Fix formatting, lint (path variable shadowing), and rebase cleanup

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: sbryngelson

examples/2D_moving_lag_bubs/case.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3
 import argparse
-import math
 import json
+import math
+
 import numpy as np
 
 # Domain extents

examples/3D_moving_lag_particles/case.py

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3
 import argparse
-import math
 import json
+import math
+
 import numpy as np
 
 # Domain extents

src/post_process/m_global_parameters.fpp

@@ -1068,7 +1068,7 @@ contains
         if (ib) MPI_IO_IB_DATA%var%sf => null()
 #endif
 
-        if (allocated(neighbor_ranks)) deallocate(neighbor_ranks)
+        if (allocated(neighbor_ranks)) deallocate (neighbor_ranks)
 
     end subroutine s_finalize_global_parameters_module
 

src/pre_process/m_global_parameters.fpp

@@ -1086,7 +1086,7 @@ contains
 
 #endif
 
-        if (allocated(neighbor_ranks)) deallocate(neighbor_ranks)
+        if (allocated(neighbor_ranks)) deallocate (neighbor_ranks)
 
     end subroutine s_finalize_global_parameters_module
 

src/simulation/m_global_parameters.fpp

@@ -714,8 +714,8 @@ contains
         bub_pp%gam_g = dflt_real; gam_g = dflt_real
         bub_pp%M_v = dflt_real; M_v = dflt_real
         bub_pp%M_g = dflt_real; M_g = dflt_real
-        bub_pp%k_v = dflt_real;
-        bub_pp%k_g = dflt_real;
+        bub_pp%k_v = dflt_real; 
+        bub_pp%k_g = dflt_real; 
         bub_pp%cp_v = dflt_real; cp_v = dflt_real
         bub_pp%cp_g = dflt_real; cp_g = dflt_real
         bub_pp%R_v = dflt_real; R_v = dflt_real
@@ -1379,15 +1379,15 @@ contains
         @:PREFER_GPU(x_cc)
         @:PREFER_GPU(dx)
 
-        if (n == 0) return;
+        if (n == 0) return; 
         @:ALLOCATE(y_cb(-1 - buff_size:n + buff_size))
         @:ALLOCATE(y_cc(-buff_size:n + buff_size))
         @:ALLOCATE(dy(-buff_size:n + buff_size))
         @:PREFER_GPU(y_cb)
         @:PREFER_GPU(y_cc)
         @:PREFER_GPU(dy)
 
-        if (p == 0) return;
+        if (p == 0) return; 
         @:ALLOCATE(z_cb(-1 - buff_size:p + buff_size))
         @:ALLOCATE(z_cc(-buff_size:p + buff_size))
         @:ALLOCATE(dz(-buff_size:p + buff_size))
@@ -1478,10 +1478,10 @@ contains
         ! Deallocating grid variables for the x-, y- and z-directions
         @:DEALLOCATE(x_cb, x_cc, dx)
 
-        if (n == 0) return;
+        if (n == 0) return; 
         @:DEALLOCATE(y_cb, y_cc, dy)
 
-        if (p == 0) return;
+        if (p == 0) return; 
         @:DEALLOCATE(z_cb, z_cc, dz)
 
         if (allocated(neighbor_ranks)) then

src/simulation/m_time_steppers.fpp

@@ -470,7 +470,6 @@ contains
             @:ALLOCATE(max_dt(0:m, 0:n, 0:p))
         end if
 
-
         ! Allocating arrays to store the bc types
         @:ALLOCATE(bc_type(1:num_dims,1:2))
 

toolchain/mfc/params/definitions.py

@@ -1253,16 +1253,13 @@ def _load():
             _r(f"simplex_params%perturb_vel_offset({d},{j})", REAL)
 
     # --- lag_params (Lagrangian bubbles) ---
-    for a in ["heatTransfer_model", "massTransfer_model", "pressure_corrector",
-              "write_bubbles", "write_bubbles_stats", "pressure_force", "gravity_force",
-              "write_void_evol" ]:
+    for a in ["heatTransfer_model", "massTransfer_model", "pressure_corrector", "write_bubbles", "write_bubbles_stats", "pressure_force", "gravity_force", "write_void_evol"]:
         _r(f"lag_params%{a}", LOG, {"bubbles"})
-    for a in ["solver_approach", "cluster_type", "smooth_type", "nBubs_glb", "drag_model",
-              "vel_model", "charNz"]:
+    for a in ["solver_approach", "cluster_type", "smooth_type", "nBubs_glb", "drag_model", "vel_model", "charNz"]:
         _r(f"lag_params%{a}", INT, {"bubbles"})
     for a in ["epsilonb", "valmaxvoid", "charwidth", "c0", "rho0", "T0", "x0", "Thost"]:
         _r(f"lag_params%{a}", REAL, {"bubbles"})
-    _r(f"lag_params%input_path", STR, {"bubbles"})
+    _r("lag_params%input_path", STR, {"bubbles"})
 
     # --- chem_params ---
     for a in ["diffusion", "reactions"]: