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Update SpeciesConc variable name to SpeciesConcVV for consistency with GEOS-Chem 14.1.0 updates #187

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Merged
merged 2 commits into from
Dec 22, 2022
Merged

Update SpeciesConc variable name to SpeciesConcVV for consistency with GEOS-Chem 14.1.0 updates #187

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f2c01cd
Update SpeciesConc variable name to SpeciesConcVV for consistency wit…
msulprizio Dec 22, 2022
ae12821
Fix typos in references to 'SpeciesConc_' variable
msulprizio Dec 22, 2022
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47 changes: 36 additions & 11 deletions gcpy/benchmark.py
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Original file line number Diff line number Diff line change
Expand Up @@ -713,20 +713,31 @@ def make_benchmark_conc_plots(
refds = reader(ref, drop_variables=gcon.skip_these_vars).load()
devds = reader(dev, drop_variables=gcon.skip_these_vars).load()

# Rename SpeciesConc_ to SpeciesConcVV_ for consistency with new
# naming introduced in GEOS-Chem 14.1.0
for v in refds.data_vars.keys():
if v.startswith('SpeciesConc_'):
spc = v.replace('SpeciesConc_', '')
refds = refds.rename({v: 'SpeciesConcVV_' + spc})
for v in devds.data_vars.keys():
if v.startswith('SpeciesConc_'):
spc = v.replace('SpeciesConc_', '')
devds = devds.rename({v: 'SpeciesConcVV_' + spc})

# -----------------------------------------------------------------
# Kludge, rename wrong variable name
if "SpeciesConcVV_PFE" in refds.data_vars.keys():
refds = refds.rename({"SpeciesConcVV_PFE": "SpeciesConcVV_pFe"})
if "SpeciesConcVV_PFE" in devds.data_vars.keys():
devds = devds.rename({"SpeciesConcVV_PFE": "SpeciesConcVV_pFe"})
# -----------------------------------------------------------------

if verbose:
print('\nPrinting refds (comparison ref)\n')
print(refds)
print('\nPrinting devds (comparison dev)\n')
print(devds)

# -----------------------------------------------------------------
# Kludge, rename wrong variable name
if "SpeciesConc_PFE" in refds.data_vars.keys():
refds = refds.rename({"SpeciesConc_PFE": "SpeciesConc_pFe"})
if "SpeciesConc_PFE" in devds.data_vars.keys():
devds = devds.rename({"SpeciesConc_PFE": "SpeciesConc_pFe"})
# -----------------------------------------------------------------

# Open met datasets if passed as arguments
refmetds = None
devmetds = None
Expand Down Expand Up @@ -835,7 +846,7 @@ def make_benchmark_conc_plots(
# ==================================================================
if not plot_by_spc_cat:
[refds, devds] = util.add_missing_variables(refds, devds)
var_prefix = 'SpeciesConc_'
var_prefix = 'SpeciesConcVV_'
varlist = [k for k in refds.data_vars.keys() if var_prefix in k]
varlist.sort()

Expand Down Expand Up @@ -900,14 +911,18 @@ def make_benchmark_conc_plots(
# FullChemBenchmark has lumped species (TransportTracers does not)
if "FullChem" in benchmark_type:
print("\nComputing lumped species for full chemistry benchmark")

print("-->Adding lumped species to ref dataset")
refds = util.add_lumped_species_to_dataset(refds)

print("-->Adding lumped species to dev dataset")
devds = util.add_lumped_species_to_dataset(devds)

if diff_of_diffs:
print("-->Adding lumped species to dev datasets")
second_refds = util.add_lumped_species_to_dataset(second_refds)
second_devds = util.add_lumped_species_to_dataset(second_devds)

util.archive_lumped_species_definitions(dst)
print("Lumped species computation complete.\n")

Expand All @@ -925,7 +940,10 @@ def make_benchmark_conc_plots(
[devds, second_devds] = util.add_missing_variables(devds, second_devds)

# Collection prefix
coll_prefix = collection.strip() + "_"
if "SpeciesConc" in collection:
coll_prefix = "SpeciesConcVV_"
else:
coll_prefix = collection.strip() + "_"

# ==================================================================
# Create the plots!
Expand Down Expand Up @@ -3402,6 +3420,13 @@ def make_benchmark_aerosol_tables(
drop_variables=gcon.skip_these_vars) # ,
# combine="nested", concat_dim="time")

# Rename SpeciesConc_ to SpeciesConcVV_ for consistency with new
# naming introduced in GEOS-Chem 14.1.0
for v in ds_spc.data_vars.keys():
if v.startswith('SpeciesConc_'):
spc = v.replace('SpeciesConc_', '')
ds_spc = ds_spc.rename({v: 'SpeciesConcVV_' + spc})

# Get troposphere mask
tropmask = get_troposphere_mask(ds_met)

Expand Down Expand Up @@ -3501,7 +3526,7 @@ def print_aerosol_metrics(data, species_list, filename, title, label):

# Whole-atmosphere and trop-only quantities [g]
# NOTE: DryDep is by nature trop-only
varname = "SpeciesConc_" + spc
varname = "SpeciesConcVV_" + spc
q[spc + "_f"] = ds_spc[varname].values * vv_to_Tg[spc]
q[spc + "_t"] = np.ma.masked_array(q[spc + "_f"], tropmask)

Expand Down
8 changes: 4 additions & 4 deletions gcpy/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -344,8 +344,8 @@ def add_bookmarks_to_pdf(
remove_prefix: str
Specifies a prefix to remove from each entry in varlist
when creating bookmarks. For example, if varlist has
a variable name "SpeciesConc_NO", and you specify
remove_prefix="SpeciesConc_", then the bookmark for
a variable name "SpeciesConcVV_NO", and you specify
remove_prefix="SpeciesConcVV_", then the bookmark for
that variable will be just "NO", etc.
verbose: bool
Set this flag to True to print extra informational output.
Expand Down Expand Up @@ -1168,7 +1168,7 @@ def add_lumped_species_to_dataset(
lspc_yaml="",
verbose=False,
overwrite=False,
prefix="SpeciesConc_",
prefix="SpeciesConcVV_",
):
"""
Function to calculate lumped species concentrations and add
Expand Down Expand Up @@ -1204,7 +1204,7 @@ def add_lumped_species_to_dataset(
also used to extract an existing dataarray in the dataset with
the correct size and dimensions to use during initialization of
new lumped species dataarrays.
Default value: "SpeciesConc_"
Default value: "SpeciesConcVV_"

Returns:
ds: xarray Dataset
Expand Down