diff --git a/config/cfg.py b/config/cfg.py
index 973314411765c7e882ae5448be980bb01c78f945..3cdf2024e1ebf2b9b85a52a0edee8c5d3591de1f 100755
--- a/config/cfg.py
+++ b/config/cfg.py
@@ -1,7 +1,7 @@
from dartwrf import utils
exp = utils.Experiment()
-exp.expname = "test_newcode"
+exp.expname = "test_newcode" #exp_v1.22_P2_rr_VIS_obs10_loc20_oe3"
exp.model_dx = 2000
exp.n_ens = 40
exp.superob_km = False # False or int (spatial averaging of observations)
@@ -16,20 +16,35 @@ exp.input_profile = '/mnt/jetfs/home/lkugler/data/initial_profiles/wrf/ens/2022-
exp.dart_nml = {'&assim_tools_nml':
- dict(assim_tools_nml='.false.',
- filter_kind='1',
- sampling_error_correction='.true.',
- # obs_impact_filename='/jetfs/home/lkugler/DART-WRF/templates/impactfactor_T.txt',
- ),
+ dict(filter_kind='1',
+ sampling_error_correction='.true.',
+ # obs_impact_filename='/jetfs/home/lkugler/DART-WRF/templates/impactfactor_T.txt',
+ ),
'&filter_nml':
- dict(ens_size=str(exp.n_ens),
- num_output_state_members=str(exp.n_ens),
- num_output_obs_members=str(exp.n_ens),
- inf_flavor=['2', '0'],
+ dict(ens_size=exp.n_ens,
+ num_output_state_members=exp.n_ens,
+ num_output_obs_members=exp.n_ens,
+ inf_flavor=['0', '0'],
),
'&location_nml':
dict(horiz_dist_only='.true.',
),
+ '&model_nml':
+ dict(wrf_state_variables =
+ [['U', 'QTY_U_WIND_COMPONENT', 'TYPE_U', 'UPDATE','999',],
+ ['V', 'QTY_V_WIND_COMPONENT', 'TYPE_V', 'UPDATE','999',],
+ ['W', 'QTY_VERTICAL_VELOCITY', 'TYPE_W', 'UPDATE','999',],
+ ['PH', 'QTY_GEOPOTENTIAL_HEIGHT', 'TYPE_GZ', 'UPDATE','999',],
+ ['THM', 'QTY_POTENTIAL_TEMPERATURE','TYPE_T', 'UPDATE','999',],
+ ['MU', 'QTY_PRESSURE', 'TYPE_MU', 'UPDATE','999',],
+ ['QVAPOR','QTY_VAPOR_MIXING_RATIO', 'TYPE_QV', 'UPDATE','999',],
+ ['QICE', 'QTY_ICE_MIXING_RATIO', 'TYPE_QI', 'UPDATE','999',],
+ ['QCLOUD','QTY_CLOUDWATER_MIXING_RATIO','TYPE_QC', 'UPDATE','999',],
+ ['CLDFRA','QTY_CLOUD_FRACTION', 'TYPE_CFRAC','UPDATE','999',],
+ ['PSFC', 'QTY_SURFACE_PRESSURE', 'TYPE_PSFC', 'UPDATE','999',],
+ ['T2', 'QTY_2M_TEMPERATURE', 'TYPE_T', 'UPDATE','999',],
+ ['TSK', 'QTY_SKIN_TEMPERATURE', 'TYPE_T', 'UPDATE','999',],
+ ['REFL_10CM','QTY_RADAR_REFLECTIVITY','TYPE_REFL', 'UPDATE','999',]]),
}
diff --git a/config/cluster.py b/config/cluster.py
new file mode 100755
index 0000000000000000000000000000000000000000..c1c779118d5b01ba92626a27d268c7c414480a74
--- /dev/null
+++ b/config/cluster.py
@@ -0,0 +1,77 @@
+import os, sys
+import datetime as dt
+from dartwrf import utils
+from config.cfg import exp
+
+"""Configuration name docs
+
+When coding, use attributes of a dictionary like this:
+$ from cfg import exp, cluster
+$ path = cluster.archivedir
+
+
+attribute name | description
+------------------------------------------------------
+name any string (currently unused)
+
+python path of python version to use
+python_enstools path of python version to use for verification script (not provided)
+ncks path to 'ncks' program; type 'which ncks' to find the path,
+ if it doesn't exist, try to load the module first ('module load nco')
+ideal path to WRF's ideal.exe
+wrfexe path to WRF's wrf.exe
+
+wrf_rundir_base path for temporary files for WRF
+dart_rundir_base path for temporary files for DART
+archive_base path for long-time output storage
+
+srcdir path to where WRF has been compiled, including the 'run' folder of WRF, e.g. /home/WRF-4.3/run
+dart_srcdir path to DART compile directory, e.g. /home/DART-9.11.9/models/wrf/work
+rttov_srcdir path to RTTOV compile directory, e.g. /home/RTTOV13/rtcoef_rttov13/
+scriptsdir path where DART-WRF scripts reside, e.g. /home/DART-WRF/scripts
+
+namelist path to a namelist template; strings like <hist_interval>, will be overwritten in scripts/prepare_namelist.py
+run_WRF path to script which runs WRF on a node of the cluster
+obs_impact_filename path to obs_impact_filename (see DART guide; module assim_tools_mod and program obs_impact_tool)
+geo_em path to NetCDF file of WRF domain (see WRF guide)
+
+slurm_cfg python dictionary, containing options of SLURM
+ defined in SLURM docs (https://slurm.schedmd.com/sbatch.html)
+ this configuration can be overwritten later on, for example:
+ 'dict(cluster.slurm_cfg, **cfg_update)' where
+ 'cfg_update = {"nodes": "2"}'
+"""
+
+cluster = utils.ClusterConfig(exp)
+cluster.name = 'srvx1'
+cluster.max_nproc = 6
+cluster.use_slurm = False
+
+# binaries
+cluster.python = 'python'
+cluster.python_verif = '/users/staff/lkugler/miniconda3/bin/python'
+cluster.ncks = '/home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.5.0/nco-5.0.1-ntu44aoxlvwtr2tsrobfr4lht7cpvccf/bin/ncks'
+cluster.ideal = '' #/jetfs/home/lkugler/bin/ideal-v4.3_v1.22.exe'
+cluster.wrfexe = '' #/jetfs/home/lkugler/bin/wrf-v4.3_v1.22.exe'
+cluster.dart_modules = ''
+cluster.wrf_modules = ''
+
+# paths for data output
+cluster.wrf_rundir_base = utils.userhome+'/AdvDA23/run_WRF/' # path for temporary files
+cluster.dart_rundir_base = utils.userhome+'/AdvDA23/run_DART/' # path for temporary files
+cluster.archive_base = utils.userhome+'/data/sim_archive/'
+
+# paths used as input
+cluster.srcdir = '/users/staff/lkugler/AdvDA23/DART/WRF-4.3/run'
+cluster.dart_srcdir = '/users/students/lehre/advDA_s2023/DART/models/wrf/work'
+cluster.rttov_srcdir = '/users/students/lehre/advDA_s2023/RTTOV13/rtcoef_rttov13/'
+cluster.scriptsdir = utils.userhome+'/AdvDA23/DART-WRF/dartwrf/'
+cluster.geo_em = '/users/students/lehre/advDA_s2023/data/geo_em.d01.nc'
+
+# templates/run scripts
+cluster.namelist = cluster.scriptsdir+'/../templates/namelist.input'
+cluster.run_WRF = cluster.scriptsdir+'/run_ens.jet.sh'
+
+cluster.slurm_cfg = {"account": "lkugler", "partition": "compute",
+ "ntasks": "1", "ntasks-per-core": "1", "mem": "50G",
+ "mail-type": "FAIL", "mail-user": "lukas.kugler@univie.ac.at"}
diff --git a/config/srvx1.py b/config/srvx1.py
index c1c779118d5b01ba92626a27d268c7c414480a74..9a22186d45adfb62e2d130eb040c5b92e525584a 100755
--- a/config/srvx1.py
+++ b/config/srvx1.py
@@ -65,12 +65,12 @@ cluster.archive_base = utils.userhome+'/data/sim_archive/'
cluster.srcdir = '/users/staff/lkugler/AdvDA23/DART/WRF-4.3/run'
cluster.dart_srcdir = '/users/students/lehre/advDA_s2023/DART/models/wrf/work'
cluster.rttov_srcdir = '/users/students/lehre/advDA_s2023/RTTOV13/rtcoef_rttov13/'
-cluster.scriptsdir = utils.userhome+'/AdvDA23/DART-WRF/dartwrf/'
+cluster.dartwrf_dir = utils.userhome+'/AdvDA23/DART-WRF/'
cluster.geo_em = '/users/students/lehre/advDA_s2023/data/geo_em.d01.nc'
# templates/run scripts
-cluster.namelist = cluster.scriptsdir+'/../templates/namelist.input'
-cluster.run_WRF = cluster.scriptsdir+'/run_ens.jet.sh'
+cluster.namelist = cluster.dartwrf_dir+'/../templates/namelist.input'
+cluster.run_WRF = cluster.dartwrf_dir+'/run_ens.jet.sh'
cluster.slurm_cfg = {"account": "lkugler", "partition": "compute",
"ntasks": "1", "ntasks-per-core": "1", "mem": "50G",
diff --git a/dartwrf/assim_synth_obs.py b/dartwrf/assim_synth_obs.py
index 64c4653c25ea6a04e4e418d96bc264b7ce457e55..9c79deb7c7214579618273d5ecd8b439871ff62f 100755
--- a/dartwrf/assim_synth_obs.py
+++ b/dartwrf/assim_synth_obs.py
@@ -50,6 +50,7 @@ def prepare_prior_ensemble(assim_time, prior_init_time, prior_valid_time, prior_
"""
print("prepare prior state estimate")
for iens in range(1, exp.n_ens + 1):
+
print("link wrfout file to DART background file")
wrfout_run = (
prior_path_exp
@@ -65,7 +66,7 @@ def prepare_prior_ensemble(assim_time, prior_init_time, prior_valid_time, prior_
copy(wrfout_run, wrfout_dart)
symlink(wrfout_dart, dart_ensdir + "/wrfinput_d01")
- # ensure prior time matches assim time (can be off intentionally)
+ # ensure prior time matches assim time (can be intentionally different)
if assim_time != prior_valid_time:
print("overwriting time in prior from nature wrfout")
shell(cluster.ncks+ " -A -v XTIME,Times "+
@@ -86,18 +87,22 @@ def prepare_prior_ensemble(assim_time, prior_init_time, prior_valid_time, prior_
os.system("rm -rf " + cluster.dart_rundir + "/obs_seq.fina*")
def write_list_of_inputfiles_prior():
- files = []
- for iens in range(1, exp.n_ens+1):
- files.append("./prior_ens" + str(iens) + "/wrfout_d01")
- write_txt(files, cluster.dart_rundir+'/input_list.txt')
+ """Instruct DART to use the prior ensemble as input
+ """
+ files = []
+ for iens in range(1, exp.n_ens+1):
+ files.append("./prior_ens" + str(iens) + "/wrfout_d01")
+ write_txt(files, cluster.dart_rundir+'/input_list.txt')
def write_list_of_inputfiles_posterior(assim_time):
- filedir = cluster.archivedir+assim_time.strftime("/%Y-%m-%d_%H:%M/assim_stage0/")
+ """Use posterior as input for DART, e.g. to evaluate the analysis in observation space
+ """
+ filedir = cluster.archivedir+assim_time.strftime("/%Y-%m-%d_%H:%M/assim_stage0/")
- files = []
- for iens in range(1, exp.n_ens+1):
- files.append(filedir+'filter_restart_d01.'+str(iens).zfill(4))
- write_txt(files, cluster.dart_rundir+'/input_list.txt')
+ files = []
+ for iens in range(1, exp.n_ens+1):
+ files.append(filedir+'filter_restart_d01.'+str(iens).zfill(4))
+ write_txt(files, cluster.dart_rundir+'/input_list.txt')
def write_list_of_outputfiles():
files = []
@@ -300,8 +305,7 @@ def evaluate(assim_time,
os.makedirs(cluster.dart_rundir, exist_ok=True) # create directory to run DART in
os.chdir(cluster.dart_rundir)
- # link DART binaries to run_DART
- os.system(cluster.python + " " + cluster.scripts_rundir + "/link_dart_rttov.py")
+ link_DART_binaries_and_RTTOV_files()
# remove any existing observation files
os.system("rm -f input.nml obs_seq.final")
@@ -488,6 +492,15 @@ def link_DART_binaries_and_RTTOV_files():
else:
pass # we dont need RTTOV anyway
+def prepare_run_DART_folder():
+ os.makedirs(cluster.dart_rundir, exist_ok=True) # create directory to run DART in
+ os.chdir(cluster.dart_rundir)
+
+ link_DART_binaries_and_RTTOV_files()
+
+ # remove any existing observation files
+ os.system("rm -f input.nml obs_seq.in obs_seq.out obs_seq.out-orig obs_seq.final")
+
def main(time, prior_init_time, prior_valid_time, prior_path_exp):
"""Assimilate observations
@@ -511,14 +524,7 @@ def main(time, prior_init_time, prior_valid_time, prior_path_exp):
"""
nproc = cluster.max_nproc
- archive_time = cluster.archivedir + time.strftime("/%Y-%m-%d_%H:%M/")
- os.makedirs(cluster.dart_rundir, exist_ok=True) # create directory to run DART in
- os.chdir(cluster.dart_rundir)
-
- link_DART_binaries_and_RTTOV_files()
-
- # remove any existing observation files
- os.system("rm -f input.nml obs_seq.in obs_seq.out obs_seq.out-orig obs_seq.final")
+ prepare_run_DART_folder()
dart_nml.write_namelist()
print("prepare nature")
diff --git a/dartwrf/config b/dartwrf/config
deleted file mode 120000
index 4088526854d4f1d637653a0436624cdcf75dceb9..0000000000000000000000000000000000000000
--- a/dartwrf/config
+++ /dev/null
@@ -1 +0,0 @@
-../config/
\ No newline at end of file
diff --git a/dartwrf/dart_nml.py b/dartwrf/dart_nml.py
index e2b490023f4097663771853945e63b15dc04aee2..37c9be9f00d0fac7b84f0128142e0ded89c69dd2 100644
--- a/dartwrf/dart_nml.py
+++ b/dartwrf/dart_nml.py
@@ -37,7 +37,7 @@ def read_namelist(filepath):
d[section] = dict()
continue
- if '/' in line:
+ if line == '/':
continue # skip end of namelist section
line = line.strip().strip(',')
@@ -57,11 +57,21 @@ def read_namelist(filepath):
val = val.strip().strip(',').split(',')
- # ensure that we have strings
- if isinstance(val, list):
- val = [str(v) for v in val]
- else:
- val = [str(val)]
+ # # ensure that we have list of strings
+ # if isinstance(val, list) and len(val) == 1:
+ # val = [val]
+
+
+ # try:
+ # # convert to float/int
+ # val = [float(v) for v in val]
+
+ # # convert to int when they are equal
+ # val = [int(v) for v in val if int(v)==v]
+ # except:
+ # it is not a numeric value => string
+ val = [v.strip() for v in val]
+
param_data.append(val)
@@ -96,15 +106,35 @@ def write_namelist_from_dict(d, filepath):
for parameter in parameters:
lines = d[section][parameter]
- if isinstance(lines, str):
- lines = [lines,]
+ # lines (list(list(str))):
+ # outer list: one element per line in the text file
+ # inner list: one element per value in that line
+
+
+ # we should have a list here
+ # if we instead have a single value, then make a list
+ # because we assume that lines consists of multiple lines
+ assert isinstance(lines, list)
for i, line in enumerate(lines):
- try:
- line = ', '.join(line) # write line (is a list)
- except:
- pass
+ assert isinstance(line, list)
+ if line == []:
+ line = ['',]
+
+
+ first_entry = line[0]
+ if isinstance(first_entry, str) and not first_entry.startswith('.'):
+ try:
+ float(first_entry)
+ line = ', '.join(str(v) for v in line)
+ except:
+ # contains strings
+ line = [entry.strip("'").strip('"') for entry in line] # remove pre-existing quotes
+ line = ', '.join('"'+v+'"' for v in line)
+ else:
+ # numerical values
+ line = ', '.join(str(v) for v in line)
if i == 0:
@@ -154,54 +184,78 @@ def _get_list_of_localizations():
l_obstypes.append(obscfg["kind"])
loc_horiz_km = obscfg["loc_horiz_km"]
+ if not loc_horiz_km >= 0:
+ raise ValueError('Invalid value for `loc_horiz_km`, set loc_horiz_km >= 0 !')
# compute horizontal localization
- loc_horiz_rad = str(to_radian_horizontal(loc_horiz_km))
+ loc_horiz_rad = to_radian_horizontal(loc_horiz_km)
l_loc_horiz_rad.append(loc_horiz_rad)
# compute vertical localization
+ # do we have vertical localization?
+ if not hasattr(obscfg, "loc_vert_km") and not hasattr(obscfg, "loc_vert_scaleheight"):
+ l_loc_vert_km.append(-1)
+ l_loc_vert_scaleheight.append(-1)
+ # if not add dummy value
+
# choose either localization by height or by scale height
if hasattr(obscfg, "loc_vert_km") and hasattr(obscfg, "loc_vert_scaleheight"):
raise ValueError("Observation config contains both loc_vert_km and loc_vert_scaleheight. Please choose one.")
elif hasattr(obscfg, "loc_vert_km"): # localization by height
- loc_vert_km = str(obscfg["loc_vert_km"])
+ loc_vert_km = obscfg["loc_vert_km"]
vert_norm_hgt = to_vertical_normalization(loc_vert_km, loc_horiz_km)
l_loc_vert_km.append(vert_norm_hgt)
elif hasattr(obscfg, "loc_vert_scaleheight"): # localization by scale height
- loc_vert_scaleheight = str(obscfg["loc_vert_scaleheight"])
+ loc_vert_scaleheight = obscfg["loc_vert_scaleheight"]
# no conversion necessary, take the values as defined in obscfg
l_loc_vert_scaleheight.append(loc_vert_scaleheight)
-
- # fail when both localization by height and scale height are requested
- if len(l_loc_vert_km) > 0 and len(l_loc_vert_scaleheight) > 0:
- raise ValueError("List of observation configurations contain both height and scale-height localization. Please choose one.")
-
# set the other (unused) list to a dummy value
if len(l_loc_vert_km) > 0:
- l_loc_vert_scaleheight = ["-1",]
+ l_loc_vert_scaleheight = [-1,]
else:
- l_loc_vert_km = ["-1",]
+ l_loc_vert_km = [-1,]
return l_obstypes, l_loc_horiz_rad, l_loc_vert_km, l_loc_vert_scaleheight
-def _to_fortran_list(l):
- """Ensure formatting with quotation mark, e.g. parameter = "arg1", "arg2",
- """
- assert isinstance(l, list)
+# def _fortran_format(l):
+
+# # do we have multiples entries?
+# # Caution: a string is iterable
+# if isinstance(l, list):
+# pass
+# else:
+# l = [l,]
+
+# # do we have strings as elements?
+# if isinstance(l[0], str):
+
+
+# return l
+
+# def _as_fortran_list(l):
+# """Convert parameter list
+
+# if l contains strings:
+# output: "arg1", "arg2", "arg3"
+# else
+# output 1,2,3
+# """
+# assert isinstance(l, list)
+
+# if isinstance(l[0], str):
+# # contains strings
+# l = ['"'+a+'"' for a in l] # add quotation marks
+
+
+
- if len(l) > 1: # multiple entries
- return ', '.join(['"'+v+'"' for v in l])
- elif len(l) == 1: # single entry
- return '"'+l[0]+'"'
- else: # no entry
- return ''
def write_namelist(just_prior_values=False):
"""Set DART namelist variables in 'input.nml' file.
@@ -225,26 +279,28 @@ def write_namelist(just_prior_values=False):
nml = read_namelist(cluster.dart_srcdir + "/input.nml")
# make sure that observations defined in `exp.observations` are assimilated
- nml['&obs_kind_nml']['assimilate_these_obs_types'] = _to_fortran_list(list_obstypes)
+ nml['&obs_kind_nml']['assimilate_these_obs_types'] = [list_obstypes]
# dont compute posterior, just evaluate prior
if just_prior_values:
- nml['&filter_nml']['compute_posterior'] = '.false.'
- nml['&filter_nml']['output_members'] = '.false.'
- nml['&filter_nml']['output_mean'] = '.false.'
- nml['&filter_nml']['output_sd'] = '.false.'
- nml['&obs_kind_nml']['assimilate_these_obs_types'] = []
- nml['&obs_kind_nml']['evaluate_these_obs_types'] = [_to_fortran_list(list_obstypes)]
+ nml['&filter_nml']['compute_posterior'] = [['.false.']]
+ nml['&filter_nml']['output_members'] = [['.false.']]
+ nml['&filter_nml']['output_mean'] = [['.false.']]
+ nml['&filter_nml']['output_sd'] = [['.false.']]
+ nml['&obs_kind_nml']['assimilate_these_obs_types'] = [[]]
+ nml['&obs_kind_nml']['evaluate_these_obs_types'] = [list_obstypes]
# write localization variables
- nml['&assim_tools_nml']['special_localization_obs_types'] = [_to_fortran_list(list_obstypes)]
- nml['&assim_tools_nml']['special_localization_cutoffs'] = [_to_fortran_list(list_loc_horiz_rad)]
+ nml['&assim_tools_nml']['special_localization_obs_types'] = [list_obstypes]
+ nml['&assim_tools_nml']['special_localization_cutoffs'] = [list_loc_horiz_rad]
- nml['&location_nml']['special_vert_normalization_obs_types'] = [_to_fortran_list(list_obstypes)]
- nml['&location_nml']['special_vert_normalization_heights'] = [_to_fortran_list(list_loc_vert_km)]
- nml['&location_nml']['special_vert_normalization_scale_heights'] = [_to_fortran_list(list_loc_vert_scaleheight)]
+ nml['&location_nml']['special_vert_normalization_obs_types'] = [list_obstypes]
+ nml['&location_nml']['special_vert_normalization_heights'] = [list_loc_vert_km]
+ nml['&location_nml']['special_vert_normalization_scale_heights'] = [list_loc_vert_scaleheight]
+ nml['&location_nml']['special_vert_normalization_levels'] = [[-1,]]
+ nml['&location_nml']['special_vert_normalization_pressures'] = [[-1,]]
# overwrite namelist with experiment configuration
for section, sdata in exp.dart_nml.items():
@@ -255,8 +311,12 @@ def write_namelist(just_prior_values=False):
for parameter, value in sdata.items():
- if isinstance(value, list) and len(value) > 1: # it is a real list
- value = [value] # value was a list of parameter values, but just one line
+ if isinstance(value, list) and len(value) > 1: # it is a list
+
+ if isinstance(value[0], list):
+ pass # nothing to do, value is list(list())
+ else:
+ value = [value] # value was a list of parameter values, but just one line
else:
value = [[value]] # value was a single entry
@@ -274,5 +334,5 @@ def write_namelist(just_prior_values=False):
write_namelist_from_dict(nml, cluster.dart_rundir + "/input.nml")
# append section for RTTOV
- rttov_nml = cluster.scriptsdir + "/../templates/obs_def_rttov.VIS.nml"
+ rttov_nml = cluster.dartwrf_dir + "/../templates/obs_def_rttov.VIS.nml"
append_file(cluster.dart_rundir + "/input.nml", rttov_nml)
\ No newline at end of file
diff --git a/dartwrf/evaluate_obs_space.py b/dartwrf/evaluate_obs_space.py
index 91cae073f7fcabd2b4f61edc575f86898252d188..5cabadeb955352a1d128edafad82d0a79b073dd0 100755
--- a/dartwrf/evaluate_obs_space.py
+++ b/dartwrf/evaluate_obs_space.py
@@ -8,7 +8,7 @@ from config.cluster import cluster
from dartwrf import assim_synth_obs as aso
def get_previous_obsseq_file(time):
- oso_input = cluster.archivedir+'/obs_seq_out' + init.strftime("/%Y-%m-%d_%H:%M_obs_seq.out-beforeQC")
+ oso_input = cluster.archivedir+'/obs_seq_out' + time.strftime("/%Y-%m-%d_%H:%M_obs_seq.out-beforeQC")
if not os.path.isfile(oso_input): # fallback
oso_input = cluster.archivedir+'/obs_seq_out' + time.strftime("/%Y-%m-%d_%H:%M_obs_seq.out")
@@ -28,15 +28,22 @@ if __name__ == "__main__":
use_other_obsseq = False
- aso.write_list_of_inputfiles_posterior(time)
+ # we need an existing run_DART folder
+ aso.prepare_run_DART_folder()
- # use the last assimilation obsseq file for the observation locations (note: observed values are not valid)
+ # # prepare nature and prior ensemble
+ aso.prepare_nature_dart(time)
+ aso.prepare_prior_ensemble(time, prior_init_time=init, prior_valid_time=time, prior_path_exp=cluster.archivedir)
+
+ # tell DART to use the prior as input
+ aso.write_list_of_inputfiles_prior()
if use_other_obsseq: # use a different obsseq file
oso_input = use_other_obsseq
else: # from same exp
-
- oso_input = get_previous_obsseq_file(time)
+
+ # use the last assimilation obsseq file for the observation locations (note: observed values are not valid)
+ oso_input = get_previous_obsseq_file(init)
shutil.copy(oso_input, cluster.dart_rundir+'/obs_seq.out')
aso.evaluate(time, output_format="%Y-%m-%d_%H:%M_obs_seq.final-evaluate")
\ No newline at end of file
diff --git a/dartwrf/prepare_wrfrundir.py b/dartwrf/prepare_wrfrundir.py
index 3abe07441de4dd0b0a0fc283f40dc26395ab32a4..32e8c984f65d376f1f3741e437350afaf90250a9 100755
--- a/dartwrf/prepare_wrfrundir.py
+++ b/dartwrf/prepare_wrfrundir.py
@@ -11,8 +11,9 @@ import datetime as dt
from config.cfg import exp
from config.cluster import cluster
-from dartwrf.utils import symlink, copy, link_contents
-from dartwrf import prepare_namelist
+
+from utils import symlink, copy, link_contents
+import prepare_namelist
if __name__ == '__main__':
diff --git a/dartwrf/workflows.py b/dartwrf/workflows.py
index 036bd46e2c935639ad34908b00d2968f55d65b2c..27d7d8dfd3c45ed0a15ee1b657616b8da04561bf 100644
--- a/dartwrf/workflows.py
+++ b/dartwrf/workflows.py
@@ -30,14 +30,20 @@ class WorkFlows(object):
# Copy scripts to self.cluster.archivedir folder
os.makedirs(self.cluster.archivedir, exist_ok=True)
try:
- shutil.copytree(self.cluster.scriptsdir, self.cluster.scripts_rundir)
+ shutil.copytree(self.cluster.dartwrf_dir, self.cluster.scripts_rundir)
print('scripts have been copied to', self.cluster.archivedir)
except FileExistsError as e:
warnings.warn(str(e))
+ if input('Scripts already exist and will not be overwritten. Continue? (Y/n) ') in ['Y', 'y']:
+ pass
+ else:
+ raise e
except:
raise
def copy_config_to_archive():
+ os.makedirs(self.cluster.scripts_rundir+'/config/', exist_ok=True)
+
# later, we can load the exp cfg with `from config.cfg import exp`
shutil.copyfile('config/'+exp_config, self.cluster.scripts_rundir+'/config/cfg.py')
@@ -54,6 +60,9 @@ class WorkFlows(object):
self.cluster = importlib.import_module('config.'+server_config.strip('.py')).cluster
self.exp = importlib.import_module('config.'+exp_config.strip('.py')).exp
+ # we set the path from where python should import dartwrf modules
+ self.cluster.python = 'export PYTHONPATH='+self.cluster.scripts_rundir+'; '+self.cluster.python
+
copy_dartwrf_to_archive()
copy_config_to_archive()
@@ -111,9 +120,7 @@ class WorkFlows(object):
txt += '}'
f.write(txt)
- _dict_to_py(_obskind_read(), self.cluster.scriptsdir+'/../config/obskind.py')
-
-
+ _dict_to_py(_obskind_read(), self.cluster.scripts_rundir+'/config/obskind.py')
# probably not needed
# shutil.copy('config/'+server_config, 'config/cluster.py') # whatever server, the config name is always the same!
@@ -133,7 +140,7 @@ class WorkFlows(object):
Returns:
None
"""
- cmd = 'cd '+self.cluster.scripts_rundir+'; '+self.cluster.python+' prepare_wrfrundir.py '+init_time.strftime('%Y-%m-%d_%H:%M')
+ cmd = self.cluster.python+' '+self.cluster.dartwrf_dir+'/dartwrf/prepare_wrfrundir.py '+init_time.strftime('%Y-%m-%d_%H:%M')
print(cmd)
os.system(cmd)
@@ -251,7 +258,7 @@ class WorkFlows(object):
if not os.path.exists(prior_path_exp):
raise IOError('prior_path_exp does not exist: '+prior_path_exp)
- cmd = ('cd '+self.cluster.scripts_rundir+'; '+self.cluster.python+' assim_synth_obs.py '
+ cmd = (self.cluster.python+' '+self.cluster.dartwrf_dir+'/dartwrf/assim_synth_obs.py '
+assim_time.strftime('%Y-%m-%d_%H:%M ')
+prior_init_time.strftime('%Y-%m-%d_%H:%M ')
+prior_valid_time.strftime('%Y-%m-%d_%H:%M ')
diff --git a/tests/input.nml.desired_output b/tests/input.nml.desired_output
index 64635bd3a885d1243c24f5553df7343b47d1c613..7362dc412778c8cd9c5219a3928f23ec31a09448 100644
--- a/tests/input.nml.desired_output
+++ b/tests/input.nml.desired_output
@@ -46,7 +46,7 @@
output_interval = 1,
num_groups = 1,
distributed_state = .true.
- compute_posterior = .true.
+ compute_posterior = .false.
output_forward_op_errors = .false.,
output_timestamps = .false.,
trace_execution = .false.,
diff --git a/tests/test_inputnml.py b/tests/test_inputnml.py
index 26466033dd02a2a1fca25dbf326359e26307fbc4..6117ef08c0bafd7cd837036c3e1c513be4c3f868 100644
--- a/tests/test_inputnml.py
+++ b/tests/test_inputnml.py
@@ -14,9 +14,10 @@ def test_input_nml():
nml = dart_nml.read_namelist(test_input)
# modify one parameter
- nml['&filter_nml']['ens_size'] = [[str(999)]]
- nml['&filter_nml']['num_output_state_members'] = [[str(999)]]
- nml['&filter_nml']['num_output_obs_members'] = [[str(999)]]
+ nml['&filter_nml']['ens_size'] = [[999,]]
+ nml['&filter_nml']['num_output_state_members'] = [[999,]]
+ nml['&filter_nml']['num_output_obs_members'] = [[999,]]
+ nml['&filter_nml']['compute_posterior'] = [['.false.']]
# save the configuration as input.nml
dart_nml.write_namelist_from_dict(nml, test_output)
@@ -26,20 +27,29 @@ def test_input_nml():
nml_desired = dart_nml.read_namelist(desired_output)
nml_test = dart_nml.read_namelist(test_output)
+ # section e.g. '&preprocess_nml'
for section, _ in nml_desired.items():
+ # param e.g. 'filter_kind'
for param, value in nml_desired[section].items():
should_have = nml_desired[section][param]
- should_have = [v.strip() for line in should_have for v in line]
-
have = nml_test[section][param]
- have = [v.strip() for line in have for v in line]
-
- if should_have != have:
- raise ValueError(section, param, 'should be', should_have, 'but is', have)
+ for i, line in enumerate(should_have):
+
+ for j, expected in enumerate(line):
+
+ if expected != have[i][j]:
+ # if one has "wrfinput" and other has 'wrfinput'
+ # thats ok
+ this = "'"+have[i][j].strip('"')+"'"
+ if this == expected:
+ pass
+ # print(this, expected)
+ else:
+ raise ValueError('expected', expected, 'got', have[i][j])
os.remove(test_output)