geoschem · yantosca · Jan 30, 2024 · Dec 7, 2023 · Dec 7, 2023 · Dec 8, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,15 @@ All notable changes to GCPy will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased] - TBD
+### Added
+- Script `gcpy/benchmark/modules/benchmark_utils.py`, with common benchmark utility functions
+- Script `gcpy/benchmark/modules/benchmark_drydep.py`, with code to create drydep velocity plots
+- YAML tag `plot_drydep` in `gcpy/benchmark/config/*.yml` files
+
+### Changed
+- YAML tag `operations_budget` is now `ops_budget_table` in `gcpy/benchmark/config/1yr_tt_benchmark.yml`
+
 ## [1.4.0] - 2023-11-20
 ### Added
 - Added C2H2 and C2H4 to `emission_species.yml`

diff --git a/gcpy/benchmark/cloud/template.1hr_benchmark.yml b/gcpy/benchmark/cloud/template.1hr_benchmark.yml
@@ -110,6 +110,7 @@ options:
     plot_emis: False
     emis_table: True
     plot_jvalues: False
+    plot_drydep: False
     plot_aod: False
     mass_table: True
     mass_accum_table: False

diff --git a/gcpy/benchmark/cloud/template.1mo_benchmark.yml b/gcpy/benchmark/cloud/template.1mo_benchmark.yml
@@ -111,6 +111,7 @@ options:
     emis_table: True
     plot_jvalues: True
     plot_aod: True
+    plot_drydep: False  # Need to save out DryDep collection for 1-mo
     mass_table: True
     mass_accum_table: False
     ops_budget_table: False

diff --git a/gcpy/benchmark/config/1mo_benchmark.yml b/gcpy/benchmark/config/1mo_benchmark.yml
@@ -111,6 +111,7 @@ options:
     emis_table: True
     plot_jvalues: True
     plot_aod: True
+    plot_drydep: False  # Need to save out DryDep collection for 1-mo
     mass_table: True
     mass_accum_table: False
     ops_budget_table: False

diff --git a/gcpy/benchmark/config/1yr_fullchem_benchmark.yml b/gcpy/benchmark/config/1yr_fullchem_benchmark.yml
@@ -113,6 +113,7 @@ options:
     emis_table: True
     plot_jvalues: True
     plot_aod: True
+    plot_drydep: True
     mass_table: True
     ops_budget_table: False
     aer_budget_table: True

diff --git a/gcpy/benchmark/config/1yr_tt_benchmark.yml b/gcpy/benchmark/config/1yr_tt_benchmark.yml
@@ -1,3 +1,4 @@
+
 ---
 # =====================================================================
 # Benchmark configuration file (**EDIT AS NEEDED**)
@@ -108,8 +109,9 @@ options:
   outputs:
     plot_conc: True
     plot_wetdep: True
+    plot_drydep: True
     rnpbbe_budget: True
-    operations_budget: False
+    ops_budget_table: False
     mass_table: True
     ste_table: True
     cons_table: True

diff --git a/gcpy/benchmark/modules/benchmark_drydep.py b/gcpy/benchmark/modules/benchmark_drydep.py
@@ -0,0 +1,175 @@
+"""
+Specific utilities for creating plots from GEOS-Chem benchmark simulations.
+"""
+import os
+import gc
+import numpy as np
+from gcpy import util
+from gcpy.plot.compare_single_level import compare_single_level
+import gcpy.benchmark.modules.benchmark_utils as bmk_util
+
+# Suppress numpy divide by zero warnings to prevent output spam
+np.seterr(divide="ignore", invalid="ignore")
+
+
+def make_benchmark_drydep_plots(
+        ref,
+        refstr,
+        dev,
+        devstr,
+        collection="DryDep",
+        dst="./benchmark",
+        subdst=None,
+        cmpres=None,
+        overwrite=False,
+        verbose=False,
+        log_color_scale=False,
+        weightsdir=".",
+        sigdiff_files=None,
+        n_job=-1,
+        time_mean=False,
+        varlist=None,
+        spcdb_dir=os.path.join(os.path.dirname(__file__), "..", "..")
+):
+    """
+    Creates six-panel comparison plots (PDF format) from GEOS-Chem
+    benchmark simualtion output.  Can be used with data collections
+    that do not require special handling (e.g. concentrations).
+
+    Args:
+        ref: str
+            Path name for the "Ref" (aka "Reference") data set.
+        refstr: str
+            A string to describe ref (e.g. version number)
+        dev: str
+            Path name for the "Dev" (aka "Development") data set.
+            This data set will be compared against the "Reference"
+            data set.
+        devstr: str
+            A string to describe dev (e.g. version number)
+
+    Keyword Args (optional):
+        collection : str
+            Name of the diagnostic collection (e.g. "DryDep")
+        dst: str
+            A string denoting the destination folder where a PDF
+            file containing plots will be written.
+            Default value: ./benchmark
+        subdst: str
+            A string denoting the sub-directory of dst where PDF
+            files containing plots will be written.  In practice,
+            subdst is only needed for the 1-year benchmark output,
+            and denotes a date string (such as "Jan2016") that
+            corresponds to the month that is being plotted.
+            Default value: None
+        benchmark_type: str
+            A string denoting the type of benchmark output to plot, options are
+            FullChemBenchmark, TransportTracersBenchmark, or CH4Benchmark.
+            Default value: "FullChemBenchmark"
+        overwrite: bool
+            Set this flag to True to overwrite files in the
+            destination folder (specified by the dst argument).
+            Default value: False.
+        verbose: bool
+            Set this flag to True to print extra informational output.
+            Default value: False.
+        n_job: int
+            Defines the number of simultaneous workers for parallel plotting.
+            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: Directory of GCPy code repository
+        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.
+    """
+
+    # Create directory for plots (if it doesn't exist)
+    dst = bmk_util.make_output_dir(
+        dst,
+        collection,
+        subdst,
+        overwrite=overwrite,
+    )
+
+    # Read data
+    refdata, devdata = bmk_util.read_ref_and_dev(
+        ref,
+        dev,
+        time_mean=time_mean
+    )
+
+    # Get common variables between Ref and Dev
+    if varlist is None:
+        varlist = bmk_util.get_common_varnames(
+            refdata,
+            devdata,
+            prefix="DryDepVel_",
+            verbose=verbose
+        )
+
+    # Create surface plots
+    sigdiff_list = []
+    pdfname = bmk_util.pdf_filename(
+        dst,
+        collection,
+        subdst,
+        plot_type="Surface"
+    )
+    compare_single_level(
+        refdata,
+        refstr,
+        devdata,
+        devstr,
+        varlist=varlist,
+        cmpres=cmpres,
+        ilev=0,
+        pdfname=pdfname,
+        log_color_scale=log_color_scale,
+        extra_title_txt=subdst,
+        sigdiff_list=sigdiff_list,
+        weightsdir=weightsdir,
+        n_job=n_job,
+        spcdb_dir=spcdb_dir
+    )
+    util.add_bookmarks_to_pdf(
+        pdfname,
+        varlist,
+        remove_prefix=collection + '_',
+        verbose=verbose
+    )
+
+    # Write significant differences to file (if there are any)
+    bmk_util.print_sigdiffs(
+        sigdiff_files,
+        sigdiff_list,
+        sigdiff_type="sfc",
+        sigdiff_cat="DryDepVel"
+    )
+
+    # -------------------------------------------
+    # Clean up
+    # -------------------------------------------
+    del refdata
+    del devdata
+    gc.collect()
+
+
+def drydepvel_species():
+    """
+    Returns a list of species for the dry deposition velocity
+    (DryDepVel) benchmark plots:
+
+    Returns:
+    --------
+    varnames (list of str): Variable names to plot
+    """
+    # These are key dry deposition species (as per Mat Evans)
+    return ["DryDepVel_ACET", "DryDepVel_HNO3", "DryDepVel_NH3",
+            "DryDepVel_NH4", "DryDepVel_NIT", "DryDepVel_NITs",
+            "DryDepVel_O3", "DryDepVel_SO4"]