import os
import numpy as np
import shutil
import xarray as xr
from compass.landice.tests.ismip6_forcing.atmosphere.create_mapfile_smb \
import build_mapping_file
from mpas_tools.io import write_netcdf
from mpas_tools.logging import check_call
from compass.step import Step
[docs]class ProcessSMB(Step):
"""
A step for processing the ISMIP6 surface mass balance data
"""
[docs] def __init__(self, test_case, input_file=None):
"""
Create the step
Parameters
----------
test_case : compass.landice.tests.ismip6_forcing.atmosphere.Atmosphere
The test case this step belongs to
input_file : file name of ismip6 forcing data processed by this step
"""
self.input_file = input_file
super().__init__(test_case=test_case, name="process_smb", ntasks=4,
min_tasks=1)
[docs] def setup(self):
"""
Set up this step of the test case
"""
config = self.config
section = config["ismip6_ais"]
base_path_ismip6 = section.get("base_path_ismip6")
base_path_mali = section.get("base_path_mali")
output_base_path = section.get("output_base_path")
mali_mesh_name = section.get("mali_mesh_name")
mali_mesh_file = section.get("mali_mesh_file")
period_endyear = section.get("period_endyear")
model = section.get("model")
scenario = section.get("scenario")
res_ismip6 = section.get("res_ismip6")
self.add_input_file(filename=mali_mesh_file,
target=os.path.join(base_path_mali,
mali_mesh_file))
input_file_list = \
self._files[period_endyear][model][scenario][res_ismip6]
for file in input_file_list:
self.add_input_file(filename=os.path.basename(file),
target=os.path.join(base_path_ismip6,
file))
output_file_esm = f"{mali_mesh_name}_SMB_{model}_{scenario}_" \
f"{period_endyear}.nc"
self.add_output_file(filename=output_file_esm)
# add processed racmo data as input as it is needed for smb correction
racmo_clim_file = f"{mali_mesh_name}_RACMO2.3p2_ANT27" \
f"_smb_climatology_1995-2017.nc"
racmo_path = f"{output_base_path}/atmosphere_forcing/" \
f"RACMO_climatology_1995-2017"
self.add_input_file(filename=racmo_clim_file,
target=os.path.join(racmo_path,
racmo_clim_file))
[docs] def run(self):
"""
Run this step of the test case
"""
logger = self.logger
config = self.config
section = config["ismip6_ais"]
mali_mesh_name = section.get("mali_mesh_name")
mali_mesh_file = section.get("mali_mesh_file")
period_endyear = section.get("period_endyear")
model = section.get("model")
scenario = section.get("scenario")
res_ismip6 = section.get("res_ismip6")
output_base_path = section.get("output_base_path")
section = config["ismip6_ais_atmosphere"]
method_remap = section.get("method_remap")
# define file names needed
# input racmo climotology file
racmo_clim_file = f"{mali_mesh_name}_RACMO2.3p2_ANT27" \
f"_smb_climatology_1995-2017.nc"
racmo_path = f"{output_base_path}/atmosphere_forcing/" \
f"RACMO_climatology_1995-2017"
# check if the processed racmo input file exists
racmo_clim_file_final = os.path.join(racmo_path, racmo_clim_file)
if not os.path.exists(racmo_clim_file_final):
raise ValueError("Processed RACMO data does not exist, "
"but it is required as an input file "
"to run this step. Please run `process_smb_racmo`"
"step prior to running this step by setting"
"the config option 'process_smb_racmo' to 'True'.")
# temporary remapped climatology and anomaly files
clim_ismip6_temp = "clim_ismip6.nc"
remapped_clim_ismip6_temp = "remapped_clim_ismip6.nc"
remapped_anomaly_ismip6_temp = "remapped_anomaly_ismip6.nc"
# renamed remapped climatology and anomaly files (final outputs)
output_clim_ismip6 = f"{mali_mesh_name}_SMB_climatology_1995-2017_" \
f"{model}_{scenario}.nc"
output_anomaly_ismip6 = f"{mali_mesh_name}_SMB_{model}_{scenario}_" \
f"{period_endyear}.nc"
# combine ismip6 forcing data covering different periods
# into a single file
input_file_list = \
self._files[period_endyear][model][scenario][res_ismip6]
i = 0
for file in input_file_list:
input_file_list[i] = os.path.basename(file)
i += 1
input_file_combined = xr.open_mfdataset(input_file_list,
concat_dim='time',
combine='nested',
engine='netcdf4')
combined_file_temp = "combined.nc"
write_netcdf(input_file_combined, combined_file_temp)
# create smb climatology data over 1995-2017
# take the time average over the period 1995-2017
# note: make sure to have the correct time indexing for each
# smb anomaly files on which climatology is calculated.
logger.info(f"Calculating climatology for {model}_{scenario} forcing"
f"over 1995-2017")
args = [f"ncra", "-O", "-F", "-d", "time,1,23",
f"{combined_file_temp}",
f"{clim_ismip6_temp}"]
check_call(args, logger=logger)
# remap and rename the ismip6 smb climatology
logger.info("Remapping ismip6 climatology onto MALI mesh...")
self.remap_ismip6_smb_to_mali(clim_ismip6_temp,
remapped_clim_ismip6_temp,
mali_mesh_name,
mali_mesh_file,
method_remap)
# rename the ismip6 variables to MALI variables
logger.info("Renaming the ismip6 variables to mali variable names...")
self.rename_ismip6_smb_to_mali_vars(remapped_clim_ismip6_temp,
output_clim_ismip6)
# remap and rename ismip6 smb anomaly
logger.info(f"Remapping the {model}_{scenario} SMB anomaly onto "
f"MALI mesh")
self.remap_ismip6_smb_to_mali(combined_file_temp,
remapped_anomaly_ismip6_temp,
mali_mesh_name,
mali_mesh_file,
method_remap)
# rename the ismip6 variables to MALI variables
logger.info("Renaming the ismip6 variables to mali variable names...")
self.rename_ismip6_smb_to_mali_vars(remapped_anomaly_ismip6_temp,
output_anomaly_ismip6)
# correct the SMB anomaly field with mali base SMB field
logger.info("Correcting the SMB anomaly field for the base SMB "
"climatology 1995-2017...")
self.correct_smb_anomaly_for_climatology(racmo_clim_file,
output_clim_ismip6,
output_anomaly_ismip6)
logger.info("Processing done successfully. "
"Removing the temporary files...")
# remove the temporary remapped and combined files
os.remove(remapped_clim_ismip6_temp)
os.remove(remapped_anomaly_ismip6_temp)
os.remove(combined_file_temp)
os.remove(clim_ismip6_temp)
os.remove(output_clim_ismip6)
# place the output file in appropriate directory
output_path = f"{output_base_path}/atmosphere_forcing/" \
f"{model}_{scenario}/1995-{period_endyear}"
if not os.path.exists(output_path):
print("Creating a new directory for the output data...")
os.makedirs(output_path)
src = os.path.join(os.getcwd(), output_anomaly_ismip6)
dst = os.path.join(output_path, output_anomaly_ismip6)
shutil.copy(src, dst)
logger.info(f"!---Done processing the file---!")
[docs] def remap_ismip6_smb_to_mali(self, input_file, output_file, mali_mesh_name,
mali_mesh_file, method_remap):
"""
Remap the input ismip6 smb forcing data onto mali mesh
Parameters
----------
input_file: str
input smb data on its native polarstereo 8km grid
output_file : str
smb data remapped on mali mesh
mali_mesh_name : str
name of the mali mesh used to name mapping files
mali_mesh_file : str, optional
The MALI mesh file if mapping file does not exist
method_remap : str, optional
Remapping method used in building a mapping file
"""
mapping_file = f"map_ismip6_8km_to_" \
f"{mali_mesh_name}_{method_remap}.nc"
# check if mapfile exists
if not os.path.exists(mapping_file):
# build a mapping file if it doesn't already exist
self.logger.info(f"Creating a mapping file. "
f"Mapping method used: {method_remap}")
build_mapping_file(self.config, self.ntasks, self.logger,
input_file, mapping_file, mali_mesh_file,
method_remap)
else:
self.logger.info("Mapping file exists. "
"Remapping the input data...")
# remap the input data
args = ["ncremap",
"-i", input_file,
"-o", output_file,
"-m", mapping_file,
"-v", "smb_anomaly"]
check_call(args, logger=self.logger)
[docs] def rename_ismip6_smb_to_mali_vars(self, remapped_file_temp, output_file):
"""
Rename variables in the remapped source input data
to the ones that MALI uses.
Parameters
----------
remapped_file_temp : str
temporary ismip6 data remapped on mali mesh
output_file : str
remapped ismip6 data renamed on mali mesh
"""
# open dataset in 20 years chunk
ds = xr.open_dataset(remapped_file_temp, chunks=dict(time=20),
engine="netcdf4")
# build dictionary for ismip6 variables that MALI takes in
ismip6_to_mali_dims = dict(
time="Time",
ncol="nCells")
ds = ds.rename(ismip6_to_mali_dims)
ismip6_to_mali_vars = dict(
smb_anomaly="sfcMassBal")
ds = ds.rename(ismip6_to_mali_vars)
# add xtime variable
xtime = []
for t_index in range(ds.sizes["Time"]):
date = ds.Time[t_index]
# forcing files do not all match even years, so round up the years
# pandas round function does not work for years, so do it manually
yr = date.dt.year.values
mo = date.dt.month.values
dy = date.dt.day.values
dec_yr = np.around(yr + (30 * (mo - 1) + dy) / 365.0)
date = f"{dec_yr.astype(int)}-01-01_00:00:00".ljust(64)
xtime.append(date)
ds["xtime"] = ("Time", xtime)
ds["xtime"] = ds.xtime.astype('S')
# drop unnecessary variables
ds = ds.drop_vars(["lon", "lon_vertices", "lat", "lat_vertices",
"area"])
# write to a new netCDF file
write_netcdf(ds, output_file)
ds.close()
[docs] def correct_smb_anomaly_for_climatology(self,
racmo_clim_file,
output_clim_ismip6_file,
output_file_final):
"""
Apply the MALI base SMB to the ismip6 SMB anomaly field
Parameters
----------
racmo_clim_file : str
RACMO climatology file (1995-2017)
output_clim_ismip6_file : str
remapped and renamed ismip6 climatology file
output_file_final : str
climatology-corrected, final ismip6 smb anomaly file
"""
ds = xr.open_dataset(output_file_final)
ds_racmo_clim = xr.open_dataset(racmo_clim_file)
ds_ismip6_clim = xr.open_dataset(output_clim_ismip6_file)
# calculate the climatology correction
corr_clim = (ds_racmo_clim["sfcMassBal"].isel(Time=0) -
ds_ismip6_clim["sfcMassBal"].isel(Time=0))
# correct the ismip6 smb anomaly
ds["sfcMassBal"] = ds["sfcMassBal"] + corr_clim
# write metadata
ds["sfcMassBal"].attrs = {"long_name" : "surface mass balance",
"units" : "kg m-2 s-1",
"coordinates" : "lat lon"}
# write to a new netCDF file
write_netcdf(ds, output_file_final)
ds.close()
# create a nested dictionary for the ISMIP6 original forcing files including relative path
# Note: these files needed to be explicitly listed because of inconsistencies that are
# present in file naming conventions in the ISMIP6 source dataset.
_files = {
"2100": {
"CCSM4": {
"RCP85": [
"AIS/Atmosphere_Forcing/ccsm4_rcp8.5/Regridded_8km/CCSM4_8km_anomaly_1995-2100.nc"]
},
"CESM2": {
"SSP585v1": [
"AIS/Atmosphere_Forcing/CESM2_ssp585/Regridded_8km/CESM2_anomaly_ssp585_1995-2100_8km_v1.nc"],
"SSP585v2": [
"AIS/Atmosphere_Forcing/CESM2_ssp585/Regridded_8km/CESM2_anomaly_ssp585_1995-2100_8km_v2.nc"]
},
"CNRM_CM6": {
"SSP126": [
"AIS/Atmosphere_Forcing/CNRM_CM6_ssp126/Regridded_8km/CNRM-CM6-1_anomaly_ssp126_1995-2100_8km_ISMIP6.nc"],
"SSP585": [
"AIS/Atmosphere_Forcing/CNRM_CM6_ssp585/Regridded_8km/CNRM-CM6-1_anomaly_ssp585_1995-2100_8km_ISMIP6.nc"]
},
"CNRM_ESM2": {
"SSP585": [
"AIS/Atmosphere_Forcing/CNRM_ESM2_ssp585/Regridded_8km/CNRM-ESM2-1_anomaly_ssp585_1995-2100_8km_ISMIP6.nc"]
},
"CSIRO-Mk3-6-0": {
"RCP85": [
"AIS/Atmosphere_Forcing/CSIRO-Mk3-6-0_rcp85/Regridded_8km/CSIRO-Mk3-6-0_8km_anomaly_rcp85_1995-2100.nc"]
},
"HadGEM2-ES": {
"RCP85": [
"AIS/Atmosphere_Forcing/HadGEM2-ES_rcp85/Regridded_8km/HadGEM2-ES_8km_anomaly_rcp85_1995-2100.nc"]
},
"IPSL-CM5A-MR": {
"RCP26": [
"AIS/Atmosphere_Forcing/IPSL-CM5A-MR_rcp26/Regridded_8km/IPSL-CM5A-MR_8km_anomaly_rcp26_1995-2100.nc"],
"RCP85": [
"AIS/Atmosphere_Forcing/IPSL-CM5A-MR_rcp85/Regridded_8km/IPSL-CM5A-MR_8km_anomaly_rcp85_1995-2100.nc"]
},
"MIROC-ESM-CHEM": {
"RCP85": [
"AIS/Atmosphere_Forcing/miroc-esm-chem_rcp8.5/Regridded_8km/MIROC-ESM-CHEM_8km_anomaly_1995-2100.nc"]
},
"NorESM1-M": {
"RCP26": [
"AIS/Atmosphere_Forcing/noresm1-m_rcp2.6/Regridded_8km/NorESM-M_8km_anomaly_rcp26_1995-2100.nc"],
"RCP85": [
"AIS/Atmosphere_Forcing/noresm1-m_rcp8.5/Regridded_8km/NorESM-M_8km_anomaly_1995-2100.nc"]
},
"UKESM1-0-LL": {
"SSP585": [
"AIS/Atmosphere_Forcing/UKESM1-0-LL/Regridded_8km/UKESM1-0-LL_anomaly_ssp585_1995-2100_8km.nc"]
}
},
"2300": {
"CCSM4": {
"RCP85": {
"4km": [
"AIS/Atmospheric_forcing/CCSM4_RCP85/Regridded_04km/CCSM4_4km_anomaly_1995-2100.nc",
"AIS/Atmospheric_forcing/CCSM4_RCP85/Regridded_04km/CCSM4_4km_anomaly_2101-2300.nc"],
"8km": [
"AIS/Atmospheric_forcing/CCSM4_RCP85/Regridded_08km/CCSM4_8km_anomaly_1995-2100.nc",
"AIS/Atmospheric_forcing/CCSM4_RCP85/Regridded_08km/CCSM4_8km_anomaly_2101-2300.nc"]
},
},
"CESM2-WACCM": {
"SSP585": {
"4km": [
"AIS/Atmospheric_forcing/CESM2-WACCM_ssp585/Regridded_4km/CESM2-WACCM_4km_anomaly_ssp585_1995-2100.nc",
"AIS/Atmospheric_forcing/CESM2-WACCM_ssp585/Regridded_4km/CESM2-WACCM_4km_anomaly_ssp585_2101-2299.nc"],
"8km": [
"AIS/Atmospheric_forcing/CESM2-WACCM_ssp585/Regridded_8km/CESM2-WACCM_8km_anomaly_ssp585_1995-2100.nc",
"AIS/Atmospheric_forcing/CESM2-WACCM_ssp585/Regridded_8km/CESM2-WACCM_8km_anomaly_ssp585_2101-2299.nc"]
},
"SSP585-repeat": {
"4km": [
"AIS/Atmospheric_forcing/CESM2-WACCM_ssp585-repeat/Regridded_4km/CESM2-WACCM_4km_anomaly_ssp585_1995-2300_v2.nc"],
"8km": [
"AIS/Atmospheric_forcing/CESM2-WACCM_ssp585-repeat/Regridded_8km/CESM2-WACCM_8km_anomaly_ssp585_1995-2300_v2.nc"]
},
},
"HadGEM2-ES": {
"RCP85": {
"4km": [
"AIS/Atmospheric_forcing/HadGEM2-ES_RCP85/Regridded_4km/HadGEM2-ES_4km_anomaly_rcp85_1995-2100.nc",
"AIS/Atmospheric_forcing/HadGEM2-ES_RCP85/Regridded_4km/HadGEM2-ES_4km_anomaly_rcp85_2101-2299.nc"],
"8km": [
"AIS/Atmospheric_forcing/HadGEM2-ES_RCP85/Regridded_8km/HadGEM2-ES_8km_anomaly_rcp85_1995-2100.nc",
"AIS/Atmospheric_forcing/HadGEM2-ES_RCP85/Regridded_8km/HadGEM2-ES_8km_anomaly_rcp85_2101-2299.nc"]
},
"RCP85-repeat": {
"4km": [
"AIS/Atmospheric_forcing/HadGEM2-ES-RCP85-repeat/Regridded_4km/HadGEM2-ES_4km_anomaly_rcp85_1995-2300_v2.nc"],
"8km": [
"AIS/Atmospheric_forcing/HadGEM2-ES-RCP85-repeat/Regridded_8km/HadGEM2-ES_8km_anomaly_rcp85_1995-2300_v2.nc"]
},
},
"NorESM1-M": {
"RCP26-repeat": {
"4km": [
"AIS/Atmospheric_forcing/NorESM1-M_RCP26-repeat/Regridded_4km/NorESM1-M_4km_anomaly_rcp26_1995-2300_v3.nc"],
"8km": [
"AIS/Atmospheric_forcing/NorESM1-M_RCP26-repeat/Regridded_8km/NorESM1-M_8km_anomaly_rcp26_1995-2300_v2.nc"]
},
"RCP85-repeat": {
"4km": [
"AIS/Atmospheric_forcing/NorESM1-M_RCP85-repeat/Regridded_4km/NorESM1-M_4km_anomaly_1995-2300_v2.nc"],
"8km": [
"AIS/Atmospheric_forcing/NorESM1-M_RCP85-repeat/Regridded_8km/NorESM1-M_8km_anomaly_1995-2300_v2.nc"]
},
},
"UKESM1-0-LL": {
"SSP126": {
"4km": [
"AIS/Atmospheric_forcing/UKESM1-0-LL_ssp126/Regridded_4km/UKESM1-0-LL_4km_anomaly_ssp126_1995-2100.nc",
"AIS/Atmospheric_forcing/UKESM1-0-LL_ssp126/Regridded_4km/UKESM1-0-LL_4km_anomaly_ssp126_2101-2300.nc"],
"8km": [
"AIS/Atmospheric_forcing/UKESM1-0-LL_ssp126/Regridded_8km/UKESM1-0-LL_8km_anomaly_ssp126_1995-2100.nc",
"AIS/Atmospheric_forcing/UKESM1-0-LL_ssp126/Regridded_8km/UKESM1-0-LL_8km_anomaly_ssp126_2101-2300.nc"]
},
"SSP585": {
"4km": [
"AIS/Atmospheric_forcing/UKESM1-0-LL_ssp585/Regridding_4km/UKESM1-0-LL_4km_anomaly_ssp585_1995-2100.nc",
"AIS/Atmospheric_forcing/UKESM1-0-LL_ssp585/Regridding_4km/UKESM1-0-LL_4km_anomaly_ssp585_2101-2300.nc"],
"8km": [
"AIS/Atmospheric_forcing/UKESM1-0-LL_ssp585/Regridding_8km/UKESM1-0-LL_8km_anomaly_ssp585_1995-2100.nc",
"AIS/Atmospheric_forcing/UKESM1-0-LL_ssp585/Regridding_8km/UKESM1-0-LL_8km_anomaly_ssp585_2101-2300.nc"]
},
"SSP585-repeat": {
"4km": [
"AIS/Atmospheric_forcing/UKESM1-0-LL_ssp585-repeat/Regridding_4km/UKESM1-0-LL_4km_anomaly_ssp585_1995-2300_v2.nc"],
"8km": [
"AIS/Atmospheric_forcing/UKESM1-0-LL_ssp585-repeat/Regridding_8km/UKESM1-0-LL_8km_anomaly_ssp585_1995-2300_v2.nc"]
}
}
}
}