
+bg_ocn_init_12=0.002396505570523
+# modern PO4 (2.159E-06) + 1%
+bg_ocn_init_8=2.189613003283920e-06
+# modern SAL + 0.33 PSU
+go_saln0=35.23
+#
+## --- MISC ----------------------------------------------------------
+#
+# (no preformed)
+bg_ctrl_bio_preformed=.false.
+# add ventillation tracers
+bg_ctrl_force_ocn_age1=.true.
+# add brine rejection SH limit
+bg_par_misc_brinerejection_jmax=19
+# wind-stress
+go_13=1.3
+ea_11=1.3
+
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+
+# maximum time-scale to geochemical reaction completion (days)
+bg_par_bio_geochem_tau=90.0
+
+# extend solubility and geochem constant T range (leave S range as default)
+gm_par_geochem_Tmin = -2.0
+gm_par_geochem_Tmax = 45.0
+gm_par_carbchem_Tmin = -2.0
+gm_par_carbchem_Tmax = 45.0
+
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# --- END -----------------------------------------------------------
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
new file mode 100644
index 000000000..39ace5762
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
@@ -0,0 +1,144 @@
+# *** CLIMATE *******************************************************
+#
+# set climate feedback (climate responding to changing pCO2)
+ea_36=y
+#
+# *** BIOLOGICAL NEW PRODUCTION *************************************
+#
+# biological scheme ID string
+# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
+bg_par_bio_prodopt="NONE"
+#
+# *** ORGANIC MATTER EXPORT RATIOS **********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** INORGANIC MATTER EXPORT RATIOS ********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** REMINERALIZATION **********************************************
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+# *** optional changes to align with PALEO recommendations **********
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# *** IRON CYCLING **************************************************
+#
+# [no iron]
+#
+# *** ECOGEM ********************************************************
+#
+# Planktic Foraminifer and Ecosystem
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#################### Nitrogen ############################
+eg_useNO3 =.false.
+eg_nquota =.false.
+################## Phosphorus ############################
+eg_usePO4 =.true.
+eg_pquota =.true.
+######################## Iron ############################
+eg_useFe =.false.
+eg_fquota =.false.
+################# Chlorophyll ############################
+eg_chlquota =.true.
+################# d13C ###################################
+eg_useDIC_13C =.true.
+# Tuned parameters
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+# ???
+eg_ns=2
+# ???
+eg_respir_a=0
+# DOM parameters
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+# ???
+eg_nsubtime=25
+eg_n_keco=1
+# exponent for modifier of CaCO3:POC export ratio
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=7
+# reduce output
+bg_ctrl_data_save_2d=.true.
+bg_ctrl_data_save_3d=.true. # JDW - set to true
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
+bg_par_atm_force_scale_val_4=-6.428
+# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 280
+bg_par_atm_force_scale_val_3=0.000280
+# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
+bg_par_ocn_force_scale_val_2=0.2
+#
+# *** MISC **********************************************************
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+# *** optional changes to align with PALEO recommendations **********
+# set mixed layer to be only diagnosed (for ECOGEM)
+go_ctrl_diagmld=.true.
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+# maximum time-scale to geochemical reaction completion (days)
+bg_par_bio_geochem_tau=90.0
+# extend solubility and geochem constant T range (leave S range as default)
+gm_par_geochem_Tmin = -2.0
+gm_par_geochem_Tmax = 45.0
+gm_par_carbchem_Tmin = -2.0
+gm_par_carbchem_Tmax = 45.0
+#
+ma_flag_ecogem=.TRUE.
+GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
+gm_ocn_select_60=.true. # preformed PO4
+gm_ocn_select_66=.true. # Csoft
+bg_ctrl_bio_preformed=.true.
+bg_ctrl_bio_remin_redox_save=.true.
+bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
+#
+# *******************************************************************
+# *** END ***********************************************************
+# *******************************************************************
+#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN
new file mode 100644
index 000000000..e6195a162
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN
@@ -0,0 +1,144 @@
+# *** CLIMATE *******************************************************
+#
+# set climate feedback (climate responding to changing pCO2)
+ea_36=y
+#
+# *** BIOLOGICAL NEW PRODUCTION *************************************
+#
+# biological scheme ID string
+# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
+bg_par_bio_prodopt="NONE"
+#
+# *** ORGANIC MATTER EXPORT RATIOS **********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** INORGANIC MATTER EXPORT RATIOS ********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** REMINERALIZATION **********************************************
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+# *** optional changes to align with PALEO recommendations **********
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# *** IRON CYCLING **************************************************
+#
+# [no iron]
+#
+# *** ECOGEM ********************************************************
+#
+# Planktic Foraminifer and Ecosystem
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#################### Nitrogen ############################
+eg_useNO3 =.false.
+eg_nquota =.false.
+################## Phosphorus ############################
+eg_usePO4 =.true.
+eg_pquota =.true.
+######################## Iron ############################
+eg_useFe =.false.
+eg_fquota =.false.
+################# Chlorophyll ############################
+eg_chlquota =.true.
+################# d13C ###################################
+eg_useDIC_13C =.true.
+# Tuned parameters
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+# ???
+eg_ns=2
+# ???
+eg_respir_a=0
+# DOM parameters
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+# ???
+eg_nsubtime=25
+eg_n_keco=1
+# exponent for modifier of CaCO3:POC export ratio
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=7
+# reduce output
+bg_ctrl_data_save_2d=.true.
+bg_ctrl_data_save_3d=.true. # JDW - set to true
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
+bg_par_atm_force_scale_val_4=-6.202
+# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
+bg_par_atm_force_scale_val_3=0.000400
+# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.5
+bg_par_ocn_force_scale_val_2=0.5
+#
+# *** MISC **********************************************************
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+# *** optional changes to align with PALEO recommendations **********
+# set mixed layer to be only diagnosed (for ECOGEM)
+go_ctrl_diagmld=.true.
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+# maximum time-scale to geochemical reaction completion (days)
+bg_par_bio_geochem_tau=90.0
+# extend solubility and geochem constant T range (leave S range as default)
+gm_par_geochem_Tmin = -2.0
+gm_par_geochem_Tmax = 45.0
+gm_par_carbchem_Tmin = -2.0
+gm_par_carbchem_Tmax = 45.0
+#
+ma_flag_ecogem=.TRUE.
+GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
+gm_ocn_select_60=.true. # preformed PO4
+gm_ocn_select_66=.true. # Csoft
+bg_ctrl_bio_preformed=.true.
+bg_ctrl_bio_remin_redox_save=.true.
+bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
+#
+# *******************************************************************
+# *** END ***********************************************************
+# *******************************************************************
+#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
new file mode 100644
index 000000000..dac971aaa
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
@@ -0,0 +1,144 @@
+# *** CLIMATE *******************************************************
+#
+# set climate feedback (climate responding to changing pCO2)
+ea_36=y
+#
+# *** BIOLOGICAL NEW PRODUCTION *************************************
+#
+# biological scheme ID string
+# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
+bg_par_bio_prodopt="NONE"
+#
+# *** ORGANIC MATTER EXPORT RATIOS **********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** INORGANIC MATTER EXPORT RATIOS ********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** REMINERALIZATION **********************************************
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+# *** optional changes to align with PALEO recommendations **********
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# *** IRON CYCLING **************************************************
+#
+# [no iron]
+#
+# *** ECOGEM ********************************************************
+#
+# Planktic Foraminifer and Ecosystem
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#################### Nitrogen ############################
+eg_useNO3 =.false.
+eg_nquota =.false.
+################## Phosphorus ############################
+eg_usePO4 =.true.
+eg_pquota =.true.
+######################## Iron ############################
+eg_useFe =.false.
+eg_fquota =.false.
+################# Chlorophyll ############################
+eg_chlquota =.true.
+################# d13C ###################################
+eg_useDIC_13C =.true.
+# Tuned parameters
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+# ???
+eg_ns=2
+# ???
+eg_respir_a=0
+# DOM parameters
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+# ???
+eg_nsubtime=25
+eg_n_keco=1
+# exponent for modifier of CaCO3:POC export ratio
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=7
+# reduce output
+bg_ctrl_data_save_2d=.true.
+bg_ctrl_data_save_3d=.true. # JDW - set to true
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
+bg_par_atm_force_scale_val_4=-6.265
+# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
+bg_par_atm_force_scale_val_3=0.000280
+# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
+bg_par_ocn_force_scale_val_2=0.2
+#
+# *** MISC **********************************************************
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+# *** optional changes to align with PALEO recommendations **********
+# set mixed layer to be only diagnosed (for ECOGEM)
+go_ctrl_diagmld=.true.
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+# maximum time-scale to geochemical reaction completion (days)
+bg_par_bio_geochem_tau=90.0
+# extend solubility and geochem constant T range (leave S range as default)
+gm_par_geochem_Tmin = -2.0
+gm_par_geochem_Tmax = 45.0
+gm_par_carbchem_Tmin = -2.0
+gm_par_carbchem_Tmax = 45.0
+#
+ma_flag_ecogem=.TRUE.
+GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
+gm_ocn_select_60=.true. # preformed PO4
+gm_ocn_select_66=.true. # Csoft
+bg_ctrl_bio_preformed=.true.
+bg_ctrl_bio_remin_redox_save=.true.
+bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
+#
+# *******************************************************************
+# *** END ***********************************************************
+# *******************************************************************
+#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN
new file mode 100644
index 000000000..69dbf5620
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN
@@ -0,0 +1,144 @@
+# *** CLIMATE *******************************************************
+#
+# set climate feedback (climate responding to changing pCO2)
+ea_36=y
+#
+# *** BIOLOGICAL NEW PRODUCTION *************************************
+#
+# biological scheme ID string
+# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
+bg_par_bio_prodopt="NONE"
+#
+# *** ORGANIC MATTER EXPORT RATIOS **********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** INORGANIC MATTER EXPORT RATIOS ********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** REMINERALIZATION **********************************************
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+# *** optional changes to align with PALEO recommendations **********
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# *** IRON CYCLING **************************************************
+#
+# [no iron]
+#
+# *** ECOGEM ********************************************************
+#
+# Planktic Foraminifer and Ecosystem
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#################### Nitrogen ############################
+eg_useNO3 =.false.
+eg_nquota =.false.
+################## Phosphorus ############################
+eg_usePO4 =.true.
+eg_pquota =.true.
+######################## Iron ############################
+eg_useFe =.false.
+eg_fquota =.false.
+################# Chlorophyll ############################
+eg_chlquota =.true.
+################# d13C ###################################
+eg_useDIC_13C =.true.
+# Tuned parameters
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+# ???
+eg_ns=2
+# ???
+eg_respir_a=0
+# DOM parameters
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+# ???
+eg_nsubtime=25
+eg_n_keco=1
+# exponent for modifier of CaCO3:POC export ratio
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=7
+# reduce output
+bg_ctrl_data_save_2d=.true.
+bg_ctrl_data_save_3d=.true. # JDW - set to true
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
+bg_par_atm_force_scale_val_4=-6.265
+# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
+bg_par_atm_force_scale_val_3=0.000400
+# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
+bg_par_ocn_force_scale_val_2=0.2
+#
+# *** MISC **********************************************************
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+# *** optional changes to align with PALEO recommendations **********
+# set mixed layer to be only diagnosed (for ECOGEM)
+go_ctrl_diagmld=.true.
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+# maximum time-scale to geochemical reaction completion (days)
+bg_par_bio_geochem_tau=90.0
+# extend solubility and geochem constant T range (leave S range as default)
+gm_par_geochem_Tmin = -2.0
+gm_par_geochem_Tmax = 45.0
+gm_par_carbchem_Tmin = -2.0
+gm_par_carbchem_Tmax = 45.0
+#
+ma_flag_ecogem=.TRUE.
+GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
+gm_ocn_select_60=.true. # preformed PO4
+gm_ocn_select_66=.true. # Csoft
+bg_ctrl_bio_preformed=.true.
+bg_ctrl_bio_remin_redox_save=.true.
+bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
+#
+# *******************************************************************
+# *** END ***********************************************************
+# *******************************************************************
+#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg
new file mode 100644
index 000000000..fbb1f3810
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg
@@ -0,0 +1,158 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+#
+# starting year
+bg_par_misc_t_start=2022.0
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.2deg
new file mode 100644
index 000000000..a3ce3de18
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.2deg
@@ -0,0 +1,158 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+## starting year
+bg_par_misc_t_start=2022.0
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.3deg
new file mode 100644
index 000000000..07942ad3a
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.3deg
@@ -0,0 +1,158 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+## starting year
+bg_par_misc_t_start=2022.0
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.4deg
new file mode 100644
index 000000000..d99432318
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.4deg
@@ -0,0 +1,157 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+# starting year
+bg_par_misc_t_start=2022.0
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
new file mode 100644
index 000000000..e72a4a6fe
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
@@ -0,0 +1,155 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006"
+bg_par_atm_force_scale_val_3=278.0E-06
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+# --- END -----------------------------------------------------------
+#
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical
new file mode 100644
index 000000000..1f5fdc476
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical
@@ -0,0 +1,159 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+
+eg_ah_size_ratio=0.0015
+eg_ss_tradeoff_a=1.0
+eg_ss_tradeoff_h=0.5
+
+eg_sn_tradeoff_a=0.8
+eg_sn_tradeoff_h=0.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historical2022.dat'
+bg_par_infile_sig_name='save_sig_historical2022.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+# starting year
+bg_par_misc_t_start=1765.0
+
+# --- END -----------------------------------------------------------
+#
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/readme.md b/genie-userconfigs/FORAMECOGEM/readme.md
new file mode 100644
index 000000000..f647b125d
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/readme.md
@@ -0,0 +1,113 @@
+This is model documentation for ForamEcoGENIE 1.1 covering Pliocene/LGM/Pre-industrial/Future
+
+# About the model
+
+## Aim
+The model won't be perfect. It aims to solve three things: (1) the essential foram trait; (2) the biogeogprahy; (3) useful in the past.
+
+Currently I intend to keep the foraminifera biomass overestimated than the observation. Because currently no model including those species distribution model can fullfil all three aspects of foram observation: distribution, biomass and export production.
+
+Other models:
+ForamClim has individual-based implementation, but use empirical (i.e., fixed) growth rate curve;
+PLAFOM has similarily overestimated annual mean biomass (N. Pachyderma > 0.1 mmol C/m3) but has mechanistic setting
+PLANKTOM has foram but only designed for solving carbonate pump. Similarily use Lombard et al. 2009 measured growth curve.
+Statistic models (Waterson et al. 2016; Zaric et al. 2005; Knecht et al. 2023) are not counted here.
+
+
+## Traits
+
+### Feeding behaviour
+Symbiont-barren non-spinose foram (e.g., N. pacheyderma): *herbivory* generalist with increased food range (2x)
+Symbiont-barren spinose foram (e.g., G. bulloides): *herbivory* with increased grazing rate (reduced half-saturation constant)
+Symbiont-facultative non-spinose foram (e.g., N. dutertei): *herbivory* generalist with increased food range (2x)
+Symbiont-obligate spinose foram (e.g., G. ruber): *carnivory* with increased grazing rate (reduced half-saturation constant)
+Same predator-prey size ratio: 10/1
+
+### Calcification/Spine trait trade-offs
+- non-spinose adult: 20-40% growth rate reduction, 20-50% mortality reduction
+- spinose adult: 20-60% growth rate reduction, 12–55% mortality reduction
+
+Reference of 0D model test: Grigoratou et al. (2019) Biogeoscience; Grigoratou et al. (2022) Marine Micropaleotonlogy;
+
+Tested alternative cost: respiration
+
+### Symbiosis
+- Independent symbiont size: 1% foraminifera shell size
+- Slight stronger photosynthesis efficiency for symbiont-obligate species (Takagi et al. 2019, Fig. 11)
+- Low autotrophy efficiency: Great amount of excessive carbon from symbionts (theoretical growth rate = 0.89 d-1, >> ~0.2 d-1 in observation)
+- Low heterotrophy efficiency: mixotrophy modelling convention (Ward and Follows. 2016 PNAS)
+
+Tested implementation: directly transfer biomass from phytoplankton, or mixotroph;
+
+
+## Limitation
++ only adult foram are incldued
++ no 3D water column ecosystem;
++ cGENIE has little primary production in the tropical oceans
++ fixed zooplankton Q10 (the respiration of foram has high Q10 (>3, Lombard et al. 2009 L&O), Photo:Respir = 2-10
+
+
+# Model Runs
+## pre-industrial spinup (0-10000)
+
+```
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL RUI_LABS/foramecogem muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN 10000
+```
+
+## Historical (1765-2022)
+
+```sh
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL RUI_LABS/foramecogem muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical 257 muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
+```
+
+## Future (2022-2100)
+
+```sh
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL RUI_LABS/foramecogem muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.[XXX]deg 78 muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical
+```
+
+## LGM
+
+```sh
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.GIteiiva.BASESFeTDTL_rb RUI_LABS/foramecogem muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1 10000
+```
+
+## Holocene
+
+```sh
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.GIteiiaa.BASESFeTDTL_rb RUI_LABS/foramecogem muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1 10000
+```
+
+## Pliocene
+muffin.CB.umQ00p0a.BASES (modern)
+muffin.CB.umQ04p5a.BASES (Pliocene open)
+muffin.CB.umQ04p5b.BASES (Pliocene close)
+
+``` sh
+## Pliocene open, 400 ppm
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5a.BASES RUI_LABS/foramecogem 20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN 10000
+
+## Modern CAS closed, 280 ppm
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ00p0a.BASES RUI_LABS/foramecogem 20220104.CB.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN 10000
+
+## Pliocene closed, 400 ppm
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES RUI_LABS/foramecogem 20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN 10000
+
+## Pliocene closed, 280 ppm
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES RUI_LABS/foramecogem 20220104.CB.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN 10000
+```
+
+
+> Full effect:4.5 Ma (open, 400 ppm) - 0 Ma (closed, 280 ppm)
+20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN
+20220104.CB.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
+
+> CO2 effect: 4.5 Ma (closed, 400 ppm) - 4.5 Ma (closed, 280 ppm)
+20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN
+20220104.CB.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
+
+> CAS effect: 4.5 Ma (open, 400 ppm) - 4.5 Ma (closed, 400 ppm)
+20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN
+20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN
+
+## K-Pg
diff --git a/genie-userconfigs/FORAMECOGEM/update_userconfig.py b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
new file mode 100644
index 000000000..ad2036840
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
@@ -0,0 +1,57 @@
+import os
+
+def update_foramecogem(directory):
+ """A quicker way to update all foramecogem related text configuration.
+ This function identifies scripts starting with muffin as targets
+ """
+
+
+ parameters = {
+ ## ecogem parameters
+ 'eg_ctrl_ncrst' : '.false.',
+ 'eg_ctrl_continuing' : '.false.',
+ 'eg_ctrl_grazing_explicit': '.true.',
+ 'eg_ctrl_debug_init': '0',
+ 'eg_ctrl_debug_eco_init': '.false.',
+ 'eg_gkernel_cap': '.false.'
+ ## foramecogenie parameters (logical)
+ 'eg_ctrl_use_foramecogenie': '.true.',
+ 'eg_ctrl_foramecogenie_oa': '.false.',
+ 'eg_ctrl_foramecogenie_bleach': '.false.',
+ ## foramecogenie parameters (numerical)
+ 'eg_par_ecogem_plankton_file': "'8P7Z4F.eco'",
+ 'eg_par_ecogem_grazing_file': "'FORAMECOGEM.zoo'",
+ 'eg_foram_symbiont_esd_scale': '0.0015',
+ 'eg_foram_auto_cost_sn': '0.5',
+ 'eg_foram_hetero_cost_sn': '0.5',
+ 'eg_foram_auto_cost_ss': '0.5',
+ 'eg_foram_hetero_cost_ss': '0.5',
+ 'eg_foram_grazing_scale_bs': '2.0',
+ 'eg_foram_grazing_scale_ss': '2.0',
+ }
+
+
+ for filename in os.listdir(directory):
+ file_path = os.path.join(directory, filename)
+ if os.path.isfile(file_path) and filename.startswith("muffin"):
+ with open(file_path, 'r') as file:
+ lines = file.readlines()
+
+ updated_lines = []
+ for line in lines:
+ for key, value in parameters.items():
+ if key in line:
+ line = f"{key}={value}\n"
+ updated_lines.append(line)
+
+ with open(file_path, 'w') as file:
+ file.writelines(updated_lines)
+
+# Check if the script is being run as a standalone program
+if __name__ == "__main__":
+ import sys
+ if len(sys.argv) > 1:
+ text_directory = sys.argv[1]
+ update_foramecogem(text_directory)
+ else:
+ print("Please provide the text directory as a command-line argument.")
From 56cda807efb87f5654315987eb3b1a84b408cbe2 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 01:06:03 +0100
Subject: [PATCH 08/89] debug, remove whitespace
---
genie-ecogem/src/fortran/ecogem_lib.f90 | 2 +-
genie-userconfigs/FORAMECOGEM/update_userconfig.py | 6 +++---
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index 7b0e9bb05..ca8308bb4 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -304,7 +304,7 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:) ::respir,biosink,mort,beta_graz,beta_mort ! Other loss parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::symbiont_auto_cost, symbiont_hetero_cost ! RY, foramecogenie symbiont cost parameter
REAL ,ALLOCATABLE,DIMENSION(:) ::auto_volume, hetero_volume, grazing_esd_scale, symbiont_esd_scale ! RY, foramecogenie size parameter
- REAL ,ALLOCATABLE,DIMENSION(:) ::respir_cost,kg_scale, ! RY, foramecogenie grazing parameter
+ REAL ,ALLOCATABLE,DIMENSION(:) ::respir_cost,kg_scale ! RY, foramecogenie grazing parameter
! Grazing kernel
REAL,ALLOCATABLE,DIMENSION(:,:)::gkernel,gkernelT
diff --git a/genie-userconfigs/FORAMECOGEM/update_userconfig.py b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
index ad2036840..bfa9deb4e 100644
--- a/genie-userconfigs/FORAMECOGEM/update_userconfig.py
+++ b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
@@ -13,7 +13,7 @@ def update_foramecogem(directory):
'eg_ctrl_grazing_explicit': '.true.',
'eg_ctrl_debug_init': '0',
'eg_ctrl_debug_eco_init': '.false.',
- 'eg_gkernel_cap': '.false.'
+ 'eg_gkernel_cap': '.false.',
## foramecogenie parameters (logical)
'eg_ctrl_use_foramecogenie': '.true.',
'eg_ctrl_foramecogenie_oa': '.false.',
@@ -22,9 +22,9 @@ def update_foramecogem(directory):
'eg_par_ecogem_plankton_file': "'8P7Z4F.eco'",
'eg_par_ecogem_grazing_file': "'FORAMECOGEM.zoo'",
'eg_foram_symbiont_esd_scale': '0.0015',
- 'eg_foram_auto_cost_sn': '0.5',
+ 'eg_foram_auto_cost_sn': '0.8',
'eg_foram_hetero_cost_sn': '0.5',
- 'eg_foram_auto_cost_ss': '0.5',
+ 'eg_foram_auto_cost_ss': '1.0',
'eg_foram_hetero_cost_ss': '0.5',
'eg_foram_grazing_scale_bs': '2.0',
'eg_foram_grazing_scale_ss': '2.0',
From 68b0b50827dd9f1e42fccfcccbd76a80bd0c6a23 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 01:56:18 +0100
Subject: [PATCH 09/89] debug: declaration and numerical feeding
(herbivory/carnivory real)
---
genie-ecogem/src/fortran/ecogem_data.f90 | 72 +++++++++++---------
genie-ecogem/src/fortran/ecogem_lib.f90 | 5 ++
genie-main/src/xml-config/xml/definition.xml | 5 ++
3 files changed, 49 insertions(+), 33 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 0bae7b045..5ac085fc8 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -314,7 +314,7 @@ SUBROUTINE sub_init_plankton()
real,dimension(npmax,1) ::pred_diam
real,dimension(1,npmax) ::prey_diam
real,dimension(npmax,npmax)::prdpry,ppopt_mat,ppsig_mat
-
+
! to convert per day rates into per second
real,parameter :: pday = 86400.0
@@ -458,6 +458,7 @@ SUBROUTINE sub_init_plankton()
grazing_esd_scale(:) = 1.0
symbiont_auto_cost(:) = 1.0
symbiont_hetero_cost(:) = 1.0
+
! modify for foraminifera only
if (pft(jp).eq.'foram_bs') then
@@ -481,10 +482,15 @@ SUBROUTINE sub_init_plankton()
pp_sig_a_array(:)=pp_sig_a
ns_array(:)=ns
mort_protect(:)=1.0
- herbivory(:)=.false.
- carnivory(:)=.false.
palatability(:)=1.0
growthcost_factor(:)=1.0
+ if (ctrl_numerical_feeding) then
+ herbivory_real(:)=0.0
+ carnivory_real(:)=0.0
+ else
+ herbivory(:)=.false.
+ carnivory(:)=.false.
+ endif
endif
! set growth costs (could do the same for autotrophy in coccolithophores) - Fanny Mar21
heterotrophy(:) = heterotrophy(:)*growthcost_factor(:)
@@ -575,28 +581,26 @@ SUBROUTINE sub_init_plankton()
prey_diam(1,:)=diameter(:) ! transpose pred diameter vector
prdpry(:,:) =matmul(pred_diam,1.0/prey_diam)
gkernel(:,:) =exp(-log(prdpry(:,:)/ppopt_mat(:,:))**2 / (2*ppsig_mat(:,:)**2)) ! [jpred,jprey] populate whole array at once, then find exceptions to set to 0.0 based on type
-
+
do jpred=1,npmax
select case(pft(jpred))
case('foram','foram_bn','foram_bs','foram_sn','foram_ss')
do jprey=1,npmax
- if(autotrophy(jprey).gt.0.0) gkernel(jpred,jprey)=gkernel(jpred,jprey) * herbivory(jpred)
- if(heterotrophy(jprey).gt.0.0) gkernel(jpred,jprey)=gkernel(jpred,jprey) * carnivory(jpred)
! foram dont eat foram, they are always brothers
if (index(pft(jprey), "foram") /= 0) gkernel(jpred, jprey)=0.0
end do
end select
end do
-
- if (gkernel_cap) gkernel(:,:) =merge(gkernel(:,:),0.0,gkernel(:,:).gt.1e-2) ! set kernel<1e-2 to 0.0 (wardetal.2018)
- gkernelT(:,:) =transpose(gkernel(:,:))
+
- ! detrital partitioning
- ! NOTE: fraction partitioned into DOM (a seperate and explicit array is created for 1-minus this -- the fraction into POM)
- beta_graz(:) =beta_graz_a - (beta_graz_a-beta_graz_b) / (1.0+beta_mort_c/diameter(:))
- beta_mort(:) =beta_mort_a - (beta_mort_a-beta_mort_b) / (1.0+beta_mort_c/diameter(:))
- endif
+ if (gkernel_cap) gkernel(:,:) =merge(gkernel(:,:),0.0,gkernel(:,:).gt.1e-2) ! set kernel<1e-2 to 0.0 (wardetal.2018)
+ gkernelT(:,:) =transpose(gkernel(:,:))
+ ! detrital partitioning
+ ! NOTE: fraction partitioned into DOM (a seperate and explicit array is created for 1-minus this -- the fraction into POM)
+ beta_graz(:) =beta_graz_a - (beta_graz_a-beta_graz_b) / (1.0+beta_mort_c/diameter(:))
+ beta_mort(:) =beta_mort_a - (beta_mort_a-beta_mort_b) / (1.0+beta_mort_c/diameter(:))
+ endif
!-----------------------------------------------------------------------------------------
! maximum photosynthetic rate
@@ -674,14 +678,18 @@ SUBROUTINE sub_init_plankton()
prdpry(:,:) =matmul(pred_diam,1.0/prey_diam)
gkernel(:,:) =exp(-log(prdpry(:,:)/ppopt_mat(:,:))**2 / (2*ppsig_mat(:,:)**2)) ! [jpred,jprey] populate whole array at once, then find exceptions to set to 0.0 based on type
do jpred=1,npmax
- select case(pft(jpred))
- case('foram')
- do jprey=1,npmax
- if(autotrophy(jprey).gt.0.0 .AND. carnivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
- if(heterotrophy(jprey).gt.0.0 .AND. herbivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
- end do
- end select
+ select case(pft(jpred))
+ case('foram')
+ do jprey=1,npmax
+ if(autotrophy(jprey).gt.0.0 .AND. carnivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
+ if(heterotrophy(jprey).gt.0.0 .AND. herbivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
+ end do
+ end select
end do
+
+ if(ctrl_numerical_feeding .AND. autotrophy(jprey).gt.0.0) gkernel(jpred,jprey)=gkernel(jpred,jprey) * herbivory_real(jpred)
+ if(ctrl_numerical_feeding .AND. heterotrophy(jprey).gt.0.0) gkernel(jpred,jprey)=gkernel(jpred,jprey) * carnivory_real(jpred)
+
if (gkernel_cap) gkernel(:,:) =merge(gkernel(:,:),0.0,gkernel(:,:).gt.1e-2) ! set kernel<1e-2 to 0.0 (wardetal.2018)
gkernelT(:,:) =transpose(gkernel(:,:))
@@ -898,14 +906,11 @@ SUBROUTINE sub_init_explicit_grazing_params
real ::loc_mort_protect
real ::loc_palatability
real ::loc_growthcost_factor
+ real ::loc_herbivory_real
+ real ::loc_carnivory_real
+ real ::loc_kg
+ real ::loc_respir
- if (ctrl_use_foramecogenie) then
- ! make herbivory and carnivory not logical but range from 0 to 1
- real ::loc_herbivory_real
- real ::loc_carnivory_real
- real ::loc_kg
- real ::loc_respir
- endif
! if setting plankton specific parameters
! check file format and determine number of lines of data
@@ -941,13 +946,13 @@ SUBROUTINE sub_init_explicit_grazing_params
READ(unit=in,fmt='(1X)')
END DO
- if (ctrl_use_foramecogenie) then
+ if (ctrl_use_foramecogenie .AND. ctrl_numerical_feeding) then
!read in richer population specifications
DO n = 1,loc_n_elements
READ(unit=in,FMT=*) &
& loc_plnktn_pft, & ! COLUMN #01: plankton PFT (not used here)
- & loc_herbivory, & ! COLUMN #02: herbivory
- & loc_carnivory, & ! COLUMN #03: carnivory
+ & loc_herbivory_real, & ! COLUMN #02: herbivory
+ & loc_carnivory_real, & ! COLUMN #03: carnivory
& loc_pp_opt_a, & ! COLUMN #04: pp_opt_a
& loc_pp_sig_a, & ! COLUMN #05: pp_sig_a
& loc_ns, & ! COLUMN #06: ns (prey switching)
@@ -957,8 +962,8 @@ SUBROUTINE sub_init_explicit_grazing_params
& loc_kg, & ! COLUMN #10: spine-derived kg modification Rui Oct21
& loc_respir ! COLUMN #11: increased respiration rate for the calcite building cost
- herbivory(n) = loc_herbivory
- carnivory(n) = loc_carnivory
+ herbivory_real(n) = loc_herbivory_real
+ carnivory_real(n) = loc_carnivory_real
pp_opt_a_array(n) = loc_pp_opt_a
pp_sig_a_array(n) = loc_pp_sig_a
ns_array(n) = loc_ns
@@ -967,6 +972,7 @@ SUBROUTINE sub_init_explicit_grazing_params
growthcost_factor(n) = loc_growthcost_factor
kg_scale(n) = loc_kg
respir_cost(n) = loc_respir
+ END DO
else
!read in population specifications
DO n = 1,loc_n_elements
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index ca8308bb4..00ac4f75b 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -140,6 +140,10 @@ MODULE ecogem_lib
! Mixotrophy parameters
real :: trophic_tradeoff,foram_auto_cost_sn,foram_auto_cost_ss,foram_hetero_cost_sn,foram_hetero_cost_ss
namelist/ini_ecogem_nml/trophic_tradeoff,foram_auto_cost_sn,foram_auto_cost_ss,foram_hetero_cost_sn,foram_hetero_cost_ss
+ real ::foram_grazing_scale_bs, foram_grazing_scale_ss, foram_symbiont_esd_scale
+ namelist/ini_ecogem_nml/foram_grazing_scale_bs, foram_grazing_scale_ss, foram_symbiont_esd_scale
+ logical :: ctrl_numerical_feeding
+ namelist/ini_ecogem_nml/ctrl_numerical_feeding
! Temperature dependence
real :: temp_A,temp_P,temp_K,temp_T0 !
namelist/ini_ecogem_nml/temp_A,temp_P,temp_K,temp_T0
@@ -292,6 +296,7 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:) ::volume,diameter ,logvol,logesd ! Size parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::autotrophy,heterotrophy ! Trophic strategy
LOGICAL ,ALLOCATABLE,DIMENSION(:) ::herbivory,carnivory ! Feeding behavior - Added by Grigoratou, Nov18
+ REAL ,ALLOCATABLE,DIMENSION(:) ::herbivory_real,carnivory_real ! Feeding behavior - Added by Grigoratou, Nov18
real ,ALLOCATABLE,DIMENSION(:) ::pp_opt_a_array,pp_sig_a_array,ns_array ! grazing parameters as arrays
REAL ,ALLOCATABLE,DIMENSION(:) ::prey_refuge ! PFT dependent traits - Added by Grigoratou, Dec18
REAL ,ALLOCATABLE,DIMENSION(:) ::mort_protect ! PFT dependent traits - Added by Grigoratou, Dec18
diff --git a/genie-main/src/xml-config/xml/definition.xml b/genie-main/src/xml-config/xml/definition.xml
index 8025ad087..4ccb67cb7 100644
--- a/genie-main/src/xml-config/xml/definition.xml
+++ b/genie-main/src/xml-config/xml/definition.xml
@@ -8902,6 +8902,11 @@ par_bio_red_PC_alpha2 scales the offset of 6.0e-3 of Galbraith & Martiny, 2015 C
.FALSE.
kill foraminifera when calcite saturation state is less than 1
+
+
+ .FALSE.
+ make carnivory/herbivory array real type instead of logical
+
40.0
From ce0598c0b809a1fc62f32b3e76ad4e81e623170d Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 02:04:33 +0100
Subject: [PATCH 10/89] all debug done!
---
genie-ecogem/src/fortran/ecogem.f90 | 4 ++--
genie-ecogem/src/fortran/ecogem_lib.f90 | 2 ++
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem.f90 b/genie-ecogem/src/fortran/ecogem.f90
index 3e5c5979e..7b3ebbd21 100644
--- a/genie-ecogem/src/fortran/ecogem.f90
+++ b/genie-ecogem/src/fortran/ecogem.f90
@@ -326,7 +326,7 @@ subroutine ecogem( &
! foram cannot live in environment with < 1 omega
! Roy et al. 2015. Biogeosciences, 12, 2873–2889, 2015
- if (ctrl_foram_oa .and. (omega(i,j,k) .lt. 1.0)) then
+ if (ctrl_foramecogenie_oa .and. (omega(i,j,k) .lt. 1.0)) then
do jp=1,npmax
! for any foram
if (index(pft(jp), "foram") /= 0) then
@@ -395,7 +395,7 @@ subroutine ecogem( &
! mortality(:) = mortality(:) * gamma_TK ! temp adjusted?
! calculate respiration
- respiration(:) = respir(:) * gamma_T !* (1.0 - exp(-1.0e10 * loc_biomass(iCarb,:))) ! reduce respiration at very low biomass
+ respiration(:) = respir(:) * gamma_TK !* (1.0 - exp(-1.0e10 * loc_biomass(iCarb,:))) ! reduce respiration at very low biomass
! calculate assimilation efficiency based on quota status
!BAW: zoolimit should be optional Totzoolimit(:) = 0.0 !total food limitation - Maria May 2019 !!! Need to check if consistent!!!
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index 00ac4f75b..3e6d083d5 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -175,6 +175,8 @@ MODULE ecogem_lib
! RY Foram symbiont bleaching, ocean acidification killing control
logical::ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa, ctrl_use_foramecogenie
namelist /ini_ecogem_nml/ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa,ctrl_use_foramecogenie
+ real::foramecogenie_bleach_temp
+ namelist /ini_ecogem_nml/foramecogenie_bleach_temp
! explicit grazing parameters
logical::ctrl_grazing_explicit
namelist /ini_ecogem_nml/ctrl_grazing_explicit
From de42f612438a8c8304f0fe585555701744973b44 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 14:11:25 +0100
Subject: [PATCH 11/89] update user-configs
---
...CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1 | 23 +++++++++++-------
...CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1 | 22 ++++++++++-------
...a.BASESFeTDTL_rb_foramecogem2.1.modernAMOC | 22 ++++++++++-------
...Q00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN | 24 ++++++++++++-------
...umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN | 24 ++++++++++++-------
...Q04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN | 24 ++++++++++++-------
...Q04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN | 24 ++++++++++++-------
...lg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg | 22 ++++++++++-------
...orlg4.BASESFeTDTL.foramecogem2.1.2100.2deg | 22 ++++++++++-------
...orlg4.BASESFeTDTL.foramecogem2.1.2100.3deg | 22 ++++++++++-------
...orlg4.BASESFeTDTL.foramecogem2.1.2100.4deg | 22 ++++++++++-------
...CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN | 23 +++++++++++-------
...rlg4.BASESFeTDTL.foramecogem2.1.historical | 21 +++++++++-------
.../FORAMECOGEM/update_userconfig.py | 2 +-
14 files changed, 181 insertions(+), 116 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1
index 7c7b6f6c8..64162005b 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1
@@ -71,18 +71,25 @@ bg_par_bio_FetoC_C=0.0
#
# *** ECOGEM ********************************************************
#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1
index ffafa57b3..4092c7bfe 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1
@@ -69,15 +69,19 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
-
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
+
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1.modernAMOC
index 3b5d3e950..f49774eb4 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1.modernAMOC
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1.modernAMOC
@@ -69,15 +69,19 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
-
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
+
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
index 39ace5762..1413a03e9 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
@@ -44,19 +44,25 @@ bg_par_bio_remin_sinkingrate_reaction=125.0
#
# *** ECOGEM ********************************************************
#
-# Planktic Foraminifer and Ecosystem
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN
index e6195a162..80ff9845a 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN
@@ -44,19 +44,25 @@ bg_par_bio_remin_sinkingrate_reaction=125.0
#
# *** ECOGEM ********************************************************
#
-# Planktic Foraminifer and Ecosystem
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
index dac971aaa..5e7568e9d 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
@@ -44,19 +44,25 @@ bg_par_bio_remin_sinkingrate_reaction=125.0
#
# *** ECOGEM ********************************************************
#
-# Planktic Foraminifer and Ecosystem
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN
index 69dbf5620..87ed08c54 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN
@@ -44,19 +44,25 @@ bg_par_bio_remin_sinkingrate_reaction=125.0
#
# *** ECOGEM ********************************************************
#
-# Planktic Foraminifer and Ecosystem
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg
index fbb1f3810..9983ba076 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg
@@ -76,15 +76,19 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
-
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
+
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.2deg
index a3ce3de18..131e7191f 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.2deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.2deg
@@ -76,15 +76,19 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
-
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
+
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.3deg
index 07942ad3a..a66f6dd17 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.3deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.3deg
@@ -76,15 +76,19 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
-
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
+
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.4deg
index d99432318..2a872830f 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.4deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.4deg
@@ -76,15 +76,19 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
-
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
+
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
index e72a4a6fe..cb15953f5 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
@@ -76,15 +76,20 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
-
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
+eg_ctrl_numerical_feeding = .true.
+
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical
index 1f5fdc476..f62d3d3c0 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical
@@ -76,15 +76,20 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_ctrl_use_foramecogenie = .true.
+eg_ctrl_foramecogenie_oa = .false.
+eg_ctrl_foramecogenie_bleach = .false.
+
+eg_par_ecogem_plankton_file = '8P7Z4F.eco'
+eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale = 0.0015
+eg_foram_auto_cost_sn = 0.8
+eg_foram_hetero_cost_sn = 0.5
+eg_foram_auto_cost_ss = 1.0
+eg_foram_hetero_cost_ss = 0.5
+eg_foram_grazing_scale_bs = 2.0
+eg_foram_grazing_scale_ss = 2.0
-eg_ah_size_ratio=0.0015
-eg_ss_tradeoff_a=1.0
-eg_ss_tradeoff_h=0.5
-
-eg_sn_tradeoff_a=0.8
-eg_sn_tradeoff_h=0.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/update_userconfig.py b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
index bfa9deb4e..64948394a 100644
--- a/genie-userconfigs/FORAMECOGEM/update_userconfig.py
+++ b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
@@ -11,7 +11,7 @@ def update_foramecogem(directory):
'eg_ctrl_ncrst' : '.false.',
'eg_ctrl_continuing' : '.false.',
'eg_ctrl_grazing_explicit': '.true.',
- 'eg_ctrl_debug_init': '0',
+ 'ma_ctrl_debug_init': '0',
'eg_ctrl_debug_eco_init': '.false.',
'eg_gkernel_cap': '.false.',
## foramecogenie parameters (logical)
From 4d59ea987cc31c4c782da9a055db2c4859f514e3 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 14:11:49 +0100
Subject: [PATCH 12/89] remove numerical_feeding!
---
genie-ecogem/src/fortran/ecogem_data.f90 | 12 +++++-------
genie-ecogem/src/fortran/ecogem_lib.f90 | 3 ---
genie-main/src/xml-config/xml/definition.xml | 5 -----
3 files changed, 5 insertions(+), 15 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 5ac085fc8..8ddd8cc84 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -906,8 +906,6 @@ SUBROUTINE sub_init_explicit_grazing_params
real ::loc_mort_protect
real ::loc_palatability
real ::loc_growthcost_factor
- real ::loc_herbivory_real
- real ::loc_carnivory_real
real ::loc_kg
real ::loc_respir
@@ -946,13 +944,13 @@ SUBROUTINE sub_init_explicit_grazing_params
READ(unit=in,fmt='(1X)')
END DO
- if (ctrl_use_foramecogenie .AND. ctrl_numerical_feeding) then
+ if (ctrl_use_foramecogenie) then
!read in richer population specifications
DO n = 1,loc_n_elements
READ(unit=in,FMT=*) &
& loc_plnktn_pft, & ! COLUMN #01: plankton PFT (not used here)
- & loc_herbivory_real, & ! COLUMN #02: herbivory
- & loc_carnivory_real, & ! COLUMN #03: carnivory
+ & loc_herbivory, & ! COLUMN #02: herbivory
+ & loc_carnivory, & ! COLUMN #03: carnivory
& loc_pp_opt_a, & ! COLUMN #04: pp_opt_a
& loc_pp_sig_a, & ! COLUMN #05: pp_sig_a
& loc_ns, & ! COLUMN #06: ns (prey switching)
@@ -962,8 +960,8 @@ SUBROUTINE sub_init_explicit_grazing_params
& loc_kg, & ! COLUMN #10: spine-derived kg modification Rui Oct21
& loc_respir ! COLUMN #11: increased respiration rate for the calcite building cost
- herbivory_real(n) = loc_herbivory_real
- carnivory_real(n) = loc_carnivory_real
+ herbivory_real(n) = loc_herbivory
+ carnivory_real(n) = loc_carnivory
pp_opt_a_array(n) = loc_pp_opt_a
pp_sig_a_array(n) = loc_pp_sig_a
ns_array(n) = loc_ns
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index 3e6d083d5..fb84bb7c9 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -142,8 +142,6 @@ MODULE ecogem_lib
namelist/ini_ecogem_nml/trophic_tradeoff,foram_auto_cost_sn,foram_auto_cost_ss,foram_hetero_cost_sn,foram_hetero_cost_ss
real ::foram_grazing_scale_bs, foram_grazing_scale_ss, foram_symbiont_esd_scale
namelist/ini_ecogem_nml/foram_grazing_scale_bs, foram_grazing_scale_ss, foram_symbiont_esd_scale
- logical :: ctrl_numerical_feeding
- namelist/ini_ecogem_nml/ctrl_numerical_feeding
! Temperature dependence
real :: temp_A,temp_P,temp_K,temp_T0 !
namelist/ini_ecogem_nml/temp_A,temp_P,temp_K,temp_T0
@@ -298,7 +296,6 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:) ::volume,diameter ,logvol,logesd ! Size parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::autotrophy,heterotrophy ! Trophic strategy
LOGICAL ,ALLOCATABLE,DIMENSION(:) ::herbivory,carnivory ! Feeding behavior - Added by Grigoratou, Nov18
- REAL ,ALLOCATABLE,DIMENSION(:) ::herbivory_real,carnivory_real ! Feeding behavior - Added by Grigoratou, Nov18
real ,ALLOCATABLE,DIMENSION(:) ::pp_opt_a_array,pp_sig_a_array,ns_array ! grazing parameters as arrays
REAL ,ALLOCATABLE,DIMENSION(:) ::prey_refuge ! PFT dependent traits - Added by Grigoratou, Dec18
REAL ,ALLOCATABLE,DIMENSION(:) ::mort_protect ! PFT dependent traits - Added by Grigoratou, Dec18
diff --git a/genie-main/src/xml-config/xml/definition.xml b/genie-main/src/xml-config/xml/definition.xml
index 4ccb67cb7..5baf0f1f4 100644
--- a/genie-main/src/xml-config/xml/definition.xml
+++ b/genie-main/src/xml-config/xml/definition.xml
@@ -8903,11 +8903,6 @@ par_bio_red_PC_alpha2 scales the offset of 6.0e-3 of Galbraith & Martiny, 2015 C
kill foraminifera when calcite saturation state is less than 1
-
- .FALSE.
- make carnivory/herbivory array real type instead of logical
-
-
40.0
temperature threshold of symbiont bleaching in Celsius
From d3fd01b0da807f08112bf563b1da1e1ae44a36d4 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 14:12:05 +0100
Subject: [PATCH 13/89] correct foram names
---
genie-ecogem/src/fortran/ecogem_data.f90 | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 8ddd8cc84..878243d76 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -403,14 +403,14 @@ SUBROUTINE sub_init_plankton()
silicify(jp) = 0.0
autotrophy(jp) = 0.0
heterotrophy(jp) = 1.0
- elseif (pft(jp).eq.'foram_bn') then
+ elseif (pft(jp).eq.'foram_bs') then
NO3up(jp) = 0.0
Nfix(jp) = 0.0
calcify(jp) = 0.0
silicify(jp) = 0.0
autotrophy(jp) = 0.0
heterotrophy(jp) = 1.0
- elseif (pft(jp).eq.'foram_bn') then
+ elseif (pft(jp).eq.'foram_sn') then
NO3up(jp) = 0.0
Nfix(jp) = 0.0
calcify(jp) = 0.0
From 3b508cacde8f596b9f7e726b40134f8062075247 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 14:17:13 +0100
Subject: [PATCH 14/89] again remove ctrl_numerical_feeding
---
genie-ecogem/src/fortran/ecogem_data.f90 | 205 +++++++++++------------
1 file changed, 99 insertions(+), 106 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 878243d76..1a9466eb4 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -484,12 +484,8 @@ SUBROUTINE sub_init_plankton()
mort_protect(:)=1.0
palatability(:)=1.0
growthcost_factor(:)=1.0
- if (ctrl_numerical_feeding) then
- herbivory_real(:)=0.0
- carnivory_real(:)=0.0
- else
- herbivory(:)=.false.
- carnivory(:)=.false.
+ herbivory(:)=.false.
+ carnivory(:)=.false.
endif
endif
! set growth costs (could do the same for autotrophy in coccolithophores) - Fanny Mar21
@@ -591,114 +587,111 @@ SUBROUTINE sub_init_plankton()
end do
end select
end do
-
- if (gkernel_cap) gkernel(:,:) =merge(gkernel(:,:),0.0,gkernel(:,:).gt.1e-2) ! set kernel<1e-2 to 0.0 (wardetal.2018)
- gkernelT(:,:) =transpose(gkernel(:,:))
- ! detrital partitioning
- ! NOTE: fraction partitioned into DOM (a seperate and explicit array is created for 1-minus this -- the fraction into POM)
- beta_graz(:) =beta_graz_a - (beta_graz_a-beta_graz_b) / (1.0+beta_mort_c/diameter(:))
- beta_mort(:) =beta_mort_a - (beta_mort_a-beta_mort_b) / (1.0+beta_mort_c/diameter(:))
- endif
-
- !-----------------------------------------------------------------------------------------
- ! maximum photosynthetic rate
- ! vmax(iDIC,:) = vmaxDIC_a * volume(:) ** vmaxDIC_b * autotrophy(:)
- vmax(iDIC,:) = (vmaxDIC_a + log10(volume(:))) / (vmaxDIC_b + vmaxDIC_c * log10(volume(:)) + log10(volume(:))**2) * autotrophy(:)
- !-----------------------------------------------------------------------------------------
- if (nquota) then ! nitrogen parameters
- qmin(iNitr,:) = qminN_a * volume(:) ** qminN_b
- qmax(iNitr,:) = qmaxN_a * volume(:) ** qmaxN_b
- if (maxval((qmin(iNitr,:)/qmax(iNitr,:))).gt.1.0) print*,"WARNING: Nitrogen Qmin > Qmax. Population inviable!"
- if (useNO3) then ! nitrate parameters
- vmax(iNO3,:) = vmaxNO3_a * volume(:) ** vmaxNO3_b * autotrophy(:) * NO3up(:)
- affinity(iNO3,:) = affinNO3_a * volume(:) ** affinNO3_b * autotrophy(:) * NO3up(:)
+ if (gkernel_cap) gkernel(:,:) =merge(gkernel(:,:),0.0,gkernel(:,:).gt.1e-2) ! set kernel<1e-2 to 0.0 (wardetal.2018)
+ gkernelT(:,:) =transpose(gkernel(:,:))
+
+ ! detrital partitioning
+ ! NOTE: fraction partitioned into DOM (a seperate and explicit array is created for 1-minus this -- the fraction into POM)
+ beta_graz(:) =beta_graz_a - (beta_graz_a-beta_graz_b) / (1.0+beta_mort_c/diameter(:))
+ beta_mort(:) =beta_mort_a - (beta_mort_a-beta_mort_b) / (1.0+beta_mort_c/diameter(:))
+ else
+ ! >>>>>>>> Noraml ECOGEM Setting
+ !-----------------------------------------------------------------------------------------
+ ! maximum photosynthetic rate
+ ! vmax(iDIC,:) = vmaxDIC_a * volume(:) ** vmaxDIC_b * autotrophy(:)
+ vmax(iDIC,:) = (vmaxDIC_a + log10(volume(:))) / (vmaxDIC_b + vmaxDIC_c * log10(volume(:)) + log10(volume(:))**2) * autotrophy(:)
+ !-----------------------------------------------------------------------------------------
+ if (nquota) then ! nitrogen parameters
+ qmin(iNitr,:) = qminN_a * volume(:) ** qminN_b
+ qmax(iNitr,:) = qmaxN_a * volume(:) ** qmaxN_b
+ if (maxval((qmin(iNitr,:)/qmax(iNitr,:))).gt.1.0) print*,"WARNING: Nitrogen Qmin > Qmax. Population inviable!"
+ if (useNO3) then ! nitrate parameters
+ vmax(iNO3,:) = vmaxNO3_a * volume(:) ** vmaxNO3_b * autotrophy(:) * NO3up(:)
+ affinity(iNO3,:) = affinNO3_a * volume(:) ** affinNO3_b * autotrophy(:) * NO3up(:)
+ endif
+ if (useNO2) then ! nitrite parameters
+ vmax(iNO2,:) = vmaxNO2_a * volume(:) ** vmaxNO2_b * autotrophy(:)
+ affinity(iNO2,:) = affinNO2_a * volume(:) ** affinNO2_b * autotrophy(:)
+ endif
+ if (useNH4) then ! ammonium parameters
+ vmax(iNH4,:) = vmaxNH4_a * volume(:) ** vmaxNH4_b * autotrophy(:)
+ affinity(iNH4,:) = affinNH4_a * volume(:) ** affinNH4_b * autotrophy(:)
+ endif
+ kexc(iNitr,:) = kexcN_a * volume(:) ** kexcN_b
+
+ ! mumax(iNitr,:) = vmax(iDIC,:)*vmax(iNO3,:) &
+ ! & /(vmax(iDIC,:)*Qmin(iNitr,:) + vmax(iNO3,:)*qmax(iNitr,:)/(qmax(iNitr,:)-qmin(iNitr,:)))
+ ! alpha(iNitr,:) = affinity(iNitr,:)/Qmin(iNitr,:)
endif
- if (useNO2) then ! nitrite parameters
- vmax(iNO2,:) = vmaxNO2_a * volume(:) ** vmaxNO2_b * autotrophy(:)
- affinity(iNO2,:) = affinNO2_a * volume(:) ** affinNO2_b * autotrophy(:)
+ !-----------------------------------------------------------------------------------------
+ if (pquota) then ! phosphorus parameters
+ qmin(iPhos,:) = qminP_a * volume(:) ** qminP_b
+ qmax(iPhos,:) = qmaxP_a * volume(:) ** qmaxP_b
+ if (maxval((qmin(iPhos,:)/qmax(iPhos,:))).gt.1.0) print*,"WARNING: Phosphate Qmin > Qmax. Population inviable!"
+ vmax(iPO4,:) = vmaxPO4_a * volume(:) ** vmaxPO4_b * autotrophy(:)
+ affinity(iPO4,:) = affinPO4_a * volume(:) ** affinPO4_b * autotrophy(:)
+ kexc(iPhos,:) = kexcP_a * volume(:) ** kexcP_b
endif
- if (useNH4) then ! ammonium parameters
- vmax(iNH4,:) = vmaxNH4_a * volume(:) ** vmaxNH4_b * autotrophy(:)
- affinity(iNH4,:) = affinNH4_a * volume(:) ** affinNH4_b * autotrophy(:)
+ !-----------------------------------------------------------------------------------------
+ if (fquota) then ! iron parameters
+ qmin(iIron,:) = qminFe_a * volume(:) ** qminFe_b
+ qmax(iIron,:) = qmaxFe_a * volume(:) ** qmaxFe_b
+ if (maxval((qmin(iIron,:)/qmax(iIron,:))).gt.1.0) print*,"WARNING: Iron Qmin > Qmax. Population inviable!"
+ vmax(iFe,:) = vmaxFe_a * volume(:) ** vmaxFe_b * autotrophy(:)
+ affinity(iFe,:) = affinFe_a * volume(:) ** affinFe_b * autotrophy(:)
+ kexc(iIron,:) = kexcFe_a * volume(:) ** kexcFe_b
endif
- kexc(iNitr,:) = kexcN_a * volume(:) ** kexcN_b
+ !-----------------------------------------------------------------------------------------
+ if (squota) then ! silicon parameters
+ qmin(iSili,:) = qminSi_a * volume(:) ** qminSi_b * silicify(:)
+ qmax(iSili,:) = qmaxSi_a * volume(:) ** qmaxSi_b * silicify(:)
+ if (maxval((qmin(iSili,:)/qmax(iSili,:))).gt.1.0) print*,"WARNING: Silicon Qmin > Qmax. Population inviable!"
+ vmax(iSiO2,:) = vmaxSiO2_a * volume(:) ** vmaxSiO2_b * autotrophy(:) * silicify(:)
+ affinity(iSiO2,:) =affinSiO2_a * volume(:) ** affinSiO2_b * autotrophy(:)
+ kexc(iSili,:) = kexcSi_a * volume(:) ** kexcSi_b * silicify(:)
+ endif
+ !-----------------------------------------------------------------------------------------
+ ! other parameters
+ qcarbon(:) = qcarbon_a * volume(:) ** qcarbon_b
+ alphachl(:) = alphachl_a * volume(:) ** alphachl_b
+ graz(:) = graz_a * volume(:) ** graz_b * heterotrophy(:)
+ kg(:) = kg_a * volume(:) ** kg_b
+ pp_opt(:) =pp_opt_a_array * volume(:) ** pp_opt_b
+ pp_sig(:) =pp_sig_a_array * volume(:) ** pp_sig_b
+ respir(:) = respir_a * volume(:) ** respir_b
+ biosink(:) = biosink_a * volume(:) ** biosink_b
+ mort(:) = (mort_a * volume(:) ** mort_b) * mort_protect(:) ! mort_protect added by Grigoratou, Dec2018 as a benefit for foram's calcification
+ do jp=1,npmax ! grazing kernel (npred,nprey)
+ ! pad predator dependent pp_opt and pp_sig so that they vary along matrix columns
+ ! (they should be constant within each row)
+ ppopt_mat(:,jp)=pp_opt !added an optimal predator-prey length ratio for each plankton group, Grigoratou, Dec18
+ ppsig_mat(:,jp)=pp_sig !added an optimal standar deviation for predator-prey length ratio for each plankton group, Grigoratou, Dec18
+ enddo
+ pred_diam(:,1)=diameter(:) ! standard prey diameter vector
+ prey_diam(1,:)=diameter(:) ! transpose pred diameter vector
+ prdpry(:,:) =matmul(pred_diam,1.0/prey_diam)
+ gkernel(:,:) =exp(-log(prdpry(:,:)/ppopt_mat(:,:))**2 / (2*ppsig_mat(:,:)**2)) ! [jpred,jprey] populate whole array at once, then find exceptions to set to 0.0 based on type
+ do jpred=1,npmax
+ select case(pft(jpred))
+ case('foram')
+ do jprey=1,npmax
+ if(autotrophy(jprey).gt.0.0 .AND. carnivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
+ if(heterotrophy(jprey).gt.0.0 .AND. herbivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
+ end do
+ end select
+ end do
- ! mumax(iNitr,:) = vmax(iDIC,:)*vmax(iNO3,:) &
- ! & /(vmax(iDIC,:)*Qmin(iNitr,:) + vmax(iNO3,:)*qmax(iNitr,:)/(qmax(iNitr,:)-qmin(iNitr,:)))
- ! alpha(iNitr,:) = affinity(iNitr,:)/Qmin(iNitr,:)
- endif
- !-----------------------------------------------------------------------------------------
- if (pquota) then ! phosphorus parameters
- qmin(iPhos,:) = qminP_a * volume(:) ** qminP_b
- qmax(iPhos,:) = qmaxP_a * volume(:) ** qmaxP_b
- if (maxval((qmin(iPhos,:)/qmax(iPhos,:))).gt.1.0) print*,"WARNING: Phosphate Qmin > Qmax. Population inviable!"
- vmax(iPO4,:) = vmaxPO4_a * volume(:) ** vmaxPO4_b * autotrophy(:)
- affinity(iPO4,:) = affinPO4_a * volume(:) ** affinPO4_b * autotrophy(:)
- kexc(iPhos,:) = kexcP_a * volume(:) ** kexcP_b
- endif
- !-----------------------------------------------------------------------------------------
- if (fquota) then ! iron parameters
- qmin(iIron,:) = qminFe_a * volume(:) ** qminFe_b
- qmax(iIron,:) = qmaxFe_a * volume(:) ** qmaxFe_b
- if (maxval((qmin(iIron,:)/qmax(iIron,:))).gt.1.0) print*,"WARNING: Iron Qmin > Qmax. Population inviable!"
- vmax(iFe,:) = vmaxFe_a * volume(:) ** vmaxFe_b * autotrophy(:)
- affinity(iFe,:) = affinFe_a * volume(:) ** affinFe_b * autotrophy(:)
- kexc(iIron,:) = kexcFe_a * volume(:) ** kexcFe_b
- endif
- !-----------------------------------------------------------------------------------------
- if (squota) then ! silicon parameters
- qmin(iSili,:) = qminSi_a * volume(:) ** qminSi_b * silicify(:)
- qmax(iSili,:) = qmaxSi_a * volume(:) ** qmaxSi_b * silicify(:)
- if (maxval((qmin(iSili,:)/qmax(iSili,:))).gt.1.0) print*,"WARNING: Silicon Qmin > Qmax. Population inviable!"
- vmax(iSiO2,:) = vmaxSiO2_a * volume(:) ** vmaxSiO2_b * autotrophy(:) * silicify(:)
- affinity(iSiO2,:) =affinSiO2_a * volume(:) ** affinSiO2_b * autotrophy(:)
- kexc(iSili,:) = kexcSi_a * volume(:) ** kexcSi_b * silicify(:)
- endif
- !-----------------------------------------------------------------------------------------
- ! other parameters
- qcarbon(:) = qcarbon_a * volume(:) ** qcarbon_b
- alphachl(:) = alphachl_a * volume(:) ** alphachl_b
- graz(:) = graz_a * volume(:) ** graz_b * heterotrophy(:)
- kg(:) = kg_a * volume(:) ** kg_b
- pp_opt(:) =pp_opt_a_array * volume(:) ** pp_opt_b
- pp_sig(:) =pp_sig_a_array * volume(:) ** pp_sig_b
- respir(:) = respir_a * volume(:) ** respir_b
- biosink(:) = biosink_a * volume(:) ** biosink_b
- mort(:) = (mort_a * volume(:) ** mort_b) * mort_protect(:) ! mort_protect added by Grigoratou, Dec2018 as a benefit for foram's calcification
- do jp=1,npmax ! grazing kernel (npred,nprey)
- ! pad predator dependent pp_opt and pp_sig so that they vary along matrix columns
- ! (they should be constant within each row)
- ppopt_mat(:,jp)=pp_opt !added an optimal predator-prey length ratio for each plankton group, Grigoratou, Dec18
- ppsig_mat(:,jp)=pp_sig !added an optimal standar deviation for predator-prey length ratio for each plankton group, Grigoratou, Dec18
- enddo
- pred_diam(:,1)=diameter(:) ! standard prey diameter vector
- prey_diam(1,:)=diameter(:) ! transpose pred diameter vector
- prdpry(:,:) =matmul(pred_diam,1.0/prey_diam)
- gkernel(:,:) =exp(-log(prdpry(:,:)/ppopt_mat(:,:))**2 / (2*ppsig_mat(:,:)**2)) ! [jpred,jprey] populate whole array at once, then find exceptions to set to 0.0 based on type
- do jpred=1,npmax
- select case(pft(jpred))
- case('foram')
- do jprey=1,npmax
- if(autotrophy(jprey).gt.0.0 .AND. carnivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
- if(heterotrophy(jprey).gt.0.0 .AND. herbivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
- end do
- end select
- end do
-
- if(ctrl_numerical_feeding .AND. autotrophy(jprey).gt.0.0) gkernel(jpred,jprey)=gkernel(jpred,jprey) * herbivory_real(jpred)
- if(ctrl_numerical_feeding .AND. heterotrophy(jprey).gt.0.0) gkernel(jpred,jprey)=gkernel(jpred,jprey) * carnivory_real(jpred)
+ if (gkernel_cap) gkernel(:,:) =merge(gkernel(:,:),0.0,gkernel(:,:).gt.1e-2) ! set kernel<1e-2 to 0.0 (wardetal.2018)
+ gkernelT(:,:) =transpose(gkernel(:,:))
- if (gkernel_cap) gkernel(:,:) =merge(gkernel(:,:),0.0,gkernel(:,:).gt.1e-2) ! set kernel<1e-2 to 0.0 (wardetal.2018)
- gkernelT(:,:) =transpose(gkernel(:,:))
+ ! detrital partitioning
+ ! NOTE: fraction partitioned into DOM (a seperate and explicit array is created for 1-minus this -- the fraction into POM)
+ beta_graz(:) =beta_graz_a - (beta_graz_a-beta_graz_b) / (1.0+beta_mort_c/diameter(:))
+ beta_mort(:) =beta_mort_a - (beta_mort_a-beta_mort_b) / (1.0+beta_mort_c/diameter(:))
+ endif
- ! detrital partitioning
- ! NOTE: fraction partitioned into DOM (a seperate and explicit array is created for 1-minus this -- the fraction into POM)
- beta_graz(:) =beta_graz_a - (beta_graz_a-beta_graz_b) / (1.0+beta_mort_c/diameter(:))
- beta_mort(:) =beta_mort_a - (beta_mort_a-beta_mort_b) / (1.0+beta_mort_c/diameter(:))
-
-
! ****************************************************************************************
! ****************************************************************************************
! Write plankton parameters to output file (opened in initialise_ecogem)
From c8b14cf1ab91fe834a9a7cecafd6d094eff135d5 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 14:21:12 +0100
Subject: [PATCH 15/89] update foramecogem.zoo grazing file
---
genie-ecogem/src/fortran/ecogem_data.f90 | 6 +--
genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo | 38 +++++++++----------
2 files changed, 22 insertions(+), 22 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 1a9466eb4..a02b09d88 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -486,8 +486,8 @@ SUBROUTINE sub_init_plankton()
growthcost_factor(:)=1.0
herbivory(:)=.false.
carnivory(:)=.false.
- endif
endif
+
! set growth costs (could do the same for autotrophy in coccolithophores) - Fanny Mar21
heterotrophy(:) = heterotrophy(:)*growthcost_factor(:)
@@ -953,8 +953,8 @@ SUBROUTINE sub_init_explicit_grazing_params
& loc_kg, & ! COLUMN #10: spine-derived kg modification Rui Oct21
& loc_respir ! COLUMN #11: increased respiration rate for the calcite building cost
- herbivory_real(n) = loc_herbivory
- carnivory_real(n) = loc_carnivory
+ herbivory(n) = loc_herbivory
+ carnivory(n) = loc_carnivory
pp_opt_a_array(n) = loc_pp_opt_a
pp_sig_a_array(n) = loc_pp_sig_a
ns_array(n) = loc_ns
diff --git a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
index 78fa2831f..d56b164da 100644
--- a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
+++ b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
@@ -3,25 +3,25 @@
\/ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
-START-OF-DATA-
-Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton 0.0 0.0 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-foram_bn 1.0 0.0 10.0 4.0 1.0 0.7 0.8 1.0 1.0 0.04
-foram_bs 1.0 0.0 10.0 2.0 1.0 0.7 0.7 1.0 0.75 0.06
-foram_sn 1.0 0.0 10.0 4.0 1.0 0.7 0.8 1.0 1.0 0.04
-foram_ss 0.0 1.0 10.0 2.0 1.0 0.7 0.7 1.0 0.8 0.06
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
+foram_bn t f 10.0 4.0 1.0 0.7 0.8 1.0 1.0 0.04
+foram_bs t f 10.0 2.0 1.0 0.7 0.7 1.0 0.75 0.06
+foram_sn t f 10.0 4.0 1.0 0.7 0.8 1.0 1.0 0.04
+foram_ss f t 10.0 2.0 1.0 0.7 0.7 1.0 0.8 0.06
-END-OF-DATA-
/\ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
From 3128c384c16c726c7ff317461aa884657597bc5b Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 14:38:26 +0100
Subject: [PATCH 16/89] Add hetero_diameter
---
genie-ecogem/src/fortran/ecogem_data.f90 | 11 +++++------
genie-ecogem/src/fortran/ecogem_lib.f90 | 2 +-
genie-ecogem/src/fortran/initialise_ecogem.f90 | 3 +++
3 files changed, 9 insertions(+), 7 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index a02b09d88..207f7cb4b 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -415,14 +415,14 @@ SUBROUTINE sub_init_plankton()
Nfix(jp) = 0.0
calcify(jp) = 0.0
silicify(jp) = 0.0
- autotrophy(jp) = 0.0
+ autotrophy(jp) = 1.0
heterotrophy(jp) = 1.0
elseif (pft(jp).eq.'foram_ss') then
NO3up(jp) = 0.0
Nfix(jp) = 0.0
calcify(jp) = 0.0
silicify(jp) = 0.0
- autotrophy(jp) = 0.0
+ autotrophy(jp) = 1.0
heterotrophy(jp) = 1.0
else
print*," "
@@ -458,8 +458,7 @@ SUBROUTINE sub_init_plankton()
grazing_esd_scale(:) = 1.0
symbiont_auto_cost(:) = 1.0
symbiont_hetero_cost(:) = 1.0
-
-
+
! modify for foraminifera only
if (pft(jp).eq.'foram_bs') then
grazing_esd_scale(:) = foram_grazing_scale_bs
@@ -496,6 +495,7 @@ SUBROUTINE sub_init_plankton()
! v1/v2 = (r1/r2)^3
auto_volume(:) = volume(:) * symbiont_esd_scale(:) ** 3
hetero_volume(:) = volume(:) * grazing_esd_scale(:) ** 3
+ hetero_diamter(:) = diameter(:) * grazing_esd_scale(:)
autotrophy(:) = autotrophy(:) * symbiont_auto_cost(:)
heterotrophy(:) = heterotrophy(:) * symbiont_hetero_cost(:)
@@ -573,7 +573,7 @@ SUBROUTINE sub_init_plankton()
ppopt_mat(:,jp)=pp_opt !added an optimal predator-prey length ratio for each plankton group, Grigoratou, Dec18
ppsig_mat(:,jp)=pp_sig !added an optimal standar deviation for predator-prey length ratio for each plankton group, Grigoratou, Dec18
enddo
- pred_diam(:,1)=diameter(:) ! standard prey diameter vector
+ pred_diam(:,1)=hetero_diameter(:) ! standard prey diameter vector
prey_diam(1,:)=diameter(:) ! transpose pred diameter vector
prdpry(:,:) =matmul(pred_diam,1.0/prey_diam)
gkernel(:,:) =exp(-log(prdpry(:,:)/ppopt_mat(:,:))**2 / (2*ppsig_mat(:,:)**2)) ! [jpred,jprey] populate whole array at once, then find exceptions to set to 0.0 based on type
@@ -588,7 +588,6 @@ SUBROUTINE sub_init_plankton()
end select
end do
-
if (gkernel_cap) gkernel(:,:) =merge(gkernel(:,:),0.0,gkernel(:,:).gt.1e-2) ! set kernel<1e-2 to 0.0 (wardetal.2018)
gkernelT(:,:) =transpose(gkernel(:,:))
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index fb84bb7c9..5df5d342b 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -308,7 +308,7 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:) ::respir,biosink,mort,beta_graz,beta_mort ! Other loss parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::symbiont_auto_cost, symbiont_hetero_cost ! RY, foramecogenie symbiont cost parameter
REAL ,ALLOCATABLE,DIMENSION(:) ::auto_volume, hetero_volume, grazing_esd_scale, symbiont_esd_scale ! RY, foramecogenie size parameter
- REAL ,ALLOCATABLE,DIMENSION(:) ::respir_cost,kg_scale ! RY, foramecogenie grazing parameter
+ REAL ,ALLOCATABLE,DIMENSION(:) ::respir_cost,kg_scale, hetero_diameter ! RY, foramecogenie grazing parameter
! Grazing kernel
REAL,ALLOCATABLE,DIMENSION(:,:)::gkernel,gkernelT
diff --git a/genie-ecogem/src/fortran/initialise_ecogem.f90 b/genie-ecogem/src/fortran/initialise_ecogem.f90
index f342115c3..da75a6bc8 100644
--- a/genie-ecogem/src/fortran/initialise_ecogem.f90
+++ b/genie-ecogem/src/fortran/initialise_ecogem.f90
@@ -338,6 +338,9 @@ SUBROUTINE initialise_ecogem( &
ALLOCATE(hetero_volume(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
+
+ ALLOCATE(hetero_diameter(npmax),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(grazing_esd_scale(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
From 67dc03a76ac52d3061245b3ab7d2a8e94335d5b7 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 14:46:28 +0100
Subject: [PATCH 17/89] fix a typo: diameter
---
genie-ecogem/src/fortran/ecogem_data.f90 | 2 +-
genie-ecogem/src/fortran/ecogem_lib.f90 | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 207f7cb4b..a0f50dcc7 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -495,7 +495,7 @@ SUBROUTINE sub_init_plankton()
! v1/v2 = (r1/r2)^3
auto_volume(:) = volume(:) * symbiont_esd_scale(:) ** 3
hetero_volume(:) = volume(:) * grazing_esd_scale(:) ** 3
- hetero_diamter(:) = diameter(:) * grazing_esd_scale(:)
+ hetero_diameter(:) = diameter(:) * grazing_esd_scale(:)
autotrophy(:) = autotrophy(:) * symbiont_auto_cost(:)
heterotrophy(:) = heterotrophy(:) * symbiont_hetero_cost(:)
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index 5df5d342b..057568b23 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -293,7 +293,7 @@ MODULE ecogem_lib
character(len=5) ,ALLOCATABLE,DIMENSION(:) ::rsrcstrng ! Inorganic resource labels
INTEGER ,ALLOCATABLE,DIMENSION(:) ::random_n ! n population replicates
INTEGER ,ALLOCATABLE,DIMENSION(:) ::nut2quota ! match nutrients to quotas
- REAL ,ALLOCATABLE,DIMENSION(:) ::volume,diameter ,logvol,logesd ! Size parameters
+ REAL ,ALLOCATABLE,DIMENSION(:) ::volume,diameter,logvol,logesd ! Size parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::autotrophy,heterotrophy ! Trophic strategy
LOGICAL ,ALLOCATABLE,DIMENSION(:) ::herbivory,carnivory ! Feeding behavior - Added by Grigoratou, Nov18
real ,ALLOCATABLE,DIMENSION(:) ::pp_opt_a_array,pp_sig_a_array,ns_array ! grazing parameters as arrays
From 215262f9e909814cf4639c59735d6df492f8364c Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 15:41:55 +0100
Subject: [PATCH 18/89] move the namelist in ecogem_lib.f90 together
---
genie-ecogem/src/fortran/ecogem_lib.f90 | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index 057568b23..ea15ce5ef 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -138,10 +138,17 @@ MODULE ecogem_lib
namelist/ini_ecogem_nml/beta_graz_a,beta_graz_b,beta_graz_c,beta_mort_a,beta_mort_b,beta_mort_c
namelist/ini_ecogem_nml/par_bio_remin_POC_frac2,par_bio_remin_CaCO3_frac2
! Mixotrophy parameters
- real :: trophic_tradeoff,foram_auto_cost_sn,foram_auto_cost_ss,foram_hetero_cost_sn,foram_hetero_cost_ss
- namelist/ini_ecogem_nml/trophic_tradeoff,foram_auto_cost_sn,foram_auto_cost_ss,foram_hetero_cost_sn,foram_hetero_cost_ss
- real ::foram_grazing_scale_bs, foram_grazing_scale_ss, foram_symbiont_esd_scale
+ real :: trophic_tradeoff
+ namelist/ini_ecogem_nml/trophic_tradeoff
+ ! foramecogenie parameters (11)
+ logical::ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa, ctrl_use_foramecogenie
+ real :: foram_auto_cost_sn, foram_auto_cost_ss, foram_hetero_cost_sn, foram_hetero_cost_ss
+ real :: foram_grazing_scale_bs, foram_grazing_scale_ss, foram_symbiont_esd_scale
+ real :: foramecogenie_bleach_temp
+ namelist/ini_ecogem_nml/foram_auto_cost_sn,foram_auto_cost_ss,foram_hetero_cost_sn,foram_hetero_cost_ss
namelist/ini_ecogem_nml/foram_grazing_scale_bs, foram_grazing_scale_ss, foram_symbiont_esd_scale
+ namelist/ini_ecogem_nml/ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa,ctrl_use_foramecogenie
+ namelist/ini_ecogem_nml/foramecogenie_bleach_temp
! Temperature dependence
real :: temp_A,temp_P,temp_K,temp_T0 !
namelist/ini_ecogem_nml/temp_A,temp_P,temp_K,temp_T0
@@ -170,11 +177,6 @@ MODULE ecogem_lib
namelist /ini_ecogem_nml/ctrl_force_T
character(LEN=127)::par_ecogem_force_T_file
namelist /ini_ecogem_nml/par_ecogem_force_T_file
- ! RY Foram symbiont bleaching, ocean acidification killing control
- logical::ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa, ctrl_use_foramecogenie
- namelist /ini_ecogem_nml/ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa,ctrl_use_foramecogenie
- real::foramecogenie_bleach_temp
- namelist /ini_ecogem_nml/foramecogenie_bleach_temp
! explicit grazing parameters
logical::ctrl_grazing_explicit
namelist /ini_ecogem_nml/ctrl_grazing_explicit
@@ -340,7 +342,6 @@ MODULE ecogem_lib
real::par_misc_t_err !
LOGICAL::par_misc_t_go = .FALSE. !
LOGICAL::par_misc_t_echo_header = .TRUE. !
- !
real::par_misc_t_tseries = 0.0
real::par_misc_t_tslice = 0.0
logical::par_misc_t_intseries = .FALSE.
From 288ce46718a55f52581ce8b0dfd471d9892c444d Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 16:15:39 +0100
Subject: [PATCH 19/89] remove eg_ctrl_numerical_feeding in user-config
---
.../muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN | 1 -
1 file changed, 1 deletion(-)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
index cb15953f5..06aafd6cc 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
@@ -79,7 +79,6 @@ eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie = .true.
eg_ctrl_foramecogenie_oa = .false.
eg_ctrl_foramecogenie_bleach = .false.
-eg_ctrl_numerical_feeding = .true.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
From a0714f830b11c9ef468040e7be652cfcfdde8f5e Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 16:33:57 +0100
Subject: [PATCH 20/89] debug: add for loop in init foram parameters
---
genie-ecogem/src/fortran/ecogem_data.f90 | 39 +++++++++++++-----------
1 file changed, 21 insertions(+), 18 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index a0f50dcc7..2be8c91c2 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -454,24 +454,27 @@ SUBROUTINE sub_init_plankton()
! initialise foram parameters
if (ctrl_use_foramecogenie) then
- symbiont_esd_scale(:) = 1.0
- grazing_esd_scale(:) = 1.0
- symbiont_auto_cost(:) = 1.0
- symbiont_hetero_cost(:) = 1.0
-
- ! modify for foraminifera only
- if (pft(jp).eq.'foram_bs') then
- grazing_esd_scale(:) = foram_grazing_scale_bs
- elseif (pft(jp).eq.'foram_sn') then
- symbiont_esd_scale(:) = foram_symbiont_esd_scale
- symbiont_auto_cost(:) = foram_auto_cost_sn
- symbiont_hetero_cost(:) = foram_hetero_cost_sn
- elseif (pft(jp).eq.'foram_ss') then
- symbiont_esd_scale(:) = foram_symbiont_esd_scale
- symbiont_auto_cost(:) = foram_auto_cost_ss
- symbiont_hetero_cost(:) = foram_hetero_cost_ss
- grazing_esd_scale(:) = foram_grazing_scale_ss
- endif
+ do jp=1,npmax
+ call lower(pft(jp))
+ symbiont_esd_scale(:) = 1.0
+ grazing_esd_scale(:) = 1.0
+ symbiont_auto_cost(:) = 1.0
+ symbiont_hetero_cost(:) = 1.0
+
+ ! modify for foraminifera only
+ if (pft(jp).eq.'foram_bs') then
+ grazing_esd_scale(:) = foram_grazing_scale_bs
+ elseif (pft(jp).eq.'foram_sn') then
+ symbiont_esd_scale(:) = foram_symbiont_esd_scale
+ symbiont_auto_cost(:) = foram_auto_cost_sn
+ symbiont_hetero_cost(:) = foram_hetero_cost_sn
+ elseif (pft(jp).eq.'foram_ss') then
+ symbiont_esd_scale(:) = foram_symbiont_esd_scale
+ symbiont_auto_cost(:) = foram_auto_cost_ss
+ symbiont_hetero_cost(:) = foram_hetero_cost_ss
+ grazing_esd_scale(:) = foram_grazing_scale_ss
+ endif
+ enddo
endif
!-----------------------------------------------------------------------------------------
From b26fa0b97a024920b7be2cdca1e18e64b9256441 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 16:45:49 +0100
Subject: [PATCH 21/89] debug: move init_array out of loop
---
genie-ecogem/src/fortran/ecogem_data.f90 | 31 ++++++++++++------------
1 file changed, 16 insertions(+), 15 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 2be8c91c2..fff859afc 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -454,25 +454,26 @@ SUBROUTINE sub_init_plankton()
! initialise foram parameters
if (ctrl_use_foramecogenie) then
- do jp=1,npmax
- call lower(pft(jp))
- symbiont_esd_scale(:) = 1.0
- grazing_esd_scale(:) = 1.0
- symbiont_auto_cost(:) = 1.0
- symbiont_hetero_cost(:) = 1.0
+ ! initialise arrays
+ symbiont_esd_scale(:) = 1.0
+ grazing_esd_scale(:) = 1.0
+ symbiont_auto_cost(:) = 1.0
+ symbiont_hetero_cost(:) = 1.0
- ! modify for foraminifera only
+ !modify foraminifera PFTs' parameters
+ do jp=1,npmax
+ call lower_case(pft(jp))
if (pft(jp).eq.'foram_bs') then
- grazing_esd_scale(:) = foram_grazing_scale_bs
+ grazing_esd_scale(jp) = foram_grazing_scale_bs
elseif (pft(jp).eq.'foram_sn') then
- symbiont_esd_scale(:) = foram_symbiont_esd_scale
- symbiont_auto_cost(:) = foram_auto_cost_sn
- symbiont_hetero_cost(:) = foram_hetero_cost_sn
+ symbiont_esd_scale(jp) = foram_symbiont_esd_scale
+ symbiont_auto_cost(jp) = foram_auto_cost_sn
+ symbiont_hetero_cost(jp) = foram_hetero_cost_sn
elseif (pft(jp).eq.'foram_ss') then
- symbiont_esd_scale(:) = foram_symbiont_esd_scale
- symbiont_auto_cost(:) = foram_auto_cost_ss
- symbiont_hetero_cost(:) = foram_hetero_cost_ss
- grazing_esd_scale(:) = foram_grazing_scale_ss
+ symbiont_esd_scale(jp) = foram_symbiont_esd_scale
+ symbiont_auto_cost(jp) = foram_auto_cost_ss
+ symbiont_hetero_cost(jp) = foram_hetero_cost_ss
+ grazing_esd_scale(jp) = foram_grazing_scale_ss
endif
enddo
endif
From c48bf39b17ba1086112af98506fdf72417992ded Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Fri, 16 Jun 2023 17:50:16 +0100
Subject: [PATCH 22/89] rename to foramecogem2.2
---
...cogem2.1 => muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2} | 0
...cogem2.1 => muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2} | 0
... muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC} | 0
...ffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN} | 0
...muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN} | 0
...ffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN} | 0
...ffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN} | 0
...g => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg} | 0
...deg => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg} | 0
...deg => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg} | 0
...deg => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg} | 0
...2.1.SPIN => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN} | 0
...al => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical} | 0
13 files changed, 0 insertions(+), 0 deletions(-)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1 => muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1 => muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1.modernAMOC => muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN => muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN => muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN => muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN => muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.2deg => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.3deg => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.4deg => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN} (100%)
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical => muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical} (100%)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1.modernAMOC
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.1p5deg
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.2deg
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.3deg
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.4deg
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
From c7e320481112f2aa89ad20f2b38d75d6e0a75186 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 17 Jun 2023 00:29:34 +0100
Subject: [PATCH 23/89] adjust spinose foram volume
---
genie-ecogem/src/fortran/ecogem_data.f90 | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index fff859afc..bf551944e 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -564,8 +564,8 @@ SUBROUTINE sub_init_plankton()
alphachl(:) = alphachl_a * auto_volume(:) ** alphachl_b
graz(:) = graz_a * hetero_volume(:) ** graz_b * heterotrophy(:)
kg(:) = kg_a * hetero_volume(:) ** kg_b * kg_scale(:)
- pp_opt(:) =pp_opt_a_array * hetero_volume(:) ** pp_opt_b
- pp_sig(:) =pp_sig_a_array * hetero_volume(:) ** pp_sig_b
+ pp_opt(:) =pp_opt_a_array * volume(:) ** pp_opt_b
+ pp_sig(:) =pp_sig_a_array * volume(:) ** pp_sig_b
respir(:) = respir_a * volume(:) ** respir_b + respir_cost(:)
biosink(:) = biosink_a * volume(:) ** biosink_b
mort(:) = (mort_a * volume(:) ** mort_b) * mort_protect(:) ! mort_protect added by Grigoratou, Dec2018 as a benefit for foram's calcification
From 6f3c1bc593629ca9655c747d51d0ad053c416228 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 17 Jun 2023 00:59:20 +0100
Subject: [PATCH 24/89] auto_volume in Si
---
genie-ecogem/src/fortran/ecogem_data.f90 | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index bf551944e..cdb2fa7c4 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -556,7 +556,7 @@ SUBROUTINE sub_init_plankton()
if (maxval((qmin(iSili,:)/qmax(iSili,:))).gt.1.0) print*,"WARNING: Silicon Qmin > Qmax. Population inviable!"
vmax(iSiO2,:) = vmaxSiO2_a * auto_volume(:) ** vmaxSiO2_b * autotrophy(:) * silicify(:)
affinity(iSiO2,:) =affinSiO2_a * auto_volume(:) ** affinSiO2_b * autotrophy(:)
- kexc(iSili,:) = kexcSi_a * auto_volume(:) ** kexcSi_b * silicify(:)
+ kexc(iSili,:) = kexcSi_a * volume(:) ** kexcSi_b * silicify(:)
endif
!-----------------------------------------------------------------------------------------
! other parameters
From 60683f6fbab65312ddb862c08d987eb4d64da882 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 17 Jun 2023 12:59:48 +0100
Subject: [PATCH 25/89] a new subroutine: sub_init_explicit_rich_grazing_params
---
genie-ecogem/src/fortran/ecogem_data.f90 | 164 ++++++++++++------
.../src/fortran/initialise_ecogem.f90 | 6 +-
2 files changed, 113 insertions(+), 57 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index cdb2fa7c4..867971dde 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -885,7 +885,8 @@ SUBROUTINE sub_init_populations()
END SUBROUTINE sub_init_populations
- ! ****************************************************************************************************************************** !
+
+ ! ****************************************************************************************************************************** !
! DEFINE AND INITIALIZE EXPLICIT GRAZER PARMAETERS FROM INPUT FILE
SUBROUTINE sub_init_explicit_grazing_params
@@ -902,10 +903,87 @@ SUBROUTINE sub_init_explicit_grazing_params
real ::loc_mort_protect
real ::loc_palatability
real ::loc_growthcost_factor
- real ::loc_kg
- real ::loc_respir
+ ! if setting plankton specific parameters
+ ! check file format and determine number of lines of data
+ loc_filename = TRIM(par_indir_name)//"/"//TRIM(par_ecogem_grazing_file)
+ CALL sub_check_fileformat(loc_filename,loc_n_elements,loc_n_start)
+
+
+ if (loc_n_elements.eq.0) then
+ print*," "
+ print*,"! ERROR !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+ print*,"! No plankton types specified in grazing input file ",TRIM(par_indir_name)//"/"//TRIM(par_ecogem_grazing_file)
+ print*,"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+ stop
+ endif
+
+ if (loc_n_elements.ne.npmax) then
+ print*," "
+ print*,"! ERROR !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+ print*,"! Different number of plankton types defined in ",TRIM(par_indir_name)//"/"//TRIM(par_ecogem_plankton_file),'and',TRIM(par_indir_name)//"/"//TRIM(par_ecogem_grazing_file)
+ print*,"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
+ stop
+ endif
+
+ !open file pipe
+ OPEN(unit=in,file=loc_filename,action='read')
+ DO n = 1,loc_n_start
+ READ(unit=in,fmt='(1X)')
+ END DO
+
+ ! re-set filepipe
+ REWIND(unit=in)
+ DO n = 1,loc_n_start
+ READ(unit=in,fmt='(1X)')
+ END DO
+ !read in population specifications
+ DO n = 1,loc_n_elements
+ READ(unit=in,FMT=*) &
+ & loc_plnktn_pft, & ! COLUMN #01: plankton PFT (not used here)
+ & loc_herbivory, & ! COLUMN #02: herbivory
+ & loc_carnivory, & ! COLUMN #03: carnivory
+ & loc_pp_opt_a, & ! COLUMN #04: pp_opt_a
+ & loc_pp_sig_a, & ! COLUMN #05: pp_sig_a
+ & loc_ns, & ! COLUMN #06: ns (prey switching)
+ & loc_mort_protect, & ! COLUMN #07: mortality_protection
+ & loc_palatability, & ! COLUMN #08: palatability - in development - Fanny Mar21
+ & loc_growthcost_factor ! COLUMN #09: growth-cost factor - in development - Fanny Mar21
+ herbivory(n) = loc_herbivory
+ carnivory(n) = loc_carnivory
+ pp_opt_a_array(n) = loc_pp_opt_a
+ pp_sig_a_array(n) = loc_pp_sig_a
+ ns_array(n) = loc_ns
+ mort_protect(n) = loc_mort_protect
+ palatability(n) = loc_palatability
+ growthcost_factor(n) = loc_growthcost_factor
+
+ END DO
+ !close file pipe
+ CLOSE(unit=in)
+
+ END SUBROUTINE sub_init_explicit_grazing_params
+ ! ****************************************************************************************************************************** !
+ ! DEFINE AND INITIALIZE EXPLICIT GRAZER PARMAETERS FROM INPUT FILE
+ SUBROUTINE sub_init_explicit_rich_grazing_params
+
+ ! local variables
+ INTEGER::n
+ INTEGER :: loc_n_elements,loc_n_start
+ CHARACTER(len=16) :: loc_plnktn_pft
+ CHARACTER(len=255):: loc_filename
+ real :: loc_herbivory
+ real :: loc_carnivory
+ real :: loc_pp_opt_a
+ real :: loc_pp_sig_a
+ real :: loc_ns
+ real :: loc_mort_protect
+ real :: loc_palatability
+ real :: loc_growthcost_factor
+ real :: loc_kg
+ real :: loc_respir
+
! if setting plankton specific parameters
! check file format and determine number of lines of data
loc_filename = TRIM(par_indir_name)//"/"//TRIM(par_ecogem_grazing_file)
@@ -940,62 +1018,38 @@ SUBROUTINE sub_init_explicit_grazing_params
READ(unit=in,fmt='(1X)')
END DO
- if (ctrl_use_foramecogenie) then
- !read in richer population specifications
- DO n = 1,loc_n_elements
- READ(unit=in,FMT=*) &
- & loc_plnktn_pft, & ! COLUMN #01: plankton PFT (not used here)
- & loc_herbivory, & ! COLUMN #02: herbivory
- & loc_carnivory, & ! COLUMN #03: carnivory
- & loc_pp_opt_a, & ! COLUMN #04: pp_opt_a
- & loc_pp_sig_a, & ! COLUMN #05: pp_sig_a
- & loc_ns, & ! COLUMN #06: ns (prey switching)
- & loc_mort_protect, & ! COLUMN #07: mortality_protection
- & loc_palatability, & ! COLUMN #08: palatability - in development - Fanny Mar21
- & loc_growthcost_factor, & ! COLUMN #09: growth-cost factor - in development - Fanny Mar21
- & loc_kg, & ! COLUMN #10: spine-derived kg modification Rui Oct21
- & loc_respir ! COLUMN #11: increased respiration rate for the calcite building cost
-
- herbivory(n) = loc_herbivory
- carnivory(n) = loc_carnivory
- pp_opt_a_array(n) = loc_pp_opt_a
- pp_sig_a_array(n) = loc_pp_sig_a
- ns_array(n) = loc_ns
- mort_protect(n) = loc_mort_protect
- palatability(n) = loc_palatability
- growthcost_factor(n) = loc_growthcost_factor
- kg_scale(n) = loc_kg
- respir_cost(n) = loc_respir
- END DO
- else
- !read in population specifications
- DO n = 1,loc_n_elements
- READ(unit=in,FMT=*) &
- & loc_plnktn_pft, & ! COLUMN #01: plankton PFT (not used here)
- & loc_herbivory, & ! COLUMN #02: herbivory
- & loc_carnivory, & ! COLUMN #03: carnivory
- & loc_pp_opt_a, & ! COLUMN #04: pp_opt_a
- & loc_pp_sig_a, & ! COLUMN #05: pp_sig_a
- & loc_ns, & ! COLUMN #06: ns (prey switching)
- & loc_mort_protect, & ! COLUMN #07: mortality_protection
- & loc_palatability, & ! COLUMN #08: palatability - in development - Fanny Mar21
- & loc_growthcost_factor ! COLUMN #09: growth-cost factor - in development - Fanny Mar21
- herbivory(n) = loc_herbivory
- carnivory(n) = loc_carnivory
- pp_opt_a_array(n) = loc_pp_opt_a
- pp_sig_a_array(n) = loc_pp_sig_a
- ns_array(n) = loc_ns
- mort_protect(n) = loc_mort_protect
- palatability(n) = loc_palatability
- growthcost_factor(n) = loc_growthcost_factor
- END DO
- endif
+ !read in richer population specifications
+ DO n = 1,loc_n_elements
+ READ(unit=in,FMT=*) &
+ & loc_plnktn_pft, & ! COLUMN #01: plankton PFT (not used here)
+ & loc_herbivory, & ! COLUMN #02: herbivory
+ & loc_carnivory, & ! COLUMN #03: carnivory
+ & loc_pp_opt_a, & ! COLUMN #04: pp_opt_a
+ & loc_pp_sig_a, & ! COLUMN #05: pp_sig_a
+ & loc_ns, & ! COLUMN #06: ns (prey switching)
+ & loc_mort_protect, & ! COLUMN #07: mortality_protection
+ & loc_palatability, & ! COLUMN #08: palatability - in development - Fanny Mar21
+ & loc_growthcost_factor, & ! COLUMN #09: growth-cost factor - in development - Fanny Mar21
+ & loc_kg, & ! COLUMN #10: spine-derived kg modification Rui Oct21
+ & loc_respir ! COLUMN #11: increased respiration rate for the calcite building cost
+
+ herbivory_real(n) = loc_herbivory
+ carnivory_real(n) = loc_carnivory
+ pp_opt_a_array(n) = loc_pp_opt_a
+ pp_sig_a_array(n) = loc_pp_sig_a
+ ns_array(n) = loc_ns
+ mort_protect(n) = loc_mort_protect
+ palatability(n) = loc_palatability
+ growthcost_factor(n) = loc_growthcost_factor
+ kg_scale(n) = loc_kg
+ respir_cost(n) = loc_respir
+ END DO
+
!close file pipe
CLOSE(unit=in)
- END SUBROUTINE sub_init_explicit_grazing_params
-
+ END SUBROUTINE sub_init_explicit_rich_grazing_params
! ****************************************************************************************************************************** !
! LOAD TIME-SERIES LOCATIONS FROM INPUT FILE SUBROUTINE sub_init_timeseries()
diff --git a/genie-ecogem/src/fortran/initialise_ecogem.f90 b/genie-ecogem/src/fortran/initialise_ecogem.f90
index da75a6bc8..3bb587ff6 100644
--- a/genie-ecogem/src/fortran/initialise_ecogem.f90
+++ b/genie-ecogem/src/fortran/initialise_ecogem.f90
@@ -369,8 +369,10 @@ SUBROUTINE initialise_ecogem( &
enddo
! get explicit grazing parameters from input file
- if(ctrl_grazing_explicit)then
- CALL sub_init_explicit_grazing_params()
+ if(ctrl_grazing_explicit .AND. .NOT. ctrl_use_foramecogenie)then
+ CALL sub_init_explicit_grazing_params()
+ else if (ctrl_grazing_explicit .AND. ctrl_use_foramecogenie)
+ CALL sub_init_explicit_rich_grazing_params()
endif
! *** initialise plankton biomass array
From ec66de05da81ae9f00956c0ff4638f70942bec1c Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 17 Jun 2023 13:07:53 +0100
Subject: [PATCH 26/89] no more numerical herb/carni, it's not meaningful
---
genie-ecogem/src/fortran/ecogem_data.f90 | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 867971dde..58828db19 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -973,8 +973,8 @@ SUBROUTINE sub_init_explicit_rich_grazing_params
INTEGER :: loc_n_elements,loc_n_start
CHARACTER(len=16) :: loc_plnktn_pft
CHARACTER(len=255):: loc_filename
- real :: loc_herbivory
- real :: loc_carnivory
+ logical :: loc_herbivory
+ logical :: loc_carnivory
real :: loc_pp_opt_a
real :: loc_pp_sig_a
real :: loc_ns
@@ -1033,8 +1033,8 @@ SUBROUTINE sub_init_explicit_rich_grazing_params
& loc_kg, & ! COLUMN #10: spine-derived kg modification Rui Oct21
& loc_respir ! COLUMN #11: increased respiration rate for the calcite building cost
- herbivory_real(n) = loc_herbivory
- carnivory_real(n) = loc_carnivory
+ herbivory(n) = loc_herbivory
+ carnivory(n) = loc_carnivory
pp_opt_a_array(n) = loc_pp_opt_a
pp_sig_a_array(n) = loc_pp_sig_a
ns_array(n) = loc_ns
From 127091a27975e8c82f681ae5ceb1a46d68f97467 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 17 Jun 2023 13:12:07 +0100
Subject: [PATCH 27/89] fix a bug cause by if-then
---
genie-ecogem/src/fortran/initialise_ecogem.f90 | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/genie-ecogem/src/fortran/initialise_ecogem.f90 b/genie-ecogem/src/fortran/initialise_ecogem.f90
index 3bb587ff6..47b2deeff 100644
--- a/genie-ecogem/src/fortran/initialise_ecogem.f90
+++ b/genie-ecogem/src/fortran/initialise_ecogem.f90
@@ -371,7 +371,7 @@ SUBROUTINE initialise_ecogem( &
! get explicit grazing parameters from input file
if(ctrl_grazing_explicit .AND. .NOT. ctrl_use_foramecogenie)then
CALL sub_init_explicit_grazing_params()
- else if (ctrl_grazing_explicit .AND. ctrl_use_foramecogenie)
+ else if (ctrl_grazing_explicit .AND. ctrl_use_foramecogenie) then
CALL sub_init_explicit_rich_grazing_params()
endif
From 7c7e18dd030b0bd7db2598d0150df73f99093373 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 17 Jun 2023 15:30:49 +0100
Subject: [PATCH 28/89] VERIFIED: herbivory don't eat zooplankton
---
genie-ecogem/src/fortran/ecogem_data.f90 | 36 ++++++++++++++++---
.../src/fortran/initialise_ecogem.f90 | 4 ++-
2 files changed, 35 insertions(+), 5 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 58828db19..7fb30a047 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -305,6 +305,32 @@ end SUBROUTINE sub_data_load_rst
! ****************************************************************************************************************************** !
+ subroutine sub_debug_foramecogem()
+ ! local variables
+ integer :: jp
+ ! -------------------------------------------------------- !
+ ! DEBUG
+ ! -------------------------------------------------------- !
+ ! loop to filter foraminifera groups
+ do jp=1,npmax
+ if (index(pft(jp), "foram") /= 0) then
+ ! reprot foraminifera parameters
+ print*, "-------------------------------"
+ print*, "foraminifera group: ", pft(jp)
+ print*, "diameter", diameter(jp)
+ print*, "volume", volume(jp)
+ print*, "auto_volume", auto_volume(jp)
+ print*, "hetero_volume", hetero_volume(jp)
+ print*, "autotrophy", autotrophy(jp)
+ print*, "heterotrophy", heterotrophy(jp)
+ print*, "Vmax C (auto)", vmax(iDIC,jp)
+ print*, "Vmax P (auto)", vmax(iPO4,jp)
+ print*, "graz (hetero)", graz(jp)
+ print*, "-------------------------------"
+ endif
+ enddo
+ end subroutine sub_debug_foramecogem
+
! ****************************************************************************************************************************** !
! INITIALISE PLANKTON
SUBROUTINE sub_init_plankton()
@@ -463,7 +489,7 @@ SUBROUTINE sub_init_plankton()
!modify foraminifera PFTs' parameters
do jp=1,npmax
call lower_case(pft(jp))
- if (pft(jp).eq.'foram_bs') then
+ if (pft(jp).eq.'foram_bs') then
grazing_esd_scale(jp) = foram_grazing_scale_bs
elseif (pft(jp).eq.'foram_sn') then
symbiont_esd_scale(jp) = foram_symbiont_esd_scale
@@ -562,8 +588,8 @@ SUBROUTINE sub_init_plankton()
! other parameters
qcarbon(:) = qcarbon_a * auto_volume(:) ** qcarbon_b !seems not used
alphachl(:) = alphachl_a * auto_volume(:) ** alphachl_b
- graz(:) = graz_a * hetero_volume(:) ** graz_b * heterotrophy(:)
- kg(:) = kg_a * hetero_volume(:) ** kg_b * kg_scale(:)
+ graz(:) = graz_a * volume(:) ** graz_b * heterotrophy(:)
+ kg(:) = kg_a * volume(:) ** kg_b * kg_scale(:)
pp_opt(:) =pp_opt_a_array * volume(:) ** pp_opt_b
pp_sig(:) =pp_sig_a_array * volume(:) ** pp_sig_b
respir(:) = respir_a * volume(:) ** respir_b + respir_cost(:)
@@ -577,7 +603,7 @@ SUBROUTINE sub_init_plankton()
ppopt_mat(:,jp)=pp_opt !added an optimal predator-prey length ratio for each plankton group, Grigoratou, Dec18
ppsig_mat(:,jp)=pp_sig !added an optimal standar deviation for predator-prey length ratio for each plankton group, Grigoratou, Dec18
enddo
- pred_diam(:,1)=hetero_diameter(:) ! standard prey diameter vector
+ pred_diam(:,1)=diameter(:) ! standard prey diameter vector
prey_diam(1,:)=diameter(:) ! transpose pred diameter vector
prdpry(:,:) =matmul(pred_diam,1.0/prey_diam)
gkernel(:,:) =exp(-log(prdpry(:,:)/ppopt_mat(:,:))**2 / (2*ppsig_mat(:,:)**2)) ! [jpred,jprey] populate whole array at once, then find exceptions to set to 0.0 based on type
@@ -588,6 +614,8 @@ SUBROUTINE sub_init_plankton()
do jprey=1,npmax
! foram dont eat foram, they are always brothers
if (index(pft(jprey), "foram") /= 0) gkernel(jpred, jprey)=0.0
+ if(autotrophy(jprey).gt.0.0 .AND. carnivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
+ if(heterotrophy(jprey).gt.0.0 .AND. herbivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
end do
end select
end do
diff --git a/genie-ecogem/src/fortran/initialise_ecogem.f90 b/genie-ecogem/src/fortran/initialise_ecogem.f90
index 47b2deeff..7b66bd417 100644
--- a/genie-ecogem/src/fortran/initialise_ecogem.f90
+++ b/genie-ecogem/src/fortran/initialise_ecogem.f90
@@ -375,9 +375,11 @@ SUBROUTINE initialise_ecogem( &
CALL sub_init_explicit_rich_grazing_params()
endif
+ if (ctrl_use_foramecogenie) call sub_debug_foramecogem()
+
! *** initialise plankton biomass array
call sub_init_plankton()
-
+
! JDW: allocate and load temperature forcing dataset
if(ctrl_force_T)then
allocate(T_input(n_i,n_j),STAT=alloc_error)
From f95bda1e77980a40b5494620702d48cdf4cd005b Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 17 Jun 2023 16:17:06 +0100
Subject: [PATCH 29/89] apply hetero volume, but just for grazing (not prey
selection)
---
genie-ecogem/src/fortran/ecogem_data.f90 | 9 +++++----
genie-ecogem/src/fortran/initialise_ecogem.f90 | 2 +-
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 7fb30a047..125589197 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -588,8 +588,8 @@ SUBROUTINE sub_init_plankton()
! other parameters
qcarbon(:) = qcarbon_a * auto_volume(:) ** qcarbon_b !seems not used
alphachl(:) = alphachl_a * auto_volume(:) ** alphachl_b
- graz(:) = graz_a * volume(:) ** graz_b * heterotrophy(:)
- kg(:) = kg_a * volume(:) ** kg_b * kg_scale(:)
+ graz(:) = graz_a * hetero_volume(:) ** graz_b * heterotrophy(:)
+ kg(:) = kg_a * hetero_volume(:) ** kg_b * kg_scale(:)
pp_opt(:) =pp_opt_a_array * volume(:) ** pp_opt_b
pp_sig(:) =pp_sig_a_array * volume(:) ** pp_sig_b
respir(:) = respir_a * volume(:) ** respir_b + respir_cost(:)
@@ -608,14 +608,15 @@ SUBROUTINE sub_init_plankton()
prdpry(:,:) =matmul(pred_diam,1.0/prey_diam)
gkernel(:,:) =exp(-log(prdpry(:,:)/ppopt_mat(:,:))**2 / (2*ppsig_mat(:,:)**2)) ! [jpred,jprey] populate whole array at once, then find exceptions to set to 0.0 based on type
+ ! set carnivory and herbivory feeding strategy for foraminifera
do jpred=1,npmax
select case(pft(jpred))
case('foram','foram_bn','foram_bs','foram_sn','foram_ss')
do jprey=1,npmax
! foram dont eat foram, they are always brothers
if (index(pft(jprey), "foram") /= 0) gkernel(jpred, jprey)=0.0
- if(autotrophy(jprey).gt.0.0 .AND. carnivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
- if(heterotrophy(jprey).gt.0.0 .AND. herbivory(jpred))gkernel(jpred,jprey)=0.0 ! if predator is carnivorous and prey is phytoplankton, - no grazing
+ if(autotrophy(jprey).gt.0.0 .AND. carnivory(jpred))gkernel(jpred,jprey)=0.0
+ if(heterotrophy(jprey).gt.0.0 .AND. herbivory(jpred))gkernel(jpred,jprey)=0.0
end do
end select
end do
diff --git a/genie-ecogem/src/fortran/initialise_ecogem.f90 b/genie-ecogem/src/fortran/initialise_ecogem.f90
index 7b66bd417..ab9bad4d5 100644
--- a/genie-ecogem/src/fortran/initialise_ecogem.f90
+++ b/genie-ecogem/src/fortran/initialise_ecogem.f90
@@ -375,7 +375,7 @@ SUBROUTINE initialise_ecogem( &
CALL sub_init_explicit_rich_grazing_params()
endif
- if (ctrl_use_foramecogenie) call sub_debug_foramecogem()
+ if (ctrl_use_foramecogenie .AND. ctrl_debug_init > 0) call sub_debug_foramecogem()
! *** initialise plankton biomass array
call sub_init_plankton()
From 32c27154ad0e46b3f9965b84f0c0d4da78e5692f Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 17 Jun 2023 22:16:34 +0100
Subject: [PATCH 30/89] change the name grazing_esd_scale to spine_esd_scale
---
genie-ecogem/src/fortran/ecogem_data.f90 | 12 ++++++------
genie-ecogem/src/fortran/ecogem_lib.f90 | 6 +++---
genie-ecogem/src/fortran/initialise_ecogem.f90 | 2 +-
genie-main/src/xml-config/xml/definition.xml | 3 +--
4 files changed, 11 insertions(+), 12 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 125589197..a34df05f3 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -482,7 +482,7 @@ SUBROUTINE sub_init_plankton()
if (ctrl_use_foramecogenie) then
! initialise arrays
symbiont_esd_scale(:) = 1.0
- grazing_esd_scale(:) = 1.0
+ spine_esd_scale(:) = 1.0
symbiont_auto_cost(:) = 1.0
symbiont_hetero_cost(:) = 1.0
@@ -490,7 +490,7 @@ SUBROUTINE sub_init_plankton()
do jp=1,npmax
call lower_case(pft(jp))
if (pft(jp).eq.'foram_bs') then
- grazing_esd_scale(jp) = foram_grazing_scale_bs
+ spine_esd_scale(jp) = foram_spine_scale_bs
elseif (pft(jp).eq.'foram_sn') then
symbiont_esd_scale(jp) = foram_symbiont_esd_scale
symbiont_auto_cost(jp) = foram_auto_cost_sn
@@ -499,7 +499,7 @@ SUBROUTINE sub_init_plankton()
symbiont_esd_scale(jp) = foram_symbiont_esd_scale
symbiont_auto_cost(jp) = foram_auto_cost_ss
symbiont_hetero_cost(jp) = foram_hetero_cost_ss
- grazing_esd_scale(jp) = foram_grazing_scale_ss
+ spine_esd_scale(jp) = foram_grazing_scale_ss
endif
enddo
endif
@@ -524,8 +524,8 @@ SUBROUTINE sub_init_plankton()
if(ctrl_use_foramecogenie)then
! v1/v2 = (r1/r2)^3
auto_volume(:) = volume(:) * symbiont_esd_scale(:) ** 3
- hetero_volume(:) = volume(:) * grazing_esd_scale(:) ** 3
- hetero_diameter(:) = diameter(:) * grazing_esd_scale(:)
+ hetero_volume(:) = volume(:) * spine_esd_scale(:) ** 3
+ hetero_diameter(:) = diameter(:) * spine_esd_scale(:)
autotrophy(:) = autotrophy(:) * symbiont_auto_cost(:)
heterotrophy(:) = heterotrophy(:) * symbiont_hetero_cost(:)
@@ -589,7 +589,7 @@ SUBROUTINE sub_init_plankton()
qcarbon(:) = qcarbon_a * auto_volume(:) ** qcarbon_b !seems not used
alphachl(:) = alphachl_a * auto_volume(:) ** alphachl_b
graz(:) = graz_a * hetero_volume(:) ** graz_b * heterotrophy(:)
- kg(:) = kg_a * hetero_volume(:) ** kg_b * kg_scale(:)
+ kg(:) = kg_a * volume(:) ** kg_b * kg_scale(:)
pp_opt(:) =pp_opt_a_array * volume(:) ** pp_opt_b
pp_sig(:) =pp_sig_a_array * volume(:) ** pp_sig_b
respir(:) = respir_a * volume(:) ** respir_b + respir_cost(:)
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index ea15ce5ef..19010cf6e 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -143,10 +143,10 @@ MODULE ecogem_lib
! foramecogenie parameters (11)
logical::ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa, ctrl_use_foramecogenie
real :: foram_auto_cost_sn, foram_auto_cost_ss, foram_hetero_cost_sn, foram_hetero_cost_ss
- real :: foram_grazing_scale_bs, foram_grazing_scale_ss, foram_symbiont_esd_scale
+ real :: foram_spine_scale_bs, foram_spine_scale_ss, foram_symbiont_esd_scale
real :: foramecogenie_bleach_temp
namelist/ini_ecogem_nml/foram_auto_cost_sn,foram_auto_cost_ss,foram_hetero_cost_sn,foram_hetero_cost_ss
- namelist/ini_ecogem_nml/foram_grazing_scale_bs, foram_grazing_scale_ss, foram_symbiont_esd_scale
+ namelist/ini_ecogem_nml/foram_spine_scale_bs, foram_spine_scale_ss, foram_symbiont_esd_scale
namelist/ini_ecogem_nml/ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa,ctrl_use_foramecogenie
namelist/ini_ecogem_nml/foramecogenie_bleach_temp
! Temperature dependence
@@ -309,7 +309,7 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:) ::graz,kg,pp_opt,pp_sig ! Grazing parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::respir,biosink,mort,beta_graz,beta_mort ! Other loss parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::symbiont_auto_cost, symbiont_hetero_cost ! RY, foramecogenie symbiont cost parameter
- REAL ,ALLOCATABLE,DIMENSION(:) ::auto_volume, hetero_volume, grazing_esd_scale, symbiont_esd_scale ! RY, foramecogenie size parameter
+ REAL ,ALLOCATABLE,DIMENSION(:) ::auto_volume, hetero_volume, spine_esd_scale, symbiont_esd_scale ! RY, foramecogenie size parameter
REAL ,ALLOCATABLE,DIMENSION(:) ::respir_cost,kg_scale, hetero_diameter ! RY, foramecogenie grazing parameter
! Grazing kernel
diff --git a/genie-ecogem/src/fortran/initialise_ecogem.f90 b/genie-ecogem/src/fortran/initialise_ecogem.f90
index ab9bad4d5..3aad2b9a9 100644
--- a/genie-ecogem/src/fortran/initialise_ecogem.f90
+++ b/genie-ecogem/src/fortran/initialise_ecogem.f90
@@ -342,7 +342,7 @@ SUBROUTINE initialise_ecogem( &
ALLOCATE(hetero_diameter(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
- ALLOCATE(grazing_esd_scale(npmax),STAT=alloc_error)
+ ALLOCATE(spine_esd_scale(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(symbiont_esd_scale(npmax),STAT=alloc_error)
diff --git a/genie-main/src/xml-config/xml/definition.xml b/genie-main/src/xml-config/xml/definition.xml
index 5baf0f1f4..c59ad4ba4 100644
--- a/genie-main/src/xml-config/xml/definition.xml
+++ b/genie-main/src/xml-config/xml/definition.xml
@@ -8918,12 +8918,11 @@ par_bio_red_PC_alpha2 scales the offset of 6.0e-3 of Galbraith & Martiny, 2015 C
stronger "grazing volume" for symbiont-barren spinose foraminifera
-
+
1.0
stronger "grazing volume" for symbiont-bearing spinose foraminifera
-
1.0
Auto trade-off parameter
From 3e51d09c89b18e4e2b979df627534410dcbecd55 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 17 Jun 2023 22:21:08 +0100
Subject: [PATCH 31/89] update more spine-related variable name
---
genie-ecogem/src/fortran/ecogem_data.f90 | 2 +-
genie-main/src/xml-config/xml/definition.xml | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index a34df05f3..173b4adcc 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -499,7 +499,7 @@ SUBROUTINE sub_init_plankton()
symbiont_esd_scale(jp) = foram_symbiont_esd_scale
symbiont_auto_cost(jp) = foram_auto_cost_ss
symbiont_hetero_cost(jp) = foram_hetero_cost_ss
- spine_esd_scale(jp) = foram_grazing_scale_ss
+ spine_esd_scale(jp) = foram_spine_scale_ss
endif
enddo
endif
diff --git a/genie-main/src/xml-config/xml/definition.xml b/genie-main/src/xml-config/xml/definition.xml
index c59ad4ba4..d6650cb93 100644
--- a/genie-main/src/xml-config/xml/definition.xml
+++ b/genie-main/src/xml-config/xml/definition.xml
@@ -8913,7 +8913,7 @@ par_bio_red_PC_alpha2 scales the offset of 6.0e-3 of Galbraith & Martiny, 2015 C
symbiont/foraminifera host size ratio
-
+
1.0
stronger "grazing volume" for symbiont-barren spinose foraminifera
From 13d04bf5910322c5fd89f58b79fbec5c9cb4a166 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 18 Jun 2023 18:28:47 +0100
Subject: [PATCH 32/89] enable omnivory for foram
---
genie-ecogem/src/fortran/ecogem_data.f90 | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 173b4adcc..3db93461d 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -615,8 +615,13 @@ SUBROUTINE sub_init_plankton()
do jprey=1,npmax
! foram dont eat foram, they are always brothers
if (index(pft(jprey), "foram") /= 0) gkernel(jpred, jprey)=0.0
- if(autotrophy(jprey).gt.0.0 .AND. carnivory(jpred))gkernel(jpred,jprey)=0.0
- if(heterotrophy(jprey).gt.0.0 .AND. herbivory(jpred))gkernel(jpred,jprey)=0.0
+ ! enable omnivory for foram
+ if(herbivory(jpred) .AND. carnivory(jpred)) then
+ CONTINUE
+ else
+ if(autotrophy(jprey).gt.0.0 .AND. carnivory(jpred)) gkernel(jpred,jprey)=0.0
+ if(heterotrophy(jprey).gt.0.0 .AND. herbivory(jpred))gkernel(jpred,jprey)=0.0
+ endif
end do
end select
end do
From 4ffe14f782a5f9324806305fae20e928f9ea9608 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 1 Jul 2023 17:00:46 +0100
Subject: [PATCH 33/89] make symbiont and spine trait universal for groups
---
genie-ecogem/src/fortran/ecogem_data.f90 | 12 +++++-----
genie-ecogem/src/fortran/ecogem_lib.f90 | 8 +++----
genie-main/src/xml-config/xml/definition.xml | 25 ++++----------------
3 files changed, 15 insertions(+), 30 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 3db93461d..9bd4e859f 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -490,16 +490,16 @@ SUBROUTINE sub_init_plankton()
do jp=1,npmax
call lower_case(pft(jp))
if (pft(jp).eq.'foram_bs') then
- spine_esd_scale(jp) = foram_spine_scale_bs
+ spine_esd_scale(jp) = foram_spine_scale
elseif (pft(jp).eq.'foram_sn') then
symbiont_esd_scale(jp) = foram_symbiont_esd_scale
- symbiont_auto_cost(jp) = foram_auto_cost_sn
- symbiont_hetero_cost(jp) = foram_hetero_cost_sn
+ symbiont_auto_cost(jp) = foram_auto_cost
+ symbiont_hetero_cost(jp) = foram_hetero_cost
elseif (pft(jp).eq.'foram_ss') then
symbiont_esd_scale(jp) = foram_symbiont_esd_scale
- symbiont_auto_cost(jp) = foram_auto_cost_ss
- symbiont_hetero_cost(jp) = foram_hetero_cost_ss
- spine_esd_scale(jp) = foram_spine_scale_ss
+ symbiont_auto_cost(jp) = foram_auto_cost
+ symbiont_hetero_cost(jp) = foram_hetero_cost
+ spine_esd_scale(jp) = foram_spine_scale
endif
enddo
endif
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index 19010cf6e..e893492ee 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -142,11 +142,11 @@ MODULE ecogem_lib
namelist/ini_ecogem_nml/trophic_tradeoff
! foramecogenie parameters (11)
logical::ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa, ctrl_use_foramecogenie
- real :: foram_auto_cost_sn, foram_auto_cost_ss, foram_hetero_cost_sn, foram_hetero_cost_ss
- real :: foram_spine_scale_bs, foram_spine_scale_ss, foram_symbiont_esd_scale
+ real :: foram_auto_cost, foram_hetero_cost
+ real :: foram_spine_scale, foram_symbiont_esd_scale
real :: foramecogenie_bleach_temp
- namelist/ini_ecogem_nml/foram_auto_cost_sn,foram_auto_cost_ss,foram_hetero_cost_sn,foram_hetero_cost_ss
- namelist/ini_ecogem_nml/foram_spine_scale_bs, foram_spine_scale_ss, foram_symbiont_esd_scale
+ namelist/ini_ecogem_nml/foram_auto_cost, foram_hetero_cost
+ namelist/ini_ecogem_nml/foram_spine_scale, foram_symbiont_esd_scale
namelist/ini_ecogem_nml/ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa,ctrl_use_foramecogenie
namelist/ini_ecogem_nml/foramecogenie_bleach_temp
! Temperature dependence
diff --git a/genie-main/src/xml-config/xml/definition.xml b/genie-main/src/xml-config/xml/definition.xml
index d6650cb93..4565b8a56 100644
--- a/genie-main/src/xml-config/xml/definition.xml
+++ b/genie-main/src/xml-config/xml/definition.xml
@@ -8913,36 +8913,21 @@ par_bio_red_PC_alpha2 scales the offset of 6.0e-3 of Galbraith & Martiny, 2015 C
symbiont/foraminifera host size ratio
-
+
1.0
- stronger "grazing volume" for symbiont-barren spinose foraminifera
+ stronger "grazing volume" for spinose foraminifera
-
- 1.0
- stronger "grazing volume" for symbiont-bearing spinose foraminifera
-
-
-
- 1.0
- Auto trade-off parameter
-
-
-
+
1.0
Auto trade-off parameter
-
+
1.0
Auto trade-off parameter
-
-
- 1.0
- Auto trade-off parameter
-
-
+
From e3981da8e40e09621b599b193145cb0e841a7513 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 1 Jul 2023 18:11:07 +0100
Subject: [PATCH 34/89] mechanistic spine effect: influence Gm and kg
---
genie-ecogem/src/fortran/ecogem_data.f90 | 19 +++++++++++--------
genie-ecogem/src/fortran/ecogem_lib.f90 | 4 ++--
.../src/fortran/initialise_ecogem.f90 | 10 +---------
3 files changed, 14 insertions(+), 19 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 9bd4e859f..57ef67f94 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -320,7 +320,6 @@ subroutine sub_debug_foramecogem()
print*, "diameter", diameter(jp)
print*, "volume", volume(jp)
print*, "auto_volume", auto_volume(jp)
- print*, "hetero_volume", hetero_volume(jp)
print*, "autotrophy", autotrophy(jp)
print*, "heterotrophy", heterotrophy(jp)
print*, "Vmax C (auto)", vmax(iDIC,jp)
@@ -524,8 +523,6 @@ SUBROUTINE sub_init_plankton()
if(ctrl_use_foramecogenie)then
! v1/v2 = (r1/r2)^3
auto_volume(:) = volume(:) * symbiont_esd_scale(:) ** 3
- hetero_volume(:) = volume(:) * spine_esd_scale(:) ** 3
- hetero_diameter(:) = diameter(:) * spine_esd_scale(:)
autotrophy(:) = autotrophy(:) * symbiont_auto_cost(:)
heterotrophy(:) = heterotrophy(:) * symbiont_hetero_cost(:)
@@ -588,14 +585,23 @@ SUBROUTINE sub_init_plankton()
! other parameters
qcarbon(:) = qcarbon_a * auto_volume(:) ** qcarbon_b !seems not used
alphachl(:) = alphachl_a * auto_volume(:) ** alphachl_b
- graz(:) = graz_a * hetero_volume(:) ** graz_b * heterotrophy(:)
- kg(:) = kg_a * volume(:) ** kg_b * kg_scale(:)
+ graz(:) = graz_a * volume(:) ** graz_b * heterotrophy(:)
+ kg(:) = kg_a * volume(:) ** kg_b
pp_opt(:) =pp_opt_a_array * volume(:) ** pp_opt_b
pp_sig(:) =pp_sig_a_array * volume(:) ** pp_sig_b
respir(:) = respir_a * volume(:) ** respir_b + respir_cost(:)
biosink(:) = biosink_a * volume(:) ** biosink_b
mort(:) = (mort_a * volume(:) ** mort_b) * mort_protect(:) ! mort_protect added by Grigoratou, Dec2018 as a benefit for foram's calcification
+ ! spine mechanism
+ ! surface area = 4 pi r^2, greater r by spine -> surface area times r^2
+ ! -> surface area/volume ratio times r^2
+ ! set z = surface/volume ratio,
+ ! then Gm/kg = a*z^-b increases by r^-2b times
+ kg(:) = kg(:) * foram_spine_scale ** (-2*kg_b)
+ graz(:) = graz(:) * foram_spine_scale ** (-2*graz_b)
+
+
! grazing parameters
do jp=1,npmax ! grazing kernel (npred,nprey)
! pad predator dependent pp_opt and pp_sig so that they vary along matrix columns
@@ -1015,7 +1021,6 @@ SUBROUTINE sub_init_explicit_rich_grazing_params
real :: loc_mort_protect
real :: loc_palatability
real :: loc_growthcost_factor
- real :: loc_kg
real :: loc_respir
! if setting plankton specific parameters
@@ -1064,7 +1069,6 @@ SUBROUTINE sub_init_explicit_rich_grazing_params
& loc_mort_protect, & ! COLUMN #07: mortality_protection
& loc_palatability, & ! COLUMN #08: palatability - in development - Fanny Mar21
& loc_growthcost_factor, & ! COLUMN #09: growth-cost factor - in development - Fanny Mar21
- & loc_kg, & ! COLUMN #10: spine-derived kg modification Rui Oct21
& loc_respir ! COLUMN #11: increased respiration rate for the calcite building cost
herbivory(n) = loc_herbivory
@@ -1075,7 +1079,6 @@ SUBROUTINE sub_init_explicit_rich_grazing_params
mort_protect(n) = loc_mort_protect
palatability(n) = loc_palatability
growthcost_factor(n) = loc_growthcost_factor
- kg_scale(n) = loc_kg
respir_cost(n) = loc_respir
END DO
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index e893492ee..d1197e7f9 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -309,8 +309,8 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:) ::graz,kg,pp_opt,pp_sig ! Grazing parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::respir,biosink,mort,beta_graz,beta_mort ! Other loss parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::symbiont_auto_cost, symbiont_hetero_cost ! RY, foramecogenie symbiont cost parameter
- REAL ,ALLOCATABLE,DIMENSION(:) ::auto_volume, hetero_volume, spine_esd_scale, symbiont_esd_scale ! RY, foramecogenie size parameter
- REAL ,ALLOCATABLE,DIMENSION(:) ::respir_cost,kg_scale, hetero_diameter ! RY, foramecogenie grazing parameter
+ REAL ,ALLOCATABLE,DIMENSION(:) ::auto_volume, spine_esd_scale, symbiont_esd_scale ! RY, foramecogenie size parameter
+ REAL ,ALLOCATABLE,DIMENSION(:) ::respir_cost ! RY, foramecogenie grazing parameter
! Grazing kernel
REAL,ALLOCATABLE,DIMENSION(:,:)::gkernel,gkernelT
diff --git a/genie-ecogem/src/fortran/initialise_ecogem.f90 b/genie-ecogem/src/fortran/initialise_ecogem.f90
index 3aad2b9a9..c0e631697 100644
--- a/genie-ecogem/src/fortran/initialise_ecogem.f90
+++ b/genie-ecogem/src/fortran/initialise_ecogem.f90
@@ -327,20 +327,12 @@ SUBROUTINE initialise_ecogem( &
! foramecogenie arrays allocation
if (ctrl_use_foramecogenie) then
- ALLOCATE(kg_scale(npmax),STAT=alloc_error)
- call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(respir_cost(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(auto_volume(npmax),STAT=alloc_error)
- call check_iostat(alloc_error,__LINE__,__FILE__)
-
- ALLOCATE(hetero_volume(npmax),STAT=alloc_error)
- call check_iostat(alloc_error,__LINE__,__FILE__)
-
- ALLOCATE(hetero_diameter(npmax),STAT=alloc_error)
- call check_iostat(alloc_error,__LINE__,__FILE__)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(spine_esd_scale(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
From c00c824c85a215d24bf3d8c95c752675dc157fa7 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 1 Jul 2023 18:19:57 +0100
Subject: [PATCH 35/89] update foramecogem usr-configs as code changed
---
genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo | 41 +++++++++----------
...CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2 | 11 ++---
...CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2 | 11 ++---
...a.BASESFeTDTL_rb_foramecogem2.2.modernAMOC | 11 ++---
...ASES.CASclosed.280_0p2.foramecogem2.2.SPIN | 11 ++---
....BASES.CASopen.400_0p5.foramecogem2.2.SPIN | 11 ++---
...ASES.CASclosed.280_0p2.foramecogem2.2.SPIN | 11 ++---
...ASES.CASclosed.400_0p2.foramecogem2.2.SPIN | 11 ++---
...lg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg | 11 ++---
...orlg4.BASESFeTDTL.foramecogem2.2.2100.2deg | 11 ++---
...orlg4.BASESFeTDTL.foramecogem2.2.2100.3deg | 11 ++---
...orlg4.BASESFeTDTL.foramecogem2.2.2100.4deg | 11 ++---
...CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN | 11 ++---
...rlg4.BASESFeTDTL.foramecogem2.2.historical | 11 ++---
.../FORAMECOGEM/update_userconfig.py | 11 ++---
15 files changed, 76 insertions(+), 119 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
index d56b164da..18b40e447 100644
--- a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
+++ b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
@@ -3,25 +3,25 @@
\/ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
-START-OF-DATA-
-Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 1.0 0.0
-foram_bn t f 10.0 4.0 1.0 0.7 0.8 1.0 1.0 0.04
-foram_bs t f 10.0 2.0 1.0 0.7 0.7 1.0 0.75 0.06
-foram_sn t f 10.0 4.0 1.0 0.7 0.8 1.0 1.0 0.04
-foram_ss f t 10.0 2.0 1.0 0.7 0.7 1.0 0.8 0.06
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+foram_bn t f 10.0 2.0 1.0 0.7 0.8 1.1 0.03
+foram_bs t f 10.0 2.0 5.0 0.7 0.8 1.0 0.05
+foram_sn t f 10.0 2.0 1.0 0.7 0.8 1.0 0.03
+foram_ss f t 10.0 2.0 5.0 0.7 0.8 1.0 0.05
-END-OF-DATA-
/\ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
@@ -38,8 +38,7 @@ COLUMN #06: ns (prey-switching - 2.0 = active, 1.0 = passive)
COLUMN #07: mortality protection (e.g., 0.7 is equivalent to 30% reduced mortality rate)
COLUMN #08: palatability (grazing protection)
COLUMN #09: growth-cost factor (e.g., a 10% cost is equivalent to a 0.9 growth-cost factor)
-COLUMN #10: half-saturation constant (affinity) of grazing rate
-COLUMN #11: extra respiration rate for building calcite spine and test
+COLUMN #10: extra respiration rate for building calcite spine and test
INFO: TRACER ASSIGNMENT RULES
-----------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
index 64162005b..6fad435c6 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
@@ -83,13 +83,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
index 4092c7bfe..a325889c7 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
@@ -75,13 +75,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
index f49774eb4..497f0b095 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
@@ -75,13 +75,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
index 1413a03e9..135af8ee1 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
@@ -56,13 +56,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
index 80ff9845a..7a58e1110 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
@@ -56,13 +56,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
index 5e7568e9d..4dd73844c 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
@@ -56,13 +56,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
index 87ed08c54..6b5803518 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
@@ -56,13 +56,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
index 9983ba076..035aee4c2 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
@@ -82,13 +82,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
index 131e7191f..0d4600037 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
@@ -82,13 +82,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
index a66f6dd17..68cee113c 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
@@ -82,13 +82,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
index 2a872830f..235a53245 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
@@ -82,13 +82,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
index 06aafd6cc..554c03620 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
@@ -82,13 +82,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
index f62d3d3c0..f802569c8 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
@@ -82,13 +82,10 @@ eg_ctrl_foramecogenie_bleach = .false.
eg_par_ecogem_plankton_file = '8P7Z4F.eco'
eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.0015
-eg_foram_auto_cost_sn = 0.8
-eg_foram_hetero_cost_sn = 0.5
-eg_foram_auto_cost_ss = 1.0
-eg_foram_hetero_cost_ss = 0.5
-eg_foram_grazing_scale_bs = 2.0
-eg_foram_grazing_scale_ss = 2.0
+eg_foram_symbiont_esd_scale = 0.01
+eg_foram_auto_cost = 0.05
+eg_foram_hetero_cost = 0.5
+eg_foram_grazing_scale = 3.0
#----------------- Nitrogen -------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/update_userconfig.py b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
index 64948394a..17cd18aa0 100644
--- a/genie-userconfigs/FORAMECOGEM/update_userconfig.py
+++ b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
@@ -21,13 +21,10 @@ def update_foramecogem(directory):
## foramecogenie parameters (numerical)
'eg_par_ecogem_plankton_file': "'8P7Z4F.eco'",
'eg_par_ecogem_grazing_file': "'FORAMECOGEM.zoo'",
- 'eg_foram_symbiont_esd_scale': '0.0015',
- 'eg_foram_auto_cost_sn': '0.8',
- 'eg_foram_hetero_cost_sn': '0.5',
- 'eg_foram_auto_cost_ss': '1.0',
- 'eg_foram_hetero_cost_ss': '0.5',
- 'eg_foram_grazing_scale_bs': '2.0',
- 'eg_foram_grazing_scale_ss': '2.0',
+ 'eg_foram_symbiont_esd_scale': '0.01',
+ 'eg_foram_auto_cost': '0.05',
+ 'eg_foram_hetero_cost': '0.5',
+ 'eg_foram_grazing_scale': '3.0',
}
From eb20cf95b7b03dd8afda5e39037568507cb3ffe9 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 2 Jul 2023 00:49:30 +0100
Subject: [PATCH 36/89] mechanistic spine: influence prey selection only
---
genie-ecogem/src/fortran/ecogem_data.f90 | 20 +++++++++++--------
genie-userconfigs/FORAMECOGEM/8P7Z4F.eco | 8 ++++----
genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo | 6 +++---
3 files changed, 19 insertions(+), 15 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 57ef67f94..e8e289e47 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -422,6 +422,8 @@ SUBROUTINE sub_init_plankton()
autotrophy(jp) = 0.0
heterotrophy(jp) = 1.0
elseif (pft(jp).eq.'foram_bn') then
+ ! symbiont-barren non-spinose foraminifera
+ ! e.g., N. pacyderma, T. quinqueloba
NO3up(jp) = 0.0
Nfix(jp) = 0.0
calcify(jp) = 0.0
@@ -429,6 +431,8 @@ SUBROUTINE sub_init_plankton()
autotrophy(jp) = 0.0
heterotrophy(jp) = 1.0
elseif (pft(jp).eq.'foram_bs') then
+ ! symbiont-barren spinose foraminifera
+ ! e.g., G. bulloides, H. pelagica
NO3up(jp) = 0.0
Nfix(jp) = 0.0
calcify(jp) = 0.0
@@ -436,6 +440,8 @@ SUBROUTINE sub_init_plankton()
autotrophy(jp) = 0.0
heterotrophy(jp) = 1.0
elseif (pft(jp).eq.'foram_sn') then
+ ! symbiont-facultative non-spinose foraminifera
+ ! e.g., N. dutertrei, G. menardii
NO3up(jp) = 0.0
Nfix(jp) = 0.0
calcify(jp) = 0.0
@@ -443,6 +449,8 @@ SUBROUTINE sub_init_plankton()
autotrophy(jp) = 1.0
heterotrophy(jp) = 1.0
elseif (pft(jp).eq.'foram_ss') then
+ ! symbiont-obligate spinose foraminifera
+ ! e.g., T. sacculifer, G. ruber
NO3up(jp) = 0.0
Nfix(jp) = 0.0
calcify(jp) = 0.0
@@ -594,13 +602,9 @@ SUBROUTINE sub_init_plankton()
mort(:) = (mort_a * volume(:) ** mort_b) * mort_protect(:) ! mort_protect added by Grigoratou, Dec2018 as a benefit for foram's calcification
! spine mechanism
- ! surface area = 4 pi r^2, greater r by spine -> surface area times r^2
- ! -> surface area/volume ratio times r^2
- ! set z = surface/volume ratio,
- ! then Gm/kg = a*z^-b increases by r^-2b times
- kg(:) = kg(:) * foram_spine_scale ** (-2*kg_b)
- graz(:) = graz(:) * foram_spine_scale ** (-2*graz_b)
-
+ ! influence selection process, but not grazing process that is determined by host's size
+ pp_sig(:) = pp_sig(:) * spine_esd_scale(:) ** 3
+ pp_opt(:) = pp_opt(:) * spine_esd_scale(:) ** 3
! grazing parameters
do jp=1,npmax ! grazing kernel (npred,nprey)
@@ -1069,7 +1073,7 @@ SUBROUTINE sub_init_explicit_rich_grazing_params
& loc_mort_protect, & ! COLUMN #07: mortality_protection
& loc_palatability, & ! COLUMN #08: palatability - in development - Fanny Mar21
& loc_growthcost_factor, & ! COLUMN #09: growth-cost factor - in development - Fanny Mar21
- & loc_respir ! COLUMN #11: increased respiration rate for the calcite building cost
+ & loc_respir ! COLUMN #10: increased respiration rate for the calcite building cost
herbivory(n) = loc_herbivory
carnivory(n) = loc_carnivory
diff --git a/genie-userconfigs/FORAMECOGEM/8P7Z4F.eco b/genie-userconfigs/FORAMECOGEM/8P7Z4F.eco
index 03d63ebe9..a70d96142 100644
--- a/genie-userconfigs/FORAMECOGEM/8P7Z4F.eco
+++ b/genie-userconfigs/FORAMECOGEM/8P7Z4F.eco
@@ -18,10 +18,10 @@
Zooplankton 190.00 1
Zooplankton 600.00 1
Zooplankton 1900.00 1
- foram_bn 155.00 1
- foram_bs 175.00 1
- foram_sn 190.00 1
- foram_ss 190.00 1
+ foram_bn 200.00 1
+ foram_bs 200.00 1
+ foram_sn 300.00 1
+ foram_ss 300.00 1
-END-OF-DATA-
/\ /\ /\
diff --git a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
index 18b40e447..40de70702 100644
--- a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
+++ b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
@@ -1,6 +1,6 @@
-01 02 03 04 05 06 07 08 09 10 11
-\/ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+01 02 03 04 05 06 07 08 09 10
+\/ \/ \/ \/ \/ \/ \/ \/ \/ \/
-START-OF-DATA-
Phytoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
@@ -18,7 +18,7 @@ Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
-foram_bn t f 10.0 2.0 1.0 0.7 0.8 1.1 0.03
+foram_bn t f 10.0 2.0 1.0 0.7 0.8 1.2 0.03
foram_bs t f 10.0 2.0 5.0 0.7 0.8 1.0 0.05
foram_sn t f 10.0 2.0 1.0 0.7 0.8 1.0 0.03
foram_ss f t 10.0 2.0 5.0 0.7 0.8 1.0 0.05
From 355e23cefcbb00084a53ba85941dd64507014a6e Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 2 Jul 2023 00:53:32 +0100
Subject: [PATCH 37/89] update foramecogem user-config
---
genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo | 8 ++++----
...CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2 | 18 ++++++++---------
...CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2 | 20 +++++++++----------
...a.BASESFeTDTL_rb_foramecogem2.2.modernAMOC | 20 +++++++++----------
...ASES.CASclosed.280_0p2.foramecogem2.2.SPIN | 18 ++++++++---------
....BASES.CASopen.400_0p5.foramecogem2.2.SPIN | 18 ++++++++---------
...ASES.CASclosed.280_0p2.foramecogem2.2.SPIN | 18 ++++++++---------
...ASES.CASclosed.400_0p2.foramecogem2.2.SPIN | 18 ++++++++---------
...lg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg | 18 ++++++++---------
...orlg4.BASESFeTDTL.foramecogem2.2.2100.2deg | 20 +++++++++----------
...orlg4.BASESFeTDTL.foramecogem2.2.2100.3deg | 20 +++++++++----------
...orlg4.BASESFeTDTL.foramecogem2.2.2100.4deg | 18 ++++++++---------
...CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN | 18 ++++++++---------
...rlg4.BASESFeTDTL.foramecogem2.2.historical | 20 +++++++++----------
.../FORAMECOGEM/update_userconfig.py | 2 +-
15 files changed, 127 insertions(+), 127 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
index 40de70702..eff61da9a 100644
--- a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
+++ b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
@@ -18,10 +18,10 @@ Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
-foram_bn t f 10.0 2.0 1.0 0.7 0.8 1.2 0.03
-foram_bs t f 10.0 2.0 5.0 0.7 0.8 1.0 0.05
-foram_sn t f 10.0 2.0 1.0 0.7 0.8 1.0 0.03
-foram_ss f t 10.0 2.0 5.0 0.7 0.8 1.0 0.05
+foram_bn t f 10.0 2.0 1.0 0.7 0.8 1.2 0.02
+foram_bs t f 10.0 2.0 5.0 0.7 0.8 1.0 0.04
+foram_sn t f 10.0 2.0 1.0 0.7 0.8 1.0 0.02
+foram_ss f t 10.0 2.0 5.0 0.7 0.8 1.0 0.04
-END-OF-DATA-
/\ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
index 6fad435c6..edfe7666a 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
@@ -77,16 +77,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
index a325889c7..7a2a7607a 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
@@ -69,16 +69,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
-
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
index 497f0b095..e0e78621e 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
@@ -69,16 +69,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
-
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
index 135af8ee1..28cc441ad 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
@@ -50,16 +50,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
index 7a58e1110..8e8a7c23b 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
@@ -50,16 +50,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
index 4dd73844c..9e8528401 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
@@ -50,16 +50,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
index 6b5803518..d3be453bc 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
@@ -50,16 +50,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
index 035aee4c2..ff926108a 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
@@ -76,16 +76,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
index 0d4600037..239925e19 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
@@ -76,16 +76,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
-
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
index 68cee113c..b5946d887 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
@@ -76,16 +76,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
-
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
index 235a53245..338f1ffa3 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
@@ -76,16 +76,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
index 554c03620..92e393f5a 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
@@ -76,16 +76,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
index f802569c8..d1048f3fe 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
@@ -76,16 +76,16 @@ eg_ctrl_debug_eco_init=.false.
eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie = .true.
-eg_ctrl_foramecogenie_oa = .false.
-eg_ctrl_foramecogenie_bleach = .false.
-
-eg_par_ecogem_plankton_file = '8P7Z4F.eco'
-eg_par_ecogem_grazing_file = 'FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale = 0.01
-eg_foram_auto_cost = 0.05
-eg_foram_hetero_cost = 0.5
-eg_foram_grazing_scale = 3.0
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.05
+eg_foram_hetero_cost=0.5
+eg_foram_grazing_scale=5.0
#----------------- Nitrogen -------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/update_userconfig.py b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
index 17cd18aa0..66820bded 100644
--- a/genie-userconfigs/FORAMECOGEM/update_userconfig.py
+++ b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
@@ -24,7 +24,7 @@ def update_foramecogem(directory):
'eg_foram_symbiont_esd_scale': '0.01',
'eg_foram_auto_cost': '0.05',
'eg_foram_hetero_cost': '0.5',
- 'eg_foram_grazing_scale': '3.0',
+ 'eg_foram_grazing_scale': '5.0',
}
From a992e25e1965fab793326782f778d3f3cff5370a Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 2 Jul 2023 12:48:28 +0100
Subject: [PATCH 38/89] update foramecogem uerconfig
---
genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo | 4 ++--
.../muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2 | 6 +++---
.../muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2 | 6 +++---
...in.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC | 6 +++---
...CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN | 6 +++---
...n.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN | 6 +++---
...CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN | 6 +++---
...CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN | 6 +++---
...muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg | 6 +++---
.../muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg | 6 +++---
.../muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg | 6 +++---
.../muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg | 6 +++---
.../muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN | 6 +++---
.../muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical | 6 +++---
genie-userconfigs/FORAMECOGEM/update_userconfig.py | 6 +++---
15 files changed, 44 insertions(+), 44 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
index eff61da9a..f53c1bfa5 100644
--- a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
+++ b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
@@ -18,9 +18,9 @@ Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
-foram_bn t f 10.0 2.0 1.0 0.7 0.8 1.2 0.02
+foram_bn t f 10.0 2.0 1.0 0.7 0.8 1.3 0.02
foram_bs t f 10.0 2.0 5.0 0.7 0.8 1.0 0.04
-foram_sn t f 10.0 2.0 1.0 0.7 0.8 1.0 0.02
+foram_sn t f 10.0 2.0 1.0 0.7 0.8 1.3 0.02
foram_ss f t 10.0 2.0 5.0 0.7 0.8 1.0 0.04
-END-OF-DATA-
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
index edfe7666a..6f4d9b6ab 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
@@ -84,9 +84,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
index 7a2a7607a..250817d32 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
@@ -76,9 +76,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
index e0e78621e..28497264c 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
@@ -76,9 +76,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
index 28cc441ad..cbc46b0dc 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
@@ -57,9 +57,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
index 8e8a7c23b..bc4a6946d 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
@@ -57,9 +57,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
index 9e8528401..33cb1addd 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
@@ -57,9 +57,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
index d3be453bc..72033a0b7 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
@@ -57,9 +57,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
index ff926108a..b045e1578 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
@@ -83,9 +83,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
index 239925e19..3704ddc77 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
@@ -83,9 +83,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
index b5946d887..792dc6233 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
@@ -83,9 +83,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
index 338f1ffa3..0a08ef1f8 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
@@ -83,9 +83,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
index 92e393f5a..59845f35c 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
@@ -83,9 +83,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
index d1048f3fe..5c5d6ae95 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
@@ -83,9 +83,9 @@ eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.05
-eg_foram_hetero_cost=0.5
-eg_foram_grazing_scale=5.0
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
#----------------- Nitrogen -------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/update_userconfig.py b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
index 66820bded..72ee57b61 100644
--- a/genie-userconfigs/FORAMECOGEM/update_userconfig.py
+++ b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
@@ -22,9 +22,9 @@ def update_foramecogem(directory):
'eg_par_ecogem_plankton_file': "'8P7Z4F.eco'",
'eg_par_ecogem_grazing_file': "'FORAMECOGEM.zoo'",
'eg_foram_symbiont_esd_scale': '0.01',
- 'eg_foram_auto_cost': '0.05',
- 'eg_foram_hetero_cost': '0.5',
- 'eg_foram_grazing_scale': '5.0',
+ 'eg_foram_auto_cost': '0.04',
+ 'eg_foram_hetero_cost': '0.35',
+ 'eg_foram_grazing_scale': '3.5',
}
From 71df912cdf5e992b31172e0a7f90d159b676424b Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 2 Jul 2023 15:48:52 +0100
Subject: [PATCH 39/89] migrate forcings files
---
.../biogem_force_flux_sed_det_SUR.dat | 37 +++
.../biogem_force_flux_sed_det_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_13C_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_sig.dat | 263 ++++++++++++++++++
.../configure_forcings_atm.dat | 24 ++
.../configure_forcings_ocn.dat | 24 ++
.../configure_forcings_sed.dat | 21 ++
.../biogem_force_flux_sed_det_SUR.dat | 37 +++
.../biogem_force_flux_sed_det_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_13C_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_sig.dat | 263 ++++++++++++++++++
.../configure_forcings_atm.dat | 24 ++
.../configure_forcings_ocn.dat | 24 ++
.../configure_forcings_sed.dat | 21 ++
.../biogem_force_flux_sed_det_SUR.dat | 37 +++
.../biogem_force_flux_sed_det_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_13C_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_sig.dat | 263 ++++++++++++++++++
.../configure_forcings_atm.dat | 24 ++
.../configure_forcings_ocn.dat | 24 ++
.../configure_forcings_sed.dat | 21 ++
.../biogem_force_flux_sed_det_SUR.dat | 37 +++
.../biogem_force_flux_sed_det_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_13C_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_sig.dat | 263 ++++++++++++++++++
.../configure_forcings_atm.dat | 24 ++
.../configure_forcings_ocn.dat | 24 ++
.../configure_forcings_sed.dat | 21 ++
.../biogem_force_flux_sed_det_SUR.dat | 37 +++
.../biogem_force_flux_sed_det_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_13C_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_sig.dat | 263 ++++++++++++++++++
.../configure_forcings_atm.dat | 24 ++
.../configure_forcings_ocn.dat | 24 ++
.../configure_forcings_sed.dat | 21 ++
.../muffin.CBE.GIteiiaa.BASESFeTDTL_rb.config | 221 +++++++++++++++
.../muffin.CBE.GIteiiva.BASESFeTDTL_rb.config | 221 +++++++++++++++
.../muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN | 181 ++++++++++++
.../muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN | 184 ++++++++++++
...fin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC | 200 +++++++++++++
....CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN | 147 ++++++++++
...in.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN | 147 ++++++++++
....CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN | 147 ++++++++++
....CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN | 147 ++++++++++
.../muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg | 159 +++++++++++
.../muffin.CBE.worlg4.BASESFeTDTL.2100.2deg | 159 +++++++++++
.../muffin.CBE.worlg4.BASESFeTDTL.2100.3deg | 159 +++++++++++
.../muffin.CBE.worlg4.BASESFeTDTL.2100.4deg | 158 +++++++++++
.../muffin.CBE.worlg4.BASESFeTDTL.SPIN | 156 +++++++++++
.../muffin.CBE.worlg4.BASESFeTDTL.historical | 161 +++++++++++
50 files changed, 4432 insertions(+)
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_flux_sed_det_SUR.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_flux_sed_det_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_restore_atm_pCO2_13C_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_restore_atm_pCO2_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_atm.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_ocn.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_sed.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_flux_sed_det_SUR.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_flux_sed_det_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_restore_atm_pCO2_13C_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_restore_atm_pCO2_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_atm.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_ocn.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_sed.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_flux_sed_det_SUR.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_flux_sed_det_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_restore_atm_pCO2_13C_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_restore_atm_pCO2_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_atm.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_ocn.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_sed.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_flux_sed_det_SUR.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_flux_sed_det_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_restore_atm_pCO2_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_atm.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_ocn.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_sed.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_flux_sed_det_SUR.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_flux_sed_det_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_restore_atm_pCO2_13C_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_restore_atm_pCO2_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_atm.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_ocn.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_sed.dat
create mode 100644 genie-main/configs/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.config
create mode 100644 genie-main/configs/muffin.CBE.GIteiiva.BASESFeTDTL_rb.config
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_flux_sed_det_SUR.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_flux_sed_det_SUR.dat
new file mode 100644
index 000000000..0e35c9e79
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_flux_sed_det_SUR.dat
@@ -0,0 +1,37 @@
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\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_flux_sed_det_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_flux_sed_det_sig.dat
new file mode 100644
index 000000000..972d7c3fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_flux_sed_det_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
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diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_restore_atm_pCO2_13C_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_restore_atm_pCO2_13C_sig.dat
new file mode 100644
index 000000000..b4149dc1a
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_restore_atm_pCO2_13C_sig.dat
@@ -0,0 +1,4 @@
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\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_restore_atm_pCO2_sig.dat
new file mode 100644
index 000000000..1250b1976
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/biogem_force_restore_atm_pCO2_sig.dat
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+-END-OF-DATA-
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_atm.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_atm.dat
new file mode 100644
index 000000000..453007a3e
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_atm.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08
+ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 03 t 0.1 f t F 2 01 01 '[carbon dioxide (CO2) partial pressure (atm)]'
+ 04 t 0.1 f t F 2 01 01 '[d13C CO2 (o/oo)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08
+
+DATA FORMAT AND ORDER:
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #03: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #04: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: force ocean surface in equilibrium with atmosphere? (needs ocean restoring forcing set) [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (2 = 2D, 0 = point, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_ocn.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_ocn.dat
new file mode 100644
index 000000000..a317b42fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_ocn.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08 09
+ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08 09
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: restrict restoring forcing to surface? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #04: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN #09: k grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_sed.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_sed.dat
new file mode 100644
index 000000000..0db3bf57b
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg/configure_forcings_sed.dat
@@ -0,0 +1,21 @@
+
+ 00 01 02 03 04 05
+ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 22 t F -1 01 01 '[detrital (refractory) material (wt%)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #04: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #05: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_flux_sed_det_SUR.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_flux_sed_det_SUR.dat
new file mode 100644
index 000000000..0e35c9e79
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_flux_sed_det_SUR.dat
@@ -0,0 +1,37 @@
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\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_flux_sed_det_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_flux_sed_det_sig.dat
new file mode 100644
index 000000000..972d7c3fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_flux_sed_det_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
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+-END-OF-DATA-
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_restore_atm_pCO2_13C_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_restore_atm_pCO2_13C_sig.dat
new file mode 100644
index 000000000..b4149dc1a
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_restore_atm_pCO2_13C_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
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\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_restore_atm_pCO2_sig.dat
new file mode 100644
index 000000000..fea4521a2
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/biogem_force_restore_atm_pCO2_sig.dat
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diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_atm.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_atm.dat
new file mode 100644
index 000000000..453007a3e
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_atm.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08
+ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 03 t 0.1 f t F 2 01 01 '[carbon dioxide (CO2) partial pressure (atm)]'
+ 04 t 0.1 f t F 2 01 01 '[d13C CO2 (o/oo)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08
+
+DATA FORMAT AND ORDER:
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #03: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #04: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: force ocean surface in equilibrium with atmosphere? (needs ocean restoring forcing set) [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (2 = 2D, 0 = point, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_ocn.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_ocn.dat
new file mode 100644
index 000000000..a317b42fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_ocn.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08 09
+ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08 09
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: restrict restoring forcing to surface? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #04: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN #09: k grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_sed.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_sed.dat
new file mode 100644
index 000000000..0db3bf57b
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg/configure_forcings_sed.dat
@@ -0,0 +1,21 @@
+
+ 00 01 02 03 04 05
+ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 22 t F -1 01 01 '[detrital (refractory) material (wt%)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #04: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #05: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_flux_sed_det_SUR.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_flux_sed_det_SUR.dat
new file mode 100644
index 000000000..0e35c9e79
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_flux_sed_det_SUR.dat
@@ -0,0 +1,37 @@
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\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_flux_sed_det_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_flux_sed_det_sig.dat
new file mode 100644
index 000000000..972d7c3fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_flux_sed_det_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
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+-END-OF-DATA-
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_restore_atm_pCO2_13C_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_restore_atm_pCO2_13C_sig.dat
new file mode 100644
index 000000000..b4149dc1a
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_restore_atm_pCO2_13C_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
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\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_restore_atm_pCO2_sig.dat
new file mode 100644
index 000000000..3af7cf679
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/biogem_force_restore_atm_pCO2_sig.dat
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diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_atm.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_atm.dat
new file mode 100644
index 000000000..453007a3e
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_atm.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08
+ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 03 t 0.1 f t F 2 01 01 '[carbon dioxide (CO2) partial pressure (atm)]'
+ 04 t 0.1 f t F 2 01 01 '[d13C CO2 (o/oo)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08
+
+DATA FORMAT AND ORDER:
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #03: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #04: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: force ocean surface in equilibrium with atmosphere? (needs ocean restoring forcing set) [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (2 = 2D, 0 = point, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_ocn.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_ocn.dat
new file mode 100644
index 000000000..a317b42fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_ocn.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08 09
+ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08 09
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: restrict restoring forcing to surface? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #04: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN #09: k grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_sed.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_sed.dat
new file mode 100644
index 000000000..0db3bf57b
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg/configure_forcings_sed.dat
@@ -0,0 +1,21 @@
+
+ 00 01 02 03 04 05
+ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 22 t F -1 01 01 '[detrital (refractory) material (wt%)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #04: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #05: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_flux_sed_det_SUR.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_flux_sed_det_SUR.dat
new file mode 100644
index 000000000..0e35c9e79
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_flux_sed_det_SUR.dat
@@ -0,0 +1,37 @@
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\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_flux_sed_det_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_flux_sed_det_sig.dat
new file mode 100644
index 000000000..972d7c3fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_flux_sed_det_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999.0 1.0
+-END-OF-DATA-
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
new file mode 100644
index 000000000..b4149dc1a
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
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+-END-OF-DATA-
\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_restore_atm_pCO2_sig.dat
new file mode 100644
index 000000000..abfa1560a
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/biogem_force_restore_atm_pCO2_sig.dat
@@ -0,0 +1,263 @@
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diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_atm.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_atm.dat
new file mode 100644
index 000000000..453007a3e
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_atm.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08
+ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 03 t 0.1 f t F 2 01 01 '[carbon dioxide (CO2) partial pressure (atm)]'
+ 04 t 0.1 f t F 2 01 01 '[d13C CO2 (o/oo)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08
+
+DATA FORMAT AND ORDER:
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #03: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #04: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: force ocean surface in equilibrium with atmosphere? (needs ocean restoring forcing set) [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (2 = 2D, 0 = point, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_ocn.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_ocn.dat
new file mode 100644
index 000000000..a317b42fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_ocn.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08 09
+ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08 09
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: restrict restoring forcing to surface? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #04: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN #09: k grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_sed.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_sed.dat
new file mode 100644
index 000000000..0db3bf57b
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg/configure_forcings_sed.dat
@@ -0,0 +1,21 @@
+
+ 00 01 02 03 04 05
+ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 22 t F -1 01 01 '[detrital (refractory) material (wt%)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #04: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #05: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_flux_sed_det_SUR.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_flux_sed_det_SUR.dat
new file mode 100644
index 000000000..0e35c9e79
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_flux_sed_det_SUR.dat
@@ -0,0 +1,37 @@
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+
\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_flux_sed_det_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_flux_sed_det_sig.dat
new file mode 100644
index 000000000..972d7c3fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_flux_sed_det_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999.0 1.0
+-END-OF-DATA-
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_restore_atm_pCO2_13C_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_restore_atm_pCO2_13C_sig.dat
new file mode 100644
index 000000000..b4149dc1a
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_restore_atm_pCO2_13C_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999.0 1.0
+-END-OF-DATA-
\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_restore_atm_pCO2_sig.dat
new file mode 100644
index 000000000..498b6a329
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/biogem_force_restore_atm_pCO2_sig.dat
@@ -0,0 +1,263 @@
+-START-OF-DATA-
+0.0 2.78000E-04
+1765.5 2.77910E-04
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+1992.5 3.56230E-04
+1993.5 3.56920E-04
+1994.5 3.58250E-04
+1995.5 3.60240E-04
+1996.5 3.62000E-04
+1997.5 3.63250E-04
+1998.5 3.65930E-04
+1999.5 3.67840E-04
+2000.5 3.69120E-04
+2001.5 3.70670E-04
+2002.5 3.72830E-04
+2003.5 3.75410E-04
+2004.5 3.76990E-04
+2005.5 3.78910E-04
+2006.5 3.81010E-04
+2007.5 3.82600E-04
+2008.5 3.84740E-04
+2009.5 3.86280E-04
+2010.5 3.88720E-04
+2011.5 3.90940E-04
+2012.5 3.93020E-04
+2013.5 3.95720E-04
+2014.5 3.97550E-04
+2015.5 3.99950E-04
+2016.5 4.03120E-04
+2017.5 4.05790E-04
+2018.5 4.08760E-04
+2019.5 4.11790E-04
+2020.5 4.14890E-04
+2021.5 4.18060E-04
+2022.5 4.21330E-04
+2099.5 450.0E-6
+999999999.0 278.0E-6
+-END-OF-DATA-
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_atm.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_atm.dat
new file mode 100644
index 000000000..453007a3e
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_atm.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08
+ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 03 t 0.1 f t F 2 01 01 '[carbon dioxide (CO2) partial pressure (atm)]'
+ 04 t 0.1 f t F 2 01 01 '[d13C CO2 (o/oo)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08
+
+DATA FORMAT AND ORDER:
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #03: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #04: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: force ocean surface in equilibrium with atmosphere? (needs ocean restoring forcing set) [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (2 = 2D, 0 = point, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_ocn.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_ocn.dat
new file mode 100644
index 000000000..a317b42fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_ocn.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08 09
+ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08 09
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: restrict restoring forcing to surface? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #04: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN #09: k grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_sed.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_sed.dat
new file mode 100644
index 000000000..0db3bf57b
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022/configure_forcings_sed.dat
@@ -0,0 +1,21 @@
+
+ 00 01 02 03 04 05
+ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 22 t F -1 01 01 '[detrital (refractory) material (wt%)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #04: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #05: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-main/configs/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.config b/genie-main/configs/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.config
new file mode 100644
index 000000000..6038d59fb
--- /dev/null
+++ b/genie-main/configs/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.config
@@ -0,0 +1,221 @@
+# *******************************************************************
+# CONFIGURATION TEMPLATE -- for a 16 level seasonally forced ocean
+# *******************************************************************
+
+# *******************************************************************
+# GENIE COMPONENT SELECTION
+# *******************************************************************
+# make .TRUE. the cGENIE modules to be included
+# *******************************************************************
+ma_flag_ebatmos=.TRUE.
+ma_flag_goldsteinocean=.TRUE.
+ma_flag_goldsteinseaice=.TRUE.
+ma_flag_biogem=.TRUE.
+ma_flag_atchem=.TRUE.
+ma_flag_sedgem=.FALSE.
+ma_flag_rokgem=.FALSE.
+ma_flag_gemlite=.FALSE.
+ma_flag_ecogem=.TRUE. #modified by RY, 27 Apr 2022
+# *******************************************************************
+
+# *******************************************************************
+# GRID & BOUNDARY CONDITION CONFIGURATION
+# *******************************************************************
+# insert the automatically generated muffingen parameter list here
+# *******************************************************************
+##################################################################################
+### cGENIE .config file parameter lines generated by muffingen v0.72 on: 190313 ###
+# INPUT FILE PATH
+ea_1='../../cgenie.muffin/genie-paleo/GIteiiaa'
+go_1='../../cgenie.muffin/genie-paleo/GIteiiaa'
+gs_1='../../cgenie.muffin/genie-paleo/GIteiiaa'
+# Grid resolution
+GENIENXOPTS='$(DEFINE)GENIENX=36'
+GENIENYOPTS='$(DEFINE)GENIENY=36'
+GOLDSTEINNLONSOPTS='$(DEFINE)GOLDSTEINNLONS=36'
+GOLDSTEINNLATSOPTS='$(DEFINE)GOLDSTEINNLATS=36'
+GOLDSTEINNLEVSOPTS='$(DEFINE)GOLDSTEINNLEVS=16'
+# Topography
+ma_fname_topo='GIteiiaa'
+# Assumed longitudinal offset of the grid
+gm_par_grid_lon_offset=-260
+# Ocean depth scalar (m) [internally, parameter: dsc]
+go_par_dsc=5000
+# Boundary conditions: EMBM
+ea_topo='GIteiiaa'
+ea_taux_u='GIteiiaa.taux_u.dat'
+ea_tauy_u='GIteiiaa.tauy_u.dat'
+ea_taux_v='GIteiiaa.taux_v.dat'
+ea_tauy_v='GIteiiaa.tauy_v.dat'
+ea_adv_u='GIteiiaa.wvelx.dat'
+ea_adv_v='GIteiiaa.wvely.dat'
+# Boundary conditions: GOLDSTEIN
+go_topo='GIteiiaa'
+# Boundary conditions: GOLDSTEIN sea-ice
+gs_topo='GIteiiaa'
+# Boundary conditions: ALBEDO!
+ea_par_albedo1d_name='GIteiiaa.albd.dat'
+# Boundary conditions: BIOGEM
+bg_par_pindir_name='../../cgenie.muffin/genie-paleo/GIteiiaa/'
+bg_par_windspeed_file='GIteiiaa.windspeed_uvaa.dat'
+# BIOGEM MISC
+# gas transfer coeff
+bg_par_gastransfer_a=0.904
+# Grid resolution of solid Earth components
+SEDGEMNLONSOPTS='$(DEFINE)SEDGEMNLONS=36'
+SEDGEMNLATSOPTS='$(DEFINE)SEDGEMNLATS=36'
+ROKGEMNLONSOPTS='$(DEFINE)ROKGEMNLONS=36'
+ROKGEMNLATSOPTS='$(DEFINE)ROKGEMNLATS=36'
+# Topography for solid Earth components
+sg_par_pindir_name='../../cgenie.muffin/genie-paleo/GIteiiaa/'
+sg_par_sed_topo_D_name='GIteiiaa.depth.dat'
+sg_par_sed_reef_mask_name='GIteiiaa.reefmask.dat'
+sg_par_sedcore_save_mask_name='GIteiiaa.sedcoremask.dat'
+rg_par_pindir_name='../../cgenie.muffin/genie-paleo/GIteiiaa/'
+rg_topo='GIteiiaa.k1'
+# GEOLOGIC AGE DEPENDENT PARAMETERS
+# Solar constant (W m-2) ... don't forget to adjust it if not modern!!
+###ma_genie_solar_constant=1368.0
+# ... also, salinity should be set 1 PSU lower if it an ice-free World
+###go_saln0=33.9
+# Orbital parameters (modern, defaults)
+###ea_par_orbit_osce=0.0167 # eccentricity
+###ea_par_orbit_oscsob=0.397789 # sine of obliquity
+###ea_par_orbit_oscgam=102.92 # longitude of perihelion
+# Ocean Mg/Ca concentrations (modern defaults, mol kg-1)
+bg_ocn_init_35=1.028E-02
+bg_ocn_init_50=5.282E-02
+##################################################################################
+# *******************************************************************
+
+# *******************************************************************
+# TRACER CONFIGURATION
+# *******************************************************************
+# the total number of tracers includes T and S
+# T and S do not need to be explicited selected and initialzied
+# *******************************************************************
+# Set number of tracers
+GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=19'
+# Select tracers
+gm_atm_select_3=.true.
+gm_atm_select_4=.true.
+gm_atm_select_5=.false. # 14C pCO2
+gm_atm_select_6=.true.
+gm_atm_select_16=.true.
+gm_ocn_select_3=.true.
+gm_ocn_select_4=.true.
+gm_ocn_select_5=.false. # 14C DIC
+gm_ocn_select_8=.true.
+gm_ocn_select_10=.true.
+gm_ocn_select_12=.true.
+gm_ocn_select_15=.true.
+gm_ocn_select_16=.true.
+gm_ocn_select_17=.false. # 14C DOC
+gm_ocn_select_20=.true.
+gm_ocn_select_22=.true.
+gm_ocn_select_90=.true.
+gm_ocn_select_42=.true.
+gm_ocn_select_35=.true.
+gm_ocn_select_38=.true.
+gm_ocn_select_40=.true.
+gm_ocn_select_48=.true. # r
+gm_ocn_select_49=.true. # b
+gm_ocn_select_50=.true.
+gm_sed_select_3=.true.
+gm_sed_select_4=.true.
+gm_sed_select_5=.false. # 14C POC
+gm_sed_select_8=.true.
+gm_sed_select_10=.true.
+gm_sed_select_13=.true.
+gm_sed_select_14=.true.
+gm_sed_select_15=.true.
+gm_sed_select_16=.false. # 14C CaCO3
+gm_sed_select_21=.true.
+gm_sed_select_22=.true.
+gm_sed_select_25=.true.
+gm_sed_select_32=.true.
+gm_sed_select_33=.true.
+gm_sed_select_34=.true.
+gm_sed_select_36=.true.
+# Set tracer initial values
+ac_atm_init_3=278.0E-06
+ac_atm_init_4=-6.5
+ac_atm_init_6=0.2095
+bg_ocn_init_3=2.244E-03
+bg_ocn_init_4=0.4
+bg_ocn_init_8=2.159E-06
+bg_ocn_init_10=1.696E-04
+bg_ocn_init_12=2.363E-03
+bg_ocn_init_15=0.0
+bg_ocn_init_16=0.0
+bg_ocn_init_20=0.0
+bg_ocn_init_22=0.0
+bg_ocn_init_90=0.650E-09
+bg_ocn_init_42=1.000E-09
+bg_ocn_init_35=1.025E-02
+bg_ocn_init_38=2.916E-02
+bg_ocn_init_40=0.0
+bg_ocn_init_48=0.0 # r
+bg_ocn_init_49=0.0 # b
+bg_ocn_init_50=5.282E-02
+# *******************************************************************
+
+# *******************************************************************
+# PHYSICAL CLIMATE CALIBRATION
+# *******************************************************************
+# based on Cao et al. [2009] with the following exceptions:
+# (1) warmer ocean start (could be 10C for a more intense greenhouse world)
+# (2) scaling of the freshwater re-balancing flux to zero
+# (3) application of a reduced sea-ice diffusivity and
+# prescribed maximum fractional area for sea-ice advection
+# (4) no diffusivity scaling factor over Antarctica
+# *******************************************************************
+# rel
+go_12=0.9000000
+# scl_tau / SclTau
+go_13=1.531013488769531300
+# ocean diffusivites iso (or horiz) / OcnHorizDiff
+go_14=1494.438354492187500000
+# ocean diffusivites dia (or vert) / OcnVertDiff
+go_15=0.000025363247914356
+# inverse minimum drag in days / InvDrag
+go_16=2.710164785385131800
+# scl_tau (should be same as GOLDSTEIN's value) / SclTau
+ea_11=1.531013488769531300
+# atm. diff. amp. for T / AtmDiffAmpT
+ea_12=5204945.000000000000000000
+# atm. diff. amp. for q / AtmDiffAmpQ
+ea_13=1173269.250000000000000000
+# dist'n width / AtmDiffWidthT
+ea_14=1.410347938537597700
+# dist'n slope / AtmDiffSlopeT
+ea_15=0.090003050863742828
+# atm. advection factor for T_z / AtmAdvectCoeffTm
+ea_16=0.001037851092405617
+# atm. advection factor for T_m / AtmAdvectCoeffQm
+ea_17=0.0000000E+00
+# atm. advection factor for q_z / AtmAdvectCoeffQz
+ea_18=0.164652019739151000
+# atm. advection factor for q_m / AtmAdvectCoeffQz
+ea_19=0.164652019739151000
+# temp0 -- start with a warm ocean
+go_10=5.0
+# temp1 -- start with a warm ocean
+go_11=5.0
+# SclFWF -- scale for zero freshwater re-balancing
+ea_28=0.0
+# reduced sea-ice eddy diffusivity
+gs_11=1000.000
+# set a fractional sea-ce coverage threshold for preventing advection
+gs_par_sica_thresh=0.99
+# set seasonal cycle
+ea_dosc=.true.
+go_dosc=.true.
+gs_dosc=.true.
+# *******************************************************************
+
+# *******************************************************************
+# USER-APPENDED OPTIONS FOLLOW ...
+# *******************************************************************
+# (the following parameter text is appended automatically)
+# *******************************************************************
diff --git a/genie-main/configs/muffin.CBE.GIteiiva.BASESFeTDTL_rb.config b/genie-main/configs/muffin.CBE.GIteiiva.BASESFeTDTL_rb.config
new file mode 100644
index 000000000..36ff08c04
--- /dev/null
+++ b/genie-main/configs/muffin.CBE.GIteiiva.BASESFeTDTL_rb.config
@@ -0,0 +1,221 @@
+# *******************************************************************
+# CONFIGURATION TEMPLATE -- for a 16 level seasonally forced ocean
+# *******************************************************************
+
+# *******************************************************************
+# GENIE COMPONENT SELECTION
+# *******************************************************************
+# make .TRUE. the cGENIE modules to be included
+# *******************************************************************
+ma_flag_ebatmos=.TRUE.
+ma_flag_goldsteinocean=.TRUE.
+ma_flag_goldsteinseaice=.TRUE.
+ma_flag_biogem=.TRUE.
+ma_flag_atchem=.TRUE.
+ma_flag_sedgem=.FALSE.
+ma_flag_rokgem=.FALSE.
+ma_flag_gemlite=.FALSE.
+ma_flag_ecogem=.TRUE. #modified RY, 16 Mar 2022
+# *******************************************************************
+
+# *******************************************************************
+# GRID & BOUNDARY CONDITION CONFIGURATION
+# *******************************************************************
+# insert the automatically generated muffingen parameter list here
+# *******************************************************************
+##################################################################################
+### cGENIE .config file parameter lines generated by muffingen v0.73 on: 190313 ###
+# INPUT FILE PATH
+ea_1='../../cgenie.muffin/genie-paleo/GIteiiva'
+go_1='../../cgenie.muffin/genie-paleo/GIteiiva'
+gs_1='../../cgenie.muffin/genie-paleo/GIteiiva'
+# Grid resolution
+GENIENXOPTS='$(DEFINE)GENIENX=36'
+GENIENYOPTS='$(DEFINE)GENIENY=36'
+GOLDSTEINNLONSOPTS='$(DEFINE)GOLDSTEINNLONS=36'
+GOLDSTEINNLATSOPTS='$(DEFINE)GOLDSTEINNLATS=36'
+GOLDSTEINNLEVSOPTS='$(DEFINE)GOLDSTEINNLEVS=16'
+# Topography
+ma_fname_topo='GIteiiva'
+# Assumed longitudinal offset of the grid
+gm_par_grid_lon_offset=-260
+# Ocean depth scalar (m) [internally, parameter: dsc]
+go_par_dsc=5000
+# Boundary conditions: EMBM
+ea_topo='GIteiiva'
+ea_taux_u='GIteiiva.taux_u.dat'
+ea_tauy_u='GIteiiva.tauy_u.dat'
+ea_taux_v='GIteiiva.taux_v.dat'
+ea_tauy_v='GIteiiva.tauy_v.dat'
+ea_adv_u='GIteiiva.wvelx.dat'
+ea_adv_v='GIteiiva.wvely.dat'
+# Boundary conditions: GOLDSTEIN
+go_topo='GIteiiva'
+# Boundary conditions: GOLDSTEIN sea-ice
+gs_topo='GIteiiva'
+# Boundary conditions: ALBEDO!
+ea_par_albedo1d_name='GIteiiva.albd.dat'
+# Boundary conditions: BIOGEM
+bg_par_pindir_name='../../cgenie.muffin/genie-paleo/GIteiiva/'
+bg_par_windspeed_file='GIteiiva.windspeed_uvaa.dat'
+# BIOGEM MISC
+# gas transfer coeff
+bg_par_gastransfer_a=0.904
+# Grid resolution of solid Earth components
+SEDGEMNLONSOPTS='$(DEFINE)SEDGEMNLONS=36'
+SEDGEMNLATSOPTS='$(DEFINE)SEDGEMNLATS=36'
+ROKGEMNLONSOPTS='$(DEFINE)ROKGEMNLONS=36'
+ROKGEMNLATSOPTS='$(DEFINE)ROKGEMNLATS=36'
+# Topography for solid Earth components
+sg_par_pindir_name='../../cgenie.muffin/genie-paleo/GIteiiva/'
+sg_par_sed_topo_D_name='GIteiiva.depth.dat'
+sg_par_sed_reef_mask_name='GIteiiva.reefmask.dat'
+sg_par_sedcore_save_mask_name='GIteiiva.sedcoremask.dat'
+rg_par_pindir_name='../../cgenie.muffin/genie-paleo/GIteiiva/'
+rg_topo='GIteiiva.k1'
+# GEOLOGIC AGE DEPENDENT PARAMETERS
+# Solar constant (W m-2) ... don't forget to adjust it if not modern!!
+###ma_genie_solar_constant=1368.0
+# ... also, salinity should be set 1 PSU lower if it an ice-free World
+###go_saln0=33.9
+# Orbital parameters (modern, defaults)
+###ea_par_orbit_osce=0.0167 # eccentricity
+###ea_par_orbit_oscsob=0.397789 # sine of obliquity
+###ea_par_orbit_oscgam=102.92 # longitude of perihelion
+# Ocean Mg/Ca concentrations (modern defaults, mol kg-1)
+bg_ocn_init_35=1.028E-02
+bg_ocn_init_50=5.282E-02
+##################################################################################
+# *******************************************************************
+
+# *******************************************************************
+# TRACER CONFIGURATION
+# *******************************************************************
+# the total number of tracers includes T and S
+# T and S do not need to be explicited selected and initialzied
+# *******************************************************************
+# Set number of tracers
+GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=19'
+# Select tracers
+gm_atm_select_3=.true.
+gm_atm_select_4=.true.
+gm_atm_select_5=.false. # 14C pCO2
+gm_atm_select_6=.true.
+gm_atm_select_16=.true.
+gm_ocn_select_3=.true.
+gm_ocn_select_4=.true.
+gm_ocn_select_5=.false. # 14C DIC
+gm_ocn_select_8=.true.
+gm_ocn_select_10=.true.
+gm_ocn_select_12=.true.
+gm_ocn_select_15=.true.
+gm_ocn_select_16=.true.
+gm_ocn_select_17=.false. # 14C DOC
+gm_ocn_select_20=.true.
+gm_ocn_select_22=.true.
+gm_ocn_select_90=.true.
+gm_ocn_select_42=.true.
+gm_ocn_select_35=.true.
+gm_ocn_select_38=.true.
+gm_ocn_select_40=.true.
+gm_ocn_select_48=.true. # r
+gm_ocn_select_49=.true. # b
+gm_ocn_select_50=.true.
+gm_sed_select_3=.true.
+gm_sed_select_4=.true.
+gm_sed_select_5=.false. # 14C POC
+gm_sed_select_8=.true.
+gm_sed_select_10=.true.
+gm_sed_select_13=.true.
+gm_sed_select_14=.true.
+gm_sed_select_15=.true.
+gm_sed_select_16=.false. # 14C CaCO3
+gm_sed_select_21=.true.
+gm_sed_select_22=.true.
+gm_sed_select_25=.true.
+gm_sed_select_32=.true.
+gm_sed_select_33=.true.
+gm_sed_select_34=.true.
+gm_sed_select_36=.true.
+# Set tracer initial values
+ac_atm_init_3=278.0E-06
+ac_atm_init_4=-6.5
+ac_atm_init_6=0.2095
+bg_ocn_init_3=2.244E-03
+bg_ocn_init_4=0.4
+bg_ocn_init_8=2.159E-06
+bg_ocn_init_10=1.696E-04
+bg_ocn_init_12=2.363E-03
+bg_ocn_init_15=0.0
+bg_ocn_init_16=0.0
+bg_ocn_init_20=0.0
+bg_ocn_init_22=0.0
+bg_ocn_init_90=0.650E-09
+bg_ocn_init_42=1.000E-09
+bg_ocn_init_35=1.025E-02
+bg_ocn_init_38=2.916E-02
+bg_ocn_init_40=0.0
+bg_ocn_init_48=0.0 # r
+bg_ocn_init_49=0.0 # b
+bg_ocn_init_50=5.282E-02
+# *******************************************************************
+
+# *******************************************************************
+# PHYSICAL CLIMATE CALIBRATION
+# *******************************************************************
+# based on Cao et al. [2009] with the following exceptions:
+# (1) warmer ocean start (could be 10C for a more intense greenhouse world)
+# (2) scaling of the freshwater re-balancing flux to zero
+# (3) application of a reduced sea-ice diffusivity and
+# prescribed maximum fractional area for sea-ice advection
+# (4) no diffusivity scaling factor over Antarctica
+# *******************************************************************
+# rel
+go_12=0.9000000
+# scl_tau / SclTau
+go_13=1.531013488769531300
+# ocean diffusivites iso (or horiz) / OcnHorizDiff
+go_14=1494.438354492187500000
+# ocean diffusivites dia (or vert) / OcnVertDiff
+go_15=0.000025363247914356
+# inverse minimum drag in days / InvDrag
+go_16=2.710164785385131800
+# scl_tau (should be same as GOLDSTEIN's value) / SclTau
+ea_11=1.531013488769531300
+# atm. diff. amp. for T / AtmDiffAmpT
+ea_12=5204945.000000000000000000
+# atm. diff. amp. for q / AtmDiffAmpQ
+ea_13=1173269.250000000000000000
+# dist'n width / AtmDiffWidthT
+ea_14=1.410347938537597700
+# dist'n slope / AtmDiffSlopeT
+ea_15=0.090003050863742828
+# atm. advection factor for T_z / AtmAdvectCoeffTm
+ea_16=0.001037851092405617
+# atm. advection factor for T_m / AtmAdvectCoeffQm
+ea_17=0.0000000E+00
+# atm. advection factor for q_z / AtmAdvectCoeffQz
+ea_18=0.164652019739151000
+# atm. advection factor for q_m / AtmAdvectCoeffQz
+ea_19=0.164652019739151000
+# temp0 -- start with a warm ocean
+go_10=5.0
+# temp1 -- start with a warm ocean
+go_11=5.0
+# SclFWF -- scale for zero freshwater re-balancing
+ea_28=0.0
+# reduced sea-ice eddy diffusivity
+gs_11=1000.000
+# set a fractional sea-ce coverage threshold for preventing advection
+gs_par_sica_thresh=0.99
+# set seasonal cycle
+ea_dosc=.true.
+go_dosc=.true.
+gs_dosc=.true.
+# *******************************************************************
+
+# *******************************************************************
+# USER-APPENDED OPTIONS FOLLOW ...
+# *******************************************************************
+# (the following parameter text is appended automatically)
+# *******************************************************************
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
new file mode 100644
index 000000000..6f4d9b6ab
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
@@ -0,0 +1,181 @@
+# *******************************************************************
+# *** muffin.CB.GIteiiaa.BASESFeTDTL.1p2tau.SPIN ********************
+# *******************************************************************
+#
+# *** CLIMATE *******************************************************
+#
+# (climate responding to changing pCO2)
+ea_36=y
+#
+# *** BIOLOGICAL NEW PRODUCTION *************************************
+#
+# biological scheme ID string
+# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
+bg_par_bio_prodopt="NONE"
+#
+# *** ORGANIC MATTER EXPORT RATIOS **********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** INORGANIC MATTER EXPORT RATIOS ********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** REMINERALIZATION **********************************************
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+# *** optional changes to align with PALEO recommendations **********
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# *** IRON CYCLING **************************************************
+#
+# iron tracer scheme
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility [Albani tuning]
+bg_par_det_Fe_sol=0.002441
+# modifier of the scavenging rate of dissolved Fe [Albani tuning]
+bg_par_scav_Fe_sf_POC=0.2250
+# exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# *** ECOGEM ********************************************************
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+################## Phosphorus ############################
+eg_usePO4 =.true.
+eg_pquota =.true.
+######################## Iron ############################
+eg_useFe =.true.
+eg_fquota =.true.
+################# Chlorophyll ############################
+eg_chlquota =.true.
+################# d13C ###################################
+eg_useDIC_13C =.true.
+# Tuned parameters
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns=2
+eg_respir_a=0
+# DOM parameters
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+# ???
+eg_nsubtime=25
+eg_n_keco=1
+# exponent for modifier of CaCO3:POC export ratio
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+#
+# *** DATA SAVING ***************************************************
+#
+# BASIC + biology + tracer + proxy diagnostics
+bg_par_data_save_level=7
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+#
+# *** FORCINGS ******************************************************
+#
+# specify forcings
+bg_par_forcing_name="GIteiiaa.RpCO2_Rp13CO2.Fsal_SUR.Albani.0ka"
+bg_par_atm_force_scale_val_3=275.0E-06
+bg_par_atm_force_scale_val_4=-6.35
+#
+# *** MISC **********************************************************
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# *** optional changes to align with PALEO recommendations **********
+
+# set mixed layer to be only diagnosed (for ECOGEM)
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+
+# (no preformed)
+bg_ctrl_bio_preformed=.false.
+# add ventillation tracers
+bg_ctrl_force_ocn_age1=.true.
+# add brine rejection SH limit
+bg_par_misc_brinerejection_jmax=19
+# wind-stress
+go_13=1.3
+ea_11=1.3
+#
+# *** TUNING ********************************************************
+#
+# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
+bg_par_misc_brinerejection_frac=0.2
+# parameter: bg_par_ocn_force_scale_val_2 -- default value (1) modified by factor: 0.20
+bg_par_ocn_force_scale_val_2=0.20
+#
+# *** INITIAL CONDITIONS ********************************************
+#
+# N/A
+#
+# *******************************************************************
+# *** END ***********************************************************
+# *******************************************************************
+#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
new file mode 100644
index 000000000..250817d32
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
@@ -0,0 +1,184 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# [Dealt with ECOGEM]
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# [Dealt with ECOGEM]
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002441
+# modifier of the scavenging rate of dissolved Fe [Albani tuning]
+bg_par_scav_Fe_sf_POC=0.2250
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="GIteiiva.RpCO2_Rp13CO2.Fsal_SUR.Albani.21ka"
+bg_par_atm_force_scale_val_3=193.0E-06
+bg_par_atm_force_scale_val_4=-6.46
+# Orbital parameters
+ea_par_orbit_osce=0.018994 # eccentricity
+ea_par_orbit_oscsob=0.389911 # sine of obliquity
+ea_par_orbit_oscgam=114.42 # longitude of perihelion (degrees)
+#
+#
+# *** TUNING ********************************************************
+#
+# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
+bg_par_misc_brinerejection_frac=0.2
+# parameter: bg_par_ocn_force_scale_val_2 -- default value (1) modified by factor: 0.05
+bg_par_ocn_force_scale_val_2=0.05
+#
+# *** INITIAL CONDITIONS ********************************************
+#
+# modern DIC (2.244E-03) + 1%
+bg_ocn_init_3=0.002275818239634
+# modern 13C DIC
+bg_ocn_init_4=0.4
+# modern ALK (2.363E-03) + 1%
+bg_ocn_init_12=0.002396505570523
+# modern PO4 (2.159E-06) + 1%
+bg_ocn_init_8=2.189613003283920e-06
+# modern SAL + 0.33 PSU
+go_saln0=35.23
+#
+# --- MISC ----------------------------------------------------------
+#
+# (no preformed)
+bg_ctrl_bio_preformed=.false.
+# add ventillation tracers
+bg_ctrl_force_ocn_age1=.true.
+# add brine rejection SH limit
+bg_par_misc_brinerejection_jmax=19
+# wind-stress
+go_13=1.3
+ea_11=1.3
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
new file mode 100644
index 000000000..28497264c
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
@@ -0,0 +1,200 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# [Dealt with ECOGEM]
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# [Dealt with ECOGEM]
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002441
+# modifier of the scavenging rate of dissolved Fe [Albani tuning]
+bg_par_scav_Fe_sf_POC=0.2250
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="GIteiiva.RpCO2_Rp13CO2.Fsal_SUR.Albani.21ka"
+bg_par_atm_force_scale_val_3=193.0E-06
+bg_par_atm_force_scale_val_4=-6.46
+# Orbital parameters
+ea_par_orbit_osce=0.018994 # eccentricity
+ea_par_orbit_oscsob=0.389911 # sine of obliquity
+ea_par_orbit_oscgam=114.42 # longitude of perihelion (degrees)
+#
+#
+# *** TUNING ********************************************************
+#
+# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
+bg_par_misc_brinerejection_frac=0.2
+# saltier Atlantic and a mdoern-like AMOC
+bg_par_ocn_force_scale_val_2=0.3
+#
+# *** INITIAL CONDITIONS ********************************************
+#
+# modern DIC (2.244E-03) + 1%
+bg_ocn_init_3=0.002275818239634
+# modern 13C DIC
+bg_ocn_init_4=0.4
+# modern ALK (2.363E-03) + 1%
+bg_ocn_init_12=0.002396505570523
+# modern PO4 (2.159E-06) + 1%
+bg_ocn_init_8=2.189613003283920e-06
+# modern SAL + 0.33 PSU
+go_saln0=35.23
+#
+## --- MISC ----------------------------------------------------------
+#
+# (no preformed)
+bg_ctrl_bio_preformed=.false.
+# add ventillation tracers
+bg_ctrl_force_ocn_age1=.true.
+# add brine rejection SH limit
+bg_par_misc_brinerejection_jmax=19
+# wind-stress
+go_13=1.3
+ea_11=1.3
+
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+
+# maximum time-scale to geochemical reaction completion (days)
+bg_par_bio_geochem_tau=90.0
+
+# extend solubility and geochem constant T range (leave S range as default)
+gm_par_geochem_Tmin = -2.0
+gm_par_geochem_Tmax = 45.0
+gm_par_carbchem_Tmin = -2.0
+gm_par_carbchem_Tmax = 45.0
+
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# --- END -----------------------------------------------------------
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
new file mode 100644
index 000000000..cbc46b0dc
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
@@ -0,0 +1,147 @@
+# *** CLIMATE *******************************************************
+#
+# set climate feedback (climate responding to changing pCO2)
+ea_36=y
+#
+# *** BIOLOGICAL NEW PRODUCTION *************************************
+#
+# biological scheme ID string
+# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
+bg_par_bio_prodopt="NONE"
+#
+# *** ORGANIC MATTER EXPORT RATIOS **********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** INORGANIC MATTER EXPORT RATIOS ********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** REMINERALIZATION **********************************************
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+# *** optional changes to align with PALEO recommendations **********
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# *** IRON CYCLING **************************************************
+#
+# [no iron]
+#
+# *** ECOGEM ********************************************************
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#################### Nitrogen ############################
+eg_useNO3 =.false.
+eg_nquota =.false.
+################## Phosphorus ############################
+eg_usePO4 =.true.
+eg_pquota =.true.
+######################## Iron ############################
+eg_useFe =.false.
+eg_fquota =.false.
+################# Chlorophyll ############################
+eg_chlquota =.true.
+################# d13C ###################################
+eg_useDIC_13C =.true.
+# Tuned parameters
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+# ???
+eg_ns=2
+# ???
+eg_respir_a=0
+# DOM parameters
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+# ???
+eg_nsubtime=25
+eg_n_keco=1
+# exponent for modifier of CaCO3:POC export ratio
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=7
+# reduce output
+bg_ctrl_data_save_2d=.true.
+bg_ctrl_data_save_3d=.true. # JDW - set to true
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
+bg_par_atm_force_scale_val_4=-6.428
+# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 280
+bg_par_atm_force_scale_val_3=0.000280
+# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
+bg_par_ocn_force_scale_val_2=0.2
+#
+# *** MISC **********************************************************
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+# *** optional changes to align with PALEO recommendations **********
+# set mixed layer to be only diagnosed (for ECOGEM)
+go_ctrl_diagmld=.true.
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+# maximum time-scale to geochemical reaction completion (days)
+bg_par_bio_geochem_tau=90.0
+# extend solubility and geochem constant T range (leave S range as default)
+gm_par_geochem_Tmin = -2.0
+gm_par_geochem_Tmax = 45.0
+gm_par_carbchem_Tmin = -2.0
+gm_par_carbchem_Tmax = 45.0
+#
+ma_flag_ecogem=.TRUE.
+GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
+gm_ocn_select_60=.true. # preformed PO4
+gm_ocn_select_66=.true. # Csoft
+bg_ctrl_bio_preformed=.true.
+bg_ctrl_bio_remin_redox_save=.true.
+bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
+#
+# *******************************************************************
+# *** END ***********************************************************
+# *******************************************************************
+#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
new file mode 100644
index 000000000..bc4a6946d
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
@@ -0,0 +1,147 @@
+# *** CLIMATE *******************************************************
+#
+# set climate feedback (climate responding to changing pCO2)
+ea_36=y
+#
+# *** BIOLOGICAL NEW PRODUCTION *************************************
+#
+# biological scheme ID string
+# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
+bg_par_bio_prodopt="NONE"
+#
+# *** ORGANIC MATTER EXPORT RATIOS **********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** INORGANIC MATTER EXPORT RATIOS ********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** REMINERALIZATION **********************************************
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+# *** optional changes to align with PALEO recommendations **********
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# *** IRON CYCLING **************************************************
+#
+# [no iron]
+#
+# *** ECOGEM ********************************************************
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#################### Nitrogen ############################
+eg_useNO3 =.false.
+eg_nquota =.false.
+################## Phosphorus ############################
+eg_usePO4 =.true.
+eg_pquota =.true.
+######################## Iron ############################
+eg_useFe =.false.
+eg_fquota =.false.
+################# Chlorophyll ############################
+eg_chlquota =.true.
+################# d13C ###################################
+eg_useDIC_13C =.true.
+# Tuned parameters
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+# ???
+eg_ns=2
+# ???
+eg_respir_a=0
+# DOM parameters
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+# ???
+eg_nsubtime=25
+eg_n_keco=1
+# exponent for modifier of CaCO3:POC export ratio
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=7
+# reduce output
+bg_ctrl_data_save_2d=.true.
+bg_ctrl_data_save_3d=.true. # JDW - set to true
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
+bg_par_atm_force_scale_val_4=-6.202
+# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
+bg_par_atm_force_scale_val_3=0.000400
+# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.5
+bg_par_ocn_force_scale_val_2=0.5
+#
+# *** MISC **********************************************************
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+# *** optional changes to align with PALEO recommendations **********
+# set mixed layer to be only diagnosed (for ECOGEM)
+go_ctrl_diagmld=.true.
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+# maximum time-scale to geochemical reaction completion (days)
+bg_par_bio_geochem_tau=90.0
+# extend solubility and geochem constant T range (leave S range as default)
+gm_par_geochem_Tmin = -2.0
+gm_par_geochem_Tmax = 45.0
+gm_par_carbchem_Tmin = -2.0
+gm_par_carbchem_Tmax = 45.0
+#
+ma_flag_ecogem=.TRUE.
+GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
+gm_ocn_select_60=.true. # preformed PO4
+gm_ocn_select_66=.true. # Csoft
+bg_ctrl_bio_preformed=.true.
+bg_ctrl_bio_remin_redox_save=.true.
+bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
+#
+# *******************************************************************
+# *** END ***********************************************************
+# *******************************************************************
+#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
new file mode 100644
index 000000000..33cb1addd
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
@@ -0,0 +1,147 @@
+# *** CLIMATE *******************************************************
+#
+# set climate feedback (climate responding to changing pCO2)
+ea_36=y
+#
+# *** BIOLOGICAL NEW PRODUCTION *************************************
+#
+# biological scheme ID string
+# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
+bg_par_bio_prodopt="NONE"
+#
+# *** ORGANIC MATTER EXPORT RATIOS **********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** INORGANIC MATTER EXPORT RATIOS ********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** REMINERALIZATION **********************************************
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+# *** optional changes to align with PALEO recommendations **********
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# *** IRON CYCLING **************************************************
+#
+# [no iron]
+#
+# *** ECOGEM ********************************************************
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#################### Nitrogen ############################
+eg_useNO3 =.false.
+eg_nquota =.false.
+################## Phosphorus ############################
+eg_usePO4 =.true.
+eg_pquota =.true.
+######################## Iron ############################
+eg_useFe =.false.
+eg_fquota =.false.
+################# Chlorophyll ############################
+eg_chlquota =.true.
+################# d13C ###################################
+eg_useDIC_13C =.true.
+# Tuned parameters
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+# ???
+eg_ns=2
+# ???
+eg_respir_a=0
+# DOM parameters
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+# ???
+eg_nsubtime=25
+eg_n_keco=1
+# exponent for modifier of CaCO3:POC export ratio
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=7
+# reduce output
+bg_ctrl_data_save_2d=.true.
+bg_ctrl_data_save_3d=.true. # JDW - set to true
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
+bg_par_atm_force_scale_val_4=-6.265
+# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
+bg_par_atm_force_scale_val_3=0.000280
+# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
+bg_par_ocn_force_scale_val_2=0.2
+#
+# *** MISC **********************************************************
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+# *** optional changes to align with PALEO recommendations **********
+# set mixed layer to be only diagnosed (for ECOGEM)
+go_ctrl_diagmld=.true.
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+# maximum time-scale to geochemical reaction completion (days)
+bg_par_bio_geochem_tau=90.0
+# extend solubility and geochem constant T range (leave S range as default)
+gm_par_geochem_Tmin = -2.0
+gm_par_geochem_Tmax = 45.0
+gm_par_carbchem_Tmin = -2.0
+gm_par_carbchem_Tmax = 45.0
+#
+ma_flag_ecogem=.TRUE.
+GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
+gm_ocn_select_60=.true. # preformed PO4
+gm_ocn_select_66=.true. # Csoft
+bg_ctrl_bio_preformed=.true.
+bg_ctrl_bio_remin_redox_save=.true.
+bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
+#
+# *******************************************************************
+# *** END ***********************************************************
+# *******************************************************************
+#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
new file mode 100644
index 000000000..72033a0b7
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
@@ -0,0 +1,147 @@
+# *** CLIMATE *******************************************************
+#
+# set climate feedback (climate responding to changing pCO2)
+ea_36=y
+#
+# *** BIOLOGICAL NEW PRODUCTION *************************************
+#
+# biological scheme ID string
+# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
+bg_par_bio_prodopt="NONE"
+#
+# *** ORGANIC MATTER EXPORT RATIOS **********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** INORGANIC MATTER EXPORT RATIOS ********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** REMINERALIZATION **********************************************
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+# *** optional changes to align with PALEO recommendations **********
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# *** IRON CYCLING **************************************************
+#
+# [no iron]
+#
+# *** ECOGEM ********************************************************
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#################### Nitrogen ############################
+eg_useNO3 =.false.
+eg_nquota =.false.
+################## Phosphorus ############################
+eg_usePO4 =.true.
+eg_pquota =.true.
+######################## Iron ############################
+eg_useFe =.false.
+eg_fquota =.false.
+################# Chlorophyll ############################
+eg_chlquota =.true.
+################# d13C ###################################
+eg_useDIC_13C =.true.
+# Tuned parameters
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+# ???
+eg_ns=2
+# ???
+eg_respir_a=0
+# DOM parameters
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+# ???
+eg_nsubtime=25
+eg_n_keco=1
+# exponent for modifier of CaCO3:POC export ratio
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+#
+# --- DATA SAVING ----------------------------------------------
+#
+bg_par_data_save_level=7
+# reduce output
+bg_ctrl_data_save_2d=.true.
+bg_ctrl_data_save_3d=.true. # JDW - set to true
+#
+# --- FORCINGS -------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
+bg_par_atm_force_scale_val_4=-6.265
+# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
+bg_par_atm_force_scale_val_3=0.000400
+# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
+bg_par_ocn_force_scale_val_2=0.2
+#
+# *** MISC **********************************************************
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+# *** optional changes to align with PALEO recommendations **********
+# set mixed layer to be only diagnosed (for ECOGEM)
+go_ctrl_diagmld=.true.
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+# relative partitioning of C into DOM
+eg_par_beta_POCtoDOC=0.75
+# maximum time-scale to geochemical reaction completion (days)
+bg_par_bio_geochem_tau=90.0
+# extend solubility and geochem constant T range (leave S range as default)
+gm_par_geochem_Tmin = -2.0
+gm_par_geochem_Tmax = 45.0
+gm_par_carbchem_Tmin = -2.0
+gm_par_carbchem_Tmax = 45.0
+#
+ma_flag_ecogem=.TRUE.
+GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
+gm_ocn_select_60=.true. # preformed PO4
+gm_ocn_select_66=.true. # Csoft
+bg_ctrl_bio_preformed=.true.
+bg_ctrl_bio_remin_redox_save=.true.
+bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
+#
+# *******************************************************************
+# *** END ***********************************************************
+# *******************************************************************
+#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
new file mode 100644
index 000000000..b045e1578
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
@@ -0,0 +1,159 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+#
+# starting year
+bg_par_misc_t_start=2022.0
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
new file mode 100644
index 000000000..3704ddc77
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
@@ -0,0 +1,159 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+## starting year
+bg_par_misc_t_start=2022.0
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
new file mode 100644
index 000000000..792dc6233
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
@@ -0,0 +1,159 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+## starting year
+bg_par_misc_t_start=2022.0
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
new file mode 100644
index 000000000..0a08ef1f8
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
@@ -0,0 +1,158 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+# starting year
+bg_par_misc_t_start=2022.0
+
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
new file mode 100644
index 000000000..59845f35c
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
@@ -0,0 +1,156 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006"
+bg_par_atm_force_scale_val_3=278.0E-06
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+# --- END -----------------------------------------------------------
+#
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
new file mode 100644
index 000000000..5c5d6ae95
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
@@ -0,0 +1,161 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_grazing_scale=3.5
+
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historical2022.dat'
+bg_par_infile_sig_name='save_sig_historical2022.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+
+# diagnosed only mixed layer depth
+go_ctrl_diagmld=.true.
+
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.false.
+
+# starting year
+bg_par_misc_t_start=1765.0
+
+# --- END -----------------------------------------------------------
+#
\ No newline at end of file
From dbe45dd77827bd2cc661c6b73d9e35ac28e3c7d3 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 2 Jul 2023 15:49:04 +0100
Subject: [PATCH 40/89] delete foramecogem old names
---
...CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2 | 181 ----------------
...CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2 | 184 ----------------
...a.BASESFeTDTL_rb_foramecogem2.2.modernAMOC | 200 ------------------
...ASES.CASclosed.280_0p2.foramecogem2.2.SPIN | 147 -------------
....BASES.CASopen.400_0p5.foramecogem2.2.SPIN | 147 -------------
...ASES.CASclosed.280_0p2.foramecogem2.2.SPIN | 147 -------------
...ASES.CASclosed.400_0p2.foramecogem2.2.SPIN | 147 -------------
...lg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg | 159 --------------
...orlg4.BASESFeTDTL.foramecogem2.2.2100.2deg | 159 --------------
...orlg4.BASESFeTDTL.foramecogem2.2.2100.3deg | 159 --------------
...orlg4.BASESFeTDTL.foramecogem2.2.2100.4deg | 158 --------------
...CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN | 156 --------------
...rlg4.BASESFeTDTL.foramecogem2.2.historical | 161 --------------
13 files changed, 2105 deletions(-)
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
deleted file mode 100644
index 6f4d9b6ab..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.2
+++ /dev/null
@@ -1,181 +0,0 @@
-# *******************************************************************
-# *** muffin.CB.GIteiiaa.BASESFeTDTL.1p2tau.SPIN ********************
-# *******************************************************************
-#
-# *** CLIMATE *******************************************************
-#
-# (climate responding to changing pCO2)
-ea_36=y
-#
-# *** BIOLOGICAL NEW PRODUCTION *************************************
-#
-# biological scheme ID string
-# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
-bg_par_bio_prodopt="NONE"
-#
-# *** ORGANIC MATTER EXPORT RATIOS **********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** INORGANIC MATTER EXPORT RATIOS ********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** REMINERALIZATION **********************************************
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-# *** optional changes to align with PALEO recommendations **********
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# *** IRON CYCLING **************************************************
-#
-# iron tracer scheme
-bg_opt_geochem_Fe='hybrid'
-# aeolian Fe solubility [Albani tuning]
-bg_par_det_Fe_sol=0.002441
-# modifier of the scavenging rate of dissolved Fe [Albani tuning]
-bg_par_scav_Fe_sf_POC=0.2250
-# exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# *** ECOGEM ********************************************************
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#----------------- Nitrogen -------------------------
-eg_useNO3 =.false.
-eg_nquota =.false.
-################## Phosphorus ############################
-eg_usePO4 =.true.
-eg_pquota =.true.
-######################## Iron ############################
-eg_useFe =.true.
-eg_fquota =.true.
-################# Chlorophyll ############################
-eg_chlquota =.true.
-################# d13C ###################################
-eg_useDIC_13C =.true.
-# Tuned parameters
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-
-eg_ns=2
-eg_respir_a=0
-# DOM parameters
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-# ???
-eg_nsubtime=25
-eg_n_keco=1
-# exponent for modifier of CaCO3:POC export ratio
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-#
-# *** DATA SAVING ***************************************************
-#
-# BASIC + biology + tracer + proxy diagnostics
-bg_par_data_save_level=7
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst=.false.
-eg_ctrl_continuing=.false.
-#
-# *** FORCINGS ******************************************************
-#
-# specify forcings
-bg_par_forcing_name="GIteiiaa.RpCO2_Rp13CO2.Fsal_SUR.Albani.0ka"
-bg_par_atm_force_scale_val_3=275.0E-06
-bg_par_atm_force_scale_val_4=-6.35
-#
-# *** MISC **********************************************************
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# *** optional changes to align with PALEO recommendations **********
-
-# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-
-# (no preformed)
-bg_ctrl_bio_preformed=.false.
-# add ventillation tracers
-bg_ctrl_force_ocn_age1=.true.
-# add brine rejection SH limit
-bg_par_misc_brinerejection_jmax=19
-# wind-stress
-go_13=1.3
-ea_11=1.3
-#
-# *** TUNING ********************************************************
-#
-# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
-bg_par_misc_brinerejection_frac=0.2
-# parameter: bg_par_ocn_force_scale_val_2 -- default value (1) modified by factor: 0.20
-bg_par_ocn_force_scale_val_2=0.20
-#
-# *** INITIAL CONDITIONS ********************************************
-#
-# N/A
-#
-# *******************************************************************
-# *** END ***********************************************************
-# *******************************************************************
-#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2 b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
deleted file mode 100644
index 250817d32..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2
+++ /dev/null
@@ -1,184 +0,0 @@
-#
-#
-# --- CLIMATE -------------------------------------------------------
-#
-# set climate feedback
-ea_36=y
-#
-# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
-#
-# biological scheme ID string
-bg_par_bio_prodopt="NONE"
-#
-# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
-#
-# [Dealt with ECOGEM]
-#
-# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
-#
-# [Dealt with ECOGEM]
-#
-# --- REMINERALIZATION ----------------------------------------------
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-#
-# --- IRON ----------------------------------------------------------
-#
-bg_opt_geochem_Fe='hybrid'
-# aeolian Fe solubility
-bg_par_det_Fe_sol=0.002441
-# modifier of the scavenging rate of dissolved Fe [Albani tuning]
-bg_par_scav_Fe_sf_POC=0.2250
-#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# --- ECOGEM ----------------------------------------------------------
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#----------------- Nitrogen -------------------------
-eg_useNO3 =.false.
-eg_nquota =.false.
-#---------------- Phosphorus -----------------------
-eg_usePO4 =.true.
-eg_pquota =.true.
-#---------------- Iron -----------------------------
-eg_useFe =.true.
-eg_fquota =.true.
-#---------------- Chlorophyll -----------------------
-eg_chlquota =.true.
-#---------------- d13C ------------------------------
-eg_useDIC_13C =.true.
-
-# Tuned
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-
-eg_ns = 2
-
-eg_respir_a = 0
-
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-
-eg_nsubtime =25
-eg_n_keco =1
-
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst=.false.
-eg_ctrl_continuing=.false.
-
-#
-# --- DATA SAVING -----------------------------------------------------
-#
-bg_par_data_save_level=10
-bg_ctrl_debug_lvl0=.true.
-ma_debug_loop=1
-#
-# --- FORCINGS ------------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="GIteiiva.RpCO2_Rp13CO2.Fsal_SUR.Albani.21ka"
-bg_par_atm_force_scale_val_3=193.0E-06
-bg_par_atm_force_scale_val_4=-6.46
-# Orbital parameters
-ea_par_orbit_osce=0.018994 # eccentricity
-ea_par_orbit_oscsob=0.389911 # sine of obliquity
-ea_par_orbit_oscgam=114.42 # longitude of perihelion (degrees)
-#
-#
-# *** TUNING ********************************************************
-#
-# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
-bg_par_misc_brinerejection_frac=0.2
-# parameter: bg_par_ocn_force_scale_val_2 -- default value (1) modified by factor: 0.05
-bg_par_ocn_force_scale_val_2=0.05
-#
-# *** INITIAL CONDITIONS ********************************************
-#
-# modern DIC (2.244E-03) + 1%
-bg_ocn_init_3=0.002275818239634
-# modern 13C DIC
-bg_ocn_init_4=0.4
-# modern ALK (2.363E-03) + 1%
-bg_ocn_init_12=0.002396505570523
-# modern PO4 (2.159E-06) + 1%
-bg_ocn_init_8=2.189613003283920e-06
-# modern SAL + 0.33 PSU
-go_saln0=35.23
-#
-# --- MISC ----------------------------------------------------------
-#
-# (no preformed)
-bg_ctrl_bio_preformed=.false.
-# add ventillation tracers
-bg_ctrl_force_ocn_age1=.true.
-# add brine rejection SH limit
-bg_par_misc_brinerejection_jmax=19
-# wind-stress
-go_13=1.3
-ea_11=1.3
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
-#
-# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
deleted file mode 100644
index 28497264c..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.2.modernAMOC
+++ /dev/null
@@ -1,200 +0,0 @@
-#
-#
-# --- CLIMATE -------------------------------------------------------
-#
-# set climate feedback
-ea_36=y
-#
-# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
-#
-# biological scheme ID string
-bg_par_bio_prodopt="NONE"
-#
-# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
-#
-# [Dealt with ECOGEM]
-#
-# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
-#
-# [Dealt with ECOGEM]
-#
-# --- REMINERALIZATION ----------------------------------------------
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-#
-# --- IRON ----------------------------------------------------------
-#
-bg_opt_geochem_Fe='hybrid'
-# aeolian Fe solubility
-bg_par_det_Fe_sol=0.002441
-# modifier of the scavenging rate of dissolved Fe [Albani tuning]
-bg_par_scav_Fe_sf_POC=0.2250
-#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# --- ECOGEM ----------------------------------------------------------
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#----------------- Nitrogen -------------------------
-eg_useNO3 =.false.
-eg_nquota =.false.
-#---------------- Phosphorus -----------------------
-eg_usePO4 =.true.
-eg_pquota =.true.
-#---------------- Iron -----------------------------
-eg_useFe =.true.
-eg_fquota =.true.
-#---------------- Chlorophyll -----------------------
-eg_chlquota =.true.
-#---------------- d13C ------------------------------
-eg_useDIC_13C =.true.
-
-# Tuned
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-
-eg_ns = 2
-
-eg_respir_a = 0
-
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-
-eg_nsubtime =25
-eg_n_keco =1
-
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst=.false.
-eg_ctrl_continuing=.false.
-
-#
-# --- DATA SAVING -----------------------------------------------------
-#
-bg_par_data_save_level=10
-bg_ctrl_debug_lvl0=.true.
-ma_debug_loop=1
-#
-# --- FORCINGS ------------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="GIteiiva.RpCO2_Rp13CO2.Fsal_SUR.Albani.21ka"
-bg_par_atm_force_scale_val_3=193.0E-06
-bg_par_atm_force_scale_val_4=-6.46
-# Orbital parameters
-ea_par_orbit_osce=0.018994 # eccentricity
-ea_par_orbit_oscsob=0.389911 # sine of obliquity
-ea_par_orbit_oscgam=114.42 # longitude of perihelion (degrees)
-#
-#
-# *** TUNING ********************************************************
-#
-# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
-bg_par_misc_brinerejection_frac=0.2
-# saltier Atlantic and a mdoern-like AMOC
-bg_par_ocn_force_scale_val_2=0.3
-#
-# *** INITIAL CONDITIONS ********************************************
-#
-# modern DIC (2.244E-03) + 1%
-bg_ocn_init_3=0.002275818239634
-# modern 13C DIC
-bg_ocn_init_4=0.4
-# modern ALK (2.363E-03) + 1%
-bg_ocn_init_12=0.002396505570523
-# modern PO4 (2.159E-06) + 1%
-bg_ocn_init_8=2.189613003283920e-06
-# modern SAL + 0.33 PSU
-go_saln0=35.23
-#
-## --- MISC ----------------------------------------------------------
-#
-# (no preformed)
-bg_ctrl_bio_preformed=.false.
-# add ventillation tracers
-bg_ctrl_force_ocn_age1=.true.
-# add brine rejection SH limit
-bg_par_misc_brinerejection_jmax=19
-# wind-stress
-go_13=1.3
-ea_11=1.3
-
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-
-# maximum time-scale to geochemical reaction completion (days)
-bg_par_bio_geochem_tau=90.0
-
-# extend solubility and geochem constant T range (leave S range as default)
-gm_par_geochem_Tmin = -2.0
-gm_par_geochem_Tmax = 45.0
-gm_par_carbchem_Tmin = -2.0
-gm_par_carbchem_Tmax = 45.0
-
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# --- END -----------------------------------------------------------
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
deleted file mode 100644
index cbc46b0dc..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
+++ /dev/null
@@ -1,147 +0,0 @@
-# *** CLIMATE *******************************************************
-#
-# set climate feedback (climate responding to changing pCO2)
-ea_36=y
-#
-# *** BIOLOGICAL NEW PRODUCTION *************************************
-#
-# biological scheme ID string
-# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
-bg_par_bio_prodopt="NONE"
-#
-# *** ORGANIC MATTER EXPORT RATIOS **********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** INORGANIC MATTER EXPORT RATIOS ********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** REMINERALIZATION **********************************************
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-# *** optional changes to align with PALEO recommendations **********
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# *** IRON CYCLING **************************************************
-#
-# [no iron]
-#
-# *** ECOGEM ********************************************************
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#################### Nitrogen ############################
-eg_useNO3 =.false.
-eg_nquota =.false.
-################## Phosphorus ############################
-eg_usePO4 =.true.
-eg_pquota =.true.
-######################## Iron ############################
-eg_useFe =.false.
-eg_fquota =.false.
-################# Chlorophyll ############################
-eg_chlquota =.true.
-################# d13C ###################################
-eg_useDIC_13C =.true.
-# Tuned parameters
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-# ???
-eg_ns=2
-# ???
-eg_respir_a=0
-# DOM parameters
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-# ???
-eg_nsubtime=25
-eg_n_keco=1
-# exponent for modifier of CaCO3:POC export ratio
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-#
-# --- DATA SAVING ----------------------------------------------
-#
-bg_par_data_save_level=7
-# reduce output
-bg_ctrl_data_save_2d=.true.
-bg_ctrl_data_save_3d=.true. # JDW - set to true
-#
-# --- FORCINGS -------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
-bg_par_atm_force_scale_val_4=-6.428
-# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 280
-bg_par_atm_force_scale_val_3=0.000280
-# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
-bg_par_ocn_force_scale_val_2=0.2
-#
-# *** MISC **********************************************************
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-# *** optional changes to align with PALEO recommendations **********
-# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.true.
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-# maximum time-scale to geochemical reaction completion (days)
-bg_par_bio_geochem_tau=90.0
-# extend solubility and geochem constant T range (leave S range as default)
-gm_par_geochem_Tmin = -2.0
-gm_par_geochem_Tmax = 45.0
-gm_par_carbchem_Tmin = -2.0
-gm_par_carbchem_Tmax = 45.0
-#
-ma_flag_ecogem=.TRUE.
-GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
-gm_ocn_select_60=.true. # preformed PO4
-gm_ocn_select_66=.true. # Csoft
-bg_ctrl_bio_preformed=.true.
-bg_ctrl_bio_remin_redox_save=.true.
-bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
-#
-# *******************************************************************
-# *** END ***********************************************************
-# *******************************************************************
-#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
deleted file mode 100644
index bc4a6946d..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.foramecogem2.2.SPIN
+++ /dev/null
@@ -1,147 +0,0 @@
-# *** CLIMATE *******************************************************
-#
-# set climate feedback (climate responding to changing pCO2)
-ea_36=y
-#
-# *** BIOLOGICAL NEW PRODUCTION *************************************
-#
-# biological scheme ID string
-# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
-bg_par_bio_prodopt="NONE"
-#
-# *** ORGANIC MATTER EXPORT RATIOS **********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** INORGANIC MATTER EXPORT RATIOS ********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** REMINERALIZATION **********************************************
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-# *** optional changes to align with PALEO recommendations **********
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# *** IRON CYCLING **************************************************
-#
-# [no iron]
-#
-# *** ECOGEM ********************************************************
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#################### Nitrogen ############################
-eg_useNO3 =.false.
-eg_nquota =.false.
-################## Phosphorus ############################
-eg_usePO4 =.true.
-eg_pquota =.true.
-######################## Iron ############################
-eg_useFe =.false.
-eg_fquota =.false.
-################# Chlorophyll ############################
-eg_chlquota =.true.
-################# d13C ###################################
-eg_useDIC_13C =.true.
-# Tuned parameters
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-# ???
-eg_ns=2
-# ???
-eg_respir_a=0
-# DOM parameters
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-# ???
-eg_nsubtime=25
-eg_n_keco=1
-# exponent for modifier of CaCO3:POC export ratio
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-#
-# --- DATA SAVING ----------------------------------------------
-#
-bg_par_data_save_level=7
-# reduce output
-bg_ctrl_data_save_2d=.true.
-bg_ctrl_data_save_3d=.true. # JDW - set to true
-#
-# --- FORCINGS -------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
-bg_par_atm_force_scale_val_4=-6.202
-# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
-bg_par_atm_force_scale_val_3=0.000400
-# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.5
-bg_par_ocn_force_scale_val_2=0.5
-#
-# *** MISC **********************************************************
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-# *** optional changes to align with PALEO recommendations **********
-# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.true.
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-# maximum time-scale to geochemical reaction completion (days)
-bg_par_bio_geochem_tau=90.0
-# extend solubility and geochem constant T range (leave S range as default)
-gm_par_geochem_Tmin = -2.0
-gm_par_geochem_Tmax = 45.0
-gm_par_carbchem_Tmin = -2.0
-gm_par_carbchem_Tmax = 45.0
-#
-ma_flag_ecogem=.TRUE.
-GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
-gm_ocn_select_60=.true. # preformed PO4
-gm_ocn_select_66=.true. # Csoft
-bg_ctrl_bio_preformed=.true.
-bg_ctrl_bio_remin_redox_save=.true.
-bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
-#
-# *******************************************************************
-# *** END ***********************************************************
-# *******************************************************************
-#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
deleted file mode 100644
index 33cb1addd..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.foramecogem2.2.SPIN
+++ /dev/null
@@ -1,147 +0,0 @@
-# *** CLIMATE *******************************************************
-#
-# set climate feedback (climate responding to changing pCO2)
-ea_36=y
-#
-# *** BIOLOGICAL NEW PRODUCTION *************************************
-#
-# biological scheme ID string
-# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
-bg_par_bio_prodopt="NONE"
-#
-# *** ORGANIC MATTER EXPORT RATIOS **********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** INORGANIC MATTER EXPORT RATIOS ********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** REMINERALIZATION **********************************************
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-# *** optional changes to align with PALEO recommendations **********
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# *** IRON CYCLING **************************************************
-#
-# [no iron]
-#
-# *** ECOGEM ********************************************************
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#################### Nitrogen ############################
-eg_useNO3 =.false.
-eg_nquota =.false.
-################## Phosphorus ############################
-eg_usePO4 =.true.
-eg_pquota =.true.
-######################## Iron ############################
-eg_useFe =.false.
-eg_fquota =.false.
-################# Chlorophyll ############################
-eg_chlquota =.true.
-################# d13C ###################################
-eg_useDIC_13C =.true.
-# Tuned parameters
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-# ???
-eg_ns=2
-# ???
-eg_respir_a=0
-# DOM parameters
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-# ???
-eg_nsubtime=25
-eg_n_keco=1
-# exponent for modifier of CaCO3:POC export ratio
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-#
-# --- DATA SAVING ----------------------------------------------
-#
-bg_par_data_save_level=7
-# reduce output
-bg_ctrl_data_save_2d=.true.
-bg_ctrl_data_save_3d=.true. # JDW - set to true
-#
-# --- FORCINGS -------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
-bg_par_atm_force_scale_val_4=-6.265
-# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
-bg_par_atm_force_scale_val_3=0.000280
-# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
-bg_par_ocn_force_scale_val_2=0.2
-#
-# *** MISC **********************************************************
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-# *** optional changes to align with PALEO recommendations **********
-# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.true.
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-# maximum time-scale to geochemical reaction completion (days)
-bg_par_bio_geochem_tau=90.0
-# extend solubility and geochem constant T range (leave S range as default)
-gm_par_geochem_Tmin = -2.0
-gm_par_geochem_Tmax = 45.0
-gm_par_carbchem_Tmin = -2.0
-gm_par_carbchem_Tmax = 45.0
-#
-ma_flag_ecogem=.TRUE.
-GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
-gm_ocn_select_60=.true. # preformed PO4
-gm_ocn_select_66=.true. # Csoft
-bg_ctrl_bio_preformed=.true.
-bg_ctrl_bio_remin_redox_save=.true.
-bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
-#
-# *******************************************************************
-# *** END ***********************************************************
-# *******************************************************************
-#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
deleted file mode 100644
index 72033a0b7..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.foramecogem2.2.SPIN
+++ /dev/null
@@ -1,147 +0,0 @@
-# *** CLIMATE *******************************************************
-#
-# set climate feedback (climate responding to changing pCO2)
-ea_36=y
-#
-# *** BIOLOGICAL NEW PRODUCTION *************************************
-#
-# biological scheme ID string
-# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
-bg_par_bio_prodopt="NONE"
-#
-# *** ORGANIC MATTER EXPORT RATIOS **********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** INORGANIC MATTER EXPORT RATIOS ********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** REMINERALIZATION **********************************************
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-# *** optional changes to align with PALEO recommendations **********
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# *** IRON CYCLING **************************************************
-#
-# [no iron]
-#
-# *** ECOGEM ********************************************************
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#################### Nitrogen ############################
-eg_useNO3 =.false.
-eg_nquota =.false.
-################## Phosphorus ############################
-eg_usePO4 =.true.
-eg_pquota =.true.
-######################## Iron ############################
-eg_useFe =.false.
-eg_fquota =.false.
-################# Chlorophyll ############################
-eg_chlquota =.true.
-################# d13C ###################################
-eg_useDIC_13C =.true.
-# Tuned parameters
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-# ???
-eg_ns=2
-# ???
-eg_respir_a=0
-# DOM parameters
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-# ???
-eg_nsubtime=25
-eg_n_keco=1
-# exponent for modifier of CaCO3:POC export ratio
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-#
-# --- DATA SAVING ----------------------------------------------
-#
-bg_par_data_save_level=7
-# reduce output
-bg_ctrl_data_save_2d=.true.
-bg_ctrl_data_save_3d=.true. # JDW - set to true
-#
-# --- FORCINGS -------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
-bg_par_atm_force_scale_val_4=-6.265
-# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
-bg_par_atm_force_scale_val_3=0.000400
-# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
-bg_par_ocn_force_scale_val_2=0.2
-#
-# *** MISC **********************************************************
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-# *** optional changes to align with PALEO recommendations **********
-# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.true.
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-# maximum time-scale to geochemical reaction completion (days)
-bg_par_bio_geochem_tau=90.0
-# extend solubility and geochem constant T range (leave S range as default)
-gm_par_geochem_Tmin = -2.0
-gm_par_geochem_Tmax = 45.0
-gm_par_carbchem_Tmin = -2.0
-gm_par_carbchem_Tmax = 45.0
-#
-ma_flag_ecogem=.TRUE.
-GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
-gm_ocn_select_60=.true. # preformed PO4
-gm_ocn_select_66=.true. # Csoft
-bg_ctrl_bio_preformed=.true.
-bg_ctrl_bio_remin_redox_save=.true.
-bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
-#
-# *******************************************************************
-# *** END ***********************************************************
-# *******************************************************************
-#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
deleted file mode 100644
index b045e1578..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.1p5deg
+++ /dev/null
@@ -1,159 +0,0 @@
-#
-#
-# --- CLIMATE -------------------------------------------------------
-#
-# set climate feedback
-ea_36=y
-#
-# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
-#
-# biological scheme ID string
-bg_par_bio_prodopt="NONE"
-#
-# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
-#
-# production fraction of dissolved organic matter
-bg_par_bio_red_DOMfrac=0.66
-#
-# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
-#
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-bg_par_bio_red_POC_CaCO3=0.0485
-# exponent for modifier of CaCO3:POC export ratio
-bg_par_bio_red_POC_CaCO3_pP=0.7440
-#
-# --- REMINERALIZATION ----------------------------------------------
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-#
-# --- IRON ----------------------------------------------------------
-#
-bg_opt_geochem_Fe='hybrid'
-# aeolian Fe solubility
-bg_par_det_Fe_sol=0.002014275
-#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# modifier of the scavenging rate of dissolved Fe
-bg_par_scav_Fe_sf_POC=0.344104
-bg_par_scav_Fe_sf_CaCO3=0.000
-bg_par_scav_Fe_sf_opal=0.000
-bg_par_scav_Fe_sf_det=0.000
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# --- ECOGEM ----------------------------------------------------------
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#----------------- Nitrogen -------------------------
-eg_useNO3 =.false.
-eg_nquota =.false.
-#---------------- Phosphorus -----------------------
-eg_usePO4 =.true.
-eg_pquota =.true.
-#---------------- Iron -----------------------------
-eg_useFe =.true.
-eg_fquota =.true.
-#---------------- Chlorophyll -----------------------
-eg_chlquota =.true.
-#---------------- d13C ------------------------------
-eg_useDIC_13C =.true.
-
-# Tuned
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-
-eg_ns = 2
-
-eg_respir_a = 0
-
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-
-eg_nsubtime =25
-eg_n_keco =1
-
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst=.false.
-eg_ctrl_continuing=.false.
-
-#
-# --- DATA SAVING -----------------------------------------------------
-#
-bg_par_data_save_level=10
-bg_ctrl_debug_lvl0=.true.
-ma_debug_loop=1
-bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
-bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
-#
-# --- FORCINGS ------------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.1p5deg"
-bg_par_atm_force_scale_val_4=-6.5
-#
-# --- MISC ----------------------------------------------------------
-#
-# starting year
-bg_par_misc_t_start=2022.0
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-#
-# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
deleted file mode 100644
index 3704ddc77..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.2deg
+++ /dev/null
@@ -1,159 +0,0 @@
-#
-#
-# --- CLIMATE -------------------------------------------------------
-#
-# set climate feedback
-ea_36=y
-#
-# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
-#
-# biological scheme ID string
-bg_par_bio_prodopt="NONE"
-#
-# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
-#
-# production fraction of dissolved organic matter
-bg_par_bio_red_DOMfrac=0.66
-#
-# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
-#
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-bg_par_bio_red_POC_CaCO3=0.0485
-# exponent for modifier of CaCO3:POC export ratio
-bg_par_bio_red_POC_CaCO3_pP=0.7440
-#
-# --- REMINERALIZATION ----------------------------------------------
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-#
-# --- IRON ----------------------------------------------------------
-#
-bg_opt_geochem_Fe='hybrid'
-# aeolian Fe solubility
-bg_par_det_Fe_sol=0.002014275
-#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# modifier of the scavenging rate of dissolved Fe
-bg_par_scav_Fe_sf_POC=0.344104
-bg_par_scav_Fe_sf_CaCO3=0.000
-bg_par_scav_Fe_sf_opal=0.000
-bg_par_scav_Fe_sf_det=0.000
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# --- ECOGEM ----------------------------------------------------------
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#----------------- Nitrogen -------------------------
-eg_useNO3 =.false.
-eg_nquota =.false.
-#---------------- Phosphorus -----------------------
-eg_usePO4 =.true.
-eg_pquota =.true.
-#---------------- Iron -----------------------------
-eg_useFe =.true.
-eg_fquota =.true.
-#---------------- Chlorophyll -----------------------
-eg_chlquota =.true.
-#---------------- d13C ------------------------------
-eg_useDIC_13C =.true.
-
-# Tuned
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-
-eg_ns = 2
-
-eg_respir_a = 0
-
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-
-eg_nsubtime =25
-eg_n_keco =1
-
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst=.false.
-eg_ctrl_continuing=.false.
-
-#
-# --- DATA SAVING -----------------------------------------------------
-#
-bg_par_data_save_level=10
-bg_ctrl_debug_lvl0=.true.
-ma_debug_loop=1
-bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
-bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
-#
-# --- FORCINGS ------------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.2deg"
-bg_par_atm_force_scale_val_4=-6.5
-#
-# --- MISC ----------------------------------------------------------
-## starting year
-bg_par_misc_t_start=2022.0
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
-#
-# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
deleted file mode 100644
index 792dc6233..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.3deg
+++ /dev/null
@@ -1,159 +0,0 @@
-#
-#
-# --- CLIMATE -------------------------------------------------------
-#
-# set climate feedback
-ea_36=y
-#
-# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
-#
-# biological scheme ID string
-bg_par_bio_prodopt="NONE"
-#
-# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
-#
-# production fraction of dissolved organic matter
-bg_par_bio_red_DOMfrac=0.66
-#
-# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
-#
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-bg_par_bio_red_POC_CaCO3=0.0485
-# exponent for modifier of CaCO3:POC export ratio
-bg_par_bio_red_POC_CaCO3_pP=0.7440
-#
-# --- REMINERALIZATION ----------------------------------------------
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-#
-# --- IRON ----------------------------------------------------------
-#
-bg_opt_geochem_Fe='hybrid'
-# aeolian Fe solubility
-bg_par_det_Fe_sol=0.002014275
-#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# modifier of the scavenging rate of dissolved Fe
-bg_par_scav_Fe_sf_POC=0.344104
-bg_par_scav_Fe_sf_CaCO3=0.000
-bg_par_scav_Fe_sf_opal=0.000
-bg_par_scav_Fe_sf_det=0.000
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# --- ECOGEM ----------------------------------------------------------
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#----------------- Nitrogen -------------------------
-eg_useNO3 =.false.
-eg_nquota =.false.
-#---------------- Phosphorus -----------------------
-eg_usePO4 =.true.
-eg_pquota =.true.
-#---------------- Iron -----------------------------
-eg_useFe =.true.
-eg_fquota =.true.
-#---------------- Chlorophyll -----------------------
-eg_chlquota =.true.
-#---------------- d13C ------------------------------
-eg_useDIC_13C =.true.
-
-# Tuned
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-
-eg_ns = 2
-
-eg_respir_a = 0
-
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-
-eg_nsubtime =25
-eg_n_keco =1
-
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst=.false.
-eg_ctrl_continuing=.false.
-
-#
-# --- DATA SAVING -----------------------------------------------------
-#
-bg_par_data_save_level=10
-bg_ctrl_debug_lvl0=.true.
-ma_debug_loop=1
-bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
-bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
-#
-# --- FORCINGS ------------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.3deg"
-bg_par_atm_force_scale_val_4=-6.5
-#
-# --- MISC ----------------------------------------------------------
-## starting year
-bg_par_misc_t_start=2022.0
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
-#
-# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
deleted file mode 100644
index 0a08ef1f8..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.2100.4deg
+++ /dev/null
@@ -1,158 +0,0 @@
-#
-#
-# --- CLIMATE -------------------------------------------------------
-#
-# set climate feedback
-ea_36=y
-#
-# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
-#
-# biological scheme ID string
-bg_par_bio_prodopt="NONE"
-#
-# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
-#
-# production fraction of dissolved organic matter
-bg_par_bio_red_DOMfrac=0.66
-#
-# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
-#
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-bg_par_bio_red_POC_CaCO3=0.0485
-# exponent for modifier of CaCO3:POC export ratio
-bg_par_bio_red_POC_CaCO3_pP=0.7440
-#
-# --- REMINERALIZATION ----------------------------------------------
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-#
-# --- IRON ----------------------------------------------------------
-#
-bg_opt_geochem_Fe='hybrid'
-# aeolian Fe solubility
-bg_par_det_Fe_sol=0.002014275
-#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# modifier of the scavenging rate of dissolved Fe
-bg_par_scav_Fe_sf_POC=0.344104
-bg_par_scav_Fe_sf_CaCO3=0.000
-bg_par_scav_Fe_sf_opal=0.000
-bg_par_scav_Fe_sf_det=0.000
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# --- ECOGEM ----------------------------------------------------------
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#----------------- Nitrogen -------------------------
-eg_useNO3 =.false.
-eg_nquota =.false.
-#---------------- Phosphorus -----------------------
-eg_usePO4 =.true.
-eg_pquota =.true.
-#---------------- Iron -----------------------------
-eg_useFe =.true.
-eg_fquota =.true.
-#---------------- Chlorophyll -----------------------
-eg_chlquota =.true.
-#---------------- d13C ------------------------------
-eg_useDIC_13C =.true.
-
-# Tuned
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-
-eg_ns = 2
-
-eg_respir_a = 0
-
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-
-eg_nsubtime =25
-eg_n_keco =1
-
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst=.false.
-eg_ctrl_continuing=.false.
-
-#
-# --- DATA SAVING -----------------------------------------------------
-#
-bg_par_data_save_level=10
-bg_ctrl_debug_lvl0=.true.
-ma_debug_loop=1
-bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
-bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
-#
-# --- FORCINGS ------------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg"
-bg_par_atm_force_scale_val_4=-6.5
-#
-# --- MISC ----------------------------------------------------------
-# starting year
-bg_par_misc_t_start=2022.0
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-#
-# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
deleted file mode 100644
index 59845f35c..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.SPIN
+++ /dev/null
@@ -1,156 +0,0 @@
-#
-#
-# --- CLIMATE -------------------------------------------------------
-#
-# set climate feedback
-ea_36=y
-#
-# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
-#
-# biological scheme ID string
-bg_par_bio_prodopt="NONE"
-#
-# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
-#
-# production fraction of dissolved organic matter
-bg_par_bio_red_DOMfrac=0.66
-#
-# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
-#
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-bg_par_bio_red_POC_CaCO3=0.0485
-# exponent for modifier of CaCO3:POC export ratio
-bg_par_bio_red_POC_CaCO3_pP=0.7440
-#
-# --- REMINERALIZATION ----------------------------------------------
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-#
-# --- IRON ----------------------------------------------------------
-#
-bg_opt_geochem_Fe='hybrid'
-# aeolian Fe solubility
-bg_par_det_Fe_sol=0.002014275
-#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# modifier of the scavenging rate of dissolved Fe
-bg_par_scav_Fe_sf_POC=0.344104
-bg_par_scav_Fe_sf_CaCO3=0.000
-bg_par_scav_Fe_sf_opal=0.000
-bg_par_scav_Fe_sf_det=0.000
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# --- ECOGEM ----------------------------------------------------------
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-#----------------- Nitrogen -------------------------
-eg_useNO3 =.false.
-eg_nquota =.false.
-#---------------- Phosphorus -----------------------
-eg_usePO4 =.true.
-eg_pquota =.true.
-#---------------- Iron -----------------------------
-eg_useFe =.true.
-eg_fquota =.true.
-#---------------- Chlorophyll -----------------------
-eg_chlquota =.true.
-#---------------- d13C ------------------------------
-eg_useDIC_13C =.true.
-
-# Tuned
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-
-eg_ns = 2
-
-eg_respir_a = 0
-
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-
-eg_nsubtime =25
-eg_n_keco =1
-
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst=.false.
-eg_ctrl_continuing=.false.
-
-#
-# --- DATA SAVING -----------------------------------------------------
-#
-bg_par_data_save_level=10
-bg_ctrl_debug_lvl0=.true.
-ma_debug_loop=1
-#
-# --- FORCINGS ------------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006"
-bg_par_atm_force_scale_val_3=278.0E-06
-bg_par_atm_force_scale_val_4=-6.5
-#
-# --- MISC ----------------------------------------------------------
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
-# --- END -----------------------------------------------------------
-#
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
deleted file mode 100644
index 5c5d6ae95..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.2.historical
+++ /dev/null
@@ -1,161 +0,0 @@
-#
-#
-# --- CLIMATE -------------------------------------------------------
-#
-# set climate feedback
-ea_36=y
-#
-# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
-#
-# biological scheme ID string
-bg_par_bio_prodopt="NONE"
-#
-# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
-#
-# production fraction of dissolved organic matter
-bg_par_bio_red_DOMfrac=0.66
-#
-# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
-#
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-bg_par_bio_red_POC_CaCO3=0.0485
-# exponent for modifier of CaCO3:POC export ratio
-bg_par_bio_red_POC_CaCO3_pP=0.7440
-#
-# --- REMINERALIZATION ----------------------------------------------
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-#
-# --- IRON ----------------------------------------------------------
-#
-bg_opt_geochem_Fe='hybrid'
-# aeolian Fe solubility
-bg_par_det_Fe_sol=0.002014275
-#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# modifier of the scavenging rate of dissolved Fe
-bg_par_scav_Fe_sf_POC=0.344104
-bg_par_scav_Fe_sf_CaCO3=0.000
-bg_par_scav_Fe_sf_opal=0.000
-bg_par_scav_Fe_sf_det=0.000
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# --- ECOGEM ----------------------------------------------------------
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
-
-
-#----------------- Nitrogen -------------------------
-eg_useNO3 =.false.
-eg_nquota =.false.
-#---------------- Phosphorus -----------------------
-eg_usePO4 =.true.
-eg_pquota =.true.
-#---------------- Iron -----------------------------
-eg_useFe =.true.
-eg_fquota =.true.
-#---------------- Chlorophyll -----------------------
-eg_chlquota =.true.
-#---------------- d13C ------------------------------
-eg_useDIC_13C =.true.
-
-# Tuned
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-
-eg_ns = 2
-
-eg_respir_a = 0
-
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-
-eg_nsubtime =25
-eg_n_keco =1
-
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst=.false.
-eg_ctrl_continuing=.false.
-
-#
-# --- DATA SAVING -----------------------------------------------------
-#
-bg_par_data_save_level=10
-bg_ctrl_debug_lvl0=.true.
-ma_debug_loop=1
-bg_par_infile_slice_name='save_timeslice_historical2022.dat'
-bg_par_infile_sig_name='save_sig_historical2022.dat'
-#
-# --- FORCINGS ------------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.historical2022"
-bg_par_atm_force_scale_val_4=-6.5
-#
-# --- MISC ----------------------------------------------------------
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
-# starting year
-bg_par_misc_t_start=1765.0
-
-# --- END -----------------------------------------------------------
-#
\ No newline at end of file
From babb5892651a137f4e509584a8cef7dde72810bc Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 2 Jul 2023 15:56:50 +0100
Subject: [PATCH 41/89] correct parameter name foram_spine_scale
---
.../FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN | 2 +-
.../FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN | 2 +-
.../FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC | 2 +-
.../muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN | 2 +-
.../FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN | 2 +-
.../muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN | 2 +-
.../muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN | 2 +-
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg | 2 +-
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg | 2 +-
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg | 2 +-
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg | 2 +-
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN | 2 +-
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical | 2 +-
genie-userconfigs/FORAMECOGEM/update_userconfig.py | 2 +-
14 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
index 6f4d9b6ab..cb941f81e 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
@@ -86,7 +86,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
index 250817d32..69a9e1da4 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
@@ -78,7 +78,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
index 28497264c..2fba78f1d 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
@@ -78,7 +78,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
index cbc46b0dc..ad4bf4d6c 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
@@ -59,7 +59,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
index bc4a6946d..0fd2ae8f8 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
@@ -59,7 +59,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
index 33cb1addd..8af7d6769 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
@@ -59,7 +59,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
index 72033a0b7..32b6d16ba 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
@@ -59,7 +59,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#################### Nitrogen ############################
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
index b045e1578..c7328d233 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
@@ -85,7 +85,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
index 3704ddc77..b96373fe4 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
@@ -85,7 +85,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
index 792dc6233..0e104776c 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
@@ -85,7 +85,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
index 0a08ef1f8..9284b90a6 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
@@ -85,7 +85,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
index 59845f35c..10360c221 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
@@ -85,7 +85,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
index 5c5d6ae95..fcff45fc9 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
@@ -85,7 +85,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_grazing_scale=3.5
+eg_foram_spine_scale=3.5
#----------------- Nitrogen -------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/update_userconfig.py b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
index 72ee57b61..56293c560 100644
--- a/genie-userconfigs/FORAMECOGEM/update_userconfig.py
+++ b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
@@ -24,7 +24,7 @@ def update_foramecogem(directory):
'eg_foram_symbiont_esd_scale': '0.01',
'eg_foram_auto_cost': '0.04',
'eg_foram_hetero_cost': '0.35',
- 'eg_foram_grazing_scale': '3.5',
+ 'eg_foram_spine_scale': '3.5',
}
From b1b4a88923ae0ec17da5b091ffaa8822ab160359 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 2 Jul 2023 16:01:00 +0100
Subject: [PATCH 42/89] update readme running command
---
...fin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC | 2 +-
genie-userconfigs/FORAMECOGEM/readme.md | 28 +++++++++----------
2 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
index 2fba78f1d..e8eed2d07 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
@@ -78,7 +78,7 @@ eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
eg_foram_symbiont_esd_scale=0.01
eg_foram_auto_cost=0.04
eg_foram_hetero_cost=0.35
-eg_foram_spine_scale=3
+eg_foram_spine_scale=3.5
#----------------- Nitrogen -------------------------
eg_useNO3 =.false.
diff --git a/genie-userconfigs/FORAMECOGEM/readme.md b/genie-userconfigs/FORAMECOGEM/readme.md
index f647b125d..06f0f30e1 100644
--- a/genie-userconfigs/FORAMECOGEM/readme.md
+++ b/genie-userconfigs/FORAMECOGEM/readme.md
@@ -57,25 +57,25 @@ qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTD
## Historical (1765-2022)
```sh
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL RUI_LABS/foramecogem muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical 257 muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL FORAMECOGEM muffin.CBE.worlg4.BASESFeTDTL.historical 257 muffin.CBE.worlg4.BASESFeTDTL.SPIN
```
## Future (2022-2100)
```sh
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL RUI_LABS/foramecogem muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.2100.[XXX]deg 78 muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.historical
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL FORAMECOGEM muffin.CBE.worlg4.BASESFeTDTL.2100.[XXX]deg 78 muffin.CBE.worlg4.BASESFeTDTL.historical
```
## LGM
```sh
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.GIteiiva.BASESFeTDTL_rb RUI_LABS/foramecogem muffin.CBE.GIteiiva.BASESFeTDTL_rb_foramecogem2.1 10000
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.GIteiiva.BASESFeTDTL_rb FORAMECOGEM muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN 10000
```
## Holocene
```sh
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.GIteiiaa.BASESFeTDTL_rb RUI_LABS/foramecogem muffin.CBE.GIteiiaa.BASESFeTDTL_rb_foramecogem2.1 10000
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.GIteiiaa.BASESFeTDTL_rb FORAMECOGEM muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN 10000
```
## Pliocene
@@ -85,29 +85,29 @@ muffin.CB.umQ04p5b.BASES (Pliocene close)
``` sh
## Pliocene open, 400 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5a.BASES RUI_LABS/foramecogem 20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN 10000
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5a.BASES FORAMECOGEM 20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.SPIN 10000
## Modern CAS closed, 280 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ00p0a.BASES RUI_LABS/foramecogem 20220104.CB.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN 10000
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ00p0a.BASES FORAMECOGEM 20220104.CB.umQ00p0a.BASES.CASclosed.280_0p2.SPIN 10000
## Pliocene closed, 400 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES RUI_LABS/foramecogem 20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN 10000
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES FORAMECOGEM 20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.SPIN 10000
## Pliocene closed, 280 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES RUI_LABS/foramecogem 20220104.CB.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN 10000
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES FORAMECOGEM 20220104.CB.umQ04p5b.BASES.CASclosed.280_0p2.SPIN 10000
```
> Full effect:4.5 Ma (open, 400 ppm) - 0 Ma (closed, 280 ppm)
-20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN
-20220104.CB.umQ00p0a.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
+20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.SPIN
+20220104.CB.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
> CO2 effect: 4.5 Ma (closed, 400 ppm) - 4.5 Ma (closed, 280 ppm)
-20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN
-20220104.CB.umQ04p5b.BASES.CASclosed.280_0p2.8P7Z4F.SPIN
+20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
+20220104.CB.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
> CAS effect: 4.5 Ma (open, 400 ppm) - 4.5 Ma (closed, 400 ppm)
-20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.8P7Z4F.SPIN
-20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.8P7Z4F.SPIN
+20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.SPIN
+20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
## K-Pg
From e0c71841c3cc5c415f03293e14d050195c4ea023 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 2 Jul 2023 16:05:57 +0100
Subject: [PATCH 43/89] add historical experiment saving data
---
.../data/input/save_sig_historical2022.dat | 290 ++++++++++++++++++
.../input/save_timeslice_historical2022.dat | 8 +
2 files changed, 298 insertions(+)
create mode 100644 genie-biogem/data/input/save_sig_historical2022.dat
create mode 100644 genie-biogem/data/input/save_timeslice_historical2022.dat
diff --git a/genie-biogem/data/input/save_sig_historical2022.dat b/genie-biogem/data/input/save_sig_historical2022.dat
new file mode 100644
index 000000000..d634db83d
--- /dev/null
+++ b/genie-biogem/data/input/save_sig_historical2022.dat
@@ -0,0 +1,290 @@
+-START-OF-DATA-
+0.5
+1.5
+2.5
+3.5
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+2014.5
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+2018.5
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+2020.5
+2021.5
+-END-OF-DATA-
+
diff --git a/genie-biogem/data/input/save_timeslice_historical2022.dat b/genie-biogem/data/input/save_timeslice_historical2022.dat
new file mode 100644
index 000000000..7348eb5e8
--- /dev/null
+++ b/genie-biogem/data/input/save_timeslice_historical2022.dat
@@ -0,0 +1,8 @@
+-START-OF-DATA-
+1765.5
+1976.5
+1994.5
+2000.5
+2009.5
+2021.5
+-END-OF-DATA-
From 554e98028bfd1bdebc829a099e56de7073c0f071 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 2 Jul 2023 18:54:20 +0100
Subject: [PATCH 44/89] add future saving timeslice dataevery 10 years
---
...ave_timeslice_historicalfuture_fakeSSP.dat | 200 ++++++++++++++++++
1 file changed, 200 insertions(+)
create mode 100644 genie-biogem/data/input/save_timeslice_historicalfuture_fakeSSP.dat
diff --git a/genie-biogem/data/input/save_timeslice_historicalfuture_fakeSSP.dat b/genie-biogem/data/input/save_timeslice_historicalfuture_fakeSSP.dat
new file mode 100644
index 000000000..53900c025
--- /dev/null
+++ b/genie-biogem/data/input/save_timeslice_historicalfuture_fakeSSP.dat
@@ -0,0 +1,200 @@
+-START-OF-DATA-
+1765.5
+1800.5
+1835.5
+1870.5
+1900.5
+1920.5
+1940.5
+1960.5
+1980.5
+2000.5
+2009.5
+2019.5
+2029.5
+2039.5
+2049.5
+2059.5
+2069.5
+2079.5
+2089.5
+2099.9
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+9999.9
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+94999.5
+95999.5
+96999.5
+97999.5
+98999.5
+99999.5
+199999.5
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+999999.5
+1999999.5
+4999999.5
+9999999.5
+19999999.5
+49999999.5
+99999999.5
+-END-OF-DATA-
From a0ee77e39b190cf5b57c92d8cfc749050c57ee55 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 2 Jul 2023 23:09:33 +0100
Subject: [PATCH 45/89] balance the foram biomass
---
genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
index f53c1bfa5..0551720a8 100644
--- a/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
+++ b/genie-userconfigs/FORAMECOGEM/FORAMECOGEM.zoo
@@ -19,9 +19,9 @@ Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
foram_bn t f 10.0 2.0 1.0 0.7 0.8 1.3 0.02
-foram_bs t f 10.0 2.0 5.0 0.7 0.8 1.0 0.04
+foram_bs t f 10.0 2.0 5.0 0.7 0.8 1.0 0.045
foram_sn t f 10.0 2.0 1.0 0.7 0.8 1.3 0.02
-foram_ss f t 10.0 2.0 5.0 0.7 0.8 1.0 0.04
+foram_ss f t 10.0 2.0 5.0 0.7 0.8 1.0 0.045
-END-OF-DATA-
/\ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
From 86524d34617b0fa66410448455bf69f92b925bb4 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Thu, 6 Jul 2023 13:16:59 +0100
Subject: [PATCH 46/89] delete unpublished code RY
---
genie-ecogem/src/fortran/ecogem.f90 | 22 ----------------------
1 file changed, 22 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem.f90 b/genie-ecogem/src/fortran/ecogem.f90
index 7b3ebbd21..b94394dc1 100644
--- a/genie-ecogem/src/fortran/ecogem.f90
+++ b/genie-ecogem/src/fortran/ecogem.f90
@@ -324,18 +324,6 @@ subroutine ecogem( &
PAR_in = PAR_out
endif
- ! foram cannot live in environment with < 1 omega
- ! Roy et al. 2015. Biogeosciences, 12, 2873–2889, 2015
- if (ctrl_foramecogenie_oa .and. (omega(i,j,k) .lt. 1.0)) then
- do jp=1,npmax
- ! for any foram
- if (index(pft(jp), "foram") /= 0) then
- ! note mortality(:) is changing in place and mort(:) is fixed
- mortality(jp) = mortality(jp) * 100
- endif
- enddo
- endif
-
! ?
up_inorg(:,:) = 0.0 ! (iomax,npmax)
qreg(:,:) = 0.0 ! (iomax,npmax)
@@ -359,16 +347,6 @@ subroutine ecogem( &
call quota_limitation(quota,limit,VLlimit,qreg,qreg_h)
call t_limitation(templocal,gamma_TP,gamma_TK)
-
- ! symbiont bleaching for foraminifera
- ! implementation: manually disable photosynthesis
- if (ctrl_foramecogenie_bleach .and. (templocal .gt. (foramecogenie_bleach_temp + 273.15))) then
- do jp=1,npmax
- if (pft(jp).eq.'foram_sn' .or. pft(jp).eq.'foram_ss') then
- VLlimit(jp) = 0.0
- endif
- enddo
- endif
call nutrient_uptake(qreg(:,:),loc_nuts(:),gamma_TK,up_inorg(:,:))
From 5578ca0bf52555eb460834785adb13e7a29c0925 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Thu, 6 Jul 2023 13:18:40 +0100
Subject: [PATCH 47/89] delete unpublished definition in ecogem_lib
---
genie-ecogem/src/fortran/ecogem_lib.f90 | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index d1197e7f9..66c7ffc4a 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -141,14 +141,12 @@ MODULE ecogem_lib
real :: trophic_tradeoff
namelist/ini_ecogem_nml/trophic_tradeoff
! foramecogenie parameters (11)
- logical::ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa, ctrl_use_foramecogenie
+ logical::ctrl_use_foramecogenie
real :: foram_auto_cost, foram_hetero_cost
real :: foram_spine_scale, foram_symbiont_esd_scale
- real :: foramecogenie_bleach_temp
namelist/ini_ecogem_nml/foram_auto_cost, foram_hetero_cost
namelist/ini_ecogem_nml/foram_spine_scale, foram_symbiont_esd_scale
- namelist/ini_ecogem_nml/ctrl_foramecogenie_bleach, ctrl_foramecogenie_oa,ctrl_use_foramecogenie
- namelist/ini_ecogem_nml/foramecogenie_bleach_temp
+ namelist/ini_ecogem_nml/ctrl_use_foramecogenie
! Temperature dependence
real :: temp_A,temp_P,temp_K,temp_T0 !
namelist/ini_ecogem_nml/temp_A,temp_P,temp_K,temp_T0
From 5d8927168f5d1d35010731ab0327af960af6b848 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Thu, 6 Jul 2023 13:19:29 +0100
Subject: [PATCH 48/89] delete definition in definition.xml
---
genie-main/src/xml-config/xml/definition.xml | 15 ---------------
1 file changed, 15 deletions(-)
diff --git a/genie-main/src/xml-config/xml/definition.xml b/genie-main/src/xml-config/xml/definition.xml
index 4565b8a56..c1af9be5a 100644
--- a/genie-main/src/xml-config/xml/definition.xml
+++ b/genie-main/src/xml-config/xml/definition.xml
@@ -8893,21 +8893,6 @@ par_bio_red_PC_alpha2 scales the offset of 6.0e-3 of Galbraith & Martiny, 2015 C
enable foramecogenie
-
- .FALSE.
- disable foraminifera autotrophy when exceed temperature threshold
-
-
-
- .FALSE.
- kill foraminifera when calcite saturation state is less than 1
-
-
-
- 40.0
- temperature threshold of symbiont bleaching in Celsius
-
-
1.0
symbiont/foraminifera host size ratio
From 7d11dd788286eefc9ecf147a1efc2903e09af6b8 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 8 Jul 2023 14:41:40 +0100
Subject: [PATCH 49/89] remove MLD setting in foramecogem
---
.../muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN | 11 -----------
.../muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN | 10 ----------
.../muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC | 10 ----------
...muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN | 7 -------
...muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN | 7 -------
...muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN | 7 -------
.../muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg | 13 +------------
.../muffin.CBE.worlg4.BASESFeTDTL.2100.2deg | 11 -----------
.../muffin.CBE.worlg4.BASESFeTDTL.2100.3deg | 11 -----------
.../muffin.CBE.worlg4.BASESFeTDTL.2100.4deg | 9 ---------
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN | 11 -----------
.../muffin.CBE.worlg4.BASESFeTDTL.historical | 9 ---------
12 files changed, 1 insertion(+), 115 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
index cb941f81e..48fae8ef8 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
@@ -140,17 +140,6 @@ bg_par_atm_force_scale_val_4=-6.35
#
# *** MISC **********************************************************
#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# *** optional changes to align with PALEO recommendations **********
-
-# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
# relative partitioning of C into DOM
eg_par_beta_POCtoDOC=0.75
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
index 69a9e1da4..dc2b55742 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
@@ -170,15 +170,5 @@ bg_par_misc_brinerejection_jmax=19
# wind-stress
go_13=1.3
ea_11=1.3
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
#
# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
index e8eed2d07..dd8a54242 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
@@ -171,16 +171,6 @@ bg_par_misc_brinerejection_jmax=19
go_13=1.3
ea_11=1.3
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
# relative partitioning of C into DOM
eg_par_beta_POCtoDOC=0.75
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
index ad4bf4d6c..465500b3b 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
@@ -116,13 +116,6 @@ bg_par_ocn_force_scale_val_2=0.2
#
# *** MISC **********************************************************
#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-# *** optional changes to align with PALEO recommendations **********
-# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.true.
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
# relative partitioning of C into DOM
eg_par_beta_POCtoDOC=0.75
# maximum time-scale to geochemical reaction completion (days)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
index 8af7d6769..70c7a0931 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
@@ -116,13 +116,6 @@ bg_par_ocn_force_scale_val_2=0.2
#
# *** MISC **********************************************************
#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-# *** optional changes to align with PALEO recommendations **********
-# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.true.
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
# relative partitioning of C into DOM
eg_par_beta_POCtoDOC=0.75
# maximum time-scale to geochemical reaction completion (days)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
index 32b6d16ba..4a63d2115 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
@@ -116,13 +116,6 @@ bg_par_ocn_force_scale_val_2=0.2
#
# *** MISC **********************************************************
#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-# *** optional changes to align with PALEO recommendations **********
-# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.true.
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
# relative partitioning of C into DOM
eg_par_beta_POCtoDOC=0.75
# maximum time-scale to geochemical reaction completion (days)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
index c7328d233..23c801054 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
@@ -145,15 +145,4 @@ bg_par_atm_force_scale_val_4=-6.5
# --- MISC ----------------------------------------------------------
#
# starting year
-bg_par_misc_t_start=2022.0
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-#
-# --- END -----------------------------------------------------------
+bg_par_misc_t_start=2022.0
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
index b96373fe4..bbd2ddcb2 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
@@ -145,15 +145,4 @@ bg_par_atm_force_scale_val_4=-6.5
# --- MISC ----------------------------------------------------------
## starting year
bg_par_misc_t_start=2022.0
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
-#
# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
index 0e104776c..f8b3c02c6 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
@@ -145,15 +145,4 @@ bg_par_atm_force_scale_val_4=-6.5
# --- MISC ----------------------------------------------------------
## starting year
bg_par_misc_t_start=2022.0
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
-#
# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
index 9284b90a6..82888cd93 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
@@ -145,14 +145,5 @@ bg_par_atm_force_scale_val_4=-6.5
# --- MISC ----------------------------------------------------------
# starting year
bg_par_misc_t_start=2022.0
-
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
#
# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
index 10360c221..b58c5e4ea 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
@@ -141,16 +141,5 @@ bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006"
bg_par_atm_force_scale_val_3=278.0E-06
bg_par_atm_force_scale_val_4=-6.5
#
-# --- MISC ----------------------------------------------------------
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
# --- END -----------------------------------------------------------
#
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
index fcff45fc9..85848ad87 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
@@ -145,15 +145,6 @@ bg_par_atm_force_scale_val_4=-6.5
#
# --- MISC ----------------------------------------------------------
#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-
-# diagnosed only mixed layer depth
-go_ctrl_diagmld=.true.
-
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-
# starting year
bg_par_misc_t_start=1765.0
From fcf5308520a0c87047d7cabb7a59000777e5e0a2 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 8 Jul 2023 21:48:24 +0100
Subject: [PATCH 50/89] Add back MLD but set fault to ctrl_diagmld
---
.../FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN | 4 +++-
.../FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN | 3 +++
.../FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC | 3 +++
.../muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN | 2 ++
.../muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN | 4 ++--
.../muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN | 2 ++
.../muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN | 2 ++
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg | 4 +++-
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg | 3 +++
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg | 2 ++
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg | 2 ++
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN | 2 ++
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical | 3 ++-
genie-userconfigs/FORAMECOGEM/readme.md | 2 +-
genie-userconfigs/FORAMECOGEM/update_userconfig.py | 3 +++
15 files changed, 35 insertions(+), 6 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
index 48fae8ef8..681b60f98 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
@@ -140,9 +140,11 @@ bg_par_atm_force_scale_val_4=-6.35
#
# *** MISC **********************************************************
#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
+
# relative partitioning of C into DOM
eg_par_beta_POCtoDOC=0.75
-
# (no preformed)
bg_ctrl_bio_preformed=.false.
# add ventillation tracers
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
index dc2b55742..846b3a3ac 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
@@ -171,4 +171,7 @@ bg_par_misc_brinerejection_jmax=19
go_13=1.3
ea_11=1.3
#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
+
# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
index dd8a54242..1a4fe475e 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
@@ -186,5 +186,8 @@ gm_par_carbchem_Tmax = 45.0
# set 'instantaneous' water column remineralziation
bg_par_bio_remin_sinkingrate_physical=9.9E9
bg_par_bio_remin_sinkingrate_reaction=125.0
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
+
#
# --- END -----------------------------------------------------------
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
index 465500b3b..29443cb75 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
@@ -116,6 +116,8 @@ bg_par_ocn_force_scale_val_2=0.2
#
# *** MISC **********************************************************
#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
# relative partitioning of C into DOM
eg_par_beta_POCtoDOC=0.75
# maximum time-scale to geochemical reaction completion (days)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
index 0fd2ae8f8..e70b3cbd6 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
@@ -117,10 +117,10 @@ bg_par_ocn_force_scale_val_2=0.5
# *** MISC **********************************************************
#
# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
+go_imld=1
# *** optional changes to align with PALEO recommendations **********
# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.true.
+go_ctrl_diagmld=.false.
# add seaice attenuation of PAR
eg_ctrl_PARseaicelimit=.false.
# relative partitioning of C into DOM
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
index 70c7a0931..4f20b6d02 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
@@ -116,6 +116,8 @@ bg_par_ocn_force_scale_val_2=0.2
#
# *** MISC **********************************************************
#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
# relative partitioning of C into DOM
eg_par_beta_POCtoDOC=0.75
# maximum time-scale to geochemical reaction completion (days)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
index 4a63d2115..18dc685ea 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
@@ -116,6 +116,8 @@ bg_par_ocn_force_scale_val_2=0.2
#
# *** MISC **********************************************************
#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
# relative partitioning of C into DOM
eg_par_beta_POCtoDOC=0.75
# maximum time-scale to geochemical reaction completion (days)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
index 23c801054..f4c87d77e 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
@@ -145,4 +145,6 @@ bg_par_atm_force_scale_val_4=-6.5
# --- MISC ----------------------------------------------------------
#
# starting year
-bg_par_misc_t_start=2022.0
\ No newline at end of file
+bg_par_misc_t_start=2022.0
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
index bbd2ddcb2..05af07ae6 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
@@ -145,4 +145,7 @@ bg_par_atm_force_scale_val_4=-6.5
# --- MISC ----------------------------------------------------------
## starting year
bg_par_misc_t_start=2022.0
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
+
# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
index f8b3c02c6..a54dc561e 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
@@ -145,4 +145,6 @@ bg_par_atm_force_scale_val_4=-6.5
# --- MISC ----------------------------------------------------------
## starting year
bg_par_misc_t_start=2022.0
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
index 82888cd93..426d6767a 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
@@ -145,5 +145,7 @@ bg_par_atm_force_scale_val_4=-6.5
# --- MISC ----------------------------------------------------------
# starting year
bg_par_misc_t_start=2022.0
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
#
# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
index b58c5e4ea..534e43f1f 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
@@ -140,6 +140,8 @@ ma_debug_loop=1
bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006"
bg_par_atm_force_scale_val_3=278.0E-06
bg_par_atm_force_scale_val_4=-6.5
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
#
# --- END -----------------------------------------------------------
#
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
index 85848ad87..8b3bb3110 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
@@ -147,6 +147,7 @@ bg_par_atm_force_scale_val_4=-6.5
#
# starting year
bg_par_misc_t_start=1765.0
-
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
# --- END -----------------------------------------------------------
#
\ No newline at end of file
diff --git a/genie-userconfigs/FORAMECOGEM/readme.md b/genie-userconfigs/FORAMECOGEM/readme.md
index 06f0f30e1..382abf5b3 100644
--- a/genie-userconfigs/FORAMECOGEM/readme.md
+++ b/genie-userconfigs/FORAMECOGEM/readme.md
@@ -51,7 +51,7 @@ Tested implementation: directly transfer biomass from phytoplankton, or mixotrop
## pre-industrial spinup (0-10000)
```
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL RUI_LABS/foramecogem muffin.CBE.worlg4.BASESFeTDTL.foramecogem2.1.SPIN 10000
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL FORAMECOGEM muffin.CBE.worlg4.BASESFeTDTL.SPIN 10000
```
## Historical (1765-2022)
diff --git a/genie-userconfigs/FORAMECOGEM/update_userconfig.py b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
index 56293c560..459143563 100644
--- a/genie-userconfigs/FORAMECOGEM/update_userconfig.py
+++ b/genie-userconfigs/FORAMECOGEM/update_userconfig.py
@@ -14,6 +14,9 @@ def update_foramecogem(directory):
'ma_ctrl_debug_init': '0',
'eg_ctrl_debug_eco_init': '.false.',
'eg_gkernel_cap': '.false.',
+ # kraus-turner mixed layer scheme
+ 'go_imld' :1,
+ 'go_ctrl_diagmld': '.false.',
## foramecogenie parameters (logical)
'eg_ctrl_use_foramecogenie': '.true.',
'eg_ctrl_foramecogenie_oa': '.false.',
From 5b5ccc50c69cff581a2a72f4cb14b3ee447579e9 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Thu, 21 Sep 2023 13:44:59 +0100
Subject: [PATCH 51/89] update readme.md
---
genie-userconfigs/FORAMECOGEM/readme.md | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/readme.md b/genie-userconfigs/FORAMECOGEM/readme.md
index 382abf5b3..53f83a7ea 100644
--- a/genie-userconfigs/FORAMECOGEM/readme.md
+++ b/genie-userconfigs/FORAMECOGEM/readme.md
@@ -29,11 +29,10 @@ Same predator-prey size ratio: 10/1
Reference of 0D model test: Grigoratou et al. (2019) Biogeoscience; Grigoratou et al. (2022) Marine Micropaleotonlogy;
-Tested alternative cost: respiration
+respiration is incorporated because the mismatch of model-data biogeography; This should be
### Symbiosis
- Independent symbiont size: 1% foraminifera shell size
-- Slight stronger photosynthesis efficiency for symbiont-obligate species (Takagi et al. 2019, Fig. 11)
- Low autotrophy efficiency: Great amount of excessive carbon from symbionts (theoretical growth rate = 0.89 d-1, >> ~0.2 d-1 in observation)
- Low heterotrophy efficiency: mixotrophy modelling convention (Ward and Follows. 2016 PNAS)
From bfcd0513163cc8624fb91f556e1262dd9d3f2a46 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 9 Oct 2023 15:02:26 +0100
Subject: [PATCH 52/89] Fix: update Pliocene user-configs in the readme
---
genie-userconfigs/FORAMECOGEM/readme.md | 20 ++++++++++----------
1 file changed, 10 insertions(+), 10 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/readme.md b/genie-userconfigs/FORAMECOGEM/readme.md
index 53f83a7ea..8aa253c88 100644
--- a/genie-userconfigs/FORAMECOGEM/readme.md
+++ b/genie-userconfigs/FORAMECOGEM/readme.md
@@ -84,29 +84,29 @@ muffin.CB.umQ04p5b.BASES (Pliocene close)
``` sh
## Pliocene open, 400 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5a.BASES FORAMECOGEM 20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.SPIN 10000
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5a.BASES FORAMECOGEM muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN 10000
## Modern CAS closed, 280 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ00p0a.BASES FORAMECOGEM 20220104.CB.umQ00p0a.BASES.CASclosed.280_0p2.SPIN 10000
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ00p0a.BASES FORAMECOGEM muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN 10000
## Pliocene closed, 400 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES FORAMECOGEM 20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.SPIN 10000
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES FORAMECOGEM muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN 10000
## Pliocene closed, 280 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES FORAMECOGEM 20220104.CB.umQ04p5b.BASES.CASclosed.280_0p2.SPIN 10000
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES FORAMECOGEM muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN 10000
```
> Full effect:4.5 Ma (open, 400 ppm) - 0 Ma (closed, 280 ppm)
-20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.SPIN
-20220104.CB.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
+muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
+muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
> CO2 effect: 4.5 Ma (closed, 400 ppm) - 4.5 Ma (closed, 280 ppm)
-20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
-20220104.CB.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
+muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
+muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
> CAS effect: 4.5 Ma (open, 400 ppm) - 4.5 Ma (closed, 400 ppm)
-20220104.CB.umQ04p5a.BASES.CASopen.400_0p5.SPIN
-20220104.CB.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
+muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
+muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
## K-Pg
From ca2c352a2d21baac9c0c43b1a3cc90cc2b5f7c92 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 15:25:11 +0100
Subject: [PATCH 53/89] feat: add export netcdf2d in ecogem
in-time mortality loss, eaten loss and respiration loss
all in eco_uptake_flux option
---
genie-ecogem/src/fortran/ecogem.f90 | 11 +++++--
.../src/fortran/ecogem_data_netCDF.f90 | 32 +++++++++++++++++++
genie-ecogem/src/fortran/ecogem_lib.f90 | 6 ++++
.../src/fortran/initialise_ecogem.f90 | 6 ++++
4 files changed, 53 insertions(+), 2 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem.f90 b/genie-ecogem/src/fortran/ecogem.f90
index b94394dc1..d864a4d5d 100644
--- a/genie-ecogem/src/fortran/ecogem.f90
+++ b/genie-ecogem/src/fortran/ecogem.f90
@@ -84,8 +84,8 @@ subroutine ecogem( &
REAL,DIMENSION(iomax,npmax) ::AP_uptake ! Auto uptake for each plankton
REAL,DIMENSION(iomax,npmax) ::HP_uptake ! Auto uptake for each plankton
!REAL,DIMENSION(npmax) ::diameter !ckc for size dependent fractionation
-
REAL,DIMENSION(npmax) ::mortality,respiration
+ REAL,DIMENSION(npmax) ::mort_loss, respir_loss, eaten_loss ! real-time carbon biomass loss
REAL,DIMENSION(npmax) ::beta_mort_1,beta_graz_1
REAL,DIMENSION(iomax+iChl,npmax) ::assimilated,unassimilated
REAL,DIMENSION(npmax) ::BioC,PP
@@ -452,6 +452,9 @@ subroutine ecogem( &
do io=1,iomax
AP_uptake(io,:) = dbiomassdt(io,:)
HP_uptake(io,:) = GrazPredEat(io,:) * assimilated(io,:)
+ mort_loss(:) = mortality(:) * loc_biomass(io,:)
+ respire_loss(:) = respiration(:) * loc_biomass(io,:)
+ eaten_loss(:)= GrazPreyEaten(iCarb, :)
enddo
endif
@@ -621,6 +624,10 @@ subroutine ecogem( &
if (eco_uptake_fluxes) then
AP_flux(io,:,i,j,k) = AP_uptake(io,:) ! mmol/m^3/s
HP_flux(io,:,i,j,k) = HP_uptake(io,:) ! mmol/m^3/s
+ ! save the global biomass loss fluxes
+ plankton_mort(:,i,j,k) = mort_loss(:)
+ plankton_eaten(:,i,j,k) = eaten_loss(:)
+ plankton_respir(:,i,j,k) = respir_loss(:)
end if
enddo
@@ -886,7 +893,7 @@ SUBROUTINE diag_ecogem_timeslice( &
end if
if (eco_uptake_fluxes) then
int_AP_timeslice(:,:,:,:,:) = int_AP_timeslice(:,:,:,:,:) + loc_dtyr * AP_flux(:,:,:,:,:) * pday ! mmol m^-3 d^-1 autotrophic flux in each plankton
- int_HP_timeslice(:,:,:,:,:) = int_HP_timeslice(:,:,:,:,:) + loc_dtyr * HP_flux(:,:,:,:,:) * pday ! mmol m^-3 d^-1 heterotrophic flux in each plankton
+ int_HP_timeslice(:,:,:,:,:) = int_HP_timeslice(:,:,:,:,:) + loc_dtyr * HP_flux(:,:,:,:,:) * pday ! mmol m^-3 d^-1 heterotrophic flux in each plankton
end if
end if
diff --git a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90 b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
index bad50ebec..44cf845d3 100644
--- a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
+++ b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
@@ -488,6 +488,19 @@ SUBROUTINE sub_save_netcdf_2d()
real::shannon(n_i,n_j),simpson(n_i,n_j),nthresh(n_i,n_j),berger(n_i,n_j)
real::picochl(n_i,n_j),nanochl(n_i,n_j),microchl(n_i,n_j)
real::nphyto
+
+ ! Decompose the biomass terms:
+ ! dB/dt = update/photosynthesis + grazing_in - grazing_out - mortality - respiration
+
+ ! update/photosynthesis is already summed up in the autoflux array
+ ! grazing in is already summed up in the heteroflux array
+ ! grazed_flux
+ real::grazed_flux(n_iomax, n_i,n_j)
+ ! mortality (carbon)
+ real::mort_flux(n_iomax,n_i,n_j)
+ ! respiration (carbon)
+ real::respir_flux(n_iomax,n_i,n_j)
+
!-----------------------------------------------------------------------
! INITIALIZE LOCAL VARIABLES
!-----------------------------------------------------------------------
@@ -553,6 +566,25 @@ SUBROUTINE sub_save_netcdf_2d()
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
endif
endif
+
+ loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
+ write (shrtstrng, "(A10,A,A1,I3.3)") "_Eaten_",trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A18,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+
+ loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
+ write (shrtstrng, "(A10,A,A1,I3.3)") "_Mortality_",trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+
+ loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
+ write (shrtstrng, "(A10,A,A1,I3.3)") "_Respiration_",trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A24,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+
end do
! Write community total biomasses and inorganic resource fluxes
write (shrtstrng, "(A10,A,A6)") "_Plankton_",trim(adjustl(quotastrng(io))),"_Total"
diff --git a/genie-ecogem/src/fortran/ecogem_lib.f90 b/genie-ecogem/src/fortran/ecogem_lib.f90
index 66c7ffc4a..00d3ff6d4 100644
--- a/genie-ecogem/src/fortran/ecogem_lib.f90
+++ b/genie-ecogem/src/fortran/ecogem_lib.f90
@@ -278,6 +278,9 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:)::export_flux ! surface export flux for each plankton (iomax,npmax,i,j,k) Fanny/Maria - Aug19
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:)::AP_flux ! surface autotrophic flux for each plankton (iomax,npmax,i,j,k)
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:)::HP_flux ! surface heterotrophic flux for each plankton (iomax,npmax,i,j,k)
+ REAL ,ALLOCATABLE,DIMENSION(:,:,:,:):: plankton_respir ! respiration carbon flux for each plankton (npmax,i,j,k), RY, Oct 2023
+ REAL ,ALLOCATABLE,DIMENSION(:,:,:,:):: plankton_mort ! mortality carbon flux for each plankton (npmax,i,j,k), RY, Oct 2023
+ REAL ,ALLOCATABLE,DIMENSION(:,:,:,:):: plankton_eaten !grazed carbon flux for each plankton (npmax,i,j,k), RY, Oct 2023
!ckc isotope uptake flux array, to trace full food web interaction
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:)::up_flux_iso !ckc rate of upstake isotopes (iimaxiso,npmax,i,j,k)
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:) ::eco_carb ! carbonate chemistry variables
@@ -376,6 +379,9 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:) ::int_export_timeslice ! Surface export flux for each plankton (iomax,npmax,i,j,k) Fanny/Maria - Aug19
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:) ::int_AP_timeslice ! Surface autotrophic uptake flux for each plankton (iomax,npmax,i,j,k)
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:) ::int_HP_timeslice ! Surface heterotrophic uptake flux for each plankton (iomax,npmax,i,j,k)
+ REAL ,ALLOCATABLE,DIMENSION(:,:,:,:) ::int_peaten_timeslice ! Surface grazed (carbon) flux for each plankton (npmax,i,j,k)
+ REAL ,ALLOCATABLE,DIMENSION(:,:,:,:) ::int_pmort_timeslice ! Surface mortality (carbon) flux for each plankton (npmax,i,j,k)
+ REAL ,ALLOCATABLE,DIMENSION(:,:,:,:) ::int_prespir_timeslice ! Surface respiration (carbon) flux for each plankton (npmax,i,j,k)
! ### ADD ADDITIONAL TIME-SLICE ARRAY DEFINITIONS HERE ######################################################################### !
diff --git a/genie-ecogem/src/fortran/initialise_ecogem.f90 b/genie-ecogem/src/fortran/initialise_ecogem.f90
index c0e631697..3ab87ff9c 100644
--- a/genie-ecogem/src/fortran/initialise_ecogem.f90
+++ b/genie-ecogem/src/fortran/initialise_ecogem.f90
@@ -151,6 +151,12 @@ SUBROUTINE initialise_ecogem( &
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(HP_flux(iomax,npmax,n_i,n_j,n_k),STAT=alloc_error) ! Hetero flux per plankton type
call check_iostat(alloc_error,__LINE__,__FILE__)
+ ALLOCATE(plankton_eaten(npmax,n_i,n_j,n_k),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+ ALLOCATE(plankton_grazed(npmax,n_i,n_j,n_k),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+ ALLOCATE(plankton_respir(npmax,n_i,n_j,n_k),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
! ecogem time-slice arrays
ALLOCATE(int_plankton_timeslice(iomax+iChl,npmax,n_i,n_j,n_k),STAT=alloc_error)
From f23da609975a505ee19063588d3273fd4099ef2c Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 15:43:59 +0100
Subject: [PATCH 54/89] fix: remove some unused variable definition
---
.../src/fortran/ecogem_data_netCDF.f90 | 48 ++++++++-----------
1 file changed, 19 insertions(+), 29 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90 b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
index 44cf845d3..68c3162c7 100644
--- a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
+++ b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
@@ -489,18 +489,6 @@ SUBROUTINE sub_save_netcdf_2d()
real::picochl(n_i,n_j),nanochl(n_i,n_j),microchl(n_i,n_j)
real::nphyto
- ! Decompose the biomass terms:
- ! dB/dt = update/photosynthesis + grazing_in - grazing_out - mortality - respiration
-
- ! update/photosynthesis is already summed up in the autoflux array
- ! grazing in is already summed up in the heteroflux array
- ! grazed_flux
- real::grazed_flux(n_iomax, n_i,n_j)
- ! mortality (carbon)
- real::mort_flux(n_iomax,n_i,n_j)
- ! respiration (carbon)
- real::respir_flux(n_iomax,n_i,n_j)
-
!-----------------------------------------------------------------------
! INITIALIZE LOCAL VARIABLES
!-----------------------------------------------------------------------
@@ -564,26 +552,28 @@ SUBROUTINE sub_save_netcdf_2d()
write (longstrng, "(A,A31,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Heterotrophic Uptake - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
- endif
- endif
+ endif
- loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A,A1,I3.3)") "_Eaten_",trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A18,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
- call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
- call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+ loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
+ write (shrtstrng, "(A10,A,A1,I3.3)") "_Eaten_",trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A18,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
- loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A,A1,I3.3)") "_Mortality_",trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
- call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
- call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+ loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
+ write (shrtstrng, "(A10,A,A1,I3.3)") "_Mortality_",trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
- loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A,A1,I3.3)") "_Respiration_",trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A24,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
- call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
- call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+ loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
+ write (shrtstrng, "(A10,A,A1,I3.3)") "_Respiration_",trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A24,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+ endif
+
+
end do
! Write community total biomasses and inorganic resource fluxes
From e0e297ef676f4c25802209f1f9219bfff49b5403 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 15:45:36 +0100
Subject: [PATCH 55/89] fix: a typo of variable name
---
genie-ecogem/src/fortran/initialise_ecogem.f90 | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/genie-ecogem/src/fortran/initialise_ecogem.f90 b/genie-ecogem/src/fortran/initialise_ecogem.f90
index 3ab87ff9c..d19a0bc08 100644
--- a/genie-ecogem/src/fortran/initialise_ecogem.f90
+++ b/genie-ecogem/src/fortran/initialise_ecogem.f90
@@ -153,7 +153,7 @@ SUBROUTINE initialise_ecogem( &
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(plankton_eaten(npmax,n_i,n_j,n_k),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
- ALLOCATE(plankton_grazed(npmax,n_i,n_j,n_k),STAT=alloc_error)
+ ALLOCATE(plankton_mort(npmax,n_i,n_j,n_k),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(plankton_respir(npmax,n_i,n_j,n_k),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
From 958644745cdfd4037df501c9e6b097f6a961cac5 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 15:47:16 +0100
Subject: [PATCH 56/89] fix: another typo of variable name
---
genie-ecogem/src/fortran/ecogem.f90 | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/genie-ecogem/src/fortran/ecogem.f90 b/genie-ecogem/src/fortran/ecogem.f90
index d864a4d5d..93713aa37 100644
--- a/genie-ecogem/src/fortran/ecogem.f90
+++ b/genie-ecogem/src/fortran/ecogem.f90
@@ -453,7 +453,7 @@ subroutine ecogem( &
AP_uptake(io,:) = dbiomassdt(io,:)
HP_uptake(io,:) = GrazPredEat(io,:) * assimilated(io,:)
mort_loss(:) = mortality(:) * loc_biomass(io,:)
- respire_loss(:) = respiration(:) * loc_biomass(io,:)
+ respir_loss(:) = respiration(:) * loc_biomass(io,:)
eaten_loss(:)= GrazPreyEaten(iCarb, :)
enddo
endif
From b94a52a7259af7f8cdc3eda7b73b33107caf2833 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 15:51:43 +0100
Subject: [PATCH 57/89] fix: Add timeslice arrays in ecogem.data
---
genie-ecogem/src/fortran/ecogem_data.f90 | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index e8e289e47..6293e4e02 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -1182,7 +1182,10 @@ SUBROUTINE sub_init_int_timeslice()
end if
if (eco_uptake_fluxes) then
int_AP_timeslice(:,:,:,:,:) = 0.0
- int_HP_timeslice(:,:,:,:,:) = 0.0
+ int_HP_timeslice(:,:,:,:,:) = 0.0
+ int_pmort_timeslice(:,:,:,:) = 0.0
+ int_peaten_timeslice(:,:,:,:) = 0.0
+ int_prespir_timeslice(:,:,:,:) = 0.0
end if
! ### ADD ADDITIONAL TIME-SLICE ARRAY INITIALIZATIONS HERE ################################################################### !
From a317282a7d45218583539790f184737a543b6c4d Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 15:54:09 +0100
Subject: [PATCH 58/89] fix: add int_xx_timeslice in diag_ecogem_timeslice
---
genie-ecogem/src/fortran/ecogem.f90 | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/genie-ecogem/src/fortran/ecogem.f90 b/genie-ecogem/src/fortran/ecogem.f90
index 93713aa37..fb62963d8 100644
--- a/genie-ecogem/src/fortran/ecogem.f90
+++ b/genie-ecogem/src/fortran/ecogem.f90
@@ -893,7 +893,10 @@ SUBROUTINE diag_ecogem_timeslice( &
end if
if (eco_uptake_fluxes) then
int_AP_timeslice(:,:,:,:,:) = int_AP_timeslice(:,:,:,:,:) + loc_dtyr * AP_flux(:,:,:,:,:) * pday ! mmol m^-3 d^-1 autotrophic flux in each plankton
- int_HP_timeslice(:,:,:,:,:) = int_HP_timeslice(:,:,:,:,:) + loc_dtyr * HP_flux(:,:,:,:,:) * pday ! mmol m^-3 d^-1 heterotrophic flux in each plankton
+ int_HP_timeslice(:,:,:,:,:) = int_HP_timeslice(:,:,:,:,:) + loc_dtyr * HP_flux(:,:,:,:,:) * pday ! mmol m^-3 d^-1 heterotrophic flux in each plankton
+ int_pmort_timeslice(:,:,:,:) = int_pmort_timeslice(:,:,:,:) + loc_dtyr * pmort_flux(:,:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton mortality flux in each plankton
+ int_peaten_timeslice(:,:,:,:) = int_peaten_timeslice(:,:,:,:) + loc_dtyr * peaten_flux(:,:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton grazing flux in each plankton
+ int_respir_timeslice(:,:,:,:) = int_respir_timeslice(:,:,:,:) + loc_dtyr * respir_flux(:,:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton respiration flux in each plankton
end if
end if
From b8135806325df6027e308467966cb87f1dbf4e1e Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 15:56:47 +0100
Subject: [PATCH 59/89] fix: correct the variable name
---
genie-ecogem/src/fortran/ecogem.f90 | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem.f90 b/genie-ecogem/src/fortran/ecogem.f90
index fb62963d8..f06bed3c7 100644
--- a/genie-ecogem/src/fortran/ecogem.f90
+++ b/genie-ecogem/src/fortran/ecogem.f90
@@ -894,9 +894,9 @@ SUBROUTINE diag_ecogem_timeslice( &
if (eco_uptake_fluxes) then
int_AP_timeslice(:,:,:,:,:) = int_AP_timeslice(:,:,:,:,:) + loc_dtyr * AP_flux(:,:,:,:,:) * pday ! mmol m^-3 d^-1 autotrophic flux in each plankton
int_HP_timeslice(:,:,:,:,:) = int_HP_timeslice(:,:,:,:,:) + loc_dtyr * HP_flux(:,:,:,:,:) * pday ! mmol m^-3 d^-1 heterotrophic flux in each plankton
- int_pmort_timeslice(:,:,:,:) = int_pmort_timeslice(:,:,:,:) + loc_dtyr * pmort_flux(:,:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton mortality flux in each plankton
- int_peaten_timeslice(:,:,:,:) = int_peaten_timeslice(:,:,:,:) + loc_dtyr * peaten_flux(:,:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton grazing flux in each plankton
- int_respir_timeslice(:,:,:,:) = int_respir_timeslice(:,:,:,:) + loc_dtyr * respir_flux(:,:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton respiration flux in each plankton
+ int_pmort_timeslice(:,:,:,:) = int_pmort_timeslice(:,:,:,:) + loc_dtyr * plankton_mort(:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton mortality flux in each plankton
+ int_peaten_timeslice(:,:,:,:) = int_peaten_timeslice(:,:,:,:) + loc_dtyr * plankton_eaten(:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton grazing flux in each plankton
+ int_respir_timeslice(:,:,:,:) = int_respir_timeslice(:,:,:,:) + loc_dtyr * plankton_respir(:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton respiration flux in each plankton
end if
end if
From 6addd8cd7150085cb87edb2bca64867ad1edc829 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 15:58:00 +0100
Subject: [PATCH 60/89] fix: typo! prespir_timeslice
---
genie-ecogem/src/fortran/ecogem.f90 | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/genie-ecogem/src/fortran/ecogem.f90 b/genie-ecogem/src/fortran/ecogem.f90
index f06bed3c7..67fe1b96b 100644
--- a/genie-ecogem/src/fortran/ecogem.f90
+++ b/genie-ecogem/src/fortran/ecogem.f90
@@ -896,7 +896,7 @@ SUBROUTINE diag_ecogem_timeslice( &
int_HP_timeslice(:,:,:,:,:) = int_HP_timeslice(:,:,:,:,:) + loc_dtyr * HP_flux(:,:,:,:,:) * pday ! mmol m^-3 d^-1 heterotrophic flux in each plankton
int_pmort_timeslice(:,:,:,:) = int_pmort_timeslice(:,:,:,:) + loc_dtyr * plankton_mort(:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton mortality flux in each plankton
int_peaten_timeslice(:,:,:,:) = int_peaten_timeslice(:,:,:,:) + loc_dtyr * plankton_eaten(:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton grazing flux in each plankton
- int_respir_timeslice(:,:,:,:) = int_respir_timeslice(:,:,:,:) + loc_dtyr * plankton_respir(:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton respiration flux in each plankton
+ int_prespir_timeslice(:,:,:,:) = int_prespir_timeslice(:,:,:,:) + loc_dtyr * plankton_respir(:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton respiration flux in each plankton
end if
end if
From a2b53c4a9c3eb5fd5d999ec74693c412165c5dba Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 16:22:36 +0100
Subject: [PATCH 61/89] fix: segment fault (not allocate before assigning
values)
---
genie-ecogem/src/fortran/initialise_ecogem.f90 | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/genie-ecogem/src/fortran/initialise_ecogem.f90 b/genie-ecogem/src/fortran/initialise_ecogem.f90
index d19a0bc08..df4081835 100644
--- a/genie-ecogem/src/fortran/initialise_ecogem.f90
+++ b/genie-ecogem/src/fortran/initialise_ecogem.f90
@@ -157,6 +157,12 @@ SUBROUTINE initialise_ecogem( &
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(plankton_respir(npmax,n_i,n_j,n_k),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
+ ALLOCATE(int_pmort_timeslice(npmax,n_i,n_j,n_k),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+ ALLOCATE(int_prespir_timeslice(npmax,n_i,n_j,n_k),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
+ ALLOCATE(int_peaten_timeslice(npmax,n_i,n_j,n_k),STAT=alloc_error)
+ call check_iostat(alloc_error,__LINE__,__FILE__)
! ecogem time-slice arrays
ALLOCATE(int_plankton_timeslice(iomax+iChl,npmax,n_i,n_j,n_k),STAT=alloc_error)
From 9ca4f96193010078e71636f066b3eabac2472b13 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 16:42:10 +0100
Subject: [PATCH 62/89] fix: avoid writing all nutrient tracers in loss terms
although the value is the same
---
.../src/fortran/ecogem_data_netCDF.f90 | 37 +++++++++++--------
1 file changed, 21 insertions(+), 16 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90 b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
index 68c3162c7..eb9758ae2 100644
--- a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
+++ b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
@@ -554,24 +554,29 @@ SUBROUTINE sub_save_netcdf_2d()
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
endif
- loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A,A1,I3.3)") "_Eaten_",trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A18,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
- call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
- call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+ ! only export carbon loss
+ if (io .eq. iCarb) then
+
+ loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
+ write (shrtstrng, "(A10,A") "_Eaten_",trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A16)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
- loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A,A1,I3.3)") "_Mortality_",trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
- call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
- call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+ loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
+ write (shrtstrng, "(A10,A,A1,I3.3)") "_Mortality_",trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
- loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A,A1,I3.3)") "_Respiration_",trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A24,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
- call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
- call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
- endif
+ loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
+ write (shrtstrng, "(A10,A,A1,I3.3)") "_Respiration_",trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A24,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+
+ endif
+ endif
From 1f026ffd6e92d85cb260c19b4ac568e4ac7eaef7 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 16:45:03 +0100
Subject: [PATCH 63/89] fix: netcdf exported variable's string format
---
genie-ecogem/src/fortran/ecogem_data_netCDF.f90 | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90 b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
index eb9758ae2..638841b70 100644
--- a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
+++ b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
@@ -558,20 +558,20 @@ SUBROUTINE sub_save_netcdf_2d()
if (io .eq. iCarb) then
loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A") "_Eaten_",trim(adjustl(quotastrng(io))),'_',jp
+ write (shrtstrng, "(A10,A,A6)") "_Eaten_",trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A,A16)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A,A1,I3.3)") "_Mortality_",trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ write (shrtstrng, "(A10,A,A6)") "_Mortality_",trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A16)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A,A1,I3.3)") "_Respiration_",trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A24,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ write (shrtstrng, "(A10,A,A6)") "_Respiration_",trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A16)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
From 989092f24ced499e3b3a34e8410468f97d3cab0d Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 16:51:58 +0100
Subject: [PATCH 64/89] fix: format the output string
---
.../src/fortran/ecogem_data_netCDF.f90 | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90 b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
index 638841b70..09ad4b62a 100644
--- a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
+++ b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
@@ -558,21 +558,22 @@ SUBROUTINE sub_save_netcdf_2d()
if (io .eq. iCarb) then
loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A,A6)") "_Eaten_",trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A16)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
- call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ ! eco2D_Eaten_C_001
+ write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D' '_Eaten_',trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A16,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A,A6)") "_Mortality_",trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A16)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
- call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D' '_Mortality_',trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A20,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A10,A,A6)") "_Respiration_",trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A16)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
- call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
+ write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D' '_Respiration_',trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
endif
From e6229279db960db691b47c0b5447cf2bee29f51d Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 16:52:49 +0100
Subject: [PATCH 65/89] fix: comma forgot
---
genie-ecogem/src/fortran/ecogem_data_netCDF.f90 | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90 b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
index 09ad4b62a..c9b14a122 100644
--- a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
+++ b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
@@ -559,19 +559,19 @@ SUBROUTINE sub_save_netcdf_2d()
loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
! eco2D_Eaten_C_001
- write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D' '_Eaten_',trim(adjustl(quotastrng(io))),'_',jp
+ write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D','_Eaten_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A,A16,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D' '_Mortality_',trim(adjustl(quotastrng(io))),'_',jp
+ write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D','_Mortality_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A,A20,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D' '_Respiration_',trim(adjustl(quotastrng(io))),'_',jp
+ write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D','_Respiration_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
From 5348208a0d35c055056feec03df0d1519920e305 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 16:58:59 +0100
Subject: [PATCH 66/89] fix: format string properly
---
genie-ecogem/src/fortran/ecogem_data_netCDF.f90 | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90 b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
index c9b14a122..464d909ff 100644
--- a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
+++ b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
@@ -558,20 +558,21 @@ SUBROUTINE sub_save_netcdf_2d()
if (io .eq. iCarb) then
loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
- ! eco2D_Eaten_C_001
- write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D','_Eaten_',trim(adjustl(quotastrng(io))),'_',jp
+ ! short string: eco2D_Eaten_C_001
+ ! long string: A, A8, A, A1 -> unit
+ write (shrtstrng, "(A5, A10, A, A1, I3.3)") 'eco2D','_Eaten_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A,A16,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D','_Mortality_',trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A20,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ write (shrtstrng, "(A5, A10, A, A1, I3.3)") 'eco2D','_Mortality_',trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A, A20,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A5, A10, A2, I3.3)") 'eco2D','_Respiration_',trim(adjustl(quotastrng(io))),'_',jp
+ write (shrtstrng, "(A5, A10, A, A2, I3.3)") 'eco2D','_Respiration_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
From a91aaa6a1aa281ddf88e54e2e9f12d927d407279 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 17:11:56 +0100
Subject: [PATCH 67/89] format string finally (maybe)
---
genie-ecogem/src/fortran/ecogem_data_netCDF.f90 | 16 +++++++++-------
1 file changed, 9 insertions(+), 7 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90 b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
index 464d909ff..c79397340 100644
--- a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
+++ b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
@@ -559,23 +559,25 @@ SUBROUTINE sub_save_netcdf_2d()
loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
! short string: eco2D_Eaten_C_001
- ! long string: A, A8, A, A1 -> unit
- write (shrtstrng, "(A5, A10, A, A1, I3.3)") 'eco2D','_Eaten_',trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A,A16,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ ! unit formatter: A2,A,A8,A,A1
+ write (shrtstrng, "(A5, A7, A1, A1, I3.3)") 'eco2D','_Eaten_',trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A, A17,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
- call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+ call sub_putvar2d(shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+ !short string: eco2D_Mortality_C_001
loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
write (shrtstrng, "(A5, A10, A, A1, I3.3)") 'eco2D','_Mortality_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A, A20,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
- call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+ call sub_putvar2d(shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+ !short string: eco2D_Respiration_C_001
loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A5, A10, A, A2, I3.3)") 'eco2D','_Respiration_',trim(adjustl(quotastrng(io))),'_',jp
+ write (shrtstrng, "(A5, A10, A, A1, I3.3)") 'eco2D','_Respiration_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
- call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
+ call sub_putvar2d(shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
endif
endif
From 788e5a90f2fc2a1c1e4c06dd589171c4f150cecd Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 17:12:59 +0100
Subject: [PATCH 68/89] format respiration
---
genie-ecogem/src/fortran/ecogem_data_netCDF.f90 | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90 b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
index c79397340..8c5fc3695 100644
--- a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
+++ b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
@@ -574,7 +574,7 @@ SUBROUTINE sub_save_netcdf_2d()
!short string: eco2D_Respiration_C_001
loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A5, A10, A, A1, I3.3)") 'eco2D','_Respiration_',trim(adjustl(quotastrng(io))),'_',jp
+ write (shrtstrng, "(A5, A13, A, A1, I3.3)") 'eco2D','_Respiration_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d(shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
From d53a5b7b5b639c513cb5dabfaf2a11138acf6348 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 23 Oct 2023 21:13:06 +0100
Subject: [PATCH 69/89] fix: update string of new exported variable
---
genie-ecogem/src/fortran/ecogem_data_netCDF.f90 | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90 b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
index 8c5fc3695..6a5a89f41 100644
--- a/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
+++ b/genie-ecogem/src/fortran/ecogem_data_netCDF.f90
@@ -560,14 +560,14 @@ SUBROUTINE sub_save_netcdf_2d()
loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
! short string: eco2D_Eaten_C_001
! unit formatter: A2,A,A8,A,A1
- write (shrtstrng, "(A5, A7, A1, A1, I3.3)") 'eco2D','_Eaten_',trim(adjustl(quotastrng(io))),'_',jp
- write (longstrng, "(A, A17,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
+ write (shrtstrng, "(A5, A7, A, A1, I3.3)") 'eco2D','_Eaten_',trim(adjustl(quotastrng(io))),'_',jp
+ write (longstrng, "(A, A16,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d(shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
!short string: eco2D_Mortality_C_001
loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
- write (shrtstrng, "(A5, A10, A, A1, I3.3)") 'eco2D','_Mortality_',trim(adjustl(quotastrng(io))),'_',jp
+ write (shrtstrng, "(A5, A11, A, A1, I3.3)") 'eco2D','_Mortality_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A, A20,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d(shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
From 8e1299f1cdf9f543b8f118e429f95dedf4199588 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Tue, 24 Oct 2023 14:28:36 +0100
Subject: [PATCH 70/89] fix: mort_loss and respir_loss should be carbon biomass
---
genie-ecogem/src/fortran/ecogem.f90 | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem.f90 b/genie-ecogem/src/fortran/ecogem.f90
index 67fe1b96b..963943487 100644
--- a/genie-ecogem/src/fortran/ecogem.f90
+++ b/genie-ecogem/src/fortran/ecogem.f90
@@ -452,8 +452,8 @@ subroutine ecogem( &
do io=1,iomax
AP_uptake(io,:) = dbiomassdt(io,:)
HP_uptake(io,:) = GrazPredEat(io,:) * assimilated(io,:)
- mort_loss(:) = mortality(:) * loc_biomass(io,:)
- respir_loss(:) = respiration(:) * loc_biomass(io,:)
+ mort_loss(:) = mortality(:) * BioC(:)
+ respir_loss(:) = respiration(:) * BioC(:)
eaten_loss(:)= GrazPreyEaten(iCarb, :)
enddo
endif
From 4d47c80a6ed8ffadafe359cfa76ec94e907f9b2f Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Thu, 23 Nov 2023 14:49:47 +0000
Subject: [PATCH 71/89] add a user-config of LGM seasonal data
---
...uffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal | 183 ++++++++++++++++++
1 file changed, 183 insertions(+)
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal
new file mode 100644
index 000000000..2421585b5
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal
@@ -0,0 +1,183 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# [Dealt with ECOGEM]
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# [Dealt with ECOGEM]
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002441
+# modifier of the scavenging rate of dissolved Fe [Albani tuning]
+bg_par_scav_Fe_sf_POC=0.2250
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+eg_ctrl_foramecogenie_oa=.false.
+eg_ctrl_foramecogenie_bleach=.false.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_spine_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+
+# Seasonaly time slice (12/48 steps)
+# enable this to get monthly 2D time slice data, but for all years
+bg_par_data_save_slice_n=12
+bg_par_infile_slice_name='save_timeslice.dat'
+
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="GIteiiva.RpCO2_Rp13CO2.Fsal_SUR.Albani.21ka"
+bg_par_atm_force_scale_val_3=193.0E-06
+bg_par_atm_force_scale_val_4=-6.46
+# Orbital parameters
+ea_par_orbit_osce=0.018994 # eccentricity
+ea_par_orbit_oscsob=0.389911 # sine of obliquity
+ea_par_orbit_oscgam=114.42 # longitude of perihelion (degrees)
+#
+#
+# *** TUNING ********************************************************
+#
+# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
+bg_par_misc_brinerejection_frac=0.2
+# parameter: bg_par_ocn_force_scale_val_2 -- default value (1) modified by factor: 0.05
+bg_par_ocn_force_scale_val_2=0.05
+#
+# *** INITIAL CONDITIONS ********************************************
+#
+# modern DIC (2.244E-03) + 1%
+bg_ocn_init_3=0.002275818239634
+# modern 13C DIC
+bg_ocn_init_4=0.4
+# modern ALK (2.363E-03) + 1%
+bg_ocn_init_12=0.002396505570523
+# modern PO4 (2.159E-06) + 1%
+bg_ocn_init_8=2.189613003283920e-06
+# modern SAL + 0.33 PSU
+go_saln0=35.23
+#
+# --- MISC ----------------------------------------------------------
+#
+# (no preformed)
+bg_ctrl_bio_preformed=.false.
+# add ventillation tracers
+bg_ctrl_force_ocn_age1=.true.
+# add brine rejection SH limit
+bg_par_misc_brinerejection_jmax=19
+# wind-stress
+go_13=1.3
+ea_11=1.3
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
+
+# --- END -----------------------------------------------------------
From bc55505398753f896ccc3e9f5cc946005195de3e Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Tue, 5 Dec 2023 17:56:06 +0000
Subject: [PATCH 72/89] Add comment in default foram PFT
---
genie-ecogem/src/fortran/ecogem_data.f90 | 13 +++++--------
1 file changed, 5 insertions(+), 8 deletions(-)
diff --git a/genie-ecogem/src/fortran/ecogem_data.f90 b/genie-ecogem/src/fortran/ecogem_data.f90
index 55d7221d7..b94ad4e73 100644
--- a/genie-ecogem/src/fortran/ecogem_data.f90
+++ b/genie-ecogem/src/fortran/ecogem_data.f90
@@ -436,6 +436,7 @@ SUBROUTINE sub_init_plankton()
autotrophy(jp) = trophic_tradeoff
heterotrophy(jp) = trophic_tradeoff
elseif (pft(jp).eq.'foram') then
+ ! default foram is symbiont-barren non-spinose
NO3up(jp) = 0.0
Nfix(jp) = 0.0
calcify(jp) = 0.0
@@ -548,14 +549,14 @@ SUBROUTINE sub_init_plankton()
! set growth costs (could do the same for autotrophy in coccolithophores) - Fanny Mar21
heterotrophy(:) = heterotrophy(:)*growthcost_factor(:)
- ! overwrite the plankton PFT parameters
+
+ ! Seprarate the symbiont and host body size (auto_volume and hetero_volume) in ForamECOGENIE
if(ctrl_use_foramecogenie)then
! v1/v2 = (r1/r2)^3
auto_volume(:) = volume(:) * symbiont_esd_scale(:) ** 3
autotrophy(:) = autotrophy(:) * symbiont_auto_cost(:)
- heterotrophy(:) = heterotrophy(:) * symbiont_hetero_cost(:)
-
- ! Seprarate the symbiont and host body size (auto_volume and hetero_volume)
+ heterotrophy(:) = heterotrophy(:) * symbiont_hetero_cost(:)
+
vmax(iDIC,:) = (vmaxDIC_a + log10(auto_volume(:))) / (vmaxDIC_b + vmaxDIC_c * log10(auto_volume(:)) + log10(auto_volume(:))**2) &
& * autotrophy(:)
! modify rates for functional types
@@ -584,7 +585,6 @@ SUBROUTINE sub_init_plankton()
kexc(iNitr,:) = kexcN_a * auto_volume(:) ** kexcN_b
endif
!-----------------------------------------------------------------------------------------
-!-----------------------------------------------------------------------------------------
if (pquota) then ! phosphorus parameters
qmin(iPhos,:) = qminP_a * auto_volume(:) ** qminP_b
qmax(iPhos,:) = qmaxP_a * auto_volume(:) ** qmaxP_b
@@ -605,9 +605,6 @@ SUBROUTINE sub_init_plankton()
qmin(iIron,:) = merge(qmin(iIron,:)*10.0,qmin(iIron,:),Nfix.eq.1.0)
qmax(iIron,:) = merge(qmax(iIron,:)*10.0,qmax(iIron,:),Nfix.eq.1.0)
affinity(iFe,:) = merge(affinity(iFe,:)/10.0,affinity(iFe,:),Nfix.eq.1.0)
-!!! FANNY CHECK
- !io = 1
- !write(*,*) 'qmin(iron)=',qmin(iIron,1:3), 'qmax(iron)=',qmax(iIron,1:3)
endif
!-----------------------------------------------------------------------------------------
if (squota) then ! silicon parameters
From 52bb7898c336d232f1a0e6b734e587950dce9395 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Tue, 5 Dec 2023 18:07:24 +0000
Subject: [PATCH 73/89] remove all bleach/acidification related parameters
---
.../FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN | 2 --
.../FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN | 2 --
.../FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC | 2 --
.../FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal | 2 --
.../muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN | 2 --
.../FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN | 2 --
.../muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN | 2 --
.../muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN | 3 +--
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg | 2 --
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg | 2 --
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg | 2 --
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg | 2 --
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN | 2 --
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical | 2 --
14 files changed, 1 insertion(+), 28 deletions(-)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
index 681b60f98..2f0b56da2 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
@@ -78,8 +78,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
index 846b3a3ac..5bc76b5f7 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN
@@ -70,8 +70,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
index 1a4fe475e..7024a21e7 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
@@ -70,8 +70,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal
index 2421585b5..dbd790d22 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal
@@ -70,8 +70,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
index 29443cb75..93e045a95 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
@@ -51,8 +51,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
index e70b3cbd6..7b198cf23 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
@@ -51,8 +51,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
index 4f20b6d02..32f6f4eee 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
@@ -51,8 +51,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
index 18dc685ea..c439f7a60 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
@@ -51,8 +51,7 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
+
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
index f4c87d77e..d875f6be4 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.1p5deg
@@ -77,8 +77,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
index 05af07ae6..21870e8c9 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.2deg
@@ -77,8 +77,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
index a54dc561e..3338d730c 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.3deg
@@ -77,8 +77,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
index 426d6767a..fa364bd73 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.2100.4deg
@@ -77,8 +77,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
index 534e43f1f..499f633e9 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.SPIN
@@ -77,8 +77,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
index 8b3bb3110..7773ac96a 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.historical
@@ -77,8 +77,6 @@ eg_gkernel_cap=.false.
eg_ctrl_grazing_explicit=.true.
eg_ctrl_use_foramecogenie=.true.
-eg_ctrl_foramecogenie_oa=.false.
-eg_ctrl_foramecogenie_bleach=.false.
eg_par_ecogem_plankton_file='8P7Z4F.eco'
eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
From fe565dc8f1a87427dba3c42b0758f215c0651eb2 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Tue, 5 Dec 2023 22:46:44 +0000
Subject: [PATCH 74/89] Add 3D2P2E4Z4F.eco based on new EcoGENIE (ANB et al.
2023)
---
genie-ecogem/data/input/3D2P2E4Z4F.eco | 45 ++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
create mode 100644 genie-ecogem/data/input/3D2P2E4Z4F.eco
diff --git a/genie-ecogem/data/input/3D2P2E4Z4F.eco b/genie-ecogem/data/input/3D2P2E4Z4F.eco
new file mode 100644
index 000000000..46aece289
--- /dev/null
+++ b/genie-ecogem/data/input/3D2P2E4Z4F.eco
@@ -0,0 +1,45 @@
+
+ 01 02 03
+ \/ \/ \/
+
+-START-OF-DATA-
+ Diatom 2.00 1
+ Diatom 20.00 1
+ Diatom 200.00 1
+ Picoplankton 0.6 1
+ Picoplankton 2.00 1
+ Eukaryote 20.00 1
+ Eukaryote 200.00 1
+ Zooplankton 6.00 1
+ Zooplankton 20.00 1
+ Zooplankton 200.00 1
+ Zooplankton 2000.00 1
+ foram_bn 200.00 1
+ foram_bs 200.00 1
+ foram_sn 300.00 1
+ foram_ss 300.00 1
+-END-OF-DATA-
+
+ /\ /\ /\
+ 01 02 03
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #01: plankton functional type name
+COLUMN #02: plankton diameter (micrometers)
+COLUMN #03: number of randomised replicates
+
+INFO: TRACER ASSIGNMENT RULES
+-----------------------------
+Plankton functional type one of: Prochlorococcus
+ Synechococcus
+ Picoeukaryote
+ Picoplankton
+ Diatom
+ Coccolithophore
+ Diazotroph
+ Eukaryote
+ Phytoplankton
+ Zooplankton
+ Mixotroph
From cab72d638b855e1e4445bb68386edf57723e6bc2 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Tue, 5 Dec 2023 23:14:10 +0000
Subject: [PATCH 75/89] Add ForamEcoGEM 2.1 test files
---
genie-ecogem/data/input/3D2P2E4Z4F.zoo | 49 ++++
.../muffin.CBE.worjh2.ForamECOGEM2.1.SPIN | 226 ++++++++++++++++++
2 files changed, 275 insertions(+)
create mode 100644 genie-ecogem/data/input/3D2P2E4Z4F.zoo
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worjh2.ForamECOGEM2.1.SPIN
diff --git a/genie-ecogem/data/input/3D2P2E4Z4F.zoo b/genie-ecogem/data/input/3D2P2E4Z4F.zoo
new file mode 100644
index 000000000..ec5539931
--- /dev/null
+++ b/genie-ecogem/data/input/3D2P2E4Z4F.zoo
@@ -0,0 +1,49 @@
+
+01 02 03 04 05 06 07 08 09 10
+\/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+Diatom f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Diatom f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Diatom f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Picoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Picoplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Eukaryote f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Eukaryote f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+Zooplankton f f 10.0 2.0 2.0 1.0 1.0 1.0 0.0
+foram_bn t f 10.0 2.0 1.0 0.7 0.8 1.3 0.02
+foram_bs t f 10.0 2.0 5.0 0.7 0.8 1.0 0.045
+foram_sn t f 10.0 2.0 1.0 0.7 0.8 1.3 0.02
+foram_ss f t 10.0 2.0 5.0 0.7 0.8 1.0 0.045
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 01 02 03 04 05 06 07 08 09 10 11
+
+DATA FORMAT AND ORDER
+---------------------
+COLUMN #01: functional type (dummy argument, the order MUST same as .eco file)
+COLUMN #02: herbivory (graze on phytoplankton only - if heterotrophy > 0.0)
+COLUMN #03: carnivory (graze on zooplankton only - if heterotrophy > 0.0)
+COLUMN #04: pp_opt_a (optimal predator:prey ratio)
+COLUMN #05: pp_sig_a (width of grazing kernel)
+COLUMN #06: ns (prey-switching - 2.0 = active, 1.0 = passive)
+COLUMN #07: mortality protection (e.g., 0.7 is equivalent to 30% reduced mortality rate)
+COLUMN #08: palatability (grazing protection)
+COLUMN #09: growth-cost factor (e.g., a 10% cost is equivalent to a 0.9 growth-cost factor)
+COLUMN #10: extra respiration rate for building calcite spine and test
+
+INFO: TRACER ASSIGNMENT RULES
+-----------------------------
+Plankton functional type one of: Prochlorococcus
+ Synechococcus
+ Picoeukaryote
+ Diatom
+ Coccolithophore
+ Diazotroph
+ Zooplankton
+ Mixotroph
+ Foram
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worjh2.ForamECOGEM2.1.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worjh2.ForamECOGEM2.1.SPIN
new file mode 100644
index 000000000..1a4e2fcd4
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worjh2.ForamECOGEM2.1.SPIN
@@ -0,0 +1,226 @@
+# *******************************************************************
+# *** Like muffin.CBE.worjh2.BASESFeTDTL.Albani with Si cycle on **********************
+# *******************************************************************
+#
+# *** CLIMATE *******************************************************
+#
+# set climate feedback (climate responding to changing pCO2)
+ea_36=y
+#
+# *** BIOLOGICAL NEW PRODUCTION *************************************
+#
+# biological scheme ID string
+# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
+bg_par_bio_prodopt="NONE"
+#
+# *** ORGANIC MATTER EXPORT RATIOS **********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** INORGANIC MATTER EXPORT RATIOS ********************************
+#
+# [dealt with by ECOGEM]
+#
+# *** REMINERALIZATION **********************************************
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=0.5
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.0557
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+# *** optional changes to align with PALEO recommendations **********
+# set 'instantaneous' water column remineralziation
+bg_par_bio_remin_sinkingrate_physical=9.9E9
+bg_par_bio_remin_sinkingrate_reaction=125.0
+#
+# --- NITROGEN ------------------------------------------------------ Fanny - June 2020
+## Nitrification
+# NH4 oxidation rate constant (yr-1)
+bg_par_nitri_mu=7.30
+# NH4 half-saturatation constant for NH4 oxidation (mol kg-1)
+bg_par_nitri_c0_NH4=0.01E-06
+# O2 half-saturatation constant for NH4 oxidation (mol kg-1)
+bg_par_nitri_c0_O2=0.02E-06
+## Denitrification
+#F switch hard threshold scheme for OM remineralisation
+bg_ctrl_bio_remin_thresh = .true.
+#F denitrification O2 threshold (40E-6, Naafs etal 2019)
+bg_par_bio_remin_cthresh_O2=30E-6
+#
+# iron tracer scheme
+# NOTE: the base-config requires TFe and TL tracers
+bg_opt_geochem_Fe='hybrid'
+# exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002441
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.225
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- Si ----------------------------------------------
+#
+# Si:C [DEFAULT: 0.175] ***** TO CHECK
+bg_par_bio_red_POC_opal=0.65
+# remin ***** TO CHECK
+bg_ctrl_bio_remin_opal_fixed=.false.
+bg_par_bio_remin_sinkingrate=125.0
+# 30Si ***** TO CHECK
+# epsilon 30Si associated with opal formation [DEFAULT: -1.1]
+bg_par_d30Si_opal_epsilon=-1.1
+#
+# *** ECOGEM ********************************************************
+#
+# ecosystem configuration
+# PFTs with diatoms, pico and eukaryotes Fanny - Jun20
+
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+eg_ctrl_use_foramecogenie=.true.
+
+eg_par_ecogem_plankton_file='3D2P2E4Z4F.eco'
+eg_par_ecogem_grazing_file='3D2P2E4Z4F.zoo'
+
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_spine_scale=3.5
+
+#################### Nitrogen ############################
+eg_useNO3 =.false.
+eg_nquota =.false.
+################## Phosphorus ############################
+eg_usePO4 =.true.
+eg_pquota =.true.
+######################## Iron ############################
+eg_useFe =.true.
+eg_fquota =.true.
+################# Chlorophyll ############################
+eg_chlquota =.true.
+################# d13C ###################################
+eg_useDIC_13C =.true.
+#################### Silicate ############################
+eg_useSiO2 =.true.
+eg_squota =.true.
+
+# Tuned - Ward et al. (2018)
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+# Si properties - Fanny June2020
+eg_vmaxSiO2_a=4.4e-2
+eg_vmaxSiO2_b=0.06
+eg_qminSi_a=0.033600
+eg_qmaxSi_a=0.176000
+eg_affinSiO2_a = 3.900
+eg_affinSiO2_b = -0.35
+
+# eukaryote photosynthetic rate - Fanny Jun20 (equivalent to 0.56 times diatoms Pmax)
+eg_vmaxDIC_a_pft_eukaryote = 2.2000
+
+# ???
+eg_ns=2
+# ???
+eg_respir_a=0
+# DOM parameters
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+# ???
+eg_nsubtime=25
+eg_n_keco=1
+# exponent for modifier of CaCO3:POC export ratio
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+#
+# *** DATA SAVING ***************************************************
+#
+# BASIC + biology + tracer + proxy diagnostics
+bg_par_data_save_level=10
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst = .false.
+eg_ctrl_continuing = .false.
+#
+# *** FORCINGS ******************************************************
+#
+bg_par_forcing_name="worjh2.RpCO2_Rp13CO2.Albani.0ka"
+bg_par_atm_force_scale_val_3=278.0E-06
+bg_par_atm_force_scale_val_4=-6.5
+#
+# *** MISC **********************************************************
+#
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld = 1
+# *** optional changes to align with PALEO recommendations **********
+# set mixed layer to be only diagnosed (for ECOGEM)
+go_ctrl_diagmld=.true.
+# add seaice attenuation of PAR
+eg_ctrl_PARseaicelimit=.true.
+# relative partitioning of C into DOM
+#eg_par_beta_POCtoDOC=0.75
+# maximum time-scale to geochemical reaction completion (days)
+bg_par_bio_geochem_tau=90.0
+# extend solubility and geochem constant T range (leave S range as default)
+gm_par_geochem_Tmin = -2.0
+gm_par_geochem_Tmax = 45.0
+gm_par_carbchem_Tmin = -2.0
+gm_par_carbchem_Tmax = 45.0
+#
+# *******************************************************************
+# *** END ***********************************************************
+# *******************************************************************
+#
+Ensemble created: 180712 ***** TO CHECK
+bg_ctrl_bio_remin_opal_fixed=.false.
+bg_par_bio_remin_sinkingrate=83.146
+bg_par_bio_red_POC_opal=0.17185
+Ensemble created: 221224
+eg_qminP_a=0.0027022
+eg_qmaxP_a=0.0216773
+eg_qminFe_a=6.8572e-07
+eg_qmaxFe_a=4.09512e-06
+eg_qminSi_a=0.043259
+eg_qmaxSi_a=0.407638
+eg_affinSiO2_a=4.7769
+eg_affinSiO2_b=-0.40131
+eg_affinPO4_a=0.94403
+eg_affinPO4_b=-0.43718
+eg_affinFe_a=0.17761
+eg_affinFe_b=-0.2574
+eg_vmaxFe_a=0.00016885
+eg_vmaxFe_b=-0.12635
+eg_vmaxSiO2_a=0.068039
+eg_vmaxSiO2_b=0.031868
+eg_par_diatom_palatability_mod=0.92802
+bg_par_bio_remin_sinkingrate_reaction=49.689
From d3da40f9959b9761733ca1dab5526c447160210f Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 5 Feb 2024 12:56:13 +0000
Subject: [PATCH 76/89] remove the awkward foramecogem2.1
---
.../muffin.CBE.worjh2.ForamECOGEM2.1.SPIN | 226 ------------------
1 file changed, 226 deletions(-)
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worjh2.ForamECOGEM2.1.SPIN
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worjh2.ForamECOGEM2.1.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worjh2.ForamECOGEM2.1.SPIN
deleted file mode 100644
index 1a4e2fcd4..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worjh2.ForamECOGEM2.1.SPIN
+++ /dev/null
@@ -1,226 +0,0 @@
-# *******************************************************************
-# *** Like muffin.CBE.worjh2.BASESFeTDTL.Albani with Si cycle on **********************
-# *******************************************************************
-#
-# *** CLIMATE *******************************************************
-#
-# set climate feedback (climate responding to changing pCO2)
-ea_36=y
-#
-# *** BIOLOGICAL NEW PRODUCTION *************************************
-#
-# biological scheme ID string
-# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
-bg_par_bio_prodopt="NONE"
-#
-# *** ORGANIC MATTER EXPORT RATIOS **********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** INORGANIC MATTER EXPORT RATIOS ********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** REMINERALIZATION **********************************************
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=0.5
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.0557
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-# *** optional changes to align with PALEO recommendations **********
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# --- NITROGEN ------------------------------------------------------ Fanny - June 2020
-## Nitrification
-# NH4 oxidation rate constant (yr-1)
-bg_par_nitri_mu=7.30
-# NH4 half-saturatation constant for NH4 oxidation (mol kg-1)
-bg_par_nitri_c0_NH4=0.01E-06
-# O2 half-saturatation constant for NH4 oxidation (mol kg-1)
-bg_par_nitri_c0_O2=0.02E-06
-## Denitrification
-#F switch hard threshold scheme for OM remineralisation
-bg_ctrl_bio_remin_thresh = .true.
-#F denitrification O2 threshold (40E-6, Naafs etal 2019)
-bg_par_bio_remin_cthresh_O2=30E-6
-#
-# iron tracer scheme
-# NOTE: the base-config requires TFe and TL tracers
-bg_opt_geochem_Fe='hybrid'
-# exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# aeolian Fe solubility
-bg_par_det_Fe_sol=0.002441
-# modifier of the scavenging rate of dissolved Fe
-bg_par_scav_Fe_sf_POC=0.225
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# --- Si ----------------------------------------------
-#
-# Si:C [DEFAULT: 0.175] ***** TO CHECK
-bg_par_bio_red_POC_opal=0.65
-# remin ***** TO CHECK
-bg_ctrl_bio_remin_opal_fixed=.false.
-bg_par_bio_remin_sinkingrate=125.0
-# 30Si ***** TO CHECK
-# epsilon 30Si associated with opal formation [DEFAULT: -1.1]
-bg_par_d30Si_opal_epsilon=-1.1
-#
-# *** ECOGEM ********************************************************
-#
-# ecosystem configuration
-# PFTs with diatoms, pico and eukaryotes Fanny - Jun20
-
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-eg_ctrl_use_foramecogenie=.true.
-
-eg_par_ecogem_plankton_file='3D2P2E4Z4F.eco'
-eg_par_ecogem_grazing_file='3D2P2E4Z4F.zoo'
-
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_spine_scale=3.5
-
-#################### Nitrogen ############################
-eg_useNO3 =.false.
-eg_nquota =.false.
-################## Phosphorus ############################
-eg_usePO4 =.true.
-eg_pquota =.true.
-######################## Iron ############################
-eg_useFe =.true.
-eg_fquota =.true.
-################# Chlorophyll ############################
-eg_chlquota =.true.
-################# d13C ###################################
-eg_useDIC_13C =.true.
-#################### Silicate ############################
-eg_useSiO2 =.true.
-eg_squota =.true.
-
-# Tuned - Ward et al. (2018)
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-# Si properties - Fanny June2020
-eg_vmaxSiO2_a=4.4e-2
-eg_vmaxSiO2_b=0.06
-eg_qminSi_a=0.033600
-eg_qmaxSi_a=0.176000
-eg_affinSiO2_a = 3.900
-eg_affinSiO2_b = -0.35
-
-# eukaryote photosynthetic rate - Fanny Jun20 (equivalent to 0.56 times diatoms Pmax)
-eg_vmaxDIC_a_pft_eukaryote = 2.2000
-
-# ???
-eg_ns=2
-# ???
-eg_respir_a=0
-# DOM parameters
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-# ???
-eg_nsubtime=25
-eg_n_keco=1
-# exponent for modifier of CaCO3:POC export ratio
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-#
-# *** DATA SAVING ***************************************************
-#
-# BASIC + biology + tracer + proxy diagnostics
-bg_par_data_save_level=10
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst = .false.
-eg_ctrl_continuing = .false.
-#
-# *** FORCINGS ******************************************************
-#
-bg_par_forcing_name="worjh2.RpCO2_Rp13CO2.Albani.0ka"
-bg_par_atm_force_scale_val_3=278.0E-06
-bg_par_atm_force_scale_val_4=-6.5
-#
-# *** MISC **********************************************************
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld = 1
-# *** optional changes to align with PALEO recommendations **********
-# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.true.
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.true.
-# relative partitioning of C into DOM
-#eg_par_beta_POCtoDOC=0.75
-# maximum time-scale to geochemical reaction completion (days)
-bg_par_bio_geochem_tau=90.0
-# extend solubility and geochem constant T range (leave S range as default)
-gm_par_geochem_Tmin = -2.0
-gm_par_geochem_Tmax = 45.0
-gm_par_carbchem_Tmin = -2.0
-gm_par_carbchem_Tmax = 45.0
-#
-# *******************************************************************
-# *** END ***********************************************************
-# *******************************************************************
-#
-Ensemble created: 180712 ***** TO CHECK
-bg_ctrl_bio_remin_opal_fixed=.false.
-bg_par_bio_remin_sinkingrate=83.146
-bg_par_bio_red_POC_opal=0.17185
-Ensemble created: 221224
-eg_qminP_a=0.0027022
-eg_qmaxP_a=0.0216773
-eg_qminFe_a=6.8572e-07
-eg_qmaxFe_a=4.09512e-06
-eg_qminSi_a=0.043259
-eg_qmaxSi_a=0.407638
-eg_affinSiO2_a=4.7769
-eg_affinSiO2_b=-0.40131
-eg_affinPO4_a=0.94403
-eg_affinPO4_b=-0.43718
-eg_affinFe_a=0.17761
-eg_affinFe_b=-0.2574
-eg_vmaxFe_a=0.00016885
-eg_vmaxFe_b=-0.12635
-eg_vmaxSiO2_a=0.068039
-eg_vmaxSiO2_b=0.031868
-eg_par_diatom_palatability_mod=0.92802
-bg_par_bio_remin_sinkingrate_reaction=49.689
From 5ebe313e5ca11188a7d37fb36a93d3d32b7d9cd2 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 5 Feb 2024 12:56:44 +0000
Subject: [PATCH 77/89] remove the foram+Hol config
---
.../muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN | 170 ------------------
1 file changed, 170 deletions(-)
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
deleted file mode 100644
index 2f0b56da2..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN
+++ /dev/null
@@ -1,170 +0,0 @@
-# *******************************************************************
-# *** muffin.CB.GIteiiaa.BASESFeTDTL.1p2tau.SPIN ********************
-# *******************************************************************
-#
-# *** CLIMATE *******************************************************
-#
-# (climate responding to changing pCO2)
-ea_36=y
-#
-# *** BIOLOGICAL NEW PRODUCTION *************************************
-#
-# biological scheme ID string
-# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
-bg_par_bio_prodopt="NONE"
-#
-# *** ORGANIC MATTER EXPORT RATIOS **********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** INORGANIC MATTER EXPORT RATIOS ********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** REMINERALIZATION **********************************************
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-# *** optional changes to align with PALEO recommendations **********
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# *** IRON CYCLING **************************************************
-#
-# iron tracer scheme
-bg_opt_geochem_Fe='hybrid'
-# aeolian Fe solubility [Albani tuning]
-bg_par_det_Fe_sol=0.002441
-# modifier of the scavenging rate of dissolved Fe [Albani tuning]
-bg_par_scav_Fe_sf_POC=0.2250
-# exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# *** ECOGEM ********************************************************
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_spine_scale=3.5
-
-#----------------- Nitrogen -------------------------
-eg_useNO3 =.false.
-eg_nquota =.false.
-################## Phosphorus ############################
-eg_usePO4 =.true.
-eg_pquota =.true.
-######################## Iron ############################
-eg_useFe =.true.
-eg_fquota =.true.
-################# Chlorophyll ############################
-eg_chlquota =.true.
-################# d13C ###################################
-eg_useDIC_13C =.true.
-# Tuned parameters
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-
-eg_ns=2
-eg_respir_a=0
-# DOM parameters
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-# ???
-eg_nsubtime=25
-eg_n_keco=1
-# exponent for modifier of CaCO3:POC export ratio
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-#
-# *** DATA SAVING ***************************************************
-#
-# BASIC + biology + tracer + proxy diagnostics
-bg_par_data_save_level=7
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst=.false.
-eg_ctrl_continuing=.false.
-#
-# *** FORCINGS ******************************************************
-#
-# specify forcings
-bg_par_forcing_name="GIteiiaa.RpCO2_Rp13CO2.Fsal_SUR.Albani.0ka"
-bg_par_atm_force_scale_val_3=275.0E-06
-bg_par_atm_force_scale_val_4=-6.35
-#
-# *** MISC **********************************************************
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld=1
-
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-# (no preformed)
-bg_ctrl_bio_preformed=.false.
-# add ventillation tracers
-bg_ctrl_force_ocn_age1=.true.
-# add brine rejection SH limit
-bg_par_misc_brinerejection_jmax=19
-# wind-stress
-go_13=1.3
-ea_11=1.3
-#
-# *** TUNING ********************************************************
-#
-# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
-bg_par_misc_brinerejection_frac=0.2
-# parameter: bg_par_ocn_force_scale_val_2 -- default value (1) modified by factor: 0.20
-bg_par_ocn_force_scale_val_2=0.20
-#
-# *** INITIAL CONDITIONS ********************************************
-#
-# N/A
-#
-# *******************************************************************
-# *** END ***********************************************************
-# *******************************************************************
-#
From a8db5415da59d87b1dfc72cab68eba96a8626cc0 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 1 Apr 2024 13:58:12 +0100
Subject: [PATCH 78/89] add a more comparable steady-state future run
---
.../biogem_force_flux_sed_det_SUR.dat | 37 +++
.../biogem_force_flux_sed_det_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_13C_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_sig.dat | 263 ++++++++++++++++++
.../configure_forcings_atm.dat | 24 ++
.../configure_forcings_ocn.dat | 24 ++
.../configure_forcings_sed.dat | 21 ++
.../muffin.CBE.worlg4.BASESFeTDTL.5000.4deg | 149 ++++++++++
8 files changed, 526 insertions(+)
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_flux_sed_det_SUR.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_flux_sed_det_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_atm.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_ocn.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_sed.dat
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_flux_sed_det_SUR.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_flux_sed_det_SUR.dat
new file mode 100644
index 000000000..0e35c9e79
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_flux_sed_det_SUR.dat
@@ -0,0 +1,37 @@
+ 4.811560e+009 4.626661e+009 3.126386e+009 2.214785e+009 1.652428e+009 1.418667e+009 1.229085e+009 1.076190e+009 9.778666e+008 9.012306e+008 8.453771e+008 7.600965e+008 7.182478e+008 5.693231e+008 5.741100e+008 6.638764e+008 7.234523e+008 5.594685e+008 7.167836e+008 8.443707e+008 7.166255e+008 4.937644e+008 3.068558e+008 4.938671e+008 8.409478e+008 1.096116e+009 1.683666e+009 1.914513e+009 2.299017e+009 3.071956e+009 3.802993e+009 4.240087e+009 4.936058e+009 5.216635e+009 5.376818e+009 5.281376e+009
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+
\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_flux_sed_det_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_flux_sed_det_sig.dat
new file mode 100644
index 000000000..972d7c3fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_flux_sed_det_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999.0 1.0
+-END-OF-DATA-
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
new file mode 100644
index 000000000..b4149dc1a
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999.0 1.0
+-END-OF-DATA-
\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
new file mode 100644
index 000000000..7167e027f
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
@@ -0,0 +1,263 @@
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diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_atm.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_atm.dat
new file mode 100644
index 000000000..453007a3e
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_atm.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08
+ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 03 t 0.1 f t F 2 01 01 '[carbon dioxide (CO2) partial pressure (atm)]'
+ 04 t 0.1 f t F 2 01 01 '[d13C CO2 (o/oo)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08
+
+DATA FORMAT AND ORDER:
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #03: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #04: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: force ocean surface in equilibrium with atmosphere? (needs ocean restoring forcing set) [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (2 = 2D, 0 = point, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_ocn.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_ocn.dat
new file mode 100644
index 000000000..a317b42fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_ocn.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08 09
+ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08 09
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: restrict restoring forcing to surface? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #04: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN #09: k grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_sed.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_sed.dat
new file mode 100644
index 000000000..0db3bf57b
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/configure_forcings_sed.dat
@@ -0,0 +1,21 @@
+
+ 00 01 02 03 04 05
+ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 22 t F -1 01 01 '[detrital (refractory) material (wt%)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #04: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #05: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
new file mode 100644
index 000000000..fa364bd73
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
@@ -0,0 +1,149 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_spine_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+# starting year
+bg_par_misc_t_start=2022.0
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
+#
+# --- END -----------------------------------------------------------
From f089726c770552f0edd21a52fa82a1d4395a9ec4 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 1 Apr 2024 14:07:26 +0100
Subject: [PATCH 79/89] update forcing for 5000.4degC
---
.../biogem_force_restore_atm_pCO2_sig.dat | 3 +-
genie-userconfigs/FORAMECOGEM/readme.md | 113 +++++++-----------
2 files changed, 46 insertions(+), 70 deletions(-)
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
index 7167e027f..dd7c5d687 100644
--- a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
@@ -258,6 +258,7 @@
2020.5 4.14890E-04
2021.5 4.18060E-04
2022.5 4.21330E-04
-4999.5. 680.0E-6
+2299.5. 680.0E-6
+4999.5. 695.0E-6
999999999.0 278.0E-6
-END-OF-DATA-
diff --git a/genie-userconfigs/FORAMECOGEM/readme.md b/genie-userconfigs/FORAMECOGEM/readme.md
index 8aa253c88..8bcf823d3 100644
--- a/genie-userconfigs/FORAMECOGEM/readme.md
+++ b/genie-userconfigs/FORAMECOGEM/readme.md
@@ -1,50 +1,52 @@
-This is model documentation for ForamEcoGENIE 1.1 covering Pliocene/LGM/Pre-industrial/Future
+================================================================
+=== readme.txt =================================================
+================================================================
-# About the model
+Provided are as part of the code release the configuration files necessary to run the key model experiments presented in the paper.
+The intention is to provide an oppertunity to question the paper assumptions and interpretation through re-analysis,
+as well as the creation of new and different experiments. (Plus, to provide a means to replicate published results.)
+This readme file details how the experiments can be run.
+Refer to the muffin manual:
+https://github.com/derpycode/muffindoc
+for details on model code installation and configuration, locating and visualizing model results, etc.
-## Aim
-The model won't be perfect. It aims to solve three things: (1) the essential foram trait; (2) the biogeogprahy; (3) useful in the past.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+PUBLICATION DETAILS [summary of manuscript/publication]
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-Currently I intend to keep the foraminifera biomass overestimated than the observation. Because currently no model including those species distribution model can fullfil all three aspects of foram observation: distribution, biomass and export production.
+[PAPER TITLE]
+Marine zooplankton acclimated to warming in the geological record face limits by the next century
-Other models:
-ForamClim has individual-based implementation, but use empirical (i.e., fixed) growth rate curve;
-PLAFOM has similarily overestimated annual mean biomass (N. Pachyderma > 0.1 mmol C/m3) but has mechanistic setting
-PLANKTOM has foram but only designed for solving carbonate pump. Similarily use Lombard et al. 2009 measured growth curve.
-Statistic models (Waterson et al. 2016; Zaric et al. 2005; Knecht et al. 2023) are not counted here.
+[AUTHOR LIST]
+Rui Ying1*, Fanny M. Monteiro2, Jamie D. Wilson3, Malin Ödalen4,5, Daniela N. Schmidt1
+1 School of Earth Sciences, University of Bristol, Bristol, UK
+2 School of Geographical Sciences, University of Bristol, Bristol, UK
+3 Department of Earth, Ocean and Ecological Sciences, University of Liverpool, Liverpool, UK
+4 GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
+5 Department of Meteorology, Stockholm University
-## Traits
+*Correspondence: rui.ying@bristol.ac.uk
-### Feeding behaviour
-Symbiont-barren non-spinose foram (e.g., N. pacheyderma): *herbivory* generalist with increased food range (2x)
-Symbiont-barren spinose foram (e.g., G. bulloides): *herbivory* with increased grazing rate (reduced half-saturation constant)
-Symbiont-facultative non-spinose foram (e.g., N. dutertei): *herbivory* generalist with increased food range (2x)
-Symbiont-obligate spinose foram (e.g., G. ruber): *carnivory* with increased grazing rate (reduced half-saturation constant)
-Same predator-prey size ratio: 10/1
-### Calcification/Spine trait trade-offs
-- non-spinose adult: 20-40% growth rate reduction, 20-50% mortality reduction
-- spinose adult: 20-60% growth rate reduction, 12–55% mortality reduction
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+EDITING LOG [list of changes made to this file, when, and by who]
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-Reference of 0D model test: Grigoratou et al. (2019) Biogeoscience; Grigoratou et al. (2022) Marine Micropaleotonlogy;
+2024/04/01 -- README.txt file created by RY
-respiration is incorporated because the mismatch of model-data biogeography; This should be
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+SUMMARY OF EXPERIMENTS [summerize experiments detailed and in which e.g. figures they appear]
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+1. Last Glacial Maximum spin up
+2. Pre-industrial spin up
+3. Historical simulation (until 2022)
+4. Idealised future simulation (2100) with 1.5, 2, 3, 4 degree C warming
-### Symbiosis
-- Independent symbiont size: 1% foraminifera shell size
-- Low autotrophy efficiency: Great amount of excessive carbon from symbionts (theoretical growth rate = 0.89 d-1, >> ~0.2 d-1 in observation)
-- Low heterotrophy efficiency: mixotrophy modelling convention (Ward and Follows. 2016 PNAS)
-
-Tested implementation: directly transfer biomass from phytoplankton, or mixotroph;
-
-
-## Limitation
-+ only adult foram are incldued
-+ no 3D water column ecosystem;
-+ cGENIE has little primary production in the tropical oceans
-+ fixed zooplankton Q10 (the respiration of foram has high Q10 (>3, Lombard et al. 2009 L&O), Photo:Respir = 2-10
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+RUNNING THE EXPERIMENTS [command lines, broken down in sub-sections for spinups, main experiments, SI, etc where appropriate]
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# Model Runs
## pre-industrial spinup (0-10000)
@@ -71,42 +73,15 @@ qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTD
qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.GIteiiva.BASESFeTDTL_rb FORAMECOGEM muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN 10000
```
-## Holocene
-
-```sh
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.GIteiiaa.BASESFeTDTL_rb FORAMECOGEM muffin.CBE.GIteiiaa.BASESFeTDTL_rb.SPIN 10000
-```
-
-## Pliocene
-muffin.CB.umQ00p0a.BASES (modern)
-muffin.CB.umQ04p5a.BASES (Pliocene open)
-muffin.CB.umQ04p5b.BASES (Pliocene close)
-
-``` sh
-## Pliocene open, 400 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5a.BASES FORAMECOGEM muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN 10000
-
-## Modern CAS closed, 280 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ00p0a.BASES FORAMECOGEM muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN 10000
-
-## Pliocene closed, 400 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES FORAMECOGEM muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN 10000
-
-## Pliocene closed, 280 ppm
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CB.umQ04p5b.BASES FORAMECOGEM muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN 10000
-```
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-> Full effect:4.5 Ma (open, 400 ppm) - 0 Ma (closed, 280 ppm)
-muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
-muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
+Note that all experiments are run from:
+$HOME/cgenie.muffin/genie-main
+(unless a different installation directory has been used)
-> CO2 effect: 4.5 Ma (closed, 400 ppm) - 4.5 Ma (closed, 280 ppm)
-muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
-muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
+================================================================
+================================================================
+================================================================
-> CAS effect: 4.5 Ma (open, 400 ppm) - 4.5 Ma (closed, 400 ppm)
-muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
-muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
-## K-Pg
From 5956cd6ddd940d7cef316786b6cf9a519775fe57 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 1 Apr 2024 14:43:48 +0100
Subject: [PATCH 80/89] no CO2 change after 2300
---
.../biogem_force_restore_atm_pCO2_sig.dat | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
index dd7c5d687..04d0c8282 100644
--- a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
@@ -258,7 +258,7 @@
2020.5 4.14890E-04
2021.5 4.18060E-04
2022.5 4.21330E-04
-2299.5. 680.0E-6
+2299.5. 695.0E-6
4999.5. 695.0E-6
999999999.0 278.0E-6
-END-OF-DATA-
From 2c2247d67a894dbc570051fee8556131ee045042 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 1 Apr 2024 14:44:08 +0100
Subject: [PATCH 81/89] apply the forcing
---
.../FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
index fa364bd73..fdd284ac6 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
@@ -137,7 +137,7 @@ bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
# --- FORCINGS ------------------------------------------------------
#
# specify forcings
-bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.2100.4deg"
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg"
bg_par_atm_force_scale_val_4=-6.5
#
# --- MISC ----------------------------------------------------------
From b3d168247fd1cf47f6be0442d0d3964b271b2f36 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 1 Apr 2024 20:24:19 +0100
Subject: [PATCH 82/89] fix a typo
---
.../biogem_force_restore_atm_pCO2_sig.dat | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
index 04d0c8282..300a21d27 100644
--- a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
@@ -258,7 +258,7 @@
2020.5 4.14890E-04
2021.5 4.18060E-04
2022.5 4.21330E-04
-2299.5. 695.0E-6
-4999.5. 695.0E-6
+2299.5 695.0E-6
+4999.5 695.0E-6
999999999.0 278.0E-6
-END-OF-DATA-
From c4e2e89e8e9d8fd05d46c35ed55c79047e7beebb Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sun, 28 Apr 2024 17:47:33 +0100
Subject: [PATCH 83/89] add GIteiiva to the fname_topo list to export opsia
---
genie-biogem/src/fortran/biogem_data_ascii.f90 | 4 ++--
genie-biogem/src/fortran/biogem_data_netCDF.f90 | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/genie-biogem/src/fortran/biogem_data_ascii.f90 b/genie-biogem/src/fortran/biogem_data_ascii.f90
index 2ad59e67c..9fd5e08bf 100644
--- a/genie-biogem/src/fortran/biogem_data_ascii.f90
+++ b/genie-biogem/src/fortran/biogem_data_ascii.f90
@@ -2252,7 +2252,7 @@ SUBROUTINE sub_data_save_runtime(dum_yr_save,dum_t)
OPEN(unit=out,file=loc_filename,action='write',status='old',position='append',iostat=ios)
call check_iostat(ios,__LINE__,__FILE__)
select case (fname_topo)
- case ('worbe2', 'worjh2', 'worjh4', 'worlg2', 'worlg4', 'wv2jh2', 'wv3jh2', 'worri4', 'p_worbe2', 'p_worjh2')
+ case ('worbe2', 'worjh2', 'worjh4', 'worlg2', 'worlg4', 'wv2jh2', 'wv3jh2', 'worri4', 'p_worbe2', 'p_worjh2', 'GIteiiva')
WRITE(unit=out,fmt='(f12.3,6f9.3)',iostat=ios) &
& loc_t, &
& loc_opsi_scale*int_misc_opsi_min_sig/int_t_sig, &
@@ -4413,4 +4413,4 @@ END SUBROUTINE sub_calc_psi
! ****************************************************************************************************************************** !
-END MODULE biogem_data_ascii
\ No newline at end of file
+END MODULE biogem_data_ascii
diff --git a/genie-biogem/src/fortran/biogem_data_netCDF.f90 b/genie-biogem/src/fortran/biogem_data_netCDF.f90
index 762823e64..ee2b282a2 100644
--- a/genie-biogem/src/fortran/biogem_data_netCDF.f90
+++ b/genie-biogem/src/fortran/biogem_data_netCDF.f90
@@ -3849,7 +3849,7 @@ SUBROUTINE sub_save_netcdf_goldstein_opsi()
call sub_putvar2d('phys_opsi',loc_iou,n_j+1,n_k+1,loc_ntrec,loc_tmp_jk,loc_mask)
! Atlantic & Pacific -- modern topos only
select case (fname_topo)
- case ('worbe2', 'worjh2', 'worjh4', 'worlg2', 'worlg4', 'wv2jh2', 'wv3jh2', 'worri4', 'p_worbe2', 'p_worjh2')
+ case ('worbe2', 'worjh2', 'worjh4', 'worlg2', 'worlg4', 'wv2jh2', 'wv3jh2', 'worri4', 'p_worbe2', 'p_worjh2', 'GIteiiva')
! Atlantic
loc_tmp_jk(:,:) = loc_scale*int_opsia_timeslice(:,:)/int_t_timeslice
loc_tmp_jk(:,n_k:0:-1) = loc_tmp_jk(:,0:n_k:1)
From 77e0aa0867b1ba3869c3beec429d15ffac8c9512 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Wed, 1 May 2024 15:27:51 +0100
Subject: [PATCH 84/89] save more historical timeslice data
---
genie-biogem/data/input/save_timeslice_historical2022.dat | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/genie-biogem/data/input/save_timeslice_historical2022.dat b/genie-biogem/data/input/save_timeslice_historical2022.dat
index 7348eb5e8..126350df7 100644
--- a/genie-biogem/data/input/save_timeslice_historical2022.dat
+++ b/genie-biogem/data/input/save_timeslice_historical2022.dat
@@ -1,5 +1,10 @@
-START-OF-DATA-
1765.5
+1800.5
+1850.5
+1900.5
+1925.5
+1950.5
1976.5
1994.5
2000.5
From fef75651557c91a36d1a333fb324b9b541e3669e Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Wed, 1 May 2024 15:30:08 +0100
Subject: [PATCH 85/89] save more timeslice in future runs
---
.../data/input/save_timeslice_historicalfuture_fakeSSP.dat | 2 ++
1 file changed, 2 insertions(+)
diff --git a/genie-biogem/data/input/save_timeslice_historicalfuture_fakeSSP.dat b/genie-biogem/data/input/save_timeslice_historicalfuture_fakeSSP.dat
index 53900c025..4c48156fd 100644
--- a/genie-biogem/data/input/save_timeslice_historicalfuture_fakeSSP.dat
+++ b/genie-biogem/data/input/save_timeslice_historicalfuture_fakeSSP.dat
@@ -11,6 +11,8 @@
2000.5
2009.5
2019.5
+2021.5
+2022.5
2029.5
2039.5
2049.5
From 05792d477784466f39bee7b398a6ca0a910f4221 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Wed, 1 May 2024 15:45:58 +0100
Subject: [PATCH 86/89] remove pliocene configs
---
....CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN | 140 -----------------
...in.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN | 145 ------------------
....CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN | 140 -----------------
....CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN | 141 -----------------
.../FORAMECOGEM/{readme.md => readme.txt} | 0
5 files changed, 566 deletions(-)
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
rename genie-userconfigs/FORAMECOGEM/{readme.md => readme.txt} (100%)
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
deleted file mode 100644
index 93e045a95..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ00p0a.BASES.CASclosed.280_0p2.SPIN
+++ /dev/null
@@ -1,140 +0,0 @@
-# *** CLIMATE *******************************************************
-#
-# set climate feedback (climate responding to changing pCO2)
-ea_36=y
-#
-# *** BIOLOGICAL NEW PRODUCTION *************************************
-#
-# biological scheme ID string
-# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
-bg_par_bio_prodopt="NONE"
-#
-# *** ORGANIC MATTER EXPORT RATIOS **********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** INORGANIC MATTER EXPORT RATIOS ********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** REMINERALIZATION **********************************************
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-# *** optional changes to align with PALEO recommendations **********
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# *** IRON CYCLING **************************************************
-#
-# [no iron]
-#
-# *** ECOGEM ********************************************************
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_spine_scale=3.5
-
-#################### Nitrogen ############################
-eg_useNO3 =.false.
-eg_nquota =.false.
-################## Phosphorus ############################
-eg_usePO4 =.true.
-eg_pquota =.true.
-######################## Iron ############################
-eg_useFe =.false.
-eg_fquota =.false.
-################# Chlorophyll ############################
-eg_chlquota =.true.
-################# d13C ###################################
-eg_useDIC_13C =.true.
-# Tuned parameters
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-# ???
-eg_ns=2
-# ???
-eg_respir_a=0
-# DOM parameters
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-# ???
-eg_nsubtime=25
-eg_n_keco=1
-# exponent for modifier of CaCO3:POC export ratio
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-#
-# --- DATA SAVING ----------------------------------------------
-#
-bg_par_data_save_level=7
-# reduce output
-bg_ctrl_data_save_2d=.true.
-bg_ctrl_data_save_3d=.true. # JDW - set to true
-#
-# --- FORCINGS -------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
-bg_par_atm_force_scale_val_4=-6.428
-# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 280
-bg_par_atm_force_scale_val_3=0.000280
-# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
-bg_par_ocn_force_scale_val_2=0.2
-#
-# *** MISC **********************************************************
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld=1
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-# maximum time-scale to geochemical reaction completion (days)
-bg_par_bio_geochem_tau=90.0
-# extend solubility and geochem constant T range (leave S range as default)
-gm_par_geochem_Tmin = -2.0
-gm_par_geochem_Tmax = 45.0
-gm_par_carbchem_Tmin = -2.0
-gm_par_carbchem_Tmax = 45.0
-#
-ma_flag_ecogem=.TRUE.
-GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
-gm_ocn_select_60=.true. # preformed PO4
-gm_ocn_select_66=.true. # Csoft
-bg_ctrl_bio_preformed=.true.
-bg_ctrl_bio_remin_redox_save=.true.
-bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
-#
-# *******************************************************************
-# *** END ***********************************************************
-# *******************************************************************
-#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
deleted file mode 100644
index 7b198cf23..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5a.BASES.CASopen.400_0p5.SPIN
+++ /dev/null
@@ -1,145 +0,0 @@
-# *** CLIMATE *******************************************************
-#
-# set climate feedback (climate responding to changing pCO2)
-ea_36=y
-#
-# *** BIOLOGICAL NEW PRODUCTION *************************************
-#
-# biological scheme ID string
-# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
-bg_par_bio_prodopt="NONE"
-#
-# *** ORGANIC MATTER EXPORT RATIOS **********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** INORGANIC MATTER EXPORT RATIOS ********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** REMINERALIZATION **********************************************
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-# *** optional changes to align with PALEO recommendations **********
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# *** IRON CYCLING **************************************************
-#
-# [no iron]
-#
-# *** ECOGEM ********************************************************
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_spine_scale=3.5
-
-#################### Nitrogen ############################
-eg_useNO3 =.false.
-eg_nquota =.false.
-################## Phosphorus ############################
-eg_usePO4 =.true.
-eg_pquota =.true.
-######################## Iron ############################
-eg_useFe =.false.
-eg_fquota =.false.
-################# Chlorophyll ############################
-eg_chlquota =.true.
-################# d13C ###################################
-eg_useDIC_13C =.true.
-# Tuned parameters
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-# ???
-eg_ns=2
-# ???
-eg_respir_a=0
-# DOM parameters
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-# ???
-eg_nsubtime=25
-eg_n_keco=1
-# exponent for modifier of CaCO3:POC export ratio
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-#
-# --- DATA SAVING ----------------------------------------------
-#
-bg_par_data_save_level=7
-# reduce output
-bg_ctrl_data_save_2d=.true.
-bg_ctrl_data_save_3d=.true. # JDW - set to true
-#
-# --- FORCINGS -------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
-bg_par_atm_force_scale_val_4=-6.202
-# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
-bg_par_atm_force_scale_val_3=0.000400
-# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.5
-bg_par_ocn_force_scale_val_2=0.5
-#
-# *** MISC **********************************************************
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld=1
-# *** optional changes to align with PALEO recommendations **********
-# set mixed layer to be only diagnosed (for ECOGEM)
-go_ctrl_diagmld=.false.
-# add seaice attenuation of PAR
-eg_ctrl_PARseaicelimit=.false.
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-# maximum time-scale to geochemical reaction completion (days)
-bg_par_bio_geochem_tau=90.0
-# extend solubility and geochem constant T range (leave S range as default)
-gm_par_geochem_Tmin = -2.0
-gm_par_geochem_Tmax = 45.0
-gm_par_carbchem_Tmin = -2.0
-gm_par_carbchem_Tmax = 45.0
-#
-ma_flag_ecogem=.TRUE.
-GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
-gm_ocn_select_60=.true. # preformed PO4
-gm_ocn_select_66=.true. # Csoft
-bg_ctrl_bio_preformed=.true.
-bg_ctrl_bio_remin_redox_save=.true.
-bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
-#
-# *******************************************************************
-# *** END ***********************************************************
-# *******************************************************************
-#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
deleted file mode 100644
index 32f6f4eee..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.280_0p2.SPIN
+++ /dev/null
@@ -1,140 +0,0 @@
-# *** CLIMATE *******************************************************
-#
-# set climate feedback (climate responding to changing pCO2)
-ea_36=y
-#
-# *** BIOLOGICAL NEW PRODUCTION *************************************
-#
-# biological scheme ID string
-# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
-bg_par_bio_prodopt="NONE"
-#
-# *** ORGANIC MATTER EXPORT RATIOS **********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** INORGANIC MATTER EXPORT RATIOS ********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** REMINERALIZATION **********************************************
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-# *** optional changes to align with PALEO recommendations **********
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# *** IRON CYCLING **************************************************
-#
-# [no iron]
-#
-# *** ECOGEM ********************************************************
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_spine_scale=3.5
-
-#################### Nitrogen ############################
-eg_useNO3 =.false.
-eg_nquota =.false.
-################## Phosphorus ############################
-eg_usePO4 =.true.
-eg_pquota =.true.
-######################## Iron ############################
-eg_useFe =.false.
-eg_fquota =.false.
-################# Chlorophyll ############################
-eg_chlquota =.true.
-################# d13C ###################################
-eg_useDIC_13C =.true.
-# Tuned parameters
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-# ???
-eg_ns=2
-# ???
-eg_respir_a=0
-# DOM parameters
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-# ???
-eg_nsubtime=25
-eg_n_keco=1
-# exponent for modifier of CaCO3:POC export ratio
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-#
-# --- DATA SAVING ----------------------------------------------
-#
-bg_par_data_save_level=7
-# reduce output
-bg_ctrl_data_save_2d=.true.
-bg_ctrl_data_save_3d=.true. # JDW - set to true
-#
-# --- FORCINGS -------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
-bg_par_atm_force_scale_val_4=-6.265
-# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
-bg_par_atm_force_scale_val_3=0.000280
-# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
-bg_par_ocn_force_scale_val_2=0.2
-#
-# *** MISC **********************************************************
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld=1
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-# maximum time-scale to geochemical reaction completion (days)
-bg_par_bio_geochem_tau=90.0
-# extend solubility and geochem constant T range (leave S range as default)
-gm_par_geochem_Tmin = -2.0
-gm_par_geochem_Tmax = 45.0
-gm_par_carbchem_Tmin = -2.0
-gm_par_carbchem_Tmax = 45.0
-#
-ma_flag_ecogem=.TRUE.
-GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
-gm_ocn_select_60=.true. # preformed PO4
-gm_ocn_select_66=.true. # Csoft
-bg_ctrl_bio_preformed=.true.
-bg_ctrl_bio_remin_redox_save=.true.
-bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
-#
-# *******************************************************************
-# *** END ***********************************************************
-# *******************************************************************
-#
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN b/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
deleted file mode 100644
index c439f7a60..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.umQ04p5b.BASES.CASclosed.400_0p2.SPIN
+++ /dev/null
@@ -1,141 +0,0 @@
-# *** CLIMATE *******************************************************
-#
-# set climate feedback (climate responding to changing pCO2)
-ea_36=y
-#
-# *** BIOLOGICAL NEW PRODUCTION *************************************
-#
-# biological scheme ID string
-# NOTE: with ECOGEM, no BIOGEM biological scheme must be selected
-bg_par_bio_prodopt="NONE"
-#
-# *** ORGANIC MATTER EXPORT RATIOS **********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** INORGANIC MATTER EXPORT RATIOS ********************************
-#
-# [dealt with by ECOGEM]
-#
-# *** REMINERALIZATION **********************************************
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-# *** optional changes to align with PALEO recommendations **********
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
-#
-# *** IRON CYCLING **************************************************
-#
-# [no iron]
-#
-# *** ECOGEM ********************************************************
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_spine_scale=3.5
-
-#################### Nitrogen ############################
-eg_useNO3 =.false.
-eg_nquota =.false.
-################## Phosphorus ############################
-eg_usePO4 =.true.
-eg_pquota =.true.
-######################## Iron ############################
-eg_useFe =.false.
-eg_fquota =.false.
-################# Chlorophyll ############################
-eg_chlquota =.true.
-################# d13C ###################################
-eg_useDIC_13C =.true.
-# Tuned parameters
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-# ???
-eg_ns=2
-# ???
-eg_respir_a=0
-# DOM parameters
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-# ???
-eg_nsubtime=25
-eg_n_keco=1
-# exponent for modifier of CaCO3:POC export ratio
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-#
-# --- DATA SAVING ----------------------------------------------
-#
-bg_par_data_save_level=7
-# reduce output
-bg_ctrl_data_save_2d=.true.
-bg_ctrl_data_save_3d=.true. # JDW - set to true
-#
-# --- FORCINGS -------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="Q_xxxxxx.RpCO2_Rp13CO2.Fsal_SUR"
-bg_par_atm_force_scale_val_4=-6.265
-# parameter: bg_par_atm_force_scale_val_3 -- default value modified by factor: 400
-bg_par_atm_force_scale_val_3=0.000400
-# parameter: bg_par_ocn_force_scale_val_2 -- default value modified by factor: 0.2
-bg_par_ocn_force_scale_val_2=0.2
-#
-# *** MISC **********************************************************
-#
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld=1
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-# maximum time-scale to geochemical reaction completion (days)
-bg_par_bio_geochem_tau=90.0
-# extend solubility and geochem constant T range (leave S range as default)
-gm_par_geochem_Tmin = -2.0
-gm_par_geochem_Tmax = 45.0
-gm_par_carbchem_Tmin = -2.0
-gm_par_carbchem_Tmax = 45.0
-#
-ma_flag_ecogem=.TRUE.
-GOLDSTEINNTRACSOPTS='$(DEFINE)GOLDSTEINNTRACS=16'
-gm_ocn_select_60=.true. # preformed PO4
-gm_ocn_select_66=.true. # Csoft
-bg_ctrl_bio_preformed=.true.
-bg_ctrl_bio_remin_redox_save=.true.
-bg_ctrl_bio_preformed_CsoftPOConly=.true. # Ppre = all Csoft
-#
-# *******************************************************************
-# *** END ***********************************************************
-# *******************************************************************
-#
diff --git a/genie-userconfigs/FORAMECOGEM/readme.md b/genie-userconfigs/FORAMECOGEM/readme.txt
similarity index 100%
rename from genie-userconfigs/FORAMECOGEM/readme.md
rename to genie-userconfigs/FORAMECOGEM/readme.txt
From 08607a786d15935c44c5833f4d027ff0cd81af3c Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Mon, 6 May 2024 07:02:08 +0100
Subject: [PATCH 87/89] remove 5000.4deg (not necessary)
---
.../muffin.CBE.worlg4.BASESFeTDTL.5000.4deg | 149 ------------------
1 file changed, 149 deletions(-)
delete mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
deleted file mode 100644
index fdd284ac6..000000000
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
+++ /dev/null
@@ -1,149 +0,0 @@
-#
-#
-# --- CLIMATE -------------------------------------------------------
-#
-# set climate feedback
-ea_36=y
-#
-# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
-#
-# biological scheme ID string
-bg_par_bio_prodopt="NONE"
-#
-# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
-#
-# production fraction of dissolved organic matter
-bg_par_bio_red_DOMfrac=0.66
-#
-# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
-#
-# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-bg_par_bio_red_POC_CaCO3=0.0485
-# exponent for modifier of CaCO3:POC export ratio
-bg_par_bio_red_POC_CaCO3_pP=0.7440
-#
-# --- REMINERALIZATION ----------------------------------------------
-#
-# DOC lifetime (yrs)
-bg_par_bio_remin_DOMlifetime=1.0
-# initial fractional abundance of POC component #2
-bg_par_bio_remin_POC_frac2=0.055
-# depth of remineralization or particulate organic matter
-bg_par_bio_remin_POC_eL1=589.9451
-# remineralization length #2 for POC
-bg_par_bio_remin_POC_eL2=1000000.0
-# initial fractional abundance of CaCO3 component #2
-bg_par_bio_remin_CaCO3_frac2=0.45
-# depth of remineralization or CaCO3
-bg_par_bio_remin_CaCO3_eL1=1.8905e+003
-# remineralization length #2 for CaCO3
-bg_par_bio_remin_CaCO3_eL2=1000000.0
-#
-# --- IRON ----------------------------------------------------------
-#
-bg_opt_geochem_Fe='hybrid'
-# aeolian Fe solubility
-bg_par_det_Fe_sol=0.002014275
-#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
-bg_par_det_Fe_sol_exp=0.500
-# modifier of the scavenging rate of dissolved Fe
-bg_par_scav_Fe_sf_POC=0.344104
-bg_par_scav_Fe_sf_CaCO3=0.000
-bg_par_scav_Fe_sf_opal=0.000
-bg_par_scav_Fe_sf_det=0.000
-# no scavenged regeneration
-bg_par_scav_fremin=0.0
-# return POFe
-bg_ctrl_bio_NO_fsedFe=.false.
-# Variable Fe:C
-bg_ctrl_bio_red_fixedFetoC=.false.
-# adjust pK'(FeL)
-bg_par_K_FeL_pP=11.0
-#(max) C/Fe organic matter ratio
-bg_par_bio_red_POFe_POC=250000.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
-bg_par_bio_FetoC_pP=-0.4225
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
-bg_par_bio_FetoC_K=103684.0
-#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
-bg_par_bio_FetoC_C=0.0
-#
-# --- ECOGEM ----------------------------------------------------------
-#
-gm_ctrl_debug_init =0
-eg_ctrl_debug_eco_init=.false.
-
-eg_gkernel_cap=.false.
-eg_ctrl_grazing_explicit=.true.
-
-eg_ctrl_use_foramecogenie=.true.
-
-eg_par_ecogem_plankton_file='8P7Z4F.eco'
-eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
-eg_foram_symbiont_esd_scale=0.01
-eg_foram_auto_cost=0.04
-eg_foram_hetero_cost=0.35
-eg_foram_spine_scale=3.5
-
-#----------------- Nitrogen -------------------------
-eg_useNO3 =.false.
-eg_nquota =.false.
-#---------------- Phosphorus -----------------------
-eg_usePO4 =.true.
-eg_pquota =.true.
-#---------------- Iron -----------------------------
-eg_useFe =.true.
-eg_fquota =.true.
-#---------------- Chlorophyll -----------------------
-eg_chlquota =.true.
-#---------------- d13C ------------------------------
-eg_useDIC_13C =.true.
-
-# Tuned
-eg_qminP_a = 3.33e-3
-eg_qminFe_a = 1.00e-6
-eg_qmaxFe_a = 4.00e-6
-
-eg_ns = 2
-
-eg_respir_a = 0
-
-eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
-eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
-eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
-
-eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
-eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
-
-eg_nsubtime =25
-eg_n_keco =1
-
-# disable ECOGEM restarts (as not currently coded up / used)
-eg_ctrl_ncrst=.false.
-eg_ctrl_continuing=.false.
-
-#
-# --- DATA SAVING -----------------------------------------------------
-#
-bg_par_data_save_level=10
-bg_ctrl_debug_lvl0=.true.
-ma_debug_loop=1
-bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
-bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
-#
-# --- FORCINGS ------------------------------------------------------
-#
-# specify forcings
-bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg"
-bg_par_atm_force_scale_val_4=-6.5
-#
-# --- MISC ----------------------------------------------------------
-# starting year
-bg_par_misc_t_start=2022.0
-# kraus-turner mixed layer scheme on (1) or off (0)
-go_imld=1
-#
-# --- END -----------------------------------------------------------
From 13993de3cbf0b74e9eb64017d1879f45ccab4e81 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Wed, 29 May 2024 17:04:13 +0100
Subject: [PATCH 88/89] complete list of forcing/user-configs as the revised
paper
---
.../biogem_force_flux_sed_det_SUR.dat | 37 +++
.../biogem_force_flux_sed_det_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_13C_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_sig.dat | 263 ++++++++++++++++++
.../configure_forcings_atm.dat | 24 ++
.../configure_forcings_ocn.dat | 24 ++
.../configure_forcings_sed.dat | 21 ++
.../biogem_force_flux_sed_det_SUR.dat | 37 +++
.../biogem_force_flux_sed_det_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_13C_sig.dat | 4 +
.../biogem_force_restore_atm_pCO2_sig.dat | 263 ++++++++++++++++++
.../configure_forcings_atm.dat | 24 ++
.../configure_forcings_ocn.dat | 24 ++
.../configure_forcings_sed.dat | 21 ++
.../biogem_force_restore_atm_pCO2_sig.dat | 3 +-
...> muffin.CBE.worlg4.BASESFeTDTL.3000.4deg} | 84 ++----
.../muffin.CBE.worlg4.BASESFeTDTL.4000.4deg | 149 ++++++++++
.../muffin.CBE.worlg4.BASESFeTDTL.5000.4deg | 149 ++++++++++
genie-userconfigs/FORAMECOGEM/readme.txt | 37 ++-
19 files changed, 1091 insertions(+), 85 deletions(-)
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_flux_sed_det_SUR.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_flux_sed_det_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_restore_atm_pCO2_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_atm.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_ocn.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_sed.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_flux_sed_det_SUR.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_flux_sed_det_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_restore_atm_pCO2_sig.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_atm.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_ocn.dat
create mode 100644 genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_sed.dat
rename genie-userconfigs/FORAMECOGEM/{muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC => muffin.CBE.worlg4.BASESFeTDTL.3000.4deg} (68%)
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.4000.4deg
create mode 100644 genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_flux_sed_det_SUR.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_flux_sed_det_SUR.dat
new file mode 100644
index 000000000..0e35c9e79
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_flux_sed_det_SUR.dat
@@ -0,0 +1,37 @@
+ 4.811560e+009 4.626661e+009 3.126386e+009 2.214785e+009 1.652428e+009 1.418667e+009 1.229085e+009 1.076190e+009 9.778666e+008 9.012306e+008 8.453771e+008 7.600965e+008 7.182478e+008 5.693231e+008 5.741100e+008 6.638764e+008 7.234523e+008 5.594685e+008 7.167836e+008 8.443707e+008 7.166255e+008 4.937644e+008 3.068558e+008 4.938671e+008 8.409478e+008 1.096116e+009 1.683666e+009 1.914513e+009 2.299017e+009 3.071956e+009 3.802993e+009 4.240087e+009 4.936058e+009 5.216635e+009 5.376818e+009 5.281376e+009
+ 1.343700e+010 9.545553e+009 7.701629e+009 6.234372e+009 5.062455e+009 4.316215e+009 3.738453e+009 3.505623e+009 3.031678e+009 3.020078e+009 2.587311e+009 1.913481e+009 1.093572e+009 8.971857e+008 9.264849e+008 1.242755e+009 1.826465e+009 2.137803e+009 1.864901e+009 1.727755e+009 1.651924e+009 1.529487e+009 1.748379e+009 2.522670e+009 2.675955e+009 2.661006e+009 4.062310e+009 5.542987e+009 8.772387e+009 1.201052e+010 1.523653e+010 1.940816e+010 2.490924e+010 2.464401e+010 2.370861e+010 1.913809e+010
+ 2.191364e+010 1.936862e+010 1.567816e+010 1.311101e+010 1.381438e+010 1.309821e+010 1.017951e+010 8.816739e+009 6.890637e+009 6.144822e+009 5.870425e+009 5.819545e+009 5.190809e+009 2.321959e+009 1.729022e+009 2.421049e+009 3.633724e+009 4.094662e+009 4.536250e+009 4.009311e+009 4.098709e+009 4.589060e+009 4.154100e+009 4.814990e+009 5.828027e+009 7.413160e+009 1.114812e+010 1.466988e+010 1.810967e+010 3.268979e+010 4.531443e+010 6.379481e+010 6.471064e+010 5.148941e+010 4.222460e+010 3.202711e+010
+ 4.773867e+010 3.897290e+010 3.218952e+010 2.669083e+010 1.482687e+010 1.635391e+010 1.414073e+010 1.094780e+010 9.099413e+009 8.012883e+009 7.210235e+009 5.979428e+009 9.014147e+009 8.293997e+009 3.545032e+009 5.985328e+009 8.540426e+009 1.116040e+010 1.261955e+010 1.088208e+010 7.575549e+009 7.317822e+009 7.669705e+009 9.462377e+009 1.044160e+010 1.340016e+010 1.454429e+010 2.019894e+010 3.982011e+010 5.705782e+010 6.992632e+010 9.423755e+010 8.465794e+010 6.647657e+010 6.425755e+010 6.108267e+010
+ 7.443235e+010 5.352486e+010 4.582047e+010 3.943678e+010 2.007783e+010 1.950609e+010 1.664325e+010 1.303115e+010 1.033725e+010 8.919119e+009 7.736178e+009 7.385119e+009 7.260686e+009 1.409092e+010 9.049464e+009 1.300443e+010 2.365146e+010 2.630307e+010 2.494975e+010 1.788698e+010 1.392681e+010 1.146293e+010 1.306816e+010 1.406366e+010 1.452892e+010 2.082970e+010 4.311414e+010 5.945157e+010 6.212489e+010 5.670328e+010 7.737460e+010 1.210547e+011 1.188417e+011 8.784818e+010 9.409373e+010 1.180628e+011
+ 1.398223e+011 8.271717e+010 5.901094e+010 3.395701e+010 2.454088e+010 2.056876e+010 1.684222e+010 1.253698e+010 9.230797e+009 8.258025e+009 7.277677e+009 7.619777e+009 6.318893e+009 1.374870e+010 1.745587e+010 4.980079e+010 5.384173e+010 4.144591e+010 3.433682e+010 1.964531e+010 1.501058e+010 1.502309e+010 1.664515e+010 1.520801e+010 1.553077e+010 3.322921e+010 7.962831e+010 1.301236e+011 1.113854e+011 8.800017e+010 1.670935e+011 1.567393e+011 1.901726e+011 1.437284e+011 9.446121e+010 3.131200e+011
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+
\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_flux_sed_det_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_flux_sed_det_sig.dat
new file mode 100644
index 000000000..972d7c3fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_flux_sed_det_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999.0 1.0
+-END-OF-DATA-
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
new file mode 100644
index 000000000..b4149dc1a
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999.0 1.0
+-END-OF-DATA-
\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_restore_atm_pCO2_sig.dat
new file mode 100644
index 000000000..743468828
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/biogem_force_restore_atm_pCO2_sig.dat
@@ -0,0 +1,263 @@
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+-END-OF-DATA-
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_atm.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_atm.dat
new file mode 100644
index 000000000..453007a3e
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_atm.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08
+ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 03 t 0.1 f t F 2 01 01 '[carbon dioxide (CO2) partial pressure (atm)]'
+ 04 t 0.1 f t F 2 01 01 '[d13C CO2 (o/oo)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08
+
+DATA FORMAT AND ORDER:
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #03: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #04: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: force ocean surface in equilibrium with atmosphere? (needs ocean restoring forcing set) [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (2 = 2D, 0 = point, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_ocn.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_ocn.dat
new file mode 100644
index 000000000..a317b42fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_ocn.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08 09
+ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08 09
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: restrict restoring forcing to surface? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #04: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN #09: k grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_sed.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_sed.dat
new file mode 100644
index 000000000..0db3bf57b
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg/configure_forcings_sed.dat
@@ -0,0 +1,21 @@
+
+ 00 01 02 03 04 05
+ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 22 t F -1 01 01 '[detrital (refractory) material (wt%)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #04: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #05: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_flux_sed_det_SUR.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_flux_sed_det_SUR.dat
new file mode 100644
index 000000000..0e35c9e79
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_flux_sed_det_SUR.dat
@@ -0,0 +1,37 @@
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+
\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_flux_sed_det_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_flux_sed_det_sig.dat
new file mode 100644
index 000000000..972d7c3fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_flux_sed_det_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999.0 1.0
+-END-OF-DATA-
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
new file mode 100644
index 000000000..b4149dc1a
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_restore_atm_pCO2_13C_sig.dat
@@ -0,0 +1,4 @@
+-START-OF-DATA-
+0.0 1.0
+999999.0 1.0
+-END-OF-DATA-
\ No newline at end of file
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_restore_atm_pCO2_sig.dat
new file mode 100644
index 000000000..5373aaf86
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/biogem_force_restore_atm_pCO2_sig.dat
@@ -0,0 +1,263 @@
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diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_atm.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_atm.dat
new file mode 100644
index 000000000..453007a3e
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_atm.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08
+ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 03 t 0.1 f t F 2 01 01 '[carbon dioxide (CO2) partial pressure (atm)]'
+ 04 t 0.1 f t F 2 01 01 '[d13C CO2 (o/oo)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08
+
+DATA FORMAT AND ORDER:
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #03: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #04: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: force ocean surface in equilibrium with atmosphere? (needs ocean restoring forcing set) [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (2 = 2D, 0 = point, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_ocn.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_ocn.dat
new file mode 100644
index 000000000..a317b42fd
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_ocn.dat
@@ -0,0 +1,24 @@
+
+ 00 01 02 03 04 05 06 07 08 09
+ \/ \/ \/ \/ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05 06 07 08 09
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include restoring forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: restrict restoring forcing to surface? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: time constant of restoring forcing (years) [DATA FORMAT: real]
+COLUMN #04: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #05: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #06: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #07: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #08: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN #09: k grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_sed.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_sed.dat
new file mode 100644
index 000000000..0db3bf57b
--- /dev/null
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg/configure_forcings_sed.dat
@@ -0,0 +1,21 @@
+
+ 00 01 02 03 04 05
+ \/ \/ \/ \/ \/ \/
+
+-START-OF-DATA-
+ 22 t F -1 01 01 '[detrital (refractory) material (wt%)]'
+-END-OF-DATA-
+
+ /\ /\ /\ /\ /\ /\
+ 00 01 02 03 04 05
+
+DATA FORMAT AND ORDER
+---------------------
+
+COLUMN #00: TRACER NUMBER
+COLUMN #01: include flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #02: scale flux forcing of tracer? [DATA FORMAT: 'T'/'F' ('t'/'f')]
+COLUMN #03: make forcing uniform over this dimension (3 == 3D, 2 == 2D, 0 == point, -1 == SURFACE, -2 == BENTHIC, ELSE spatially explicit forcing) [DATA FORMAT: interger]
+COLUMN #04: i grid location of point forcing [DATA FORMAT: interger]
+COLUMN #05: j grid location of point forcing [DATA FORMAT: interger]
+COLUMN END: TRACER DESCRIPTION
diff --git a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
index 300a21d27..c8c2b901d 100644
--- a/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
+++ b/genie-forcings/worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg/biogem_force_restore_atm_pCO2_sig.dat
@@ -258,7 +258,6 @@
2020.5 4.14890E-04
2021.5 4.18060E-04
2022.5 4.21330E-04
-2299.5 695.0E-6
-4999.5 695.0E-6
+4999.5 1000.0E-6
999999999.0 278.0E-6
-END-OF-DATA-
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.3000.4deg
similarity index 68%
rename from genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
rename to genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.3000.4deg
index 7024a21e7..2cdcad86c 100644
--- a/genie-userconfigs/FORAMECOGEM/muffin.CBE.GIteiiva.BASESFeTDTL_rb.modernAMOC
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.3000.4deg
@@ -12,11 +12,15 @@ bg_par_bio_prodopt="NONE"
#
# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
#
-# [Dealt with ECOGEM]
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
#
# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
#
-# [Dealt with ECOGEM]
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
#
# --- REMINERALIZATION ----------------------------------------------
#
@@ -39,11 +43,14 @@ bg_par_bio_remin_CaCO3_eL2=1000000.0
#
bg_opt_geochem_Fe='hybrid'
# aeolian Fe solubility
-bg_par_det_Fe_sol=0.002441
-# modifier of the scavenging rate of dissolved Fe [Albani tuning]
-bg_par_scav_Fe_sf_POC=0.2250
+bg_par_det_Fe_sol=0.002014275
#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
# no scavenged regeneration
bg_par_scav_fremin=0.0
# return POFe
@@ -124,68 +131,19 @@ eg_ctrl_continuing=.false.
bg_par_data_save_level=10
bg_ctrl_debug_lvl0=.true.
ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
#
# --- FORCINGS ------------------------------------------------------
#
# specify forcings
-bg_par_forcing_name="GIteiiva.RpCO2_Rp13CO2.Fsal_SUR.Albani.21ka"
-bg_par_atm_force_scale_val_3=193.0E-06
-bg_par_atm_force_scale_val_4=-6.46
-# Orbital parameters
-ea_par_orbit_osce=0.018994 # eccentricity
-ea_par_orbit_oscsob=0.389911 # sine of obliquity
-ea_par_orbit_oscgam=114.42 # longitude of perihelion (degrees)
-#
-#
-# *** TUNING ********************************************************
-#
-# parameter: bg_par_misc_brinerejection_frac -- default value (1) modified by factor: 0.2
-bg_par_misc_brinerejection_frac=0.2
-# saltier Atlantic and a mdoern-like AMOC
-bg_par_ocn_force_scale_val_2=0.3
-#
-# *** INITIAL CONDITIONS ********************************************
-#
-# modern DIC (2.244E-03) + 1%
-bg_ocn_init_3=0.002275818239634
-# modern 13C DIC
-bg_ocn_init_4=0.4
-# modern ALK (2.363E-03) + 1%
-bg_ocn_init_12=0.002396505570523
-# modern PO4 (2.159E-06) + 1%
-bg_ocn_init_8=2.189613003283920e-06
-# modern SAL + 0.33 PSU
-go_saln0=35.23
-#
-## --- MISC ----------------------------------------------------------
-#
-# (no preformed)
-bg_ctrl_bio_preformed=.false.
-# add ventillation tracers
-bg_ctrl_force_ocn_age1=.true.
-# add brine rejection SH limit
-bg_par_misc_brinerejection_jmax=19
-# wind-stress
-go_13=1.3
-ea_11=1.3
-
-# relative partitioning of C into DOM
-eg_par_beta_POCtoDOC=0.75
-
-# maximum time-scale to geochemical reaction completion (days)
-bg_par_bio_geochem_tau=90.0
-
-# extend solubility and geochem constant T range (leave S range as default)
-gm_par_geochem_Tmin = -2.0
-gm_par_geochem_Tmax = 45.0
-gm_par_carbchem_Tmin = -2.0
-gm_par_carbchem_Tmax = 45.0
-
-# set 'instantaneous' water column remineralziation
-bg_par_bio_remin_sinkingrate_physical=9.9E9
-bg_par_bio_remin_sinkingrate_reaction=125.0
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.3000.4deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+# starting year
+bg_par_misc_t_start=2022.0
# kraus-turner mixed layer scheme on (1) or off (0)
go_imld=1
-
#
-# --- END -----------------------------------------------------------
\ No newline at end of file
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.4000.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.4000.4deg
new file mode 100644
index 000000000..cad00ba6c
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.4000.4deg
@@ -0,0 +1,149 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_spine_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.4000.4deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+# starting year
+bg_par_misc_t_start=2022.0
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
new file mode 100644
index 000000000..fdd284ac6
--- /dev/null
+++ b/genie-userconfigs/FORAMECOGEM/muffin.CBE.worlg4.BASESFeTDTL.5000.4deg
@@ -0,0 +1,149 @@
+#
+#
+# --- CLIMATE -------------------------------------------------------
+#
+# set climate feedback
+ea_36=y
+#
+# --- BIOLOGICAL NEW PRODUCTION -------------------------------------
+#
+# biological scheme ID string
+bg_par_bio_prodopt="NONE"
+#
+# --- ORGANIC MATTER EXPORT RATIOS ----------------------------------
+#
+# production fraction of dissolved organic matter
+bg_par_bio_red_DOMfrac=0.66
+#
+# --- INORGANIC MATTER EXPORT RATIOS --------------------------------
+#
+# underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+bg_par_bio_red_POC_CaCO3=0.0485
+# exponent for modifier of CaCO3:POC export ratio
+bg_par_bio_red_POC_CaCO3_pP=0.7440
+#
+# --- REMINERALIZATION ----------------------------------------------
+#
+# DOC lifetime (yrs)
+bg_par_bio_remin_DOMlifetime=1.0
+# initial fractional abundance of POC component #2
+bg_par_bio_remin_POC_frac2=0.055
+# depth of remineralization or particulate organic matter
+bg_par_bio_remin_POC_eL1=589.9451
+# remineralization length #2 for POC
+bg_par_bio_remin_POC_eL2=1000000.0
+# initial fractional abundance of CaCO3 component #2
+bg_par_bio_remin_CaCO3_frac2=0.45
+# depth of remineralization or CaCO3
+bg_par_bio_remin_CaCO3_eL1=1.8905e+003
+# remineralization length #2 for CaCO3
+bg_par_bio_remin_CaCO3_eL2=1000000.0
+#
+# --- IRON ----------------------------------------------------------
+#
+bg_opt_geochem_Fe='hybrid'
+# aeolian Fe solubility
+bg_par_det_Fe_sol=0.002014275
+#exponent for aeolian Fe solubility [use 1.0 for uniform solubility]
+bg_par_det_Fe_sol_exp=0.500
+# modifier of the scavenging rate of dissolved Fe
+bg_par_scav_Fe_sf_POC=0.344104
+bg_par_scav_Fe_sf_CaCO3=0.000
+bg_par_scav_Fe_sf_opal=0.000
+bg_par_scav_Fe_sf_det=0.000
+# no scavenged regeneration
+bg_par_scav_fremin=0.0
+# return POFe
+bg_ctrl_bio_NO_fsedFe=.false.
+# Variable Fe:C
+bg_ctrl_bio_red_fixedFetoC=.false.
+# adjust pK'(FeL)
+bg_par_K_FeL_pP=11.0
+#(max) C/Fe organic matter ratio
+bg_par_bio_red_POFe_POC=250000.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- power
+bg_par_bio_FetoC_pP=-0.4225
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- scaling
+bg_par_bio_FetoC_K=103684.0
+#[FeT] dependent Fe:C ratio [Ridgwell, 2001] -- constant
+bg_par_bio_FetoC_C=0.0
+#
+# --- ECOGEM ----------------------------------------------------------
+#
+gm_ctrl_debug_init =0
+eg_ctrl_debug_eco_init=.false.
+
+eg_gkernel_cap=.false.
+eg_ctrl_grazing_explicit=.true.
+
+eg_ctrl_use_foramecogenie=.true.
+
+eg_par_ecogem_plankton_file='8P7Z4F.eco'
+eg_par_ecogem_grazing_file='FORAMECOGEM.zoo'
+eg_foram_symbiont_esd_scale=0.01
+eg_foram_auto_cost=0.04
+eg_foram_hetero_cost=0.35
+eg_foram_spine_scale=3.5
+
+#----------------- Nitrogen -------------------------
+eg_useNO3 =.false.
+eg_nquota =.false.
+#---------------- Phosphorus -----------------------
+eg_usePO4 =.true.
+eg_pquota =.true.
+#---------------- Iron -----------------------------
+eg_useFe =.true.
+eg_fquota =.true.
+#---------------- Chlorophyll -----------------------
+eg_chlquota =.true.
+#---------------- d13C ------------------------------
+eg_useDIC_13C =.true.
+
+# Tuned
+eg_qminP_a = 3.33e-3
+eg_qminFe_a = 1.00e-6
+eg_qmaxFe_a = 4.00e-6
+
+eg_ns = 2
+
+eg_respir_a = 0
+
+eg_beta_mort_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_mort_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_mort_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+eg_beta_graz_a = 0.8 # Maximum fraction to DOM as ESD --> zero
+eg_beta_graz_b = 0.4 # Minimum fraction to DOM as ESD --> infinity
+eg_beta_graz_c = 100.0 # Size at 50:50 partition (default = 100 µm^3)
+
+eg_par_bio_red_POC_CaCO3 = 0.0285 # underlying export CaCO3 as a proportion of particulate organic matter (i.e., CaCO3/POC)
+eg_par_bio_red_POC_CaCO3_pP = 0.7440 # exponent for modifier of CaCO3:POC export ratio
+
+eg_nsubtime =25
+eg_n_keco =1
+
+# disable ECOGEM restarts (as not currently coded up / used)
+eg_ctrl_ncrst=.false.
+eg_ctrl_continuing=.false.
+
+#
+# --- DATA SAVING -----------------------------------------------------
+#
+bg_par_data_save_level=10
+bg_ctrl_debug_lvl0=.true.
+ma_debug_loop=1
+bg_par_infile_slice_name='save_timeslice_historicalfuture_fakeSSP.dat'
+bg_par_infile_sig_name='save_timeseries_historicalfuture_FINE.dat'
+#
+# --- FORCINGS ------------------------------------------------------
+#
+# specify forcings
+bg_par_forcing_name="worlg4.RpCO2_Rp13CO2.FeMahowald2006.5000.4deg"
+bg_par_atm_force_scale_val_4=-6.5
+#
+# --- MISC ----------------------------------------------------------
+# starting year
+bg_par_misc_t_start=2022.0
+# kraus-turner mixed layer scheme on (1) or off (0)
+go_imld=1
+#
+# --- END -----------------------------------------------------------
diff --git a/genie-userconfigs/FORAMECOGEM/readme.txt b/genie-userconfigs/FORAMECOGEM/readme.txt
index 8bcf823d3..705ac18a5 100644
--- a/genie-userconfigs/FORAMECOGEM/readme.txt
+++ b/genie-userconfigs/FORAMECOGEM/readme.txt
@@ -38,42 +38,39 @@ EDITING LOG [list of changes made to this file, when, and by who]
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
SUMMARY OF EXPERIMENTS [summerize experiments detailed and in which e.g. figures they appear]
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-1. Last Glacial Maximum spin up
-2. Pre-industrial spin up
-3. Historical simulation (until 2022)
-4. Idealised future simulation (2100) with 1.5, 2, 3, 4 degree C warming
+1. Last Glacial Maximum spin up (Fig. 1), adapted from Odalen et al. 2022 with ECOGEM enabled
+2. Pre-industrial spin up (Fig. 1), same physical configuration as Ward et al. 2018 (ECOGEM 1.0)
+3. Historical transient simulation (until 2022) (Fig. 3), running based on preindustrial spinup
+4. Idealised future simulation (2100) with 1.5, 2, 3, 4 degree C warming (Fig. 3)
+Other important files:
+8P7Z4F.zoo: plankton functional type configuration
+FORAMECOGEM.zoo: the explicit trait parameters of foraminifera
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
RUNNING THE EXPERIMENTS [command lines, broken down in sub-sections for spinups, main experiments, SI, etc where appropriate]
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-# Model Runs
-## pre-industrial spinup (0-10000)
-
-```
+# Main experiments
+1. pre-industrial spinup (0-10000)
qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL FORAMECOGEM muffin.CBE.worlg4.BASESFeTDTL.SPIN 10000
-```
-
-## Historical (1765-2022)
-```sh
-qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL FORAMECOGEM muffin.CBE.worlg4.BASESFeTDTL.historical 257 muffin.CBE.worlg4.BASESFeTDTL.SPIN
-```
-## Future (2022-2100)
+2. Historical (1765-2022)
+qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL FORAMECOGEM muffin.CBE.worlg4.BASESFeTDTL.historical 257 muffin.CBE.worlg4.BASESFeTDTL.SPIN `
-```sh
+3. Future (2022-2100)
qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.worlg4.BASESFeTDTL FORAMECOGEM muffin.CBE.worlg4.BASESFeTDTL.2100.[XXX]deg 78 muffin.CBE.worlg4.BASESFeTDTL.historical
-```
-## LGM
-```sh
+4. LGM spin up
qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.GIteiiva.BASESFeTDTL_rb FORAMECOGEM muffin.CBE.GIteiiva.BASESFeTDTL_rb.SPIN 10000
-```
+# SI model runs
+1. LGM spinup with seasonal output: muffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal (same command of running as above)
+2. Future warming under different rates: muffin.CBE.worlg4.BASESFeTDTL.{2100, 3000, 4000, 5000}.4deg
+
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Note that all experiments are run from:
From 4cab453bf05995becfcdd5b6284659c6644a4677 Mon Sep 17 00:00:00 2001
From: "Rui Ying (Mac)" <38958822+ruiying-ocean@users.noreply.github.com>
Date: Sat, 6 Jul 2024 00:21:49 +0100
Subject: [PATCH 89/89] add update_flux in the revised manuscript
---
genie-userconfigs/FORAMECOGEM/readme.txt | 1 +
1 file changed, 1 insertion(+)
diff --git a/genie-userconfigs/FORAMECOGEM/readme.txt b/genie-userconfigs/FORAMECOGEM/readme.txt
index 705ac18a5..876b25b10 100644
--- a/genie-userconfigs/FORAMECOGEM/readme.txt
+++ b/genie-userconfigs/FORAMECOGEM/readme.txt
@@ -70,6 +70,7 @@ qsub -j y -o cgenie_log -V -S /bin/bash runmuffin.sh muffin.CBE.GIteiiva.BASESFe
# SI model runs
1. LGM spinup with seasonal output: muffin.CBE.GIteiiva.BASESFeTDTL_rb.seasonal (same command of running as above)
2. Future warming under different rates: muffin.CBE.worlg4.BASESFeTDTL.{2100, 3000, 4000, 5000}.4deg
+3. one might also reproduce the carbon uptake flux and calculate turnover time by adding 'eg_eco_uptake_fluxes=.true.'
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++