geoschem · yantosca · Oct 15, 2025 · Oct 14, 2025 · Oct 15, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -25,6 +25,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Bumped `pypdf` from version 4.2.0 to 6.0.0 in `docs/environments/gcpy_environment_py312.yml`
 - Bumped `pypdf` from version 5.3.1 to 6.0.0 in `docs/environments/gcpy_environment_py313.yml`
 - Moved `Ap` and `Bp` parameters that define vertical grids from `grid.py` to `vgrid_defs.py`
+- Changed `mamba` to `conda` in `benchmarks/benchmark_slurm.sh`
+- Separated plot and table options for clarity in  `benchmarks/config/*yml` and  `benchmarks/cloud/*.yml`
 
 ### Fixed
 - Fixed grid area calculation scripts of `grid_area` in `gcpy/gcpy/cstools.py`

diff --git a/gcpy/benchmark/benchmark_slurm.sh b/gcpy/benchmark/benchmark_slurm.sh
@@ -28,7 +28,7 @@ export OMP_STACKSIZE=500m
 export MPLBACKEND=agg
 
 # Turn on Python environment (edit for your setup)
-mamba activate gcpy_env
+conda activate gcpy_env
 
 # Specify a YAML file with benchmark options
 # Uncomment the file that you wish:
@@ -40,7 +40,7 @@ config="1mo_benchmark.yml"
 python -m gcpy.benchmark.run_benchmark "${config}" > "${config/.yml/.log}" 2>&1
 
 # Turn off python environment
-mamba deactivate
+conda deactivate
 
 exit 0
 
diff --git a/gcpy/benchmark/cloud/template.1hr_benchmark.yml b/gcpy/benchmark/cloud/template.1hr_benchmark.yml
@@ -114,24 +114,33 @@ options:
   # outputs: Specifies the plots and tables to generate
   #
   outputs:
+    #
+    # Benchmark plots
+    #
+    plot_aod: False
     plot_conc: False
+    plot_drydep: False
     plot_emis: False
-    emis_table: True
     plot_jvalues: False
-    plot_drydep: False
-    plot_aod: False
-    mass_table: True
+    plot_options:
+      by_spc_cat: True
+      by_hco_cat: True
+    #
+    # Benchmark tables
+    #
+    emis_table: True
     mass_accum_table: False
-    ops_budget_table: False
+    mass_table: True
     OH_metrics: True
+    ops_budget_table: False
+    sanity_check_table: True
     ste_table: True # GCC only
-    timing_table: True
     summary_table: True
-    sanity_check_table: True
-    plot_options:
-      by_spc_cat: True
-      by_hco_cat: True
-    # Comparison plots for other collections
+    timing_table: True
+    #
+    # Comparison plots for selected collections
+    # (not normally used for benchmarks)
+    #
     plot_budget: False
     plot_2d_met: False
     plot_3d_met: False

diff --git a/gcpy/benchmark/cloud/template.1mo_benchmark.yml b/gcpy/benchmark/cloud/template.1mo_benchmark.yml
@@ -114,24 +114,32 @@ options:
   # outputs: Specifies the plots and tables to generate
   #
   outputs:
+    #
+    # Benchmark plots
+    #
+    plot_aod: True
     plot_conc: True
+    plot_drydep: True
     plot_emis: True
-    emis_table: True
     plot_jvalues: True
-    plot_aod: True
-    plot_drydep: True
-    mass_table: True
+    plot_options:
+      by_spc_cat: True
+      by_hco_cat: True
+    #
+    # Benchmark tables
+    #
+    emis_table: True
     mass_accum_table: False
-    ops_budget_table: False
+    mass_table: True
     OH_metrics: True
+    ops_budget_table: False
+    sanity_check_table: True
     ste_table: True # GCC only
     timing_table: True
-    summary_table: True
-    sanity_check_table: True
-    plot_options:
-      by_spc_cat: True
-      by_hco_cat: True
-    # Comparison plots for other collections
+    #
+    # Comparison plots for selected collections
+    # (not normally used for benchmarks)
+    #
     plot_budget: False
     plot_2d_met: False
     plot_3d_met: False

diff --git a/gcpy/benchmark/config/1mo_benchmark.yml b/gcpy/benchmark/config/1mo_benchmark.yml
@@ -114,30 +114,38 @@ options:
   # outputs: Specifies the plots and tables to generate
   #
   outputs:
+    #
+    # Benchmark plots
+    #
+    plot_aod: True
     plot_conc: True
+    plot_drydep: True
     plot_emis: True
-    emis_table: True
     plot_jvalues: True
-    plot_aod: True
-    plot_drydep: False  # Need to save out DryDep collection for 1-mo
-    mass_table: True
+    plot_options:
+      by_spc_cat: True
+      by_hco_cat: True
+    #
+    # Benchmark tables
+    #
+    emis_table: True
     mass_accum_table: False
-    ops_budget_table: False
+    mass_table: True
     OH_metrics: True
+    ops_budget_table: False
+    sanity_check_table: True
     ste_table: True # GCC only
-    timing_table: True
     summary_table: True
-    sanity_check_table: True
-    plot_options:
-      by_spc_cat: True
-      by_hco_cat: True
-    # Comparison plots for other collections
+    timing_table: True
+    #
+    # Comparison plots for selected collections
+    # (not normally used for benchmarks)
+    #
     plot_budget: False
     plot_2d_met: False
     plot_3d_met: False
     plot_uvflux: False
-
-#
+  #
   # n_cores: Specify the number of cores to use.
   # -1: Use $OMP_NUM_THREADS         cores
   # -2: Use $OMP_NUM_THREADS - 1     cores

diff --git a/gcpy/benchmark/config/1yr_fullchem_benchmark.yml b/gcpy/benchmark/config/1yr_fullchem_benchmark.yml
@@ -126,23 +126,37 @@ options:
   # outputs: Specifies the plots and tables to generate
   #
   outputs:
+    #
+    # Benchmark plots
+    #
+    plot_aod: True
     plot_conc: True
+    plot_drydep: True
     plot_emis: True
-    emis_table: True
     plot_jvalues: True
-    plot_aod: True
-    plot_drydep: True
+    plot_options:
+      by_spc_cat: True
+      by_hco_cat: True
+    #
+    # Benchmark tables
+    #
+    emis_table: True
+    mass_accum_table: False
     mass_table: True
+    OH_metrics: True
     ops_budget_table: False
-    aer_budget_table: True
-    Ox_budget_table: True
+    sanity_check_table: True
     ste_table: True # GCC only
-    OH_metrics: True
+    summary_table: False
     timing_table: True
-    plot_models_vs_obs: True
-    plot_options:
-      by_spc_cat: True
-      by_hco_cat: True
+    #
+    # Comparison plots for selected collections
+    # (not normally used for benchmarks)
+    #
+    plot_budget: False
+    plot_2d_met: False
+    plot_3d_met: False
+    plot_uvflux: False
   #
   # n_cores: Specify the number of cores to use.
   # -1: Use $OMP_NUM_THREADS         cores

diff --git a/gcpy/benchmark/config/1yr_tt_benchmark.yml b/gcpy/benchmark/config/1yr_tt_benchmark.yml
@@ -1,4 +1,3 @@
-
 ---
 # =====================================================================
 # Benchmark configuration file (**EDIT AS NEEDED**)
@@ -115,15 +114,28 @@ options:
   # outputs: Specifies the plots and tables to generate
   #
   outputs:
+    #
+    # Benchmark plots
+    #
     plot_conc: True
-    plot_wetdep: True
     plot_drydep: True
-    rnpbbe_budget: True
-    ops_budget_table: False
+    plot_wetdep: True
+    #
+    # Benchmark tables
+    #
+    cons_table: True
     mass_table: True
+    ops_budget_table: False
+    rnpbbe_budget: True
     ste_table: True
-    cons_table: True
     timing_table: False
+    #
+    # Comparison plots for selected collections
+    # (not normally used for benchmarks)
+    #
+    plot_budget: False
+    plot_2d_met: False
+    plot_3d_met: False
   #
   # n_cores: Specify the number of cores to use.
   # -1: Use $OMP_NUM_THREADS         cores