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Merge PR #309 (Mass cons tables include Ref and Dev)
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This merge brings PR #309 (Update mass conservation tables to include
Ref & Dev in the same file, by @yantosca) into the GCPy 1.5.0
development stream.

This PR modifies the PassiveTracer mass table so that Ref, Dev,
Dev - Ref, and % diff are included in the same file.

Signed-off-by: Bob Yantosca <[email protected]>
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yantosca committed May 15, 2024
2 parents 18f03d5 + af8ef64 commit 936ce78
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -29,6 +29,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
- Benchmark script `gcpy/benchmark/modules/benchmark_scrape_gchp_timers.py`
- 1-year benchmark scripts now produce GCC vs GCC and GCHP vs GCHP timing tables
- Functions `gcc_vs_gcc_dirs`, `gchp_vs_gcc_dirs`, `gchp_vs_gchp_dirs`, and `get_log_filepaths` in `gcpy/benchmark/modules/benchmark_utils.py`
- Script `gcpy/benchmark/modules/benchmark_mass_cons_table.py`, with code to create mass conservation tables
- Expanded statistics output in benchmark mass conservation tables
- Function `get_datetimes_from_filenames` in `gcpy/benchmark/modules/benchmark_utils.py`
- Function `replace_whitespace` in `gcpy/util.py`

### Changed
- Bump pip from 23.2.1 to 23.3 (dependabot suggested this)
Expand Down Expand Up @@ -72,6 +76,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
- Environment file `docs/environment_files/requirements.txt`
- Removed `awscli` from the GCPy environment; version 2 is no longer available on conda-forge or PyPi
- GitHub config files `.github/stale.yml` and `.github/no-response.yml`
- Routine `make_benchmark_mass_conservation_table` in `benchmark_funcs.py`; this is now obsolete

## [1.4.2] - 2024-01-26
### Added
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166 changes: 0 additions & 166 deletions gcpy/benchmark/modules/benchmark_funcs.py
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Expand Up @@ -4915,172 +4915,6 @@ def make_benchmark_operations_budget(
gc.collect()


def make_benchmark_mass_conservation_table(
datafiles,
runstr,
dst="./benchmark",
overwrite=False,
areapath=None,
spcdb_dir=os.path.dirname(__file__)
):
"""
Creates a text file containing global mass of the PassiveTracer
from Transport Tracer simulations across a series of restart files.
Args:
datafiles: list of str
Path names of restart files.
runstr: str
Name to put in the filename and header of the output file
Keyword Args (optional):
dst: str
A string denoting the destination folder where the file
containing emissions totals will be written.
Default value: "./benchmark"
overwrite: bool
Set this flag to True to overwrite files in the
destination folder (specified by the dst argument).
Default value: False
areapath: str
Path to a restart file containing surface area data.
Default value: None
spcdb_dir: str
Path to the species_database.yml
Default value: points to gcpy/gcpy folder
"""

# ==================================================================
# Initialize
# ==================================================================

# Create the destination folder
util.make_directory(dst, overwrite)

# Load a YAML file containing species properties (such as
# molecular weights), which we will need for unit conversions.
properties = util.read_config_file(
os.path.join(
spcdb_dir,
"species_database.yml"
),
quiet=True
)

# Get the species name
spc_name = 'PassiveTracer'

# Get a list of properties for the given species
species_properties = properties.get(spc_name)

# Specify target units
target_units = "Tg"

dates = []
masses = []

# ==================================================================
# Make sure that surface area data is found
# ==================================================================
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=xr.SerializationWarning)


# ==================================================================
# Calculate global mass for the tracer at all restart dates
# ==================================================================
for f in datafiles:
ds = xr.open_dataset(f, drop_variables=skip_these_vars)

# Save date in desired format
#datestr = str(pd.to_datetime(ds.time.values[0]))
#dates.append(datestr[:4] + '-' + datestr[5:7] + '-' + datestr[8:10])

# Find the area variable in Dev
if areapath is None:
area = util.get_area_from_dataset(ds)
else:
area = util.get_area_from_dataset(
xr.open_dataset(
areapath,
drop_variables=skip_these_vars
)
)

# Assume typical restart file name format, but avoid using dates
# from within files which may be incorrect for the initial restart
datestr = f.split('/')[-1].split('.')[2][:9]
dates.append(datestr[:4] + '-' + datestr[4:6] + '-' + datestr[6:8])

# Select for GCC or GCHP
delta_p = ds['Met_DELPDRY'] if 'Met_DELPDRY' in list(ds.data_vars) else ds['DELP_DRY']

# ==============================================================
# Convert units of Ref and save to a DataArray
# (or skip if Ref contains NaNs everywhere)
# ==============================================================
# Select for GCC or GCHP
if 'SpeciesRst_PassiveTracer' in list(ds.data_vars):
attrs = ds['SpeciesRst_PassiveTracer'].attrs
da = ds['SpeciesRst_PassiveTracer'].astype(np.float64)
da.attrs = attrs
else:
attrs = ds['SPC_PassiveTracer'].attrs
da = ds['SPC_PassiveTracer'].astype(np.float64)
da.attrs = attrs
da = convert_units(
da,
spc_name,
species_properties,
target_units,
area_m2=area,
delta_p=delta_p
)

# Save total global mass
masses.append(np.sum(da.values))

# Clean up
del ds
del da
gc.collect()

# Calclate max and min mass, absolute diff, percent diff
max_mass = np.max(masses)
min_mass = np.min(masses)
# Convert absdiff to grams
absdiff = (max_mass-min_mass) * 10**12
pctdiff = (max_mass-min_mass)/min_mass * 100

# ==================================================================
# Print masses to file
# ==================================================================
# Create file
outfilename = os.path.join(dst, f"Passive_mass.{runstr}.txt")

with open(outfilename, 'w') as f:
titlestr = ' Global Mass of Passive Tracer in ' + runstr + ' '
#headers
print('%' * (len(titlestr)+4), file=f)
print(titlestr, file=f)
print('%' * (len(titlestr)+4), file=f)
print('', file=f)
print(' Date' + ' ' * 8 + 'Mass [Tg]', file=f)
print(' ' + '-' * 10 + ' ' + '-' * 16, file=f)
#masses
for i in range(len(masses)):
print(f" {dates[i]} {masses[i] : 11.13f}", file=f)
print(' ', file=f)
print(' Summary', file=f)
print(' ' + '-' * 30, file=f)
print(f" Max mass = {max_mass : 2.13f} Tg", file=f)
print(f" Min mass = {min_mass : 2.13f} Tg", file=f)
print(f" Abs diff = {absdiff : >16.3f} g", file=f)
print(f" Pct diff = {pctdiff : >16.10f} %", file=f)

gc.collect()


def get_species_database_dir(config):
"""
Returns the directory in which the species_database.yml file is
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