def setup_analytical_spin(self, number, st_yr_spin, en_yr_spin):
"""
Adjust the CABLE namelist file with the various flags for the
analytical spin step
"""
out_log_fname = "%s_log_analytic_%d.txt" % (self.experiment_id, number)
out_log_fname = os.path.join(self.log_dir, out_log_fname)
if os.path.isfile(out_log_fname):
os.remove(out_log_fname)
self.out_fname_CASA = "%s_out_CASA_analytic_%d.nc" % \
(self.experiment_id, number)
self.out_fname_CASA = os.path.join(self.output_dir,
self.out_fname_CASA)
if os.path.isfile(self.out_fname_CASA):
os.remove(self.out_fname_CASA)
replace_dict = {
"filename%log": "'%s'" % (out_log_fname),
"icycle":
"%d" % (self.biogeochem + 10), # Need to add 10 for spinup
"cable_user%CASA_DUMP_READ": ".TRUE.",
"cable_user%CASA_DUMP_WRITE": ".FALSE.",
"cable_user%CASA_NREP": "1",
"cable_user%SOIL_STRUC":
"'default'", # THIS needs to be default, we don't turn sli on here, presumably because it is too slow but does this make sense?
"leaps": ".FALSE.",
"spincasa": ".TRUE.",
#"casafile%c2cdumppath": "'./'",
"cable_user%CASA_SPIN_STARTYEAR": "%d" % (st_yr_spin),
"cable_user%CASA_SPIN_ENDYEAR": "%d" % (en_yr_spin),
"casafile%out": "'%s'" % (self.out_fname_CASA),
}
adjust_nml_file(self.nml_fname, replace_dict)
def inital_spin_setup(self, site, met_fname, sci_config, number=None):
"""
Initial setup for CASA spinup from zero
"""
base_nml_fn = os.path.join(self.grid_dir, "%s" % (self.nml_fname))
nml_fname = "cable_%s.nml" % (site)
shutil.copy(base_nml_fn, nml_fname)
self.nml_fname = nml_fname
out_fname = "%s_out_cable_spin_%d.nc" % (self.experiment_id, number)
out_fname = os.path.join(self.output_dir, out_fname)
out_log_fname = "%s_log_spin_%d.txt" % (self.experiment_id, number)
out_log_fname = os.path.join(self.log_dir, out_log_fname)
cable_rst_ofname = "%s_cable_rst_%d.nc" % (self.experiment_id, number)
cable_rst_ofname = os.path.join(self.restart_dir, cable_rst_ofname)
casa_rst_ofname = "%s_casa_rst_%d.nc" % (self.experiment_id, number)
casa_rst_ofname = os.path.join(self.restart_dir, casa_rst_ofname)
replace_dict = {
"filename%met": "'%s'" % (met_fname),
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_in": "' '",
"filename%restart_out": "'%s'" % (cable_rst_ofname),
"casafile%cnpipool": "' '",
"casafile%cnpepool": "'%s'" % (casa_rst_ofname),
"filename%type": "'%s'" % (self.grid_fname),
"filename%veg": "'%s'" % (self.veg_fname),
"filename%soil": "'%s'" % (self.soil_fname),
"fixedCO2": "%.2f" % (self.co2_conc),
"casafile%phen": "'%s'" % (self.phen_fname),
"casafile%cnpbiome": "'%s'" % (self.cnpbiome_fname),
"cable_user%FWSOIL_SWITCH": "'standard'",
"cable_user%GS_SWITCH": "'medlyn'",
"cable_user%RunIden": "'%s'" % (self.experiment_id),
"cable_user%vcmax": "'%s'" % (self.vcmax),
"l_vcmaxFeedbk": "%s" % (self.vcmax_feedback),
"l_laiFeedbk": ".TRUE.", # prognoistic LAI
"icycle": "%d" % (self.biogeochem_id),
"cable_user%CASA_OUT_FREQ": "'monthly'",
"output%casa": ".TRUE.",
"leaps": ".TRUE.",
"cable_user%CASA_fromZero": ".TRUE.",
"cable_user%CASA_DUMP_READ": ".FALSE.",
"cable_user%CASA_DUMP_WRITE": ".FALSE.",
"cable_user%CASA_NREP": "0",
"spincasa": ".FALSE.",
"output%restart": ".TRUE.",
}
# Make sure the dict isn't empty
if bool(sci_config):
replace_dict = merge_two_dicts(replace_dict, sci_config)
adjust_nml_file(self.nml_fname, replace_dict)
def worker(self, met_files, url, rev):
for fname in met_files:
site = os.path.basename(fname).split(".")[0].split("_")[0]
base_nml_fn = os.path.join(self.grid_dir, "%s" % (self.nml_fname))
nml_fname = "cable_%s.nml" % (site)
shutil.copy(base_nml_fn, nml_fname)
(out_fname, out_log_fname) = self.clean_up_old_files(site)
# ./plot_E_vs_psi_leaf.py, looks a reasonable match to obs
# we don't hit the max, but the bulk of the values are in the right place
Kmax_value = 0.4
#b_plant = 3.7616378326944595 # calculated from vlc
#c_plant = 10.289003851919992 # calculated from vlc
b_plant = 3.7989857501917563 # calculated from vlc, using p98
c_plant = 8.054967903830414 # calculated from vlc, using p98
vcmax = 30. # Belinda estimated this from their data
fname = change_traits(fname, site, Kmax_value, b_plant, c_plant,
vcmax, self.zse)
# Add LAI to met file?
if self.fixed_lai is not None or self.lai_dir is not None:
fname = change_LAI(fname,
site,
fixed=self.fixed_lai,
lai_dir=self.lai_dir)
replace_dict = {
"filename%met": "'%s'" % (fname),
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_out": "' '",
"filename%type": "'%s'" % (self.grid_fname),
"output%restart": ".FALSE.",
#"fixedCO2": "%.2f" % (self.co2_conc),
"casafile%phen": "'%s'" % (self.phen_fname),
"casafile%cnpbiome": "'%s'" % (self.cnpbiome_fname),
"cable_user%GS_SWITCH": "'medlyn'",
"cable_user%GW_MODEL": ".FALSE.",
"cable_user%or_evap": ".FALSE.",
"redistrb": ".FALSE.",
"spinup": ".FALSE.",
"cable_user%litter": ".TRUE.",
"cable_user%FWSOIL_SWITCH": "'%s'" % (self.fwsoil),
}
adjust_nml_file(nml_fname, replace_dict)
self.run_me(nml_fname)
add_attributes_to_output_file(nml_fname, out_fname, url, rev)
shutil.move(nml_fname, os.path.join(self.namelist_dir, nml_fname))
if self.fixed_lai is not None or self.lai_dir is not None:
os.remove("%s_tmp.nc" % (site))
def worker(self, met_files, url, rev):
for fname in met_files:
site = os.path.basename(fname).split(".")[0]
base_nml_fn = os.path.join(self.grid_dir, "%s" % (self.nml_fname))
nml_fname = "cable_%s.nml" % (site)
shutil.copy(base_nml_fn, nml_fname)
(out_fname, out_log_fname) = self.clean_up_old_files(site)
# Add LAI to met file?
if self.fixed_lai is not None or self.lai_dir is not None:
fname = change_LAI(fname,
site,
fixed=self.fixed_lai,
lai_dir=self.lai_dir)
if self.fwsoil == "hydraulics":
if site == "WombatStateForestOzFlux2":
fname = change_iveg(fname, site, 20)
else:
fname = change_iveg(fname, site, 19)
elif self.fwsoil == "standard":
fname = change_iveg(fname, site, 2)
replace_dict = {
"filename%met": "'%s'" % (fname),
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_out": "' '",
"filename%type": "'%s'" % (self.grid_fname),
"filename%veg": "'%s'" % (self.veg_fname),
"filename%soil": "'%s'" % (self.soil_fname),
"output%restart": ".FALSE.",
"fixedCO2": "%.2f" % (self.co2_conc),
"casafile%phen": "'%s'" % (self.phen_fname),
"casafile%cnpbiome": "'%s'" % (self.cnpbiome_fname),
"cable_user%GS_SWITCH": "'medlyn'",
"cable_user%GW_MODEL": ".FALSE.",
"cable_user%or_evap": ".FALSE.",
"redistrb": ".FALSE.",
"spinup": ".TRUE.",
"cable_user%FWSOIL_SWITCH": "'%s'" % (self.fwsoil),
}
adjust_nml_file(nml_fname, replace_dict)
self.run_me(nml_fname)
add_attributes_to_output_file(nml_fname, out_fname, url, rev)
shutil.move(nml_fname, os.path.join(self.namelist_dir, nml_fname))
if self.fixed_lai is not None or self.lai_dir is not None:
os.remove("%s_tmp.nc" % (site))
os.remove("new_sumbal")
def worker(self, met_files, url, rev):
fname = met_files
site = os.path.basename(fname).split(".")[0].split("_")[0]
print(fname)
ring = os.path.basename(fname).split(".")[0].split("_")[2]
base_nml_fn = os.path.join(self.grid_dir, "%s" % (self.nml_fname))
nml_fname = "cable_%s_%s_%s.nml" % (site, self.met_fname,
self.case_name)
shutil.copy(base_nml_fn, nml_fname)
(out_fname, out_log_fname,
out_restart_fname) = self.clean_up_old_files(site, ring)
# Add LAI to met file?
if self.fixed_lai is not None or self.lai_dir is not None:
fname = change_LAI(fname,
site,
fixed=self.fixed_lai,
lai_dir=self.lai_dir)
replace_dict = {
"filename%met": "'%s'" % (fname),
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"spinup": ".FALSE.",
#"filename%restart_in": "'%s'" % (out_restart_fname),
"filename%restart_out": "'%s'" % (out_restart_fname),
"filename%type": "'%s'" % (self.grid_fname),
#"filename%gw_elev": "'%s'" % (self.elev_fname)
"filename%veg": "'%s'" % (self.veg_fname),
"filename%soil": "'%s'" % (self.soil_fname),
"output%restart": ".TRUE.",
"casafile%phen": "'%s'" % (self.phen_fname),
"casafile%cnpbiome": "'%s'" % (self.cnpbiome_fname),
#"cable_user%FWSOIL_SWITCH": "'Haverd2013'",
#"cable_user%FWSOIL_SWITCH": "'standard'",
"cable_user%FWSOIL_SWITCH": "'hie_exp'",
"cable_user%GS_SWITCH": "'medlyn'",
"cable_user%GW_MODEL": ".TRUE.",
"cable_user%or_evap": ".FALSE.",
"cable_user%MetType": "site",
"gw_params%BC_hysteresis": ".FALSE.",
"gw_params%HC_SWC": "FALSE",
"gw_params%ssgw_ice_switch": ".TRUE.",
"cable_user%litter": ".TRUE.",
}
adjust_nml_file(nml_fname, replace_dict)
self.run_me(nml_fname)
add_attributes_to_output_file(nml_fname, out_fname, url, rev)
shutil.move(nml_fname, os.path.join(self.namelist_dir, nml_fname))
if self.fixed_lai is not None or self.lai_dir is not None:
os.remove("%s_tmp.nc" % (site))
def worker(self, met_files, url, rev, param_names, param_values, out_fname,
out_log_fname):
for fname in met_files:
site = os.path.basename(fname).split("_")[0]
base_nml_fn = os.path.join(self.grid_dir, "%s" % (self.nml_fname))
nml_fname = "cable_%s.nml" % (site)
shutil.copy(base_nml_fn, nml_fname)
(out_fname, out_log_fname) = self.clean_up_old_files(site)
# Add LAI to met file?
if self.fixed_lai is not None or self.lai_dir is not None:
fname = change_LAI(fname,
site,
fixed=self.fixed_lai,
lai_dir=self.lai_dir)
# Set tree, grass and bare fracs, measurement height etc
fname = set_site_info(fname, site)
replace_dict = {
"filename%met": "'%s'" % (fname),
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_out": "' '",
"filename%type": "'%s'" % (self.grid_fname),
"filename%veg": "'%s'" % (self.veg_fname),
"filename%soil": "'%s'" % (self.soil_fname),
"output%restart": ".FALSE.",
#"output%patch": ".TRUE.", # get all patches
"output%patch": ".FALSE.", # get all patches
"fixedCO2": "%.2f" % (self.co2_conc),
"casafile%phen": "'%s'" % (self.phen_fname),
"casafile%cnpbiome": "'%s'" % (self.cnpbiome_fname),
"cable_user%FWSOIL_SWITCH": "'standard'",
"cable_user%GS_SWITCH": "'medlyn'",
"cable_user%GW_MODEL": ".FALSE.",
"cable_user%or_evap": ".FALSE.",
"spinup": ".FALSE.",
"verbose": ".FALSE.",
}
adjust_nml_file(nml_fname, replace_dict)
self.run_me(nml_fname)
add_attributes_to_output_file(nml_fname, out_fname, url, rev)
shutil.move(nml_fname, os.path.join(self.namelist_dir, nml_fname))
if self.fixed_lai is not None or self.lai_dir is not None:
os.remove("%s_tmp.nc" % (site))
def worker(self, met_files, url, rev):
for fname in met_files:
species = '_'.join((os.path.basename(fname).split("_")[2:4]))
num = os.path.basename(fname).split("_")[-1].split(".")[0]
site = "%s_%s" % (species, num)
base_nml_fn = os.path.join(self.grid_dir, "%s" % (self.nml_fname))
nml_fname = "cable_%s.nml" % (site)
shutil.copy(base_nml_fn, nml_fname)
(out_fname, out_log_fname) = self.clean_up_old_files(site)
spp_traits = self.traits[self.traits.species == \
species.replace("_", " ")]
if len(spp_traits) > 0:
b_plant = float(spp_traits.b_plant.values[0])
c_plant = float(spp_traits.c_plant.values[0])
vcmax = float(spp_traits.vcmax.values[0])
fname_new = change_traits(fname, id, site, b_plant, c_plant,
vcmax)
replace_dict = {
"filename%met": "'%s'" % (fname_new),
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_out": "' '",
"filename%type": "'%s'" % (self.grid_fname),
"output%restart": ".FALSE.",
"fixedCO2": "%.2f" % (self.co2_conc),
"casafile%phen": "'%s'" % (self.phen_fname),
"casafile%cnpbiome": "'%s'" % (self.cnpbiome_fname),
"cable_user%GS_SWITCH": "'medlyn'",
"cable_user%GW_MODEL": ".FALSE.",
"cable_user%or_evap": ".FALSE.",
"redistrb": ".FALSE.",
"spinup": ".FALSE.",
"cable_user%litter": ".TRUE.",
"cable_user%FWSOIL_SWITCH": "'%s'" % (self.fwsoil),
}
adjust_nml_file(nml_fname, replace_dict)
self.run_me(nml_fname)
add_attributes_to_output_file(nml_fname, out_fname, url, rev)
shutil.move(nml_fname, os.path.join(self.namelist_dir, nml_fname))
os.remove(fname_new)
os.remove("new_sumbal")
def worker(self, met_files, url, rev, sci_config, repo_id, sci_id):
cwd = os.getcwd()
for fname in met_files:
site = os.path.basename(fname).split(".")[0]
base_nml_fn = os.path.join(self.grid_dir, "%s" % (self.nml_fname))
nml_fname = "cable_%s_R%s_S%s.nml" % (site, repo_id, sci_id)
shutil.copy(base_nml_fn, nml_fname)
#nml_fname = os.path.join(cwd, nml_fname)
(out_fname,
out_log_fname) = self.clean_up_old_files(site, repo_id, sci_id)
# Add LAI to met file?
if self.fixed_lai is not None or self.lai_dir is not None:
fname = change_LAI(fname,
site,
fixed=self.fixed_lai,
lai_dir=self.lai_dir)
replace_dict = {
"filename%met": "'%s'" % (fname),
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_out": "' '",
"filename%type": "'%s'" % (self.grid_fname),
"filename%veg": "'%s'" % (self.veg_fname),
"filename%soil": "'%s'" % (self.soil_fname),
"output%restart": ".FALSE.",
"fixedCO2": "%.2f" % (self.co2_conc),
"casafile%phen": "'%s'" % (self.phen_fname),
"casafile%cnpbiome": "'%s'" % (self.cnpbiome_fname),
"spinup": ".FALSE.",
}
# Make sure the dict isn't empty
if bool(sci_config):
replace_dict = merge_two_dicts(replace_dict, sci_config)
adjust_nml_file(nml_fname, replace_dict)
self.run_me(nml_fname)
add_attributes_to_output_file(nml_fname, out_fname, sci_config,
url, rev)
shutil.move(nml_fname, os.path.join(self.namelist_dir, nml_fname))
if self.fixed_lai is not None or self.lai_dir is not None:
os.remove("%s_tmp.nc" % (site))
def setup_analytical_spin(self, st_yr, en_yr, number=None):
"""
Adjust the CABLE namelist file with the various flags for the
analytical spin step
"""
out_fname = "%s_out_cable_aspin_%d.nc" % (self.experiment_id, number)
out_fname = os.path.join(self.output_dir, out_fname)
out_log_fname = "%s_log_aspin_%d.txt" % (self.experiment_id, number)
out_log_fname = os.path.join(self.log_dir, out_log_fname)
# This step doesn't write an output CABLE rst file.
cable_rst_ifname = "%s_cable_rst_%d.nc" % (self.experiment_id,
number - 1)
cable_rst_ifname = os.path.join(self.restart_dir, cable_rst_ifname)
casa_rst_ifname = "%s_casa_rst_%d.nc" % (self.experiment_id,
number - 1)
casa_rst_ifname = os.path.join(self.restart_dir, casa_rst_ifname)
# This will overwrite the current restart file for CASA but that is
# fine.
casa_rst_ofname = "%s_casa_rst_%d.nc" % (self.experiment_id, number)
casa_rst_ofname = os.path.join(self.restart_dir, casa_rst_ofname)
replace_dict = {
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_in": "'%s'" % (cable_rst_ifname),
"casafile%cnpipool": "'%s'" % (casa_rst_ifname),
"casafile%cnpepool": "'%s'" % (casa_rst_ofname),
#"casafile%cnpepool": "' '",
"icycle":
"%d" % (self.biogeochem_id + 10), # Need to add 10 for spinup
"cable_user%CASA_DUMP_READ": ".TRUE.",
"cable_user%CASA_DUMP_WRITE": ".FALSE.",
"cable_user%CASA_NREP": "1",
"spincasa": ".TRUE.",
"cable_user%CASA_SPIN_STARTYEAR": "%d" % (st_yr),
"cable_user%CASA_SPIN_ENDYEAR": "%d" % (en_yr),
#"cable_user%YearStart": "%d" % (st_yr),
#"cable_user%YearEnd": "%d" % (en_yr),
"output%restart": ".TRUE.",
"leaps": ".FALSE.",
}
adjust_nml_file(self.nml_fname, replace_dict)
def worker(self, met_files, url, rev):
for fname in met_files:
site = os.path.basename(fname).split(".")[0]
print(site)
base_nml_fn = os.path.join(self.grid_dir, "%s" % (self.nml_fname))
nml_fname = "cable_%s.nml" % (site)
shutil.copy(base_nml_fn, nml_fname)
(out_fname, out_log_fname) = self.clean_up_old_files(site)
# Add LAI to met file?
if self.fixed_lai is not None or self.lai_dir is not None:
fname = change_LAI(fname,
site,
fixed=self.fixed_lai,
lai_dir=self.lai_dir)
replace_dict = {
"filename%met": "'%s'" % (fname),
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_out": "' '",
"filename%type": "'%s'" % (self.grid_fname),
"filename%veg": "'%s'" % (self.veg_fname),
"filename%soil": "'%s'" % (self.soil_fname),
"output%restart": ".FALSE.",
"fixedCO2": "%.2f" % (self.co2_conc),
"casafile%phen": "'%s'" % (self.phen_fname),
"casafile%cnpbiome": "'%s'" % (self.cnpbiome_fname),
"cable_user%FWSOIL_SWITCH": "'Haverd2013'",
"cable_user%GS_SWITCH": "'medlyn'",
"cable_user%GW_MODEL": ".FALSE.",
"cable_user%or_evap": ".FALSE.",
#"elev_fname": "'%s'" % (self.elev_fname),
}
adjust_nml_file(nml_fname, replace_dict)
self.run_me(nml_fname)
add_attributes_to_output_file(nml_fname, out_fname, url, rev)
shutil.move(nml_fname, os.path.join(self.namelist_dir, nml_fname))
if self.fixed_lai is not None or self.lai_dir is not None:
os.remove("%s_tmp.nc" % (site))
def setup_transient(self, st_yr_trans, en_yr_trans, st_yr, en_yr):
"""
Adjust the CABLE namelist file for the transient run, i.e. 1850 to XXXX
"""
replace_dict = {
"RunType": '"transient"',
"CO2NDepFile": "'%s'" % (self.co2_ndep_fname),
"spinstartyear": "%d" % (st_yr),
"spinendyear": "%d" % (en_yr),
}
adjust_nml_file(self.site_nml_fname, replace_dict)
out_log_fname = "%s_log_transient.txt" % (self.experiment_id)
out_log_fname = os.path.join(self.log_dir, out_log_fname)
if os.path.isfile(out_log_fname):
os.remove(out_log_fname)
self.out_fname = "%s_out_cable_transient.nc" % (self.experiment_id)
self.out_fname = os.path.join(self.output_dir, self.out_fname)
if os.path.isfile(self.out_fname):
os.remove(self.out_fname)
self.out_fname_CASA = "%s_out_casa_transient.nc" % (self.experiment_id)
self.out_fname_CASA = os.path.join(self.output_dir,
self.out_fname_CASA)
if os.path.isfile(self.out_fname_CASA):
os.remove(self.out_fname_CASA)
replace_dict = {
"filename%out": "'%s'" % (self.out_fname),
"casafile%out": "'%s'" % (self.out_fname_CASA),
"filename%log": "'%s'" % (out_log_fname),
"cable_user%CASA_DUMP_READ": ".FALSE.",
"cable_user%CASA_DUMP_WRITE": ".FALSE.",
"cable_user%CASA_NREP": "0",
"cable_user%SOIL_STRUC": "'%s'" % (self.soil_flag),
"output%restart": ".TRUE.",
"output%averaging": "'monthly'",
"spinup": ".FALSE.",
"icycle": "%d" % (self.biogeochem),
"cable_user%POPLUC": ".F.",
"cable_user%YearStart": "%d" % (st_yr_trans),
"cable_user%YearEnd": "%d" % (en_yr_trans),
}
adjust_nml_file(self.nml_fname, replace_dict)
def setup_simulation(self, st_yr, en_yr):
"""
Adjust the CABLE namelist file for the experiment years
"""
replace_dict = {
"RunType": '"historical"',
"CO2NDepFile": "'%s'" % (self.co2_ndep_fname),
"spinstartyear": "%d" % (st_yr),
"spinendyear": "%d" % (en_yr)
}
adjust_nml_file(self.site_nml_fname, replace_dict)
out_log_fname = "%s_log_simulation.txt" % (self.experiment_id)
out_log_fname = os.path.join(self.log_dir, out_log_fname)
if os.path.isfile(out_log_fname):
os.remove(out_log_fname)
self.out_fname = "%s_out_cable.nc" % (self.experiment_id)
self.out_fname = os.path.join(self.output_dir, self.out_fname)
self.out_fname_CASA = "%s_out_casa.nc" % (self.experiment_id)
self.out_fname_CASA = os.path.join(self.output_dir,
self.out_fname_CASA)
if os.path.isfile(self.out_fname):
os.remove(self.out_fname)
replace_dict = {
"filename%log": "'%s'" % (out_log_fname),
"output%averaging": "'daily'",
"icycle": "%d" % (self.biogeochem),
"cable_user%YearStart": "%d" % (st_yr),
"cable_user%YearEnd": "%d" % (en_yr),
"filename%out": "'%s'" % (self.out_fname),
"cable_user%POPLUC": ".F.",
"cable_user%CASA_DUMP_READ": ".FALSE.",
"cable_user%CASA_DUMP_WRITE": ".FALSE.",
"cable_user%SOIL_STRUC": "'%s'" % (self.soil_flag),
"spincasa": ".FALSE.",
"spinup": ".FALSE.",
"l_laiFeedbk": ".TRUE.",
"output%averaging": "'all'",
"casafile%out": "'%s'" % (self.out_fname_CASA),
}
adjust_nml_file(self.nml_fname, replace_dict)
def setup_re_spin(self, number=None):
"""
Adjust the CABLE namelist file with the various flags for another spin
"""
out_log_fname = "%s_log_ccp%d.txt" % (self.experiment_id, number)
out_log_fname = os.path.join(self.log_dir, out_log_fname)
if os.path.isfile(out_log_fname):
os.remove(out_log_fname)
self.out_fname = "%s_out_cable_ccp%d.nc" % (self.experiment_id, number)
self.out_fname = os.path.join(self.output_dir, self.out_fname)
if os.path.isfile(self.out_fname):
os.remove(self.out_fname)
self.out_fname_CASA = "%s_out_CASA_ccp%d.nc" % \
(self.experiment_id, number)
self.out_fname_CASA = os.path.join(self.output_dir,
self.out_fname_CASA)
if os.path.isfile(self.out_fname_CASA):
os.remove(self.out_fname_CASA)
replace_dict = {
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_in": "'%s'" % (self.cable_restart_fname),
"cable_user%climate_restart_in":
"'%s'" % (self.climate_restart_fname),
"cable_user%POP_restart_in": "'%s'" % (self.pop_restart_fname),
"casafile%cnpipool": "'%s'" % (self.casa_restart_fname),
"cable_user%POP_fromZero": ".F.",
"cable_user%CASA_fromZero": ".F.",
"cable_user%POP_rst": "'./'",
"cable_user%CLIMATE_fromZero": ".F.",
"cable_user%CASA_DUMP_READ": ".FALSE.",
"cable_user%CASA_DUMP_WRITE": ".TRUE.",
"cable_user%CASA_NREP": "0",
"cable_user%SOIL_STRUC": "'%s'" % (self.soil_flag),
"icycle": "%d" % (self.biogeochem),
"leaps": ".TRUE.",
"spincasa": ".FALSE.",
#"casafile%c2cdumppath": "'./'",
"output%restart": ".TRUE.",
"filename%out": "'%s'" % (self.out_fname),
"casafile%out": "'%s'" % (self.out_fname_CASA),
}
adjust_nml_file(self.nml_fname, replace_dict)
def setup_nml_file(self):
replace_dict = {
"filename%met": "''", # not needed for GSWP3 run
"filename%type": "'%s'" % (self.grid_fname),
"filename%veg": "'%s'" % (self.veg_fname),
"filename%soil": "'%s'" % (self.soil_fname),
"gswpfile%mask": "'%s'" % (self.mask_fname),
"output%averaging": "'monthly'",
"spinup": ".FALSE.",
"cable_user%FWSOIL_SWITCH": "'standard'",
"cable_user%GS_SWITCH": "'medlyn'",
"cable_user%GW_MODEL": ".FALSE.",
"cable_user%or_evap": ".FALSE.",
"cable_user%GSWP3": ".TRUE.",
"cable_user%MetType": "'gswp3'",
"verbose": ".FALSE.",
}
adjust_nml_file(self.nml_fname, replace_dict)
def setup_re_spin(self, number=None):
"""
Adjust the CABLE namelist file with the various flags for another spin
"""
out_fname = "%s_out_cable_spin_%d.nc" % (self.experiment_id, number)
out_fname = os.path.join(self.output_dir, out_fname)
out_log_fname = "%s_log_spin_%d.txt" % (self.experiment_id, number)
out_log_fname = os.path.join(self.log_dir, out_log_fname)
cable_rst_ifname = "%s_cable_rst_%d.nc" % (self.experiment_id,
number - 1)
cable_rst_ifname = os.path.join(self.restart_dir, cable_rst_ifname)
cable_rst_ofname = "%s_cable_rst_%d.nc" % (self.experiment_id, number)
cable_rst_ofname = os.path.join(self.restart_dir, cable_rst_ofname)
casa_rst_ifname = "%s_casa_rst_%d.nc" % (self.experiment_id,
number - 1)
casa_rst_ifname = os.path.join(self.restart_dir, casa_rst_ifname)
casa_rst_ofname = "%s_casa_rst_%d.nc" % (self.experiment_id, number)
casa_rst_ofname = os.path.join(self.restart_dir, casa_rst_ofname)
replace_dict = {
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_in": "'%s'" % (cable_rst_ifname),
"filename%restart_out": "'%s'" % (cable_rst_ofname),
"casafile%cnpipool": "'%s'" % (casa_rst_ifname),
"casafile%cnpepool": "'%s'" % (casa_rst_ofname),
"cable_user%CASA_fromZero": ".FALSE.",
"cable_user%CASA_DUMP_READ": ".FALSE.",
"cable_user%CASA_DUMP_WRITE": ".TRUE.",
"cable_user%CASA_NREP": "0",
"output%restart": ".TRUE.",
"spincasa": ".FALSE.",
"icycle": "%d" % (self.biogeochem_id),
"leaps": ".TRUE.",
}
adjust_nml_file(self.nml_fname, replace_dict)
def worker(self, met_files, url, rev):
for fname in met_files:
site = "AWAP_pixel"
lat = os.path.basename(fname).split("_")[3]
lon1 = os.path.basename(fname).split("_")[4].split(".")[0]
lon2 = os.path.basename(fname).split("_")[4].split(".")[1]
lon = "%s.%s" % (lon1, lon2)
lat = float(lat)
lon = float(lon)
base_nml_fn = os.path.join(self.grid_dir, "%s" % (self.nml_fname))
nml_fname = "cable_%s.nml" % (site)
shutil.copy(base_nml_fn, nml_fname)
(out_fname, out_log_fname) = self.clean_up_old_files(site)
# Add LAI to met file?
if self.fixed_lai is not None or self.lai_dir is not None:
fname = change_LAI(fname,
site,
fixed=self.fixed_lai,
lai_dir=self.lai_dir)
if self.fwsoil == "hydraulics":
if lat == -30.40 and lon == 151.60:
fname = change_iveg(fname, site, 21) # GRW
if lat == -31.10 and lon == 142.50:
fname = change_iveg(fname, site, 21) # GRW
elif lat == -31.10 and lon == 150.95:
fname = change_iveg(fname, site, 22) # SAW
elif lat == -30.00 and lon == 141.40:
fname = change_iveg(fname, site, 22) # SAW
else:
print("problem")
sys.exit()
replace_dict = {
"filename%met": "'%s'" % (fname),
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_out": "' '",
"filename%type": "'%s'" % (self.grid_fname),
"filename%veg": "'%s'" % (self.veg_fname),
"filename%soil": "'%s'" % (self.soil_fname),
"output%restart": ".FALSE.",
"fixedCO2": "%.2f" % (self.co2_conc),
"casafile%phen": "'%s'" % (self.phen_fname),
"casafile%cnpbiome": "'%s'" % (self.cnpbiome_fname),
"cable_user%GS_SWITCH": "'medlyn'",
"cable_user%GW_MODEL": ".FALSE.",
"cable_user%or_evap": ".FALSE.",
"redistrb": ".FALSE.",
"spinup": ".FALSE.",
"cable_user%litter": ".TRUE.",
"cable_user%FWSOIL_SWITCH": "'%s'" % (self.fwsoil),
}
adjust_nml_file(nml_fname, replace_dict)
self.run_me(nml_fname)
add_attributes_to_output_file(nml_fname, out_fname, url, rev)
shutil.move(nml_fname, os.path.join(self.namelist_dir, nml_fname))
if self.fixed_lai is not None or self.lai_dir is not None:
os.remove("%s_tmp.nc" % (site))
os.remove("new_sumbal")
def setup_simulation(self, met_fname, historical=True, number=None):
"""
Adjust the CABLE namelist file for the experiment years
"""
out_fname = "%s_out_cable_simulation.nc" % (self.experiment_id)
out_fname = os.path.join(self.output_dir, out_fname)
out_log_fname = "%s_log_simulation.txt" % (self.experiment_id)
out_log_fname = os.path.join(self.log_dir, out_log_fname)
cable_rst_ifname = "%s_cable_rst_%d.nc" % (self.experiment_id, number)
cable_rst_ifname = os.path.join(self.restart_dir, cable_rst_ifname)
casa_rst_ifname = "%s_casa_rst_%d.nc" % (self.experiment_id, number)
casa_rst_ifname = os.path.join(self.restart_dir, casa_rst_ifname)
if historical:
out_fname = "%s_out_cable_historical.nc" % (self.experiment_id)
out_fname = os.path.join(self.output_dir, out_fname)
cable_rst_ofname = "%s_cable_rst_%d.nc" % (self.experiment_id,
number)
cable_rst_ofname = os.path.join(self.restart_dir, cable_rst_ofname)
casa_rst_ofname = "%s_casa_rst_%d.nc" % (self.experiment_id,
number)
casa_rst_ofname = os.path.join(self.restart_dir, casa_rst_ofname)
replace_dict = {
"filename%met": "'%s'" % (met_fname),
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_in": "'%s'" % (cable_rst_ifname),
"filename%restart_out": "'%s'" % (cable_rst_ofname),
"casafile%cnpipool": "'%s'" % (casa_rst_ifname),
"casafile%cnpepool": "'%s'" % (casa_rst_ofname),
"icycle": "%d" % (self.biogeochem_id),
"cable_user%CASA_DUMP_READ": ".FALSE.",
"cable_user%CASA_DUMP_WRITE": ".FALSE.",
"spincasa": ".FALSE.",
"spinup": ".FALSE.",
"output%restart": ".TRUE.",
"output%averaging": "'daily'",
"leaps": ".TRUE.",
}
else:
replace_dict = {
"filename%met": "'%s'" % (met_fname),
"filename%out": "'%s'" % (out_fname),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_in": "'%s'" % (cable_rst_ifname),
"filename%restart_out": "' '",
"casafile%cnpipool": "'%s'" % (casa_rst_ifname),
"casafile%cnpepool": "' '",
"icycle": "%d" % (self.biogeochem_id),
"cable_user%CASA_DUMP_READ": ".FALSE.",
"cable_user%CASA_DUMP_WRITE": ".FALSE.",
"spincasa": ".FALSE.",
"spinup": ".FALSE.",
"output%restart": ".FALSE.",
"output%averaging": "'daily'",
"leaps": ".TRUE.",
}
adjust_nml_file(self.nml_fname, replace_dict)
return (out_fname)
def create_new_nml_file(self, log_fname, out_fname, restart_in_fname,
restart_out_fname, year, co2_conc):
out_log_fname = os.path.join(self.log_dir, log_fname)
out_fname = os.path.join(self.output_dir, out_fname)
# i.e. no restart file for first spinup year
if restart_in_fname == "missing":
restart_in_fname = ""
else:
restart_in_fname = os.path.join(self.restart_dir, restart_in_fname)
restart_out_fname = os.path.join(self.restart_dir, restart_out_fname)
if self.met_data == "GSWP3":
rainf_fn = os.path.join(
self.met_dir, "Rainf/GSWP3.BC.Rainf.3hrMap.%s.nc" % (year))
snowf_fn = os.path.join(
self.met_dir, "Snowf/GSWP3.BC.Snowf.3hrMap.%s.nc" % (year))
lwdown_fn = os.path.join(
self.met_dir, "LWdown/GSWP3.BC.LWdown.3hrMap.%s.nc" % (year))
swdown_fn = os.path.join(
self.met_dir, "SWdown/GSWP3.BC.SWdown.3hrMap.%s.nc" % (year))
psurf_fn = os.path.join(
self.met_dir, "PSurf/GSWP3.BC.PSurf.3hrMap.%s.nc" % (year))
qair_fn = os.path.join(self.met_dir,
"Qair/GSWP3.BC.Qair.3hrMap.%s.nc" % (year))
wind_fn = os.path.join(self.met_dir,
"Wind/GSWP3.BC.Wind.3hrMap.%s.nc" % (year))
tair_fn = (os.path.join(
self.met_dir, "Tair/GSWP3.BC.Tair.3hrMap.%s.nc" % (year)))
elif self.met_data == "AWAP":
rainf_fn = os.path.join(self.met_dir,
"Rainf/AWAP.Rainf.3hr.%s.nc" % (year))
snowf_fn = os.path.join(self.met_dir,
"Snowf/AWAP.Snowf.3hr.%s.nc" % (year))
lwdown_fn = os.path.join(self.met_dir,
"LWdown/AWAP.LWdown.3hr.%s.nc" % (year))
swdown_fn = os.path.join(self.met_dir,
"SWdown/AWAP.SWdown.3hr.%s.nc" % (year))
psurf_fn = os.path.join(self.met_dir,
"PSurf/AWAP.PSurf.3hr.%s.nc" % (year))
qair_fn = os.path.join(self.met_dir,
"Qair/AWAP.Qair.3hr.%s.nc" % (year))
wind_fn = os.path.join(self.met_dir,
"Wind/AWAP.Wind.3hr.%s.nc" % (year))
tair_fn = (os.path.join(self.met_dir,
"Tair/AWAP.Tair.3hr.%s.nc" % (year)))
replace_dict = {
"filename%log": "'%s'" % (out_log_fname),
"filename%out": "'%s'" % (out_fname),
"filename%restart_in": "'%s'" % (restart_in_fname),
"filename%restart_out": "'%s'" % (restart_out_fname),
"fixedCO2": "%f" % (co2_conc),
"ncciy": "%s" % (
year
), # 0 for not using gswp; 4-digit year input for year of gswp met
"CABLE_USER%YearStart": "0", # needs to be 0 so the ncciy is set
"CABLE_USER%YearEnd": "0", # needs to be 0 so the ncciy is set
"gswpfile%rainf": "'%s'" % (rainf_fn),
"gswpfile%snowf": "'%s'" % (snowf_fn),
"gswpfile%LWdown": "'%s'" % (lwdown_fn),
"gswpfile%SWdown": "'%s'" % (swdown_fn),
"gswpfile%PSurf": "'%s'" % (psurf_fn),
"gswpfile%Qair": "'%s'" % (qair_fn),
"gswpfile%Tair": "'%s'" % (tair_fn),
"gswpfile%wind": "'%s'" % (wind_fn),
}
adjust_nml_file(self.nml_fname, replace_dict)
# save copy as we go for debugging - remove later
shutil.copyfile(
self.nml_fname,
os.path.join(self.namelist_dir, "cable_%d.nml" % (year)))
def initial_setup(self, st_yr_spin, en_yr_spin, st_yr, en_yr):
"""
Setup CABLE namelist file for spinup from zero
"""
if not os.path.exists(self.restart_dir):
os.makedirs(self.restart_dir)
if not os.path.exists(self.output_dir):
os.makedirs(self.output_dir)
if not os.path.exists(self.log_dir):
os.makedirs(self.log_dir)
if not os.path.exists(self.dump_dir):
os.makedirs(self.dump_dir)
base_nml_fn = os.path.join(self.grid_dir, "%s" % (self.nml_fname))
if os.path.isfile(self.nml_fname):
os.remove(self.nml_fname)
shutil.copy(base_nml_fn, self.nml_fname)
#shutil.copyfile(os.path.join(self.driver_dir, "cable.nml"),
# self.nml_fname)
shutil.copyfile(os.path.join(self.driver_dir, "site.nml"),
self.site_nml_fname)
self.out_fname = os.path.join(
self.output_dir, "%s_out_cable_zero.nc" % (self.experiment_id))
if os.path.isfile(self.out_fname):
os.remove(self.out_fname)
self.out_fname_CASA = os.path.join(
self.output_dir, "%s_out_CASA_zero.nc" % (self.experiment_id))
if os.path.isfile(self.out_fname_CASA):
os.remove(self.out_fname_CASA)
out_log_fname = os.path.join(self.log_dir,
"%s_log_zero.txt" % (self.experiment_id))
if os.path.isfile(out_log_fname):
os.remove(out_log_fname)
replace_dict = {
"RunType": '"spinup"',
"CO2NDepFile": "'%s'" % (self.co2_ndep_fname),
"spinstartyear": "%d" % (st_yr),
"spinendyear": "%d" % (en_yr),
"spinCO2": "284.7",
"spinNdep": "0.79",
"spinPdep": "0.144",
}
adjust_nml_file(self.site_nml_fname, replace_dict)
replace_dict = {
"filename%met": "'%s'" % (self.met_fname),
"filename%out": "'%s'" % (self.out_fname),
"casafile%out": "'%s'" % (self.out_fname_CASA),
"filename%log": "'%s'" % (out_log_fname),
"filename%restart_out": "'%s'" % (self.cable_restart_fname),
"cable_user%climate_restart_out":
"'%s'" % (self.climate_restart_fname),
"cable_user%POP_restart_out": "'%s'" % (self.pop_restart_fname),
"casafile%cnpepool": "'%s'" % (self.casa_restart_fname),
"filename%restart_in": "''",
"cable_user%climate_restart_in": "''",
"cable_user%POP_restart_in": "''",
"filename%type": "'%s'" % self.grid_fname,
"filename%veg": "'%s'" % (self.veg_fname),
"filename%soil": "'%s'" % (self.soil_fname),
"output%restart": ".TRUE.",
"casafile%phen": "'%s'" % (self.phen_fname),
"casafile%cnpbiome": "'%s'" % (self.cnpbiome_fname),
"cable_user%RunIden": "'%s'" % (self.experiment_id),
"cable_user%POP_out": "'ini'",
"cable_user%POP_rst": "'./'",
"cable_user%POP_fromZero": ".T.",
"cable_user%CASA_fromZero": ".T.",
"cable_user%CLIMATE_fromZero": ".T.",
"cable_user%CALL_CLIMATE": "%s" % (self.clim_flag),
"cable_user%SOIL_STRUC": "'%s'" % (self.soil_flag),
"cable_user%vcmax": "'%s'" % (self.vcmax),
"cable_user%YearStart": "%d" % (st_yr_spin),
"cable_user%YearEnd": "%d" % (en_yr_spin),
"cable_user%CASA_SPIN_STARTYEAR": "%d" % (st_yr_spin),
"cable_user%CASA_SPIN_ENDYEAR": "%d" % (en_yr_spin),
"cable_user%CALL_POP": "%s" % (self.pop_flag),
"output%averaging": "'monthly'",
"icycle": "%d" % (self.biogeochem),
"l_vcmaxFeedbk": "%s" % (self.vcmax_feedback),
"spinup": ".FALSE.",
"cable_user%FWSOIL_SWITCH": "'Haverd2013'",
"cable_user%GS_SWITCH": "'medlyn'",
"cable_user%limit_labile": ".F.",
"cable_user%SSNOW_POTEV": "'P-M'",
"cable_user%CASA_NREP":
"0", # number of times to repeat CASA forcing
"delsoilM": "0.01",
"delsoilT": "0.1",
"output%casa": ".TRUE.",
"output%grid": "'land'",
"leaps": ".FALSE.",
"cable_user%litter": ".true.",
"cable_user%CASA_OUT_FREQ": "'monthly'",
"cable_user%MetType": "'site'",
"cable_user%PHENOLOGY_SWITCH": "'modis'",
}
adjust_nml_file(self.nml_fname, replace_dict)
cwd = os.getcwd()
(url, rev) = get_svn_info(cwd, self.cable_src)
# delete local executable, copy a local copy and use that
local_exe = "cable"
if os.path.isfile(local_exe):
os.remove(local_exe)
shutil.copy(self.cable_exe, local_exe)
self.cable_exe = local_exe
return (url, rev)
