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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project follows a GNU standard version numbering of major.minor.patch with

  • major for substantial changes to code functionality,

  • minor for additions of modules and functionality, and

  • patch for technical changes and bugfixes without extending the functionality of the code.

  • if applicable, categories to include in the CHANGELOG.md are:

    • Added
    • Changed
    • Deprecated
    • Removed
    • Fixed
    • Security

[Unreleased]

[6.0.6] - 2026-03-25

Contributors

author: Stephen Wirth (wirth@pik-potsdam.de), Werner von Bloh (bloh@pik-potsdam.de) code review: Sibyll Schaphoff (sibylls@pik-potsdam.de), Christoph Müller (cmueller@pik-potsdam.de)

Added

  • DEBUG print statements for negative input to infiltration in daily_agriculture(), daily_agriculture_grass(), daily_agriculture_tree(), daily_biomass_grass(), daily_biomass_tree(), daily_woodplantation(), and daily_natural()
  • Missing regridding of climate data added to the regridlpj utility

Changed

  • Replace hardcoded Sphagnum_moss index (13) with strcmp(config->pftpar[p].name,"Sphagnum moss") in 5 landuse files
  • Fix PFT numbering comments in pft.cjson to reflect actual positions (1-14)
  • Updated biome_classification.c to use findpftname() instead of hard-coded macros
  • Removed macros from pftpar.h
  • Added missing PFTs to biome_classification.c
  • String comparison in landusechange_for_reservoir.c replaced by call to ispftinstand()
  • Default value of LPJINPATH set to /p/projects/lpjml/inputs/public_standard in configure.sh

Removed

  • Removed boreal broadleaved summergreen tree from needleleaved fpc sum in biome_classification.c
  • Removed daily_setaside.c which was unused

Fixed

  • Double accounting of irrigation water interception in daily_grassland.c
  • C balance error in deforest()
  • Balance checks in update_daily_cell(), grasslandreduction() and landusechange()
  • DEBUG print statement in restart2yaml.c
  • Sign error in daily carbon balance check in update_daily_cell(), daily_grassland(), and daily_agriculture() when methane is enabled: absorbed atmospheric CH4 oxidized within the same timestep was double-counted
  • Global water balance check in updatedaily_grid() now uses daily increments of annual flux accumulators and per-cell daily storage snapshots instead of annual _last storage fields, eliminating errors when starting from a restart file; reservoir irrigation buffer (dfout_irrigation_daily) now included in surface storage accounting
  • Misplaced printcell() corrected in update_monthly_grid.c causing SEGV if -DDEBUG is set
  • Correct number of cells written in JSON metafile in regridirrig
  • Error message corrected for nitrogen balance check in daily_natural.c to avoid SEGV without land use enabled
  • Missing fclose(file) added in getnsoilcode.c
  • Reading of landcovermap corrected in landcover.c

[6.0.5] - 2026-03-17

Contributors

Added

  • Base temp and hlimit values are read from crop PHU JSON or NetCDF file and compared to values read from the PFT JSON file. lpjml stops in case of different values.
  • Warning is printed if no JSON or NetCDF file is read for crop PHU input or file contains no "basetemp" or "hlimit" data.
  • Band names for mapping are read from JSON metafiles and NetCDF input files.
  • Globale attribute "title" is read from climate and land-use input files and checked for matching titles.
  • Global attribute "climate" is read for crop PHU and livestock density output and compared to title of climate input.
  • File magic added to support LPJmL clm and restart files for the file command. Content of the magic file has to copied to the ~/.magic file.
  • Arrays "hlimit" and "basetemp" copied from JSON metafile to NetCDF file in clm2cdf.
  • Option -drainage added to script regridlpj to regrid drainage, elevation, reservoir and neighbour irrigation file.
  • Options -metafile and -json added to regriddrain and regridirrig to use JSON metafiles for input and write JSON metafiles for output.
  • Support for float and double datatype added to readintdata_netcdf.c.

Changed

  • JSON metafiles instead of CLM files used in input.cjson for land-use, fertilizer, manure, sowing data and crop PHU input in order to read CFT maps.
  • JSON metafiles are read for climate input to get title.
  • Maps in lpjml_config.cjson are commented out. If defined they are used instead of the maps defined in the input files.
  • The global attributes in JSON metafiles are printed on separate lines.
  • If unit string is identical scaling is set to 1 for NetCDF files and udunits is not called.
  • Updated standard input data set to citable and publishable data sets (https://doi.org/10.5281/zenodo.19064225), making use of JSON file metadata where applicable.
  • The regridlpj utility uses now JSON metafiles for regridding the input data.
  • Population input for SPITFIRE can be read in units of total number or density, boolean type for "population" replaced by strings "no", "number" and "density".
  • Default map name changed to "map" in utility mathclm.

Fixed

  • Datatype Config is called by reference in filesexist() function to avoid pointer error in lpjcheck.
  • Typos in help text in regridclm.c corrected.
  • Unit for fertilizer and manure input fixed in filesexist.c.
  • opencoord() function fixed to set file format for metafiles correctly.
  • Check for successfull opening of second file corrected for metafiles in mathclm.c.
  • Header file support_pedotransfer_stub.h updated to allow successfull compilation of tests.

[6.0.4] - 2026-03-06

Contributors

Added

  • Added benchmark folder with R scripts (simulate_default.R, benchmark_default.R, benchmark_utils.R) to simulate default scenarios and run benchmarks.
  • Added support for separate methane/no_methane output configurations in benchmark scripts.
  • Option -check_balance added to configure.sh to enable balance checks on function level.

Changed

  • Argument -couple $(hostname) added to call of lpjml in slurm.jcf if -couple option is set for lpjsubmit.
  • Wait for coupled program to finish added in slurm script.
  • Fixed several potential floating point exceptions in nuptake_tree.c, nuptake_grass.c, nuptake_crop.c and littersom.c
  • Printing of balance error messages replaced by call to fail() in pedotransfer.c, allocation_grass.c, litter_update_grass.c, turnover_grass.c and update_annual_cell.c
  • Function fail.c changed to print "Program terminated unsucessfully" on new line.
  • Check balance error messages reformatted.
  • Fixed global water balance error in sowingcft.c and flux_sum.c.
  • Fixed FPE in allocation_grass.c.
  • Hard-coded error limits for balance checks in functions replaced by global parameter "carbon_fcn", "nitrogen_fcn, and "w_fcn".
  • Global balance check in updatedaily_grid.c only done if running on one task.
  • Compile flag -DNO_FAIL_BALANCE replaced by configuration flag "fail_on_balance" in lpjml_config.cjson.
  • "delta_year" keyword moved from input.cjson to lpjml_config.cjson.
  • Missing -DNO_METHANE flag added to lpjml_config_pnv.cjson.
  • Time step of "temp" output changed from daily to monthly.

Removed

  • Support for cloudiness and short wave only setting for climate input removed, only "radiation" and "radiation_lwdown" allowed.
  • Output "sun" and "sun_image" removed.
  • Unused files nooutput_gbw.c and update_monthly.c removed.
  • Unused array layer_exists in soil struct removed.

Fixed

  • Function openconfig.c corrected to avoid segmentation violation if lpjml/lpjcheck is called with -couple hostname option.
  • Changed nupsum==0 to nupsum<epsilon in nuptake_crop.c, nuptake_grass.c and nuptake_tree.c to avoid potential FPEs.
  • Function cutpfts.c corrected to close carbon balance.
  • Water balance check in infil_perc.c and annual_grass.c corrected to avoid false water balance errors.
  • Balance error messages corrected in cultivate.c.
  • Carbon balance closed in update_wetland.c.
  • Variable s renamed to sn in grasslandreduction() to avoid SEGV.
  • Misplaced reading of NO3 and NH4 depositions deleted in getclimate.c.
  • Check for negative vm added in photosynthesis.c to avoid nitrogen balance errors.
  • tillage() function changed to avoid carbon balance errors.
  • Utility regridclm corrected to avoid SEGV if file size does not match header.
  • Parameter "fburnt" in lpjparam.cjson is always read, was always zero if "luc_timber" was set to false.
  • Help text corrected in printclm.c.
  • Misplaced free(climate) causing double free corruption removed in initclimate.c.

[6.0.3] - 2026-02-23

Contributors

Added

  • Model can be run with monthly water use for household, industry and livestock which is available from Zenodo, reading in annual input is still possible.

Fixed

  • Pointers to IMAGE related data initialized to NULL in lpjprint.c.

[6.0.2] - 2026-01-17

Contributors

Added

  • Warning message added in lpjml, lpjcheck,cdf2soil, txt2grid and cdf2coord if cell size cannot be resolved by grid data in short format.
  • Function isfloatcoord() added in coord.c to check whether coordinate must be stored as a float variable, test function test_isfloatcoord.c added.
  • Test functions for vmaxlimit_tree, vmaxlimit_grass, vmaxlimit_crop, bisect, leftmostzero and getbufferavg functions added.

Changed

  • Error about first simulation year is less than first year of climate data replaced by warning in initclimate.c and filesexist.c.
  • First and last simulation year in spinup changed from 1901 to 1700 in lpjml_config.cjson.
  • Number of spinup years changed from 4000 to 3799 in lpjml_config.cjson in order to get bit-identical results.
  • Test files for unit test and shell scripts added to tar and zip file in Makefile.
  • First year of climate data set instead of first simulation year used in initsoiltemp.c.
  • Unused argument ncft removed from check_stand_fracs.c and update_wetland.c.
  • Redundant calculation of stand fraction sum removed in check_stand_fracs.c.

Removed

  • Unused source file src/lpj/part.c removed.

Fixed

  • Expected number of bands set correctly for raw input files in openinputdata.c.
  • Hard-coded filename test.lpj replaced by temporary filename in test_append.c, test_getnoread.c, test_indexarray.c, test_isdefined.c, test_isnull.c, test_restart.c, and test_writename.c in order to allow parallel execution of tests.
  • Arguments corrected in calls of lpjml functions in lpj_poem.c.
  • Missing -print_noread option added in INSTALL.
  • setupannual_grid.c corrected to compile with -DIMAGE -DCOUPLED flag.
  • Error message for different datatypes corrected in lpjcat.c.
  • Variables initialized to zero and NULL in phenology_gsi.c, lpjcat.c and restart2yaml.c to avoid warnings in gcc.
  • Man page for lpjml, lpjcheck, lpjrun, lpjfiles, json2restart and restart2yaml corrected.
  • Missing option -nooutput added to man page of lpjfiles.
  • Help text for -h option of lpjfiles, restart2yaml, printclm and regridclm corrected.
  • Check for NULL pointer for pfts array corrected in lpjcat.c.
  • Function fread() replaced by freadint() in regridirrig.c to account for different byte order.
  • Missing deallocation of items array added in sendhash.c.
  • Filename for population density input corrected in regridlpj.
  • Header files added for unit tests to compile tests successfully.
  • Function albedo_crop.c and fwritecell.c changed to compile with -DCOUPLING_WITH_FMS setting.
  • Misplaced check for NULL pointer for wind removed in dailyclimate.c, unnecessary check for NULL pointer for wind removed.
  • Missing delta_prec and delta_temp filenames added in fprintfiles.c.
  • Missing dependency on climate.h added to Makefile in src/landuse.
  • Double occurrence of "outputyear" removed in lpjml_config_pnv.cjson.

[6.0.1] - 2025-12-18

Contributors

Changed

  • Declaration of mixsoilenergy() moved from setaside.c to landuse.h.

Removed

  • Unused functions snow.old(), soiltemp() and related functions removed.
  • Setting without permafrost removed
  • Soil variables state[], alag, amp, and meanw1 removed.

[6.0.0] - 2025-11-25

Contributors

Added

  • extensive development for calculating methane and wetland dynamics (Schaphoff et al. in prep.), including:
    • calculation of the water table in infil_perc.c (merged infil_perc_rain.c and infil_perc_irr.c)
    • calculation of a dynamic wetland area in update_wetlands.c
    • extends soil pools by the oxygen pool
    • ground water pool added
    • calculates subdaily littersom.c
      • oxic decomposition depending on oxygen content
      • diffusion of methane and oxygen
      • methane production and oxidation added
      • nitrification depending on oxygen content
    • root respiration consumes oygen
    • new routines ebullition and plant_gas_transport.c
    • extensive restructuring of landusechange.c
    • new SETASIDE_WETLAND added, converted from wetlands to grow rice
    • rice always irrigated and assuming a levelled water table
    • introducing new, inundation insensitive, PFTs: tropical broadleaved evergreen tree floodtolerant, C3 graminoid flood tolerant, Sphagnum moss
    • new PFT parameters ist_m. idt_d, and alpha_e for inundation tolerance and ebullition suppression
    • new soil parameters psi_sat, b. efold. ctimax
    • configuration flag with_methane added to run LPJmL6 with or without methane and oxygen dynamics (original daily version of littersom is called)
    • reading new inputs slope_mean, slope_max, slope_min,kbf value,CH4 (atmospheric CH4 concentration), hydrotopes (CTI values),climate delta values (optional),icefrac (optional)
    • boolean flag "natNBP_only" defined to calculate NBP from natural vegetaton only
    • optional input for ice cover can be read by setting "with_glaciers" : true
    • optional reading in of climate anomalies for CLIMBER applications, enabled by setting "anomaly" : true.

Changed

  • CN_GC4_MX set to 42.71
  • K_LATOSA set to 4e3 for all trees
  • adjusted beta_root, resist, ligthextcoeff, gmin parameters
  • adjusted phenology parameters wscal base, tmax base

[5.10.2] - 2025-10-24

Contributors

Added

  • Option -with_timing added to configure.sh to enable timing, corresponding man page updated.
  • Flag -DUSE_TIMING enables now timing for several LPJmL functions for performance analysis.
  • Macros timing_start() and timing_stop() defined to allow timing of specific functions.

Changed

  • Flag -DUSE_TIMING removed from default compilation flags. Has to be enabled by ./configure.sh -with_timing.
  • Timing function for socket I/O are replaced by two separate items read_socket and write_socket.

Fixed

  • pft->fapar computation for maize in albedo_crop.c
  • albedo_green_leaves computation for crops in albedo_crop.c
  • pft->albedo, which is now a sum of albedo_green_leaves, albedo_brown_litter, and albedo_soil

[5.10.1] - 2025-09-30

Contributors

Added

  • Variable phen added to output in fprintpft.c.
  • Compile option NRECOVERY_COST added to INSTALL and man page of configure.sh.
  • Check for valid swc_bnf parameters added in fscanpftpar.c.
  • Wirth et al. (2024) article added to REFERENCES.
  • New parameter "tscal_b" added in lpjparam.cjson.
  • New virtual function getb() added to type Pft.

Changed

  • 2 boolean flags phen_to_one and rainyseason added to tree parameter. These are used in phenology_gsi.c instead of string compare with tree names.
  • Unused argument aet_layer removed from nitrogen_stress() function.
  • phi_bnf parameter calculated from swc_bnf parameter instead of reading from pft.cjson file in fscanpftpar.c.
  • Hard-coded parameter in temperature dependent calculation of b replaced by global parameter tscal_b.
  • Calculation of b in setupannual_grid.c replaced by call to new virtual PFT function getb().

Removed

  • Parameter phi_bnf removed from pft.cjson.
  • Variable b removed from restart file.
  • Unused macro RESTART_VERSION removed from header.h.

Fixed

  • Arguments of npp function corrected in daily_woodplantation.c. The current version leads to a too strong reduction in NPP.
  • nuptake_crop.c changed to compile with -DDEBUG_N option.
  • update_daily_cell.c changed to compile with -DDEBUG option.
  • daily_agriculture_tree.c changed to compile with -DDEBUG2 option.
  • Typo in error message in bstruct_writearrayindex.c corrected.
  • Error message corrected in bstruct_wopen.c.
  • Error number corrected in bstruct_finish.c.
  • Argument temp added to f_turnover_tree function to compile with -DNRECOVERY_COST option.

[5.10.0] - 2025-08-14

Contributors

Added

  • option to specify year after which deforestation is no longer feeding product pools but biomass is burnt instead: luc_burn_startyear (disabled)
  • option to specify costs for N recovery upon turnover (pre-compiler switch NRECOVERY_COST, disabled)

Changed

  • parameter changes:
    • alphaa from 0.5 to 0.7 for natural vegetation;
    • theta from 0.9 to 0.95;
    • fn_turnover PFT1: 0.5, PFT2: 0.5, PFT3: 0.7, PFT4: 0.3, PFT5: 0.3, PFT6: 0.7, PFT7: 0.3, PFT8: 0.3; updated values from Sophia et al. 2024 for all other PFTs except crops
    • cnratio_leaf.low/median/high for all PFTs updated from TRY data
    • b (ratio of dark respiration Rd to maximum photosynthetic capacity Vcmax) set to 0.031 for C3 and C4 plants (value for 25°C, from Wang et al. 2020, consistent with TRY data)
    • aphen_min from 60 to 90 and aphen_max from 245 to 180
    • nfixpot from 0.01 to 0.5 (middle of proposed range in Yu and Zhuang 2020)
    • turnover parameter for leaves&roots set to 2 for TeNE and 3 BoNE
    • temperature boundary between temperate and boreal zone changed from -2°C to -5°C
  • acclimation of b to mean vegetation period temperature (following Wang et al. 2020)
  • calculation of structural leaf N content (leaf N independent of Vcmax) based on ncleaf.low in both ndemand_xx and vmaxlimit_xx (was ncleaf.medium in ndemand_xx)
  • scaling of vmax with f_LAI removed
  • N recovery from turnover directly added to bm_inc.nitrogen
  • N uptake now separated for uptake of NH4 and NO3 with parameters from Craig et al. 2025 (median of values)
  • trees are burnt (instead of added to the litter) when running with luc_timber=FALSE
  • beginning of vegetative period for tropical raingreen trees set at beginning of 6 month period with highest precipitation sum
  • leaf shedding for deciduous trees induced after aphen_max or when phen<0.1 after aphen_min
  • phen permanently set to 1 for tropical evergreen trees

Fixed

  • corrected conversion of vmax in computation of N demand, which was incorrectly scaled with 24/daylength
  • corrected temperature sensitivity of N demand (k_temp changed from 0.02 to 0.0693)
  • corrected f_NCplant to comply with equation from Smith et al. 2014
  • corrected phenology of trees:
    • leaf turnover of raingreen trees at leaf shedding (same as for summergreen trees, had continuous daily leaf turnover like evergreen trees)
    • phen set to zero at leaf shedding until restart of phenological cycle to prevent phen>1 without leaf carbon

[5.9.28] - 2025-07-31

Contributors

Added

  • Option -h added to utilities addheader, cdf2bin, regridclm, regridsoil and printclm to print help text.
  • Notice added in configure.sh that make clean; make all has to be performed after change in configuration.
  • Support for short datatype added in cmpbin utility.
  • Shell script allbin2cdf added to convert all binary raw output files in a directory to NetCDF files.
  • Option -nounit added to bin2cdf to set unit if unit is defined in the metafile as an empty string.

Changed

  • If option -ncell 0 is used in addheader utility then the number of cells is calculated from the file size of the binary file.
  • Utilities grid2clm and cft2clm are replaced by alias to addheader.
  • File default.md converted from DOS to Linux format.
  • If scaling factor is set as an option in bin2cdf then this scaling factor is used instead that one defined in the JSON metafile.
  • Man pages updated.

Fixed

  • Missing free(axis->comment) added in freeaxis() to avoid memory leak.
  • Missing deallocation of list added in open_config.c.
  • Function nc_close() replaced by closeclimate_netcdf() in cdf2clm.c and cdf2bin.c to avoid memory leak.
  • Argument for error message corrected in getcellindex.c and getcountry.c.
  • Typo in man page of configure.sh fixed.
  • Comment for pft initialized in initsetting_netcdf.c.
  • Access to undefined pft_name.comment removed in bin2cdf.c to avoid SEGV.
  • Short data handled correctly for metafile input in bin2cdf.
  • Missing check for sum operator added in utility mathclm. Without this check number of bands in output file is always set to 1.
  • Man page for mathclm corrected for option -v.

[5.9.27] - 2025-07-15

Contributors

Added

  • Utility restart2yaml added to convert the new restart files into human readable YAML or JSON files.
  • Utility json2restart added to convert JSON files into restart files.
  • alias restart2json added for restart2yaml -json.
  • Output of time spent in reading and writing the restart file added.
  • Option -print_noread added to lpjml to print variable names not read from restart file.
  • Check added that PFT names in restart file match PFT names in LPJmL configuration file.
  • Unit tests added for bstruct library functions.

Changed

  • Restart file format changed to include metadata. A binary JSON-like structure has been implemented. The order of the objects read can be different from the order objects have been written, but performance of reading can be degraded.
  • Utility lpjcat updated to support the new restart file format.
  • Preprint's doi:10.5194/egusphere-2023-2946 changed to the final BNF paper doi:10.5194/gmd-17-7889-2024 in .zenodo.json.

[5.9.26] - 2025-07-14

Contributors

Changed

  • New functions setupannual_grid, initmonthly_grid(), updatedaily_grid() and updateannual_grid() defined to minimize lines of code in iterateyear.c and iterate.c and minimize duplicate code in lpj_poem.c.
  • Parts of code in iterateyear.c has been moved to update_daily_cell.c and update_monthly_grid.c.
  • lpj_climber4.c renamed to lpj_poem.c.
  • update_daily.c renamed to update_daily_cell.c.
  • update_monthly.c renamed to update_monthly_grid.c.
  • AFTER_STRESS debugging output in update_daily_cell.c (former updatedaily.c) moved after N update really happened.

Fixed

  • Macro isequilyear() has been defined for calling equilibration function in a consistent way (issue #375).

[5.9.25] - 2025-05-22

Contributors

Changed

  • Axis names and missing values for NetCDF output are read from JSON file netcdf.cjson instead of being hard coded.
  • Warnings in addheader replaced by terminating errors.
  • Function openinputfile() returns an error if cell size differs in JSON metafile.
  • Function openmetafile() returns an error if binary file is empty.
  • Output format for cell size updated in fprintheader.c, fprintoutputjson.c, fprintjson.c, and openinputfile.c.

Added

  • New utility splitclm added to copy specific bands from a clm file.
  • Environment variables LPJNOPP and LPJPEDANTIC added. If set to true, preprocessor is disabled and pedantic checking is enabled, respectively.
  • Info about --help option added in case of error in command line arguments.
  • Option -config added to cdf2clm, bin2cdf, country2cdf and clm2cdf in order to read axis names and missing values from a JSON file. File netcdf.json added as a template.
  • Option -json added to arr2clm, asc2clm, txt2grid, txt2clm, getcountry, and cdf2coord in order to create additional JSON metafiles.
  • Option -inpath added to regridlpj in order to set directory where data can be found.
  • Options -zero and -search added to regridlpj.
  • Option -double added to txt2grid in order to create grid files with coordinate values of type double.
  • Option -timestep added to addheader, txt2clm and bin2cdf.
  • Option sum, tsum and tmean to mathclm added.
  • Check for correct setting of nstep and nbands added in txt2clm.

Fixed

  • Misspelled -fsanitize=address option corrected in Makefile.mpich.
  • Missing free(cmd) added in fprintincludes.c.
  • Parsing of options corrected in fprintincludes.c.
  • Utility bin2cdf fixed for timestep>1.

[5.9.24] - 2025-05-15

Contributors

Added

  • Merge request template .gitlab/merge_request_templates/default.md that includes several checklists.

[5.9.23] - 2025-05-08

Contributors

Changed

  • Option -check of configure.sh enables now run-time checks of memory leaks and memory access out of bounds and undefined variables for gcc and icx compiler. Optimization is not disabled. Use options -debug -check to disable.
  • Datatype List used in fprintfiles.c.
  • All allocated memory is now freed in utilities.
  • Prescribed landcover input file changed in input.cjson to a file with the same number of natural PFTs.
  • All remaining unsafe calls to sprintf() replaced by calls to snprinf() or getsprinf().

Fixed

  • Check for missing values for integer input corrected in readclimate_netcdf.c.
  • Memory leak fixed in filesexist.c.
  • Calculation of global area fixed in printglobal.c.
  • Check for null attribute pointer added in fprintjson.c.
  • Uninitialized grid name initialized in mathclm.c.
  • Call to snprintf() replaced by getsprintf() in reservoir2cdf.c.
  • Datatype for index and writing the header corrected in lpjcat.c.
  • Functions for qsort(), bisect(), and leftmostzero() changed to avoid run-time errors with -check option.
  • Pointer set to NULL if k_estis NULL in initmanage.c.
  • Missing argument added in opening aquifer file for IMAGE.
  • Scaling of coordinates fixed in joingrid.c.
  • Fraction pointer initialized to NULL in freadresdata.c to avoid SEGV in lpjprint.c if reservoir data is read from restart file.
  • Index set correctly for outflow cells in regriddrain.c.
  • Check for maximum discharge length corrected in printdrain.c.
  • Number of years of clm file set to 1 in grid2clm.c.
  • Function fscanlandcovermap.c corrected (issue #48).
  • Access out of bounds for soil->freezdepth fixed in soiltemp.c.
  • Format specifier changed in cat2bsq.c and cutclm.c to compile without warnings using the clang compiler (issue #372).

[5.9.22] - 2025-03-14

Contributors

Changed

  • input_netcdf.cjson changed to the default dataset of input.cjson but in NetCDF format.
  • Code changed to compile under Windows OS.
  • New function getsprintf() added to allocate and print formatted output into string. Function replaces call to snprintf() function.
  • Default settings for GIT_HASH and GIT_REPO added.
  • Duplicate filenames removed from list of input/output filenames in utility lpjfiles.

Added

  • Option -int added to utility cdf2clm.
  • Option -latlon added to utility cdf2coord in order to change the order of the CLM grid file.
  • Utility cdf2reservoir added to convert NetCDF reservoir file into CLM file.
  • Utility reservoir2cdf added to convert CLM reservoir file into a NetCDF file using the soil code NetCDF file.
  • Macro NETCDF_INPUT added in lpjml_config.cjson to enable NetCDF input.
  • Reservoir, irrigation neighbor and drainage data can now be in NetCDF format:
"drainage" :           { "fmt" : "cdf", "var" : "index", "name" : "cru_netcdf/drainage.nc"},
"neighb_irrig" :       { "fmt" : "cdf", "var" : "index", "name" : "cru_netcdf/neighb_irrig.nc"},
"river" :              { "fmt" : "cdf", "var" : "riverlen", "name" : "cru_netcdf/drainage.nc"},
"reservoir" :          { "fmt" : "cdf", "var" : "year", "name" : "cru_netcdf/reservoir.nc"},
"capacity_reservoir" : { "fmt" : "cdf", "var" : "capacity", "name" : "cru_netcdf/reservoir.nc"},
"area_reservoir" :     { "fmt" : "cdf", "var" : "area", "name" : "cru_netcdf/reservoir.nc"},
"inst_cap_reservoir" : { "fmt" : "cdf", "var" : "inst_cap", "name" : "cru_netcdf/reservoir.nc"},
"height_reservoir" :   { "fmt" : "cdf", "var" : "height", "name" : "cru_netcdf/reservoir.nc"},
"purpose_reservoir" :  { "fmt" : "cdf", "var" : "purpose", "name" : "cru_netcdf/reservoir.nc"},

Fixed

  • River length is now correctly read in initdrain.c for data in NetCDF format.
  • Man page of cvrtclm corrected.
  • Missing check for open NetCDF file added to openclimate.c.

[5.9.21] - 2025-03-13

Contributors

Added

  • "coupled_host" and "coupled_port" added to LPJmL configuration to specify where the coupled model is running and which port is used for communication.

[5.9.20] - 2025-03-13

Contributors

Added

  • Check for correct number of time steps added in openclimate_netcdf.c.
  • Option timestep added to setclm.

Changed

  • Function freegrid() is calling freecell() to avoid redundant code.
  • References in man pages updated.
  • -v option of cdf2clm prints leap days setting for daily time step.
  • Missing file CHANGELOG.md added to tar and zip file.
  • Longitude and latitude boundaries excluded as variables in cdf2grid.
  • Ids for sowing date and crop PHU input added to couplerpar.h.
  • Length of GIT repository output limited in copyright.c.

Fixed

  • Memory leaks in utility lpjprint closed.
  • Handling of NaN as missing value corrected in reading NetCDF files.
  • Doubled initialization of standtype array corrected in lpj_clinber4.c.
  • Option type corrected in setclm.
  • Handling of different endianness corrected in setclm.
  • If version is changed with setclm only version is updated in the clm file.
  • Check that CO2 data is coming completely from socket corrected in readco2.c.
  • Number of years are now calculated correctly from number of days in case of leap days if number of leap days reaches 365.
  • Check for identical filenames corrected in cutclm.c.
  • Missing else added in readclimate().

[5.9.19] - 2025-03-12

Contributors

Added

  • Option -partition added to lpjsubmit script.

Changed

  • Man page of lpjsubmit refers only to slurm commands.
  • If icc compiler is found, this compiler is used.
  • enablefpc.c updated to compile under Mac OS.

Removed

  • Support for old PIK cluster removed.
  • Support for LoadLeveler batch queueing system removed.
  • Support for AIX OS removed.
  • Alias for lpjml and obsolete lpjml.sh removed in lpj_paths.sh.

[5.9.18] - 2025-01-31

Contributors

Fixed

  • basetemp and hlimit parameters fixed to fit to standard growing season inputs (issue #346).
  • laimax values corrected from 5 to 7 for temperate cereals, rice, and tropical cereals

[5.9.17] - 2025-01-29

Contributors

Added

  • Option -cmd added to lpjsubmit in order to execute a command before lpjml is called.
  • Command module list added to slurm script to show all loaded modules.

Removed

  • Obsolete #ifdef WITHOUT_NITROGEN check removed from pft.cjson.

Fixed

  • ALLOM3 parameter corrected to 4.0 for oil palm in pft.cjson (issue #369).
  • Missing break added in convert_water.c.

[5.9.16] - 2024-11-15

Contributors

Added

  • GIT repository and GIT hash printed in the LPJmL banner and in output of NetCDF and JSON files.
  • Options -repo and -hash added to lpjml to print GIT repository and hash.
  • The JSON file created by createconfig contains now name and hash of GIT repository.
  • Command lpjml -v prints GIT repository and hash.
  • Target hash added to Makefile to update hash after committing changes to the GIT repository.

Changed

  • LPJ_VERSION macro in lpj.h replaced by function getversion().

Removed

  • Obsolete header columns cereal and maize removed from fprintcountrypar.c.

Fixed

  • Missing dependency on getbuild.c for target lpjml added in src/Makefile.
  • xiar replaced by ar in Makefile.hpc2024 in order to compile with intel/oneAPI/2025.0.0.
  • Typos in error messages in filesexist.c and cdf2soil.cfixed.
  • Missing check for open file added to joingrid.c.

[5.9.15] - 2024-11-07

Contributors

Added

  • Option -scale added to bin2cdf in order to scale output.
  • Option -notime added to bin2cdf in order to omit time axis.
  • time_bnds, lat_bnds, and lon_bnds arrays added to NetCDF output for lpjml runs and the bin2cdf utility.
  • Check for identical output filenames added in fscanoutput.c.

Changed

  • If "with_days" is set to true in the lpjml configuration file, time axis of yearly output is also set in units of days instead of years.
  • Time in NetCDF output is always set in the middle between the lower and upper time boundaries.

Removed

  • Unused file cflux_sum.c removed.
  • Conversion of obsolete file manage.par removed from utility manage2js.

Fixed

  • Separate output for each year by setting "name" : "filename_%d" is now written correctly (issue #360).
  • Number of bands set to 1 in metafile of grid NetCDF output.
  • Name of longitude/latitude variables correctly derived in getlatlon_netcdf.c.
  • Misspelled option -netdcdf4 corrected to -netcdf4 in clm2cdf.c.
  • lpj_climber4.c updated to compile without errors.
  • Writing different variables into one NetCDF file fixed in create_netcdf.c. Only NetCDF outputs with one band and same time step can be written to one file.
  • Formatting of man pages corrected.
  • Missing shift 1 for -crumonthly case added in regridlpj.

[5.9.14] - 2024-09-30

Contributors

Fixed

  • pft->vscal not set to NDAYYEAR in update_annual.c. (issue #364).
  • freezefrac2soil.c corrected to avoid division by zero.
  • size of option array for sowing_date_option and crop_phu_option now correctly specified in fscanconfig.c.

[5.9.13] - 2024-09-26

Contributors

Changed

  • USE_NETCDF4 compile option replaced by "netcdf4" boolean flag in the LPJmL configuration file. If set compression of NetCDF4 files can be enabled and PFT names are written as strings instead of character arrays.
  • Formatting of man pages harmonized.
  • If lpjml is compiled without -DUSE_NETCDF flag then fscanconfig.c and fscanoutput.c return with an error for NetCDF files specified for input/output.

Added

  • Option -netcdf4 added to bin2cdf, clm2cdf, country2cdf, and drainage2cdf utility to enable NetCDF4 format.
  • Boolean flag "netcdf4" added to LPJmL configuration file in order to enable NetCDF4 format.
  • Option -compress added to drainage2cdf utility to enable file compression.
  • Man page for drainage2cdf added.
  • Check for valid compression value added for lpjml and utilities.
  • Missing option "global_netcdf" added to LPJmL config file.

Removed

  • Obsolete man page for writeregioncode() removed.

Fixed

  • Missing deallocation of memory added in cpl_init.c, fscanlandcovermap.c, fscanoutput.c, writearea.c, create_pft_netcdf.c, newgrid.c, fscanagtreemap.c, celldata.c in case of error.
  • Syntax error fixed in update_daily.c in IMAGE coupling.
  • Typo in README corrected.
  • establishmentpft.c, cdf2coord.c and cdf2grid.c modified to compile without warnings using gcc.
  • Debug flag in send_token_coupler.c and openoutput_coupler.c corrected to DEBUG_COUPLER.
  • Code changed to compile without errors/warnings for -DIMAGE -DCOUPLED setting.
  • Calculation of offsets and counts corrected in readintdata_netdf.c and missing loop over bands added.

[5.9.12] - 2024-09-24

Contributors

Added

  • added SLURM option --cpus-per-task=1 to lpjsubmit template bin/lpjsubmit_hpc to avoid that mpirun uses several CPUs per process

[5.9.11] - 2024-09-23

Contributors

Added

  • tree.fruit biomass is now explicitly handled in timber_harvest() and pools scaled accordingly in annual_woodplantation.c even though these are currently always zero anyways.

Fixed

  • added missing scaling of bm_inc.nitrogen after part of it was added to litter in harvest of wood plantations as in issue #358

[5.9.10] - 2024-09-23

Contributors

Removed

  • Option "no" for nitrogen setting removed, only "lim" and "unlim" allowed. Corresponding parameter files lpjparam_non.cjson and pft_non.cjson removed.
  • Removed commented-out code in allocation_tree.c

Fixed

  • Missing check for zero added in allocation_grass.c to avoid division by zero.

[5.9.9] - 2024-09-04

Contributors

Added

  • new options PRESCRIBED_SDATE_ALL_RAINFED and PRESCRIBED_SDATE_ALL_IRRIG to allow using the same sowing dates based on the rainfed or irrigated seasons respectively
  • new options PRESCRIBED_CROP_PHU_ALL_RAINFED and PRESCRIBED_CROP_PHU_ALL_IRRIG to allow using the same PHU requirements based on the rainfed or irrigated seasons respectively

Changed

  • refactored crop_option_restart to crop_phu_option_restart in struct Config and crop_option to crop_phu_option in struct Restartheader for greater clarity
  • refactored options "new" to "vbussel15" and "old" to "bondau07" for crop_phu_options where "vbussel15" is an implementation based on van Bussel et al. 2015

Removed

  • removed unnecessary check for file of prescribed sdates in fileexist.c

Fixed

  • fixed missing initialization of pointer map in cft2bin.c that caused abortion of compilation with -Werror otherwise

[5.9.8] - 2024-09-02

Contributors

Changed

  • included latest reference in .zenodo.json for syncing github and gitlab repositories. Future transfer of code between gitlab and github should be smoother now as both are at the same commit history now

[5.9.7] - 2024-08-30

Contributors

Changed

  • order of freezing of different water soil water components changed: free water freezes last to simply mathematical description of model

[5.9.6] - 2024-08-29

Contributors

Added

  • Utility cdf2grid added to convert grid files in NetCDF format into grid CLM files.
  • Option -json and -raw added to cdf2coord utility to write additional JSON metafile and to write without CLM header.

Changed

  • Check added that dimension must be greater 1 for variable in NetCDF file in cdf2coord.c, input_netcdf.c and coord_netcdf.c.
  • Datatype of longitude/latitude array in coord_netcdf.c changed from float to double for consistency, variable name correctly printed in error messages.
  • Intel and clang compiler recognized in printflags.c.

Fixed

  • Test for null corrected for "output" in fscanoutput.c.
  • Missing break added in switch statement in receiver_coupler.c.
  • Code changed to compile successfully without -DSAFE, -DUSE_NETCDF, and -DUDUNITS compilation flag.
  • Unit for "estab_storage_n" corrected to "gN/m2" in outputvars.cjson.
  • Scaling set to 1 if datatype is not short in cdf2coord.c and cdf2clm.

[5.9.5] - 2024-07-19

Contributors

Fixed

  • Fix a regression for NBP output in fwriteoutput introduced in version 5.9.4

[5.9.4] - 2024-07-18

Contributors

Added

  • Warning added if time step of output is longer than output interval.
  • Cycle length of spinup and number of spinup years checked for positive values in fscanconfig.c.
  • File size of CLM input files is checked for consistency with header and lpjml is stopped accordingly.
  • Utility drainage2cdf added to convert CLM drainage file into a NetCDF file using the soil code NetCDF file (issue #355).

Changed

  • Setting "const_lai_max" renamed to "laimax_const" for consistency.
  • Keyword "laimax_interpolate" renamed to "laimax_manage".
  • Region-specific fractions for residue burning replaced by global parameter "bifratio" and "fuelratio".
  • lpjml now terminates with an error message instead of a warning on invalid country codes to avoid invalid access to country-specific parameters.
  • Country code files can now have only one band. Files with 2 bands are still supported, but region code ignored.
  • Filename and source is written into configuration file created by regridlpj.
  • null allowed for "global_attrs", "inpath", "outpath", "restartpath", "output", and "checkpoint_filename" to disable the feature.

Removed

  • "laimax_interpolate", "firewood", "black_fallow", "till_fallow", "cropsheatfrost", and "grassland_fixed_pft" settings and corresponding code removed (issue #350).
  • Obsolete function daily_setaside.c removed. Function is not necessary any more for coupling to POEM.
  • Obsolete constants removed in conf.h.
  • Unused parameter "residue_rate", "residue_pool", "residue_cn", "residue_fbg" removed.
  • Functions for reading region-specific parameters removed.
  • Obsolete region parameter file manage_reg.cjson removed
  • Obsolete outputs "region", "flux_firewood", "flux_firewood_n" removed.
  • Region definitions removed from managepar.h.

Fixed

  • Typos in error messages corrected in bin2cdf.c and clm2cdf.c.
  • Output of turnover corrected in fprintpar_grass.c.
  • Output of options fixed in openconfig.c if environment variable LPJOPTIONS is set.
  • Calculation of average fixed in statclm.
  • res_remove calculation fixed for residue fires in harvest_crop.c to close carbon and nitrogen balance.
  • Missing update of FLUX_ESTABN_MG added in turnover_tree.c.
  • Function initdrain()corrected to handle river routing files in NetCDF format.

[5.9.3] - 2024-07-18

Contributors

Added

  • Output "nbp" for net biosphere productivity and "tws" for total water storage added.
  • fail added to mail type in lpjsubmit_hpc.
  • Option -map added to cdf2bin and cdf2clm to read map from NetCDF file and write it into JSON metafile.
  • "sim_name" and all other global attributes are written into JSON file for cdf2bin utility.

Fixed

  • Scaling of "littertemp" output fixed.
  • Unit corrected for "rootmoist" output and scaling corrected.
  • Correct number of output files printed in lpjfiles utility if separate output files for each year are enabled.

Changed

  • DEPTH_NAME and BNDS_NAME excluded for search for variable in NetCDF file if no variable name is provided.
  • Check added that dimension must be greater 1 for variable in NetCDF file.

[5.9.2] - 2024-07-18

Contributors

Added

  • fire_grass burns grass leaf biomass based on fire resistence parameter (function did nothing before)
  • Burning of fruits added to fire_tree, although stands with fruit trees currently do not experience fire

Changed

  • Unit and description of FIREF output changed from fire return interval to fire fraction to harmonize output between GlobFirM and SpitFire

Fixed

  • Added missing update of FPCs after fire before establishment

[5.9.1] - 2024-07-11

Contributors

Added

  • Missing regridding of wateruse and livestock density input added in regridlpj.

Changed

  • Compile option -Werror added to stop compilation of icx/gcc after warning. This feature can be disabled by using the -noerror option of configure.sh.
  • Filename and source is written into configuration file created by regridlpj.
  • All missing output indices are printed in case that the "outputvar" array is too short.

Fixed

  • Incorrect scaling removed in utility printharvest.
  • Uninitialized PFT pointer set to first PFT in harvest_stand.c.
  • Uninitialized variable n_attr set to zero in utility printclm.
  • Prescribed land cover is now read correctly if landcover map size differs from number of natural PFTs.
  • Check for land use type WP corrected in landusechange.c (issue #354).
  • Code fixed to remove all warnings if compiled with icx/gcc.
  • regridclm now used for regridding of soil file in regridlpj.
  • Missing seek to offset added in filesexist.c
  • Misplaced deallocation of memory for unit corrected in printclm.

[5.9.0] - 2024-07-08

Contributors

Added

  • Added GPL_HEAT macro to change number of gridpoints per soil layer used for heat convection.
  • Added percolation_heattransfer switch to disable convection/percolation heattransfer.
  • Added littertemp output variable for litter temperature.
  • Added fast implicit crank nicolson heat conduction scheme for non-phase change conditions apply_heatconduction_of_a_day.c.

Changed

  • Replaced soiltemp soil temperature and snow and litter heat conduction routines with update_soil_thermal_state.c; soiltemp remains in the repository for POEM/FMS coupling.
  • Use enthalpy (thermal energy) as state variable for soil thermal regime instead of temperature.
  • Numeric heat conduction method is a finite element enthalpy scheme apply_heatconduction_of_a_day.c.
  • Numeric heat convection method is improved by closing the energy balance for water infil and percolation.
  • Conduction through snow and litter cover is now part of the numerical method for the soil.
  • Snow and litter temperatures are now calculated by interpolating air and top gridpoint temperature.
  • Snow melt by snow temperature greater than 0 deg is removed.
  • Litter heat insulation is now based on literature values for litter thermal conductivity.

[5.8.17] - 2024-06-14

Contributors

Added

  • List of required modules on new PIK cluster added in INSTALL.
  • configure.sh script recognizes new PIK cluster and sets mpiicx/icx compiler accordingly.
  • New site-specific Makefile.hpc2024 and Makefile.icx for parallel/sequential compilation on new cluster added.
  • New lpjsubmit_hpc slurm script added for new PIK cluster. configure.sh sets symbolic link of lpjsubmit to this script.

Changed

  • All occurrences of the deprecated function MPI_Type_extent replaced by MPI_Type_get_extent to allow compilation with OpenMPI.
  • *.tmp files added to .gitignore.

Fixed

  • Functions mpi_write.c, mpi_write_txt.c, mpi_read_socket.c and mpi_write_socket.c changed to avoid SEGV on new PIK cluster.

[5.8.16] - 2024-06-07

Contributors

Changed

  • .zenodo.org updated to be compliant with PIK publication rules:
    • added "active-development" and "Potsdam Institute for Climate Impact Research" to keywords
    • added Christoph as "contributor", which seems to be the only way to have a visible contact person

[5.8.15] - 2024-05-30

Contributors

Added

  • A preprocessed JSON configuration file can be written if the following setting is added to the *.cjson configuration file:
"json_config_filename" : "output/lpjml_config_restart.json", /* Filename of preprocessed configuration file written or null to disable this feature */

Fixed

  • The right allocated storage for config->coupled_model is checked for NULL in fscanconfig.c.

[5.8.14] - 2024-05-27

Contributors

Fixed

  • fixed PFT pool scaling in mix_veg_grass() and mix_veg_tree()

[5.8.13] - 2024-05-23

Contributors

Changed

  • PFT parameter lai_sapl has been set back to its original value of 0.001 for grasses (tropical, temperate, polar)

[5.8.12] - 2024-05-07

Contributors

Added

  • added link to LPJmL Zenodo archive to README

Changed

  • changed ifndef usage in lpjml_config.cjson to ifdef to avoid confusion

Fixed

  • fixed handling of monthly and daily outputs in iterateyear.c to ensure that last annual timestep of outputs is written after update_annual() is called

[5.8.11] - 2024-04-10

Contributors

Added

  • added four new outputs for managed land: deposition (NDEPO_MG), biological nitrogen fixation (BNF_MG), applied nitrogen (NAPPLIED_MG) and nitrogen establishment flux (FLUX_ESTABN_MG)

[5.8.10] - 2024-04-04

Contributors

Changed

  • In outputvars.cjson, the variable field for output grid has been changed back to "grid" (instead of "soil"). If NetCDF output is written the variable name would be cell id, if raw output is written the variable name would be the coordinates. "grid" is used as generic naming here, long_name is used to describe this exception ("grid information (raw: coordinates, cdf: cell_id)")

[5.8.9] - 2024-03-14

Contributors

Changed

  • NetCDF output files are now in a more ISIMIP3 compliant format, datatype of time, lat, and lon is now double, depth_bnds added to layer specific output. Standard and long name can be specified in outputvars.json.
  • Deprecated function MPI_Extent replaced by MPI_Get_extent in mpi_write.c.
  • Functions create_netcdf.c/create_pft_netcdf.c and create1_netcdf.c/create1_pft_netcdf.c have been merged.
  • Function findcoord() improved to find cell indices, returns now true if coord is within cell.
  • STYLESHEET file converted to markup.
  • Cell size in regridclm is set to cell size of target grid, warning is printed if cell size differs.
  • Format and suffix of output files have been removed in lpjml_config.cjson and are now set by "default_fmt" and "default_suffix":
{ "id" : "npp", "file" : { "name" : "output/mnpp"}},
  • LPJINPATH set to /p/projects/lpjml/input/historical in regridlpj if not defined.
  • "descr" in outputvars.cjson renamed to "long_name".

Added

  • More options added to lpjml_config.cjson to customize format of output:
  "default_fmt" : "raw",     /* default format for output files: "raw","txt","cdf","clm","sock" */
  "default_suffix" : ".bin", /* default file suffix for output files */
  "grid_type" : "short",     /* set datatype of grid file ("short", "float", "double") */
  "flush_output" : false,    /* flush output to file every time step */
  "absyear" : false,         /* absolute years instead of years relative to baseyear (true/false) */
  "rev_lat" : false,         /* reverse order of latitudes in NetCDF output (true/false) */
  "with_days" : true,        /* use days as units for monthly output in NetCDF files */
  "nofill" : false,          /* do not fill NetCDF files at creation (true/false) */
  "baseyear" : 1901,         /* base year for output in NetCDF files */
  • Global attributes for NetCDF output files can be set in the lpjml_config.cjson file:
 "global_attrs" : {"institution" : "Potsdam Institute for Climate Impact Research",
                    "contact" : "", /* name and email address */
                    /* any name and string value can be added: "name" : "value", */
                    "comment" : ""  /* additional comments */
                   }, /* Global attributes for NetCDF output files */
  • "standard_name" for output can be set in outputvars.cjson. If not defined standard name is set to variable name.
  • Chunking defined for NetCDF files if compiled with -DUSE_NETCDF4.
  • Option -metafile added to regridclm and binsum. If metafile contains name of grid file, the filename of the source grid can be omitted:
regridclm -metafile grid_new.clm temp.clm.json temp_new.clm
binsum -metafile mnpp.bin.json anpp.bin
  • NetCDF files can be created with bin2cdf and clm2cdf from the JSON metafiles containing all global attributes:
bin2cdf -metafile soilc_layer.bin.json soilc_layer.nc
clm2cdf -metafile temp.clm.json temp.nc
  • "landcovermap" added to define mapping of the prescribed FPC input to PFTs.
  • -hostfile option added to lpjrun.
  • New utilities added:
    • cmpbin - compares binary ouput files
    • statclm - prints minimum, maximum and average of clm files
    • regriddrain - regrids drainage file to new grid
  • Option -metafile and -f added to mathclm.
  • cdf2clm stores all global attributes of NetCDF file in JSON metafile if -json option is set.
  • Option -nopp added to lpjml. This option disables preprocessing of the config file by cpp.
  • Option -ofiles added to lpjml and lpjcheck to print list of all available output files.
  • Option -pedantic added to lpjcheck and lpjml to stop on warning.
  • Option -json added to regridclm and regridsoil utilities to create additional JSON metafiles.
  • Compile flag -DSTRICT_JSON added to enable more strict syntax checking of JSON files.
  • Remark message in fscankeywords.c added if number instead of string is used in JSON file.

Fixed

  • Missing deallocation added in freeconfig.c and memory leak in fscanpftpar.c fixed.
  • Missing argument after option handling fixed in cdf2bin and countr2cdf.
  • Missing $dir/ added to manure data in regridlpj.
  • Correct default landuse, sowing data and crop PHU file set in regridlpj.

[5.8.8] - 2024-03-07

Contributors

Fixed

  • missing family names added in CITATION.cff

Changed

  • renamed double_harvest.c to separate_harvests.c and update_double_harvest.c to update_separate_harvests.c and changed entries in Makefiles accordingly
  • renamed functions double_harvest() to separate_harvests() and update_double_harvest() to update_separate_harvests() throughout the code
  • renamed the struct Double_harvest to Separate_harvest and the variable of type Separate_harvest in struct Pftcrop from dh to sh
  • renamed double_harvest flag in struct Config to separate_harvests

[5.8.7] - 2024-03-06

Contributors

Added

  • new output PFT_WATER_SUPPLY to calculate water stress PFT-specific.

Changed

  • output writing for the new output (conf.h , outputvar.cjson , createpftnames.c , fwriteoutput.c , outputsize.c , water_stressed.c).
  • isopen() call removed (fwriteoutput.c).

[5.8.6] - 2024-02-29

Fixed

  • Divsion by zero avoided for calculation of nc_ratio in ndemand_tree.c and ndemand_grass.c (issue #341).
  • Default directory for input files to current directory set and directory created in regridlpj.
  • Correct id 11 set for "tamp" input in input.cjson (issue #347).
  • Correct filename used in error message in utility mathclm.
  • Datatype of Version 4 CLM files correctly handled in cutclm, catclm, mergeclm, regridclm.

Changed

  • Hard coded CFT indices (e.g. MAIZE) have been replaced by their names.
  • Datatype of bmgr_harvest_day_nh and bmgr_harvest_day_nh changed to int.
  • Function freadseed() used in freadrestartheader.c.
  • First value of CO2 data file used for simulation years before first year of CO2 data.
  • CO2 data replaced by TRENDY data in input.cjson.

Added

  • Man page for regridclm and regridsoil added.
  • New keywords "cft_fertday_temp" and "cft_fertday_tropic" added in lpjparam.cjsonto specify the CFT names where the fertilizer application dates are taken from for grasslands.
  • Missing filename of tillage input added to lpjfiles utility.
  • Option -h added to lpjsubmit. Options -v and -l added to configure.sh.
  • New keyword "error_limits" defined in lpjparam.cjson to set maximum balance errors allowed in simulation:
 "error_limits" :
    {
      "carbon" : 1.0,       /* maximum error in local carbon balance (gC/m2) */
      "nitrogen" : 0.2,     /* maximum error in local nitrogen balance (gN/m2) */
      "water_local" : 1.5,  /* maximum error in local water balance (mm) */
      "water_global" : 1e-3 /* maximum error in global water balance (mm) */
    },

Removed

  • Option --propagate removed from srun in lpjsubmit_slurm.
  • Hard-coded parameter k_l removed in littersom.c.
  • Parameter "residues_in_soil_notillage" removed.
  • Parameter "co2_p" removed.
  • Keyword in "till_startyear" removed from lpjml_config.cjson.

[5.8.5] - 2024-01-31

Contributors

Added

  • added .zenodo.json for interaction with zenodo archives
  • added CITATION.cff file

Changed

  • updated AUTHORS file

[5.8.4] - 2024-01-22

Contributors

Fixed:

  • Removed lines 240 and 241 in landuse/annual_biomass_tree.c to get rid of the carbon balance error, which shows up in cells with significant bioenergy tree fractions in the landuse input.

[5.8.3] - 2024-01-21

Contributors

Added

  • allowed range for coordinates checked in readcoord().
  • allowed formats ("raw", "clm", "clm2") for input files checked in openmetafile().
  • Output scaling added to writearea.c.

Changed

  • Error messages changed for more clarity.

Fixed

  • NetCDF output for grid file corrected if cells are skipped.
  • var_len correctly set for input with no time axis in openclimate_netcdf.c.

[5.8.2] - 2023-12-21

Contributors

Changed

  • wateruse from "yes" to "all"
  • sowing_date_option from "fixed_sdate" to "prescribed_sdate"
  • crop_phu_option from "new" to "prescribed"
  • tillage_type from "all" to "read"
  • residue_treatment from "fixed_residue_remove" to "read_residue_data"
  • grazing from "default" to "livestock"
  • prescribe_lsuha from FALSE to TRUE
  • set nspinup to 420 instead of 390 for LU spinup
  • updated paths to land management input files in input.cjson
  • set all available LandInG1.0 inputs as the default option

[5.8.1] - 2023-12-11

Contributors

Added

  • tmin, tmax, humid GSWP3-W5E5 inputs added to input.cjson.
  • missing parameters added in lpjparam_non.cjson and pft_non.cjson.

Changed

  • set gml.noaa data as default CO2 input.
  • GSWP3-W5E5 climate is now the default.
  • regridlpj utility script updated for new inputs

Removed

  • GLDAS climate input removed.

Fixed

  • scaling fixed for daily output and unit 1/second in fwriteoutput.c (issue #332).
  • #ifdef and #elif statements fixed in lpjml_config.cjson and input.cjson.
  • computation of root biomass based on carbon fixed in nuptake_grass and nuptake_tree (issue #330)
  • fixed bug in allocation_tree (issue #330)

[5.8.0] - 2023-11-30

Contributors

Added

  • new keyword "cultivation_types" added to specify an array of cultivation types read from the pft.cjson file:
  "cultivation_types" : ["none","biomass","annual crop"],
  • wood plantation and agricultural tree PFTs added to pft.cjson.
  • '"k_est"' establishment density array added for agricultural trees to "countrypar" in manage_irrig_systems_with_dummy_laimax_data.cjson.
  • Makros to select different climate (CRU_MONTHLY, CRU_NETCDF, GLDAS) as well as land use, fertilizer and manure (OLD_LU, MADRAT) inputs added to input.cjson.
  • Makro to disable nitrogen cycle (WITHOUT_NITROGEN) added to lpjml_config.cjson.
  • Makros definition and description added to lpjml_config.cjson.

Changed

  • file ending from js to cjson.
  • renamed lpjml.cjson to lpjml_config.cjson.
  • extended input.cjson to include CRU, GSWP3-W5E5 and GLDAS climate inputs and LandInG, MADRAT and "Old" land use, fertilizer and manure inputs.
  • Moved mappings from input.cjson to lpjml_config.cjson.
  • Moved soil depths array and fuel bulk density factors from soil.cjson to lpjparam.cjson.

Removed

  • lpjml_*js, param_*js, lpjparam_*js, pft_*.js, input_*.js and manage_*.js files for specific projects.

[5.7.10] - 2023-11-13

Contributors

Added

  • name of grid file and "terr_area" output file written to output JSON files. A link to the corresponding JSON file is added.
  • list of utilities added to INSTALL file.
  • -json flag added to cdf2clm utility.
  • last year of CO2 data is checked at run time and last year of simulation is changed accordingly.

Changed

  • fscanfloat() accepts now also integer input.

Removed

  • obsolete constant definitions in conf.h.

Fixed

  • opening of grid file in JSON metafile format fixed in opencoord().
  • default soil map is set for soil data in NetCDF format.
  • missing carbon influx added to NBP calculation in flux_sum.c.

[5.7.9] - 2023-10-23

Contributors

Changed

  • constant wood density has been replaced by PFT-specific parameter "wood_density".

Removed

  • Unused flag "biomass_grass_harvest" removed from configuration.

Fixed

  • update of pft->establish.nitrogen corrected in turnover_tree.c.
  • C and N in manure from grazing livestock goes to litter (as described in Heinke et al. 2023 instead of going to soil pools directly.

[5.7.8] - 2023-09-22

Contributors

Fixed

  • bug in landusechange.c where land transfers between rainfed and irrigated setaside stands were not taken into account when determining rainfed and irrigated areas to deforest/regrow
  • false positive carbon balance errors in turnover_tree.c if the code is compiled with CHECK_BALANCE switch

[5.7.7] - 2023-09-20

Contributors

Added

  • grassland specific variables deficit_lsu_ne and deficit_lsu_mp added to fprint_grassland.c and therefore are printed by lpjprint.

Removed

  • obsolete definition of constants removed in conf.h.

Fixed

  • division by zero resulting in a floating point exception if lpjml is run with -fpe option fixed in littersom.c and harvest_stand.c.
  • index in "cft_nir" output is now correctly calculated for agriculture_tree/agrculture_grass stands in distribute_water.c.
  • pft->npp_bnf set to zero for the auto fertilization setting in the N uptake functions. Fertilization only applied if N deficit is greater than zero.

[5.7.6] - 2023-09-11

Added

  • reallocation of N added in allometry_tree.c if tree height exceeds the maximum height.
  • reproduction costs for nitrogen added to turnover_tree.c.
  • missing output "harvestc_agr" updated and written to file.

Changed

  • check for sum>1 for warnings has been replaced by sum>1+epsilon in getlanduse().
  • ml.landfrac scaling of output has been replaced by acual stand fraction.
  • output_gbw_* functions have been merged into one output_gbw function.

Removed

  • misplaced CFT_AIRRIG update has been removed from daily_woodplantation.c.

Fixed

  • missing #include "grass.h" added in sowingcft.c.
  • arguments of setaside calls in annual_woodplantation.c and annual_biomass_tree.c have been corrected.
  • update of LITFALLN corrected in timber_burn.c.
  • output written to correct N2O_DENIT_* file in denitrification.c.
  • missing reservoirfrac added to scaling for outputs in daily_agriculture_grass.c and daily_agriculture_tree.c.

[5.7.5] - 2023-08-23

Added

  • outputs:
    • IRRIG_STOR
    • RIVERVOL
    • SWC_VOL

Changed:

  • unit of output RES_STORAGE changed from hm3 to dm3 to be in line with IRRIG_STOR, RIVERVOL, LAKEVOL, SWC_VOL

Fixed

  • check for land-use fractions to not exceed 100% after scaling with landfrac, re-scale to 100%, print warning see !173
  • add turnover before allocation in cultcftstand to prevent sporadic C balance errors when running with intercrops, see!175
  • number of wet days not read if daily precipitation input is used. A warning is additionally printed to set "random_prec" to false.
  • boolean "river_routing" is read before "with_lakes" flag to avoid uninitialized variable.

[5.7.4] - 2023-08-17

Changed

  • changed quadratic soil evaporation function to sigmoid form and a minimum amount of evaporation of 5% of the available energy, following Sun et al. 2013, as described in !168

[5.7.3] - 2023-08-16

Fixed

  • correct accounting of blue water transpiration on agriculture stands in outputs
  • missing variable initialization for bioenergy grass
  • landuse change from irrigated to rainfed setaside moved area to wrong target setaside

[5.7.2] - 2023-08-11

Changed:

  • removed timestep attributes (monthly/annual) in all output descriptions that are not timestep specific

Added

  • outputs:
    • PFT_WATER_DEMAND: PFT specific water demand
    • RD: dark respiration
    • NDEPOS: total N deposition as sum of NH4 and NO3 deposition

[5.7.1] - 2023-08-10

Fixed

  • wrong use of &f instead of f, in fscanparam.c. Bug was introduced in version 5.6.26 and caused that parameter files could not be read properly

[5.7.0] - 2023-08-10

Added

  • land fraction can now be read from file, with a new flag "landfrac_from_file" and a new input "landfrac"
  • If setting "landfrac_from_file : true" cell areas in LPJmL are scaled down by land fraction from input file. If land fraction is zero, land fraction is set to minlandfrac and a warning is printed.
  • new flag "with_lakes" defined
  • new outputs "terr_area", "land_area" and "lake_area" defined writing the terrestrial area (land and lakes), land area and lake area of each cell
  • new parameters "minlandfrac" and "tinyfrac" added to lpjparams.js
  • option -area filename added to the printglobal utility to scale with the cell areas read from the file specified.

Changed

  • Lake fraction and land-use fractions are rescaled by the reciprocal of land fraction. If lake fraction is greater than one, lake fraction is set to one and a warning is printed.
  • Lakes can be enabled without river routing by setting "with_lakes" : true. Variable dmass_lake is always written to restart file.
  • lake fraction is read in utility lpjprint and printed
  • flag "shuffle_spinup_climate" only read if "nspinup" is non-zero.
  • Terrestrial area and harvest fraction are read in utility printharvest. Output format changed to CSV.

[5.6.27] - 2023-08-08

Removed

  • removed large chunks of code in allocation_daily_crop.c that was inactive

Fixed

  • fixed output PFT_VEGC to not include bm_inc.nitrogen for crops in daily_agriculture.c
  • fixed global flux summation for flux.soil.carbon and flux.soil.nitrogen (+= instead of =), bug was introduced in version 5.6.25

[5.6.26] - 2023-08-07

changed

  • avoid daily leaf turnover for biomass grass and harvest leaf turnover as dead biomass at harvest event instead (reduces litter and increases harvest)
  • introduce harvest dates depending on green/brown harvest instead of C threshold for biomass grass
  • literature-based C/N ratios and fn_turnover for biomass grass depending on green/brown harvest configuration
  • results and literature references can be found in issue #275.

Added

  • introduced #define flag to change from green harvest (default) to brown harvest: #define BMGR_BROWN
  • two options include green harvest (fresh biomass, high N content - usually used for biofuels) and brown harvest (dry biomass, high lignin content, low N content - usually used for combustion)
  • brown harvest uses later harvest dates (defined in lpjparam.js) and higher N recovery (as lower fn_turnover defined in pft.js) than green harvest
  • the #define flag is required to read the correct flag-specific parameter from the lpjparam.js and pft.js, see issue #311

[5.6.25] - 2023-07-29

Added

  • New outputs added for N fluxes from timber extraction and for N pools in wood product pools
  • New outputs added for estab_storage C and N
  • Added missing N fluxes, estab_storage, and reservoirs to globalflux output
  • Added new fluxes to man pages

Fixed

  • Corrected/added units in comments in output.h
  • Corrected units in flux_sum man page
  • Corrected N2O_DENIT output, which now no longer also includes N2O_NIT values
  • Corrected writing of mineral N pools to outputs, so that also mineral N in frozen soil layers is included
  • Corrected writing of VEGN for crops, so that bm_inc.nitrogen is no longer included to avoid double accounting

Removed

  • Removed unecessary initialization of output variables to zero in update_annual.c, which is done in initoutputdata.c

[5.6.24] - 2023-07-29

Fixed

  • The number of bands is now correctly checked for the read_residue_data input.

[5.6.23] - 2023-07-28

Changed

  • Instead of the soil code the index of the grid cell is written into the NetCDF file for "grid" output.

[5.6.22] - 2023-07-27

Changed

  • Configuration files lpjml_netcdf.js, lpjml_non.js, param_non.js, and lpjparam_non.js updated to latest lpjml version.

Removed

  • Predefined daily outputs ("d_lai"-"d_pet") and corresponding functions removed.

  • Version numbers removed from man pages.

Fixed

  • Variable issocket always initialized to FALSE in readfilename.c.

[5.6.21] - 2023-07-21

Changed

  • Flag "nitrogen_coupled" disabled for lpjml offline runs. Water stress is always coupled with nitrogen stress. Only if lpjml is compiled with -DCOUPLING_WITH_FMS flag is enabled.

  • Flag "new_trf" renamed to "transp_suction_fcn".

[5.6.20] - 2023-07-13

Added

  • New flags "fix_co2" and "fix_co2_year" added.

Changed

  • Flag "istimber" renamed to "luc_timber".

  • Flag "new_phenology" renamed to "gsi_phenology".

  • Flag "shuffle_climate" renamed to "shuffle_spinup_climate".

  • The settings for fixed input data have been updated. For climate and N deposition input an interval can be specified from which data is taken after the specified year. In can specified whether random shuffling or cycling is used:

"fix_climate" : false,                /* fix climate after specified year */
"fix_climate_year" : 1901,            /* year after climate is fixed */
"fix_climate_interval" : [1901,1930],
"fix_climate_shuffle" : true,          /* randomly shuffle climate in the interval */
"fix_deposition_with_climate" : false, /* fix N deposition same as climate */
"fix_deposition" : false,              /* fix N deposition after specified year */
"fix_deposition_year" : 1901,          /* year after deposition is fixed */
"fix_deposition_interval" : [1901,1930],
"fix_deposition_shuffle" : true,       /* randomly shuffle depositions in the interval */
"fix_landuse" : false,                 /* fix land use after specfied year */
"fix_landuse_year" : 1901,             /* year after land use is fixed */
"fix_co2" : false,                     /* fix atmospheric CO2  after specfied year */
"fix_co2_year" : 1901,                 /* year after CO2 is fixed */

Removed

  • Obsolete flag "const_climate" removed.

[5.6.19] - 2023-07-06

Added

  • Help option -h added to bin2cdf and clm2cdf utility.

  • Target lpjcheck added to Makefile to create only the lpjcheck utility.

Changed

  • The version of all man pages has been set to the LPJmL version number, date of last modification removed.

  • The different versions of the utilities have been replaced by a reference to the LPJmL version.

Removed

  • All html files have been removed from the repository.

  • Obsolete link lpj to lpjml removed.

[5.6.18] - 2023-07-04

Fixed

  • Soil array wpwp is now correctly initialized with soilpar->wpwp for the "prescribed_soilpar" setting.

[5.6.17] - 2023-06-30

Fixed

  • Replaced logical or by logical and in survive.c. This solves issue #309.

[5.6.16] - 2023-06-30

Fixed

  • Removed excess pft->nind in all harvest routines in harvest_stand.c.

[5.6.15] - 2023-06-30

Added

  • Check for matching size of discharge queues read from restart file added to initriver() function in initdrain.c. If the size differs from the value calculated from the river lengths the queues will be resized and initialized to zero. Error message is additionally printed.

[5.6.14] - 2023-06-08

Removed

  • Support for the deprecated *.conf configuration file format has been removed. Only JSON files are allowed for configuration files and metafiles for input.

  • Man pages for the description of the *.conf file format removed.

Changed

  • Strings in JSON configuration files can now be longer than 256 characters.

[5.6.13] - 2023-05-16

Added

  • Missing update of "harvestc" and "harvestn" output added in annual_biomass_tree.c, annual_woodplantation.c, daily_agriculture_tree.c, and annual_agriculture_tree.c.

[5.6.12] - 2023-05-12

Added

  • Missing agsub litter pool added to "litc", "litn", "mg_litc", "litc_agr", "mgrass_litc", "mgrass_litn" outputs and in global flux of litc.

  • Output of "litc_ag" and "litc_all" now written to output file.

Changed

  • Item ag in struct Litter renamed to agtop.

  • Functions litter_ag_grass(), litter_ag_nitrogen_tree(), litter_ag_sum(), litter_ag_sum_quick(), litter_ag_tree() renamed to litter_agtop_grass(), litter_agtop_nitrogen_tree(), litter_agtop_sum(), litter_agtop_sum_quick(), litter_agtop_tree().

  • Index in outnames array in fwriteoutput.c corrected for "mgrass_soilc", "mgrass_soiln", "mgrass_litc", "mgrass_litn"outputs.

[5.6.11] - 2023-05-11

Fixed

  • Invalid access to pointers soil->wsat-soil->wpwp has been replaced by access to layer specific data soil->wsat[l]-soil->wpwp[l] in infil_perc_rain.c and infil_perc_irr.c. See issue #303.

[5.6.10] - 2023-05-10

Added

  • PFT specific output for biological nitrogen fixation with grid and PFT scaling in npp_contr_biol_n_fixation.c and biologicalNfixation.c.

Changed

  • Adjusted optimum temperature limits ("temp_bnf_opt") of herbaceous PFTs for NPP controled biological nitrogen fixation in pft.js.

[5.6.9] - 2023-05-10

Added

  • Missing break statement added in harvest_stand.c. See issue #302

  • Missing deallocation of decomp_litter_pft added in freesoil.c.

  • Missing deallocation of with_tillage_filename added in freeconfig.c.

Changed

  • If input comes from socket connection the existence of the file is not checked anymore.

  • The memcpy arguments in cpl.h are now in the right order.

[5.6.8] - 2023-04-28

Added

  • flag "start_coupling" added in configuration file. If lpjml is coupled to an external model via
  "coupled_model" : "model",

this flag allows so set a year when input is received from the external model. Before that year input is read from input file. If flag is omitted or set to null coupling starts at the first year.

Changed

  • For input received from an external model a file name can additionally be specified where input is read from before the specified coupling year:
  "with_tillage" : { "fmt" : "clm", "socket" : true, "name" : "tillage.clm"},

  • lpjcheck and lpjml checks for specified filenames if they are necessary for the coupled run

  • JSON metafiles are also created for NetCDF output

[5.6.7] - 2023-04-27

Added

  • CHANGELOG.md added see issue #298

Changed

  • leading zeros removed in patch identifier of the version number

History

  • all versions prior to 5.6.7 have not been documented by a changelog or similar but in the respective merge requests (internal link accessible at PIK only)