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):
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):
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, 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 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 clean_up(self, url, rev, end=True, tag=None):
"""
Move restart files to a directory and delete various files we no longer
need that CABLE spits out as it spins up.
"""
add_attributes_to_output_file(self.nml_fname, self.out_fname, url, rev)
add_attributes_to_output_file(self.nml_fname, self.out_fname_CASA, url,
rev)
if end:
for f in glob.glob("c2c_*_dump.nc"):
shutil.move(f, os.path.join(self.dump_dir, f))
f = "cnpfluxOut.csv"
if os.path.isfile(f):
os.remove(f)
f = "new_sumbal"
if os.path.isfile(f):
os.remove(f)
#for f in glob.glob("*.out"):
# os.remove(f)
for f in glob.glob("restart_*.nc"):
os.remove(f)
else:
old = self.cable_restart_fname
new = "%s_%s.nc" % (old[:-3], tag)
if os.path.isfile(old):
shutil.copyfile(old, new)
old = self.casa_restart_fname
new = "%s_%s.nc" % (old[:-3], tag)
if os.path.isfile(old):
shutil.copyfile(old, new)
old = self.climate_restart_fname
new = "%s_%s.nc" % (old[:-3], tag)
if os.path.isfile(old):
shutil.copyfile(old, new)
if self.use_pop:
old = self.pop_restart_fname
new = "%s_%s.nc" % (old[:-3], tag)
if os.path.isfile(old):
shutil.copyfile(old, new)
def worker(self, met_files, url, rev, sci_config):
num = 0
not_stabilised = True
for fname in met_files:
site = os.path.basename(fname).split(".")[0].split("_")[0]
self.experiment_id = "%s_%s" % (site, self.biogeochem_cyc)
print("\n%s\n" % (site))
(st_yr, en_yr) = self.get_met_years(fname)
(fname_spin, fname_trans,
fname_sim) = self.generate_met_files(site, st_yr, en_yr, fname)
# Initial setup and first spin ...
print("\nSpinup stage: %d\n" % (num))
self.inital_spin_setup(site, fname_spin, sci_config, num)
self.run_me()
self.clean_up(num, tag="spin")
num += 1
while not_stabilised:
print("\nSpinup stage: %d\n" % (num))
self.setup_re_spin(number=num)
self.run_me()
self.clean_up(num, tag="spin")
print("\nAnalytical stage: %d\n" % (num))
self.setup_analytical_spin(st_yr, en_yr, number=num)
self.run_me()
self.clean_up(num, tag="spin_analytic")
not_stabilised = check_steady_state(self.experiment_id,
self.restart_dir, num)
num += 1
# one final spin
print("\nFinal spin\n")
self.setup_re_spin(number=num)
self.run_me()
# Run transiet simulation from 1850
print("\nHistorical\n")
(out_fname) = self.setup_simulation(fname_trans,
historical=True,
number=num)
self.run_me()
self.clean_up(number=None, tag="historical")
print("\nSimulation\n")
(out_fname) = self.setup_simulation(fname_sim,
historical=False,
number=num)
self.run_me()
self.clean_up(number=None, tag="simulation")
add_attributes_to_output_file(self.nml_fname, out_fname, url, rev)
ofname = os.path.join(self.namelist_dir, self.nml_fname)
shutil.move(self.nml_fname, ofname)
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")
