geoschem · yantosca · Jan 21, 2026 · Dec 18, 2025 · Dec 19, 2025 · Dec 17, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Added new constants for default lon/lat and stretched-grid settings in `gcpy/constants.py`
 - Added PyDoc headers in routines where they were missing
 - Added `examples/grids/display_gcclassic_grid_info.py`  to display info about a GEOS-Chem Classic horizontal grid
+- Added functions `get_molwt_from_metadata` and `read_species_metadata` to `gcpy/util.py`
+- Added function `get_species_database_files` to `gcpy/benchmark/modules/benchmark_utils.py`
+- Added constant `SPECIES_DATABASE` to `gcpy/benchmark/modules/benchmark_utils.py`
 
 ### Changed
 - Modified criteria for terminating read of log files in `benchmark_scrape_gcclassic_timers.py` to avoid being spoofed by  output that is attached by Intel VTune
@@ -39,16 +42,21 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Updated default GCPy Python environment to use Python 3.13 (instead of 3.12)
 - Benchmark routines now look for `species_database.yml` in the `Ref` and `Dev` run directories
 - Replaced `get_species_database_dir` with `get_species_database_files` in `gcpy/benchmark/modules/benchmark_funcs.py`
-- Replaced `spcdb_dir` YAML tag with directory-specific `species_metadata` tags to specify paths to `species_database.yml` files  
+- Updated `gcpy/benchmark/modules/benchmark_scrape_gchp_timers.py` to look for GCHP timers in `allPEs.log` if not found in the log file
+- Updated routine `make_benchmark_aerosol_tables` to include all dust species in the aerosol burdens table
 
 ### Fixed
 - Fixed grid area calculation scripts of `grid_area` in `gcpy/gcpy/cstools.py`
 - Fixed various security issues in GitHub Actions workflows
 - Fixed colorbar bounds for case of comparing cubed-sphere grids
 - Fixed the restart regridding for stretched GCHP when target lat/lon is exactly 0.0 in `gcpy/regrid_restart_file.py`
+- Fixed computation of the global AOD benchmark table caused by hardwired species names
+- Fixed error in `create_benchmark_emissions_table` where all species were assumed to be in Ref and Dev even if they were not
 
 ### Removed
 - Removed `PdfMerger()` from `compare_single_level` and `compare_zonal_mean`, it has been removed in pypdf >= 5.0.0
+- Removed `paths:spcdb_dir` YAML tag in benchmark configuration files
+- Removed `st_Ox` from `benchmark_categories.yml`; this species is no longer used in TransportTracers simulations
 
 ## [1.6.2] - 2025-06-12
 ### Added

diff --git a/gcpy/benchmark/cloud/template.1hr_benchmark.yml b/gcpy/benchmark/cloud/template.1hr_benchmark.yml
@@ -29,16 +29,17 @@ paths:
   main_dir: ${GEOSCHEM_BENCHMARK_WORKING_DIR}
   results_dir: BenchmarkResults
   weights_dir: ${GEOSCHEM_BENCHMARK_WORKING_DIR}/weights
-  spcdb_dir: default
 #
 # data: Contains configurations for ref and dev runs
-#   version:         Version string (must not contain spaces)
-#   dir:             Path to run directory
-#   outputs_subdir:  Subdirectory w/ GEOS-Chem diagnostic files
-#   restarts_subdir: Subdirectory w/ GEOS-Chem restarts
-#   bmk_start:       Simulation start date (YYYY-MM-DDThh:mm:ss)
-#   bmk_end:         Simulation end date (YYYY-MM-DDThh:mm:ss)
-#   resolution:      GCHP resolution string
+#   version:          Version string (must not contain spaces)
+#   dir:              Path to run directory
+#   outputs_subdir:   Subdirectory w/ GEOS-Chem diagnostic files
+#   restarts_subdir:  Subdirectory w/ GEOS-Chem restarts
+#   logs_subdir:      Subdirectory w/ GEOS-Chem log files
+#   logs_template:    Template for log file names (may include tokens)
+#   bmk_start:        Simulation start date (YYYY-MM-DDThh:mm:ss)
+#   bmk_end:          Simulation end date (YYYY-MM-DDThh:mm:ss)
+#   resolution:       GCHP resolution string
 #
 data:
   ref:

diff --git a/gcpy/benchmark/cloud/template.1mo_benchmark.yml b/gcpy/benchmark/cloud/template.1mo_benchmark.yml
@@ -32,13 +32,15 @@ paths:
   spcdb_dir: default
 #
 # data: Contains configurations for ref and dev runs
-#   version:         Version string (must not contain spaces)
-#   dir:             Path to run directory
-#   outputs_subdir:  Subdirectory w/ GEOS-Chem diagnostic files
-#   restarts_subdir: Subdirectory w/ GEOS-Chem restarts
-#   bmk_start:       Simulation start date (YYYY-MM-DDThh:mm:ss)
-#   bmk_end:         Simulation end date (YYYY-MM-DDThh:mm:ss)
-#   resolution:      GCHP resolution string
+#   version:          Version string (must not contain spaces)
+#   dir:              Path to run directory
+#   outputs_subdir:   Subdirectory w/ GEOS-Chem diagnostic files
+#   restarts_subdir:  Subdirectory w/ GEOS-Chem restarts
+#   logs_subdir:      Subdirectory w/ GEOS-Chem log files
+#   logs_template:    Template for log file names (may include tokens)
+#   bmk_start:        Simulation start date (YYYY-MM-DDThh:mm:ss)
+#   bmk_end:          Simulation end date (YYYY-MM-DDThh:mm:ss)
+#   resolution:       GCHP resolution string
 #
 data:
   ref:

diff --git a/gcpy/benchmark/config/1mo_benchmark.yml b/gcpy/benchmark/config/1mo_benchmark.yml
@@ -21,24 +21,22 @@
 #   main_dir:    High-level directory containing ref & dev rundirs
 #   results_dir: Directory where plots/tables will be created
 #   weights_dir: Path to regridding weights
-#   spcdb_dir:   Folder in which the species_database.yml file is
-#                located.  If set to "default", then will look for
-#                species_database.yml in one of the Dev rundirs.
 #
 paths:
   main_dir: /path/to/benchmark/main/dir
   results_dir: /path/to/BenchmarkResults
   weights_dir: /n/holylfs06/LABS/jacob_lab/Shared/GEOS-CHEM/gcgrid/gcdata/ExtData/GCHP/RegriddingWeights
-  spcdb_dir: default
 #
 # data: Contains configurations for ref and dev runs
-#   version:         Version string (must not contain spaces)
-#   dir:             Path to run directory
-#   outputs_subdir:  Subdirectory w/ GEOS-Chem diagnostic files
-#   restarts_subdir: Subdirectory w/ GEOS-Chem restarts
-#   bmk_start:       Simulation start date (YYYY-MM-DDThh:mm:ss)
-#   bmk_end:         Simulation end date (YYYY-MM-DDThh:mm:ss)
-#   resolution:      GCHP resolution string
+#   version:          Version string (must not contain spaces)
+#   dir:              Path to run directory
+#   outputs_subdir:   Subdirectory w/ GEOS-Chem diagnostic files
+#   restarts_subdir:  Subdirectory w/ GEOS-Chem restarts
+#   logs_subdir:      Subdirectory w/ GEOS-Chem log files
+#   logs_template:    Template for log file names (may include tokens)
+#   bmk_start:        Simulation start date (YYYY-MM-DDThh:mm:ss)
+#   bmk_end:          Simulation end date (YYYY-MM-DDThh:mm:ss)
+#   resolution:       GCHP resolution string
 #
 data:
   ref:

diff --git a/gcpy/benchmark/config/1yr_ch4_benchmark.yml b/gcpy/benchmark/config/1yr_ch4_benchmark.yml
@@ -21,15 +21,11 @@
 #   main_dir:    High-level directory containing ref & dev rundirs
 #   results_dir: Directory where plots/tables will be created
 #   weights_dir: Path to regridding weights
-#   spcdb_dir:   Folder in which the species_database.yml file is
-#                located.  If set to "default", then will look for
-#                species_database.yml in one of the Dev rundirs.
 #
 paths:
   main_dir: /path/to/benchmark/main/dir    # EDIT AS NEEDED
   results_dir: /path/to/BenchmarkResults   # EDIT AS NEEDED
   weights_dir: /n/holylfs06/LABS/jacob_lab/Shared/GEOS-CHEM/gcgrid/gcdata/ExtData/GCHP/RegriddingWeights
-  spcdb_dir: default
   #
   # Observational data dirs are on Harvard Cannon, edit if necessary
   #
@@ -43,13 +39,15 @@ paths:
       site_file: allozonesondes_site_elev.csv
 #
 # data: Contains configurations for ref and dev runs
-#   version:         Version string (must not contain spaces)
-#   dir:             Path to run directory
-#   outputs_subdir:  Subdirectory w/ GEOS-Chem diagnostic files
-#   restarts_subdir: Subdirectory w/ GEOS-Chem restarts
-#   bmk_start:       Simulation start date (YYYY-MM-DDThh:mm:ss)
-#   bmk_end:         Simulation end date (YYYY-MM-DDThh:mm:ss)
-#   resolution:      GCHP resolution string
+#   version:          Version string (must not contain spaces)
+#   dir:              Path to run directory
+#   outputs_subdir:   Subdirectory w/ GEOS-Chem diagnostic files
+#   restarts_subdir:  Subdirectory w/ GEOS-Chem restarts
+#   logs_subdir:      Subdirectory w/ GEOS-Chem log files
+#   logs_template:    Template for log file names (may include tokens)
+#   bmk_start:        Simulation start date (YYYY-MM-DDThh:mm:ss)
+#   bmk_end:          Simulation end date (YYYY-MM-DDThh:mm:ss)
+#   resolution:       GCHP resolution string
 #
 data:
   ref:

diff --git a/gcpy/benchmark/config/1yr_fullchem_benchmark.yml b/gcpy/benchmark/config/1yr_fullchem_benchmark.yml
@@ -21,16 +21,12 @@
 #   main_dir:     High-level directory containing ref & dev rundirs
 #   results_dir:  Directory where plots/tables will be created
 #   weights_dir:  Path to regridding weights
-#   spcdb_dir:    Folder in which the species_database.yml file is
-#                  located.  If set to "default", then will look for
-#                  species_database.yml in one of the Dev rundirs.
 #   obs_data:     Paths to observations (for models vs. obs plots)
 #
 paths:
   main_dir: /path/to/benchmark/main/dir
   results_dir: /path/to/BenchmarkResults
   weights_dir: /n/holylfs06/LABS/jacob_lab/Shared/GEOS-CHEM/gcgrid/gcdata/ExtData/GCHP/RegriddingWeights
-  spcdb_dir: default
   #
   # Observational data dirs are on Harvard Cannon, edit if necessary
   #
@@ -44,13 +40,16 @@ paths:
       site_file: allozonesondes_site_elev.csv
 #
 # data: Contains configurations for ref and dev runs
-#   version:         Version string (must not contain spaces)
-#   dir:             Path to run directory
-#   outputs_subdir:  Subdirectory w/ GEOS-Chem diagnostic files
-#   restarts_subdir: Subdirectory w/ GEOS-Chem restarts
-#   bmk_start:       Simulation start date (YYYY-MM-DDThh:mm:ss)
-#   bmk_end:         Simulation end date (YYYY-MM-DDThh:mm:ss)
-#   resolution:      GCHP resolution string
+#   version:          Version string (must not contain spaces)
+#   dir:              Path to run directory
+#   outputs_subdir:   Subdirectory w/ GEOS-Chem diagnostic files
+#   restarts_subdir:  Subdirectory w/ GEOS-Chem restarts
+#   logs_subdir:      Subdirectory w/ GEOS-Chem log files
+#   logs_template:    Template for log file names (may include tokens)
+#   bmk_start:        Simulation start date (YYYY-MM-DDThh:mm:ss)
+#   bmk_end:          Simulation end date (YYYY-MM-DDThh:mm:ss)
+#   resolution:       GCHP resolution string
+#
 #
 data:
   ref:
@@ -134,15 +133,18 @@ options:
     plot_drydep: True
     plot_emis: True
     plot_jvalues: True
+    plot_models_vs_obs: True
     plot_options:
       by_spc_cat: True
       by_hco_cat: True
     #
     # Benchmark tables
     #
+    aer_budget_table: True
     emis_table: True
     mass_accum_table: False
     mass_table: True
+    Ox_budget_table: True
     OH_metrics: True
     ops_budget_table: False
     sanity_check_table: True

diff --git a/gcpy/benchmark/config/1yr_tt_benchmark.yml b/gcpy/benchmark/config/1yr_tt_benchmark.yml
@@ -21,24 +21,23 @@
 #   main_dir:    High-level directory containing ref & dev rundirs
 #   results_dir: Directory where plots/tables will be created
 #   weights_dir: Path to regridding weights
-#   spcdb_dir:   Folder in which the species_database.yml file is
-#                located.  If set to "default", then will look for
-#                species_database.yml in one of the Dev rundirs.
 #
 paths:
   main_dir: /path/to/benchmark/main/dir
   results_dir: /path/to/BenchmarkResults
   weights_dir: /n/holylfs06/LABS/jacob_lab/Shared/GEOS-CHEM/gcgrid/gcdata/ExtData/GCHP/RegriddingWeights
-  spcdb_dir: default
 #
 # data: Contains configurations for ref and dev runs
-#   version:         Version string (must not contain spaces)
-#   dir:             Path to run directory
-#   outputs_subdir:  Subdirectory w/ GEOS-Chem diagnostic files
-#   restarts_subdir: Subdirectory w/ GEOS-Chem restarts
-#   bmk_start:       Simulation start date (YYYY-MM-DDThh:mm:ss)
-#   bmk_end:         Simulation end date (YYYY-MM-DDThh:mm:ss)
-#   resolution:      GCHP resolution string
+#   version:          Version string (must not contain spaces)
+#   dir:              Path to run directory
+#   outputs_subdir:   Subdirectory w/ GEOS-Chem diagnostic files
+#   restarts_subdir:  Subdirectory w/ GEOS-Chem restarts
+#   logs_subdir:      Subdirectory w/ GEOS-Chem log files
+#   logs_template:    Template for log file names (may include tokens)
+#   bmk_start:        Simulation start date (YYYY-MM-DDThh:mm:ss)
+#   bmk_end:          Simulation end date (YYYY-MM-DDThh:mm:ss)
+#   resolution:       GCHP resolution string
+#
 #
 data:
   ref:

diff --git a/gcpy/benchmark/modules/benchmark_categories.yml b/gcpy/benchmark/modules/benchmark_categories.yml
@@ -256,7 +256,6 @@ TransportTracersBenchmark:
       - e90_n
       - e90_s
       - st80_25
-      - stOX
   WetLossConv:
     WetLossConv:
       - Pb210

diff --git a/gcpy/benchmark/modules/benchmark_drydep.py b/gcpy/benchmark/modules/benchmark_drydep.py
@@ -18,6 +18,7 @@ def make_benchmark_drydep_plots(
         refstr,
         dev,
         devstr,
+        spcdb_files,
         collection="DryDep",
         dst="./benchmark",
         subdst=None,
@@ -30,7 +31,6 @@ def make_benchmark_drydep_plots(
         n_job=-1,
         time_mean=False,
         varlist=None,
-        spcdb_dir=None,
 ):
     """
     Creates six-panel comparison plots (PDF format) from GEOS-Chem
@@ -48,6 +48,8 @@ def make_benchmark_drydep_plots(
             data set.
         devstr: str
             A string to describe dev (e.g. version number)
+        spcdb_files : list 
+            Paths to species_database.yml files in Ref & Dev rundirs
 
     Keyword Args (optional):
         collection : str
@@ -79,20 +81,13 @@ def make_benchmark_drydep_plots(
             Set to 1 to disable parallel plotting. Value of -1 allows the
             application to decide.
             Default value: -1
-        spcdb_dir: str
-            Directory of species_datbase.yml file
-            Default value: None
         time_mean : bool
             Determines if we should average the datasets over time
             Default value: False
         varlist: list of str
             List of variables to plot.  If varlist is None, then
             all common variables in Ref & Dev will be plotted.
     """
-    # Make sure the species database folder is passed
-    if spcdb_dir is None:
-        msg = "The spcdb_dir argument has not been specified!"
-        raise ValueError(msg)
 
     # Replace whitespace in the ref and dev labels
     refstr = util.replace_whitespace(refstr)
@@ -144,7 +139,7 @@ def make_benchmark_drydep_plots(
         sigdiff_list=sigdiff_list,
         weightsdir=weightsdir,
         n_job=n_job,
-        spcdb_dir=spcdb_dir
+        spcdb_files=spcdb_files,
     )
     util.add_bookmarks_to_pdf(
         pdfname,
-Original file line number
+Diff line change
@@ Expand Up / @@ -256,7 +256,6 @@ TransportTracersBenchmark: @@
           - e90_n
           - e90_s
           - st80_25
-          - stOX
       WetLossConv:
         WetLossConv:
           - Pb210
@@ Expand Down @@