diff --git a/scripts/apply_obs_op_dart.py b/scripts/apply_obs_op_dart.py
index 5b380c68ec9b9564c41d9f12abac6adbff47e63b..3dfa4a5ef36851762a214f73e6ea4a389b36cddf 100644
--- a/scripts/apply_obs_op_dart.py
+++ b/scripts/apply_obs_op_dart.py
@@ -7,56 +7,13 @@ from config.cfg import exp, cluster
from utils import symlink, copy, mkdir, sed_inplace, append_file, print
import create_obsseq as osq
import assim_synth_obs as aso
-from assim_synth_obs import read_prior_obs, set_DART_nml, generate_observations, assimilate
import pre_assim
+import wrfout_add_geo
-def run_operator(obscfg, time):
- """
- time_for_dart (dt.datetime) : needs to be consistent with wrfout files!
- """
+"""Apply observation operator to some ensemble state
+i.e. wrfout files in an archive directory
- # get observation file (obs not important, but their locations)
- # this should correspond to configuration to have same locations as in real assim
- os.chdir(cluster.dartrundir)
-
- n_obs = obscfg['n_obs']
- error_var = (obscfg['err_std'])**2
- sat_channel = obscfg.get('sat_channel', False)
- cov_loc = obscfg['cov_loc_radius_km']
- dist_obs = obscfg.get('distance_between_obs_km', False)
-
- obs_coords = osq.calc_obs_locations(n_obs, coords_from_domaincenter=False,
- distance_between_obs_km=dist_obs,
- fpath_obs_locations=None)
- osq.sat(time, sat_channel, obs_coords, error_var,
- output_path=cluster.dartrundir)
- assert os.path.exists(cluster.dartrundir + '/obs_seq.in')
-
- # prepare dummy nature
- os.system('cp ./advance_temp1/wrfout_d01 ./wrfout_d01')
- import wrfout_add_geo
- wrfout_add_geo.run(cluster.dartrundir+'/geo_em.d01.nc',
- cluster.dartrundir+'/wrfout_d01')
-
- print('running perfect model obs')
- os.system('mpirun -np 12 ./perfect_model_obs')
-
- # set namelist for filter (calc only forward op)
- aso.set_DART_nml(sat_channel=sat_channel,
- just_prior_values=True)
-
- # run filter
- assert os.path.exists(cluster.dartrundir+'/obs_seq.out')
- print('running filter')
- os.system('mpirun -np 40 ./filter')
-
- # copy output to archive
- savedir = cluster.archivedir()+'/obs_seq_final_1min/'
- mkdir(savedir)
- obsname = obscfg['kind']
-
- copy(cluster.dartrundir+'/obs_seq.final', savedir+fout)
- print('output of observation operator saved to', fout)
+"""
if __name__ == '__main__':
@@ -66,6 +23,7 @@ if __name__ == '__main__':
print(prev_forecast_init, time)
# link ensemble states to run_DART directory
+ # we want the observation operator applied to these states!
pre_assim.run(time, prev_forecast_init, exppath_firstguess)
savedir = cluster.archivedir()+'/obs_seq_final_1min/'
@@ -85,9 +43,16 @@ if __name__ == '__main__':
just_prior_values=True)
osq.create_obsseq_in(time, obscfg)
- aso.generate_observations()
+
+ # prepare dummy nature (this Hx is irrelevant)
+ os.chdir(cluster.dartrundir)
+ os.system('cp ./advance_temp1/wrfout_d01 ./wrfout_d01')
+ wrfout_add_geo.run(cluster.dartrundir+'/geo_em.d01.nc',
+ cluster.dartrundir+'/wrfout_d01')
+ aso.run_perfect_model_obs()
aso.assimilate()
archive_stage = savedir+kind
+ # only the prior state values are of interest in this file
aso.archive_diagnostics(archive_stage, time.strftime('/%Y-%m-%d_%H:%M_obs_seq.final'))
diff --git a/scripts/assim_synth_obs.py b/scripts/assim_synth_obs.py
index c4f1de40a75756c94564a7523ed0b0f977af9585..bff396dfcbaf028308dbe1a10940f7639f7c009b 100755
--- a/scripts/assim_synth_obs.py
+++ b/scripts/assim_synth_obs.py
@@ -67,27 +67,6 @@ def read_obsseqout(f):
obs.append(observed)
return true, obs
-# def edit_obserr_in_obsseq(fpath_obsseqin, OEs):
-# """
-# overwrite observation errors in a obs_seq.out file
-# according to the values in OEs
-# """
-# # write to txt (write whole obs_seq.out again)
-# obsseq = open(fpath_obsseqin, 'r').readlines()
-# obsseq_new = obsseq.copy()
-# i_obs = 0
-# for i, line in enumerate(obsseq):
-# if 'kind\n' in line:
-# i_line_oe = i+9 # 9 for satellite obs
-# obsseq_new[i_line_oe] = ' '+str(OEs[i_obs])+' \n'
-# i_obs += 1
-
-# os.rename(fpath_obsseqin, fpath_obsseqin+'-bak') # backup
-# # write cloud dependent errors (actually whole file)
-# with open(fpath_obsseqin, 'w') as f:
-# for line in obsseq_new:
-# f.write(line)
-
def set_DART_nml(sat_channel=False, cov_loc_radius_km=32, cov_loc_vert_km=False,
just_prior_values=False):
@@ -95,7 +74,7 @@ def set_DART_nml(sat_channel=False, cov_loc_radius_km=32, cov_loc_vert_km=False,
cov_loc_radian = cov_loc_radius_km/earth_radius_km
if just_prior_values:
- template = cluster.scriptsdir+'/../templates/input.prioronly.nml'
+ template = cluster.scriptsdir+'/../templates/input.eval.nml'
else:
template = cluster.scriptsdir+'/../templates/input.nml'
copy(template, cluster.dartrundir+'/input.nml')
@@ -128,6 +107,7 @@ def set_DART_nml(sat_channel=False, cov_loc_radius_km=32, cov_loc_vert_km=False,
append_file(cluster.dartrundir+'/input.nml', rttov_nml)
def obs_operator_ensemble():
+ # assumes that prior ensemble is already linked to advance_temp<i>/wrfout_d01
print('running obs operator on ensemble forecast')
os.chdir(cluster.dartrundir)
@@ -139,11 +119,11 @@ def obs_operator_ensemble():
# ens members are already linked to advance_temp<i>/wrfout_d01
copy(cluster.dartrundir+'/advance_temp'+str(iens)+'/wrfout_d01',
cluster.dartrundir+'/wrfout_d01')
-
- wrfout_add_geo.run(cluster.dartrundir+'/geo_em.d01.nc', cluster.dartrundir+'/wrfout_d01')
-
# DART may need a wrfinput file as well, which serves as a template for dimension sizes
symlink(cluster.dartrundir+'/wrfout_d01', cluster.dartrundir+'/wrfinput_d01')
+
+ # add geodata
+ wrfout_add_geo.run(cluster.dartrundir+'/geo_em.d01.nc', cluster.dartrundir+'/wrfout_d01')
# run perfect_model obs (forward operator)
os.system('mpirun -np 12 ./perfect_model_obs > /dev/null')
@@ -160,25 +140,26 @@ def obs_operator_ensemble():
else:
raise NotImplementedError()
-def obs_operator_nature():
+def obs_operator_nature(time):
print('running obs operator on nature run')
- prepare_nature_dart()
-
- os.chdir(cluster.dartrundir)
- os.remove(cluster.dartrundir+'/obs_seq.out')
- os.system('mpirun -np 12 ./perfect_model_obs')
+ prepare_nature_dart(time)
+ run_perfect_model_obs()
true, _ = read_obsseqout(cluster.dartrundir+'/obs_seq.out')
return true
-def prepare_nature_dart():
+
+def link_nature_to_dart_truth(time):
# get wrfout_d01 from nature run
shutil.copy(time.strftime(cluster.nature_wrfout),
cluster.dartrundir+'/wrfout_d01')
+ # DART may need a wrfinput file as well, which serves as a template for dimension sizes
+ symlink(cluster.dartrundir+'/wrfout_d01', cluster.dartrundir+'/wrfinput_d01')
+
+def prepare_nature_dart(time):
+ link_nature_to_dart_truth(time)
wrfout_add_geo.run(cluster.dartrundir+'/geo_em.d01.nc', cluster.dartrundir+'/wrfout_d01')
- # DART may need a wrfinput file as well, which serves as a template for dimension sizes
- symlink(cluster.dartrundir+'/wrfout_d01', cluster.dartrundir+'/wrfinput_d01')
def calc_obserr_WV73(Hx_nature, Hx_prior):
@@ -196,8 +177,7 @@ def calc_obserr_WV73(Hx_nature, Hx_prior):
OEs[iobs] = oe_nature
return OEs
-def generate_observations():
- print('generate actual observations')
+def run_perfect_model_obs():
os.chdir(cluster.dartrundir)
try_remove(cluster.dartrundir+'/obs_seq.out')
if not os.path.exists(cluster.dartrundir+'/obs_seq.in'):
@@ -212,16 +192,17 @@ def assimilate():
raise RuntimeError('obs_seq.out does not exist in '+cluster.dartrundir)
os.system('mpirun -np 48 ./filter')
-def archive_diagnostics(archive_stage, fname_final):
+def archive_diagnostics(archive_dir, time):
print('archive obs space diagnostics')
- mkdir(archive_stage)
- copy(cluster.dartrundir+'/obs_seq.final', archive_stage+'/'+fname_final)
+ mkdir(archive_dir)
+ copy(cluster.dartrundir+'/obs_seq.final',
+ archive_dir+time.strftime('/%Y-%m-%d_%H:%M_obs_seq.final'))
- try:
- print('archive regression diagnostics')
- copy(cluster.dartrundir+'/reg_diagnostics', archive_stage+'/reg_diagnostics')
- except Exception as e:
- warnings.warn(str(e))
+ # try: # what are regression diagnostics?!
+ # print('archive regression diagnostics')
+ # copy(cluster.dartrundir+'/reg_diagnostics', archive_dir+'/reg_diagnostics')
+ # except Exception as e:
+ # warnings.warn(str(e))
def recycle_output():
print('move output to input')
@@ -289,7 +270,7 @@ if __name__ == "__main__":
osq.create_obsseq_in(time, obscfg, zero_error=True) # zero error to get truth vals
- Hx_nat = obs_operator_nature()
+ Hx_nat = obs_operator_nature(time)
Hx_prior = obs_operator_ensemble() # files are already linked to DART directory
obscfg['err_std'] = calc_obserr_WV73(Hx_nat, Hx_prior)
@@ -297,10 +278,12 @@ if __name__ == "__main__":
obscfg['err_std'] = np.ones(n_obs) * obscfg['err_std']
osq.create_obsseq_in(time, obscfg) # now with correct errors
- generate_observations()
+ prepare_nature_dart(time)
+ run_perfect_model_obs()
assimilate()
- archive_diagnostics(archive_stage, '/obs_seq.final')
+ dir_obsseq = cluster.archivedir()+'/obs_seq_final/assim_stage'+str(istage)+'_'+kind
+ archive_diagnostics(dir_obsseq, time)
if istage < n_stages-1:
# recirculation: filter output -> input
@@ -311,7 +294,7 @@ if __name__ == "__main__":
elif istage == n_stages-1:
# last assimilation, continue integration now
copy(cluster.dartrundir+'/input.nml', archive_stage+'/input.nml')
- pass # call update wrfinput from filteroutput later
+ archive_output_mean(archive_stage)
else:
RuntimeError('this should never occur?!')
diff --git a/scripts/prepare_namelist.py b/scripts/prepare_namelist.py
index fb6c588e715de04fd60d49d0ea353b65b8e3bc33..d69b5dee1c51085b9a9c76df0b2f34ef8193ac13 100755
--- a/scripts/prepare_namelist.py
+++ b/scripts/prepare_namelist.py
@@ -1,11 +1,17 @@
import os, sys, shutil, warnings
import datetime as dt
+from config.cfg import exp, cluster
-sys.path.append(os.getcwd())
+sys.path.append(cluster.scriptsdir)
from config.cfg import exp, cluster
from utils import sed_inplace, copy, symlink, mkdir
-def run(cluster, iens, begin, end, hist_interval=5, radt=5):
+def run(iens, begin, end, hist_interval=5, radt=5, archive=True):
+ """
+ Args:
+ archive (bool): if True, write to archivedir of experiment
+ if False, write to WRF run directory
+ """
rundir = cluster.wrf_rundir(iens)
print(rundir)
copy(cluster.namelist, rundir+'/namelist.input')
@@ -15,10 +21,14 @@ def run(cluster, iens, begin, end, hist_interval=5, radt=5):
sed_inplace(rundir+'/namelist.input', '<hist_interval>', str(int(hist_interval)))
sed_inplace(rundir+'/namelist.input', '<radt>', str(int(radt)))
- archdir = cluster.archivedir()+begin.strftime('/%Y-%m-%d_%H:%M/'+str(iens)+'/')
+ if archive:
+ archdir = cluster.archivedir()+begin.strftime('/%Y-%m-%d_%H:%M/'+str(iens)+'/')
+ os.makedirs(archdir, exist_ok=True)
+ else:
+ archdir = './'
print('namelist for run from', begin, end, 'output to', archdir)
sed_inplace(rundir+'/namelist.input', '<archivedir>', archdir)
- os.makedirs(archdir, exist_ok=True)
+
# set times
for k, v in {'<y1>': '%Y', '<m1>': '%m', '<d1>': '%d',
@@ -29,15 +39,16 @@ def run(cluster, iens, begin, end, hist_interval=5, radt=5):
sed_inplace(rundir+'/namelist.input', k, end.strftime(v))
#########################
- try:
- print('copy wrfinput of this run to archive')
- wrfin_old = rundir+'/wrfinput_d01'
- init_dir = cluster.archivedir()+begin.strftime('/%Y-%m-%d_%H:%M/')+str(iens)
- os.makedirs(init_dir, exist_ok=True)
- wrfin_arch = init_dir+'/wrfinput_d01'
- copy(wrfin_old, wrfin_arch)
- except Exception as e:
- warnings.warn(str(e))
+ if archive:
+ try:
+ print('copy wrfinput of this run to archive')
+ wrfin_old = rundir+'/wrfinput_d01'
+ init_dir = cluster.archivedir()+begin.strftime('/%Y-%m-%d_%H:%M/')+str(iens)
+ os.makedirs(init_dir, exist_ok=True)
+ wrfin_arch = init_dir+'/wrfinput_d01'
+ copy(wrfin_old, wrfin_arch)
+ except Exception as e:
+ warnings.warn(str(e))
if __name__ == '__main__':
@@ -48,4 +59,4 @@ if __name__ == '__main__':
print('prepare namelists for all ens members')
for iens in range(1, exp.n_ens+1):
- run(cluster, iens, begin, end, hist_interval=intv, radt=radt)
+ run(iens, begin, end, hist_interval=intv, radt=radt)
diff --git a/scripts/run_obs_diag.py b/scripts/run_obs_diag.py
index e9df5d5c9478f5f55a00ff38db8a5cb9b6050d40..4710f5bf5c7b8fbddb1041bd59934bb55f369d37 100644
--- a/scripts/run_obs_diag.py
+++ b/scripts/run_obs_diag.py
@@ -2,31 +2,40 @@ import os, sys, shutil, glob
from config.cfg import exp, cluster
from utils import symlink, copy, sed_inplace, append_file
-def run(folder_obs_seq_final):
- rundir_program = '/home/fs71386/lkugler/data/DART-WRF/rundir/'
+rundir_program = '/home/fs71386/lkugler/data/DART-WRF/rundir/'
- files = sorted(glob.glob(folder_obs_seq_final+'/*.final')) # input for obs_diag program
+
+def prepare(obserr_iszero='.true.'):
+ copy(cluster.scriptsdir+'/../templates/input.eval.nml',
+ rundir_program+'/input.nml')
+ sed_inplace(rundir_program+'/input.nml', '<n_ens>', str(int(exp.n_ens)))
+ sed_inplace(rundir_program+'/input.nml', '<zero_error_obs>', obserr_iszero)
+ sed_inplace(rundir_program+'/input.nml', '<horiz_dist_only>', '.false.') # dummy
+ sed_inplace(rundir_program+'/input.nml', '<vert_norm_hgt>', '5000.0') # dummy
+
+ append_file(rundir_program+'/input.nml', cluster.scriptsdir+'/../templates/obs_def_rttov.VIS.nml')
+
+
+def write_input_filelist(filepaths):
fpath = rundir_program+'/obsdiag_inputlist.txt'
print('writing', fpath)
-
if os.path.exists(fpath):
os.remove(fpath)
with open(fpath, 'w') as f:
- for fin in files:
+ for fin in filepaths:
f.write(fin)
f.write('\n')
+
+def run_obsdiag(filepaths, f_out='./obsdiag.nc'):
+ write_input_filelist(filepaths)
+
for obserr_iszero in ['.true.', '.false.']:
- print('ensure correct input.nml')
- copy(cluster.scriptsdir+'/../templates/input.prioronly.nml',
- rundir_program+'/input.nml')
- sed_inplace(rundir_program+'/input.nml', '<n_ens>', str(int(exp.n_ens)))
- sed_inplace(rundir_program+'/input.nml', '<zero_error_obs>', obserr_iszero)
- append_file(rundir_program+'/input.nml', cluster.scriptsdir+'/../templates/obs_def_rttov.VIS.nml')
-
- # run obs_diag
- print('running obs_diag program')
+ prepare(obserr_iszero=obserr_iszero)
+
+ # run_allinoneplace obs_diag
+ print('------ running obs_diag program')
os.chdir(rundir_program)
symlink(cluster.dart_srcdir+'/obs_diag', rundir_program+'/obs_diag')
try:
@@ -36,24 +45,29 @@ def run(folder_obs_seq_final):
os.system('./obs_diag >& obs_diag.log') # caution, this overwrites obs_seq_to_netcdf
# move output to archive
- outdir = '/'.join(folder_obs_seq_final.split('/')[:-1])
+ #outdir = outdir #'/'.join(folder_obs_seq_final.split('/')[:-1])
if obserr_iszero == '.true.':
- fout = '/obs_diag_wrt_truth.nc'
+ fout = outdir+'/'+f_out[:-3]+'_wrt_truth.nc'
elif obserr_iszero == '.false.':
- fout = '/obs_diag_wrt_obs.nc'
- print('moving output to', outdir+fout)
- copy(rundir_program+'/obs_diag_output.nc', outdir+fout)
+ fout = outdir+'/'+f_out[:-3]+'_wrt_obs.nc'
+ shutil.move(rundir_program+'/obs_diag_output.nc', fout)
+ print(fout, 'saved.')
- print('running obs_seq_to_netcdf program')
- shutil.copy(cluster.dart_srcdir+'/obs_seq_to_netcdf-bak', cluster.dart_srcdir+'/obs_seq_to_netcdf')
- symlink(cluster.dart_srcdir+'/obs_seq_to_netcdf', rundir_program+'/obs_seq_to_netcdf')
+def run_obs_seq_to_netcdf(filepaths, f_out='./obs_epoch.nc'):
+
+ write_input_filelist(filepaths)
+ print('------ running obs_seq_to_netcdf program')
+ shutil.copy(cluster.dart_srcdir+'/obs_seq_to_netcdf-bak', rundir_program+'/obs_seq_to_netcdf')
os.system('./obs_seq_to_netcdf >& obs_seq_to_netcdf.log') # caution, overwrites its own binary?!
- print('moving output to', outdir+'/obs_seq...')
- os.system('mv '+rundir_program+'/obs_epoch_*.nc '+outdir+'/')
+ shutil.move(rundir_program+'/obs_epoch_001.nc', f_out)
+ print(f_out, 'saved.')
if __name__ == '__main__':
- #folder_obs_seq_final = '/home/fs71386/lkugler/data/sim_archive/exp_v1.11_LMU_filter2/obs_seq_final/'
+ #folder_obs_seq_final = '/home/fs71386/lkugler/data/DART-WRF/rundir/test'
folder_obs_seq_final = str(sys.argv[1])
- run(folder_obs_seq_final)
+ files = sorted(glob.glob(folder_obs_seq_final+'/*.final')) # input for obs_diag program
+
+ run_obsdiag(files, outdir=folder_obs_seq_final) # input must be files with posterior data!!
+ run_obs_seq_to_netcdf(files, outdir=folder_obs_seq_final) # input can be files without posterior data
diff --git a/templates/input.eval.nml b/templates/input.eval.nml
new file mode 100644
index 0000000000000000000000000000000000000000..df66d8ea49826c9a97038fead9e9a0af10450b37
--- /dev/null
+++ b/templates/input.eval.nml
@@ -0,0 +1,578 @@
+&perfect_model_obs_nml
+ read_input_state_from_file = .true.
+ single_file_in = .false.
+ input_state_files = 'wrfout_d01'
+ init_time_days = -1
+ init_time_seconds = -1
+
+ write_output_state_to_file = .false.
+ single_file_out = .false.
+ output_state_files = 'perfect_output_d01.nc'
+ output_interval = 1
+
+ obs_seq_in_file_name = "obs_seq.in"
+ obs_seq_out_file_name = "obs_seq.out"
+ first_obs_days = -1
+ first_obs_seconds = -1
+ last_obs_days = -1
+ last_obs_seconds = -1
+
+ async = 0
+ adv_ens_command = "../shell_scripts/advance_model.csh"
+
+ trace_execution = .true.
+ output_timestamps = .false.
+ print_every_nth_obs = -1
+ output_forward_op_errors = .false.
+ silence = .false.
+ /
+
+&filter_nml
+ async = 0,
+ adv_ens_command = "../shell_scripts/advance_model.csh",
+ ens_size = <n_ens>,
+ obs_sequence_in_name = "obs_seq.out",
+ obs_sequence_out_name = "obs_seq.final",
+ input_state_file_list = "input_list.txt"
+ output_state_file_list = "output_list.txt"
+ init_time_days = -1,
+ init_time_seconds = -1,
+ first_obs_days = -1,
+ first_obs_seconds = -1,
+ last_obs_days = -1,
+ last_obs_seconds = -1,
+ num_output_state_members = <n_ens>,
+ num_output_obs_members = <n_ens>,
+ output_interval = 1,
+ num_groups = 1,
+ distributed_state = .true.
+ compute_posterior = .false.
+ output_forward_op_errors = .false.,
+ output_timestamps = .false.,
+ trace_execution = .false.,
+
+ stages_to_write = 'preassim'
+ output_members = .false.
+ output_mean = .false.
+ output_sd = .false.
+ write_all_stages_at_end = .false.
+
+ inf_flavor = 0, 0,
+ inf_initial_from_restart = .true., .false.,
+ inf_sd_initial_from_restart = .true., .false.,
+ inf_initial = 1.0, 1.00,
+ inf_lower_bound = 1.0, 1.0,
+ inf_upper_bound = 1000000.0, 1000000.0,
+ inf_damping = 0.9, 1.0,
+ inf_sd_initial = 0.6, 0.0,
+ inf_sd_lower_bound = 0.6, 0.0,
+ inf_sd_max_change = 1.05, 1.05,
+ /
+
+&quality_control_nml
+ input_qc_threshold = 3.0,
+ outlier_threshold = -1.0,
+ enable_special_outlier_code = .false.
+ /
+
+&fill_inflation_restart_nml
+ write_prior_inf = .false.
+ prior_inf_mean = 1.00
+ prior_inf_sd = 0.6
+
+ write_post_inf = .false.
+ post_inf_mean = 1.00
+ post_inf_sd = 0.6
+
+ input_state_files = 'wrfinput_d01', 'wrfinput_d02'
+ single_file = .false.
+ verbose = .false.
+ /
+
+&smoother_nml
+ num_lags = 0,
+ start_from_restart = .false.,
+ output_restart = .false.,
+ restart_in_file_name = 'smoother_ics',
+ restart_out_file_name = 'smoother_restart',
+ /
+
+# cutoff is in radians; for the earth, 0.05 is about 300 km.
+# cutoff is defined to be the half-width of the localization radius,
+# so 0.05 radians for cutoff is about an 600 km effective
+# localization radius, where the influence of an obs decreases
+# to ~half at 300 km, and ~0 at the edges of the area.
+&assim_tools_nml
+ filter_kind = 1,
+ cutoff = <cov_loc_radian>,
+ sort_obs_inc = .false.,
+ spread_restoration = .false.,
+ sampling_error_correction = .true.,
+ adaptive_localization_threshold = -1,
+ output_localization_diagnostics = .false.,
+ localization_diagnostics_file = 'localization_diagnostics',
+ convert_all_state_verticals_first = .true.
+ convert_all_obs_verticals_first = .true.
+ print_every_nth_obs = 0,
+ /
+
+&cov_cutoff_nml
+ select_localization = 1,
+ /
+
+&obs_sequence_nml
+ write_binary_obs_sequence = .false.,
+ /
+
+&preprocess_nml
+ overwrite_output = .true.,
+ input_obs_kind_mod_file = '../../../assimilation_code/modules/observations/DEFAULT_obs_kind_mod.F90',
+ output_obs_kind_mod_file = '../../../assimilation_code/modules/observations/obs_kind_mod.f90',
+ input_obs_def_mod_file = '../../../observations/forward_operators/DEFAULT_obs_def_mod.F90',
+ output_obs_def_mod_file = '../../../observations/forward_operators/obs_def_mod.f90',
+ input_files = '../../../observations/forward_operators/obs_def_reanalysis_bufr_mod.f90',
+ '../../../observations/forward_operators/obs_def_radar_mod.f90',
+ '../../../observations/forward_operators/obs_def_metar_mod.f90',
+ '../../../observations/forward_operators/obs_def_dew_point_mod.f90',
+ '../../../observations/forward_operators/obs_def_rel_humidity_mod.f90',
+ '../../../observations/forward_operators/obs_def_altimeter_mod.f90',
+ '../../../observations/forward_operators/obs_def_gps_mod.f90',
+ '../../../observations/forward_operators/obs_def_vortex_mod.f90',
+ '../../../observations/forward_operators/obs_def_gts_mod.f90',
+ '../../../observations/forward_operators/obs_def_rttov_mod.f90',
+ /
+
+&obs_kind_nml
+ evaluate_these_obs_types = 'RADIOSONDE_TEMPERATURE',
+ 'RADIOSONDE_U_WIND_COMPONENT',
+ 'RADIOSONDE_V_WIND_COMPONENT',
+ 'SAT_U_WIND_COMPONENT',
+ 'SAT_V_WIND_COMPONENT',
+ 'AIRCRAFT_U_WIND_COMPONENT',
+ 'AIRCRAFT_V_WIND_COMPONENT',
+ 'AIRCRAFT_TEMPERATURE',
+ 'ACARS_U_WIND_COMPONENT',
+ 'ACARS_V_WIND_COMPONENT',
+ 'ACARS_TEMPERATURE',
+ 'GPSRO_REFRACTIVITY',
+ 'DOPPLER_RADIAL_VELOCITY',
+ 'RADAR_REFLECTIVITY',
+ 'MSG_4_SEVIRI_RADIANCE',
+ 'MSG_4_SEVIRI_TB',
+ 'MSG_4_SEVIRI_BDRF',
+ 'LAND_SFC_PRESSURE',
+ 'SYNOP_SURFACE_PRESSURE',
+ 'SYNOP_TEMPERATURE',
+ 'SYNOP_SPECIFIC_HUMIDITY'
+ assimilate_these_obs_types = 'RADIOSONDE_SPECIFIC_HUMIDITY',
+ /
+
+# Notes for obs_def_radar_mod_nml:
+# (1) Reflectivity limit can be applied to observations and/or forward operator.
+# (2) The default constants below match the WRF defaults. They will need to
+# be changed for other cases, depending on which microphysics scheme is used.
+#
+
+&obs_def_radar_mod_nml
+ apply_ref_limit_to_obs = .false.,
+ reflectivity_limit_obs = -10.0,
+ lowest_reflectivity_obs = -10.0,
+ apply_ref_limit_to_fwd_op = .false.,
+ reflectivity_limit_fwd_op = -10.0,
+ lowest_reflectivity_fwd_op = -10.0,
+ max_radial_vel_obs = 1000000,
+ allow_wet_graupel = .false.,
+ microphysics_type = 5 ,
+ allow_dbztowt_conv = .false.,
+ dielectric_factor = 0.224,
+ n0_rain = 8.0e6,
+ n0_graupel = 4.0e6,
+ n0_snow = 3.0e6,
+ rho_rain = 1000.0,
+ rho_graupel = 400.0,
+ rho_snow = 100.0,
+ /
+
+
+# Notes for model_nml:
+# (1) vert_localization_coord must be one of:
+# 1 = model level
+# 2 = pressure
+# 3 = height
+# 4 = scale height
+
+# set default_state_variables to .false. to use the explicit list.
+# otherwise it uses a hardcoded default list: U, V, W, PH, T, MU, QV only.
+# see ../wrf_state_variables_table for a full list of what wrf fields are
+# supported in the DART state vector, and what settings should be used here.
+# 'UPDATE' and 'NO_COPY_BACK' are supported in the 4th column; 'NO_UPDATE' is
+# not yet supported.
+
+&model_nml
+ default_state_variables = .false.,
+ 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',
+ 'T', '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',
+ wrf_state_bounds = 'QVAPOR','0.0','NULL','CLAMP',
+ 'QRAIN', '0.0','NULL','CLAMP',
+ 'QCLOUD','0.0','NULL','CLAMP',
+ 'QICE','0.0','NULL','CLAMP',
+ 'CLDFRA','0.0','1.0','CLAMP',
+ num_domains = 1,
+ calendar_type = 3,
+ assimilation_period_seconds = 21600,
+ vert_localization_coord = 3,
+ center_search_half_length = 500000.,
+ center_spline_grid_scale = 10,
+ sfc_elev_max_diff = -1.0,
+ circulation_pres_level = 80000.0,
+ circulation_radius = 108000.0,
+ allow_obs_below_vol = .false.
+ /
+
+# vert_normalization_X is amount of X equiv to 1 radian in horiz.
+# vert localization is 'cutoff' times the pressure/height/levels,
+# only if horiz_dist_only is set to .false. in the namelist below.
+# the default nlon/nlat should be good for most experiments. it sets
+# an internal structure that speeds up searches. don't change it
+# based on your grid size. nlon must be an odd number.
+&location_nml
+ horiz_dist_only = <horiz_dist_only>,
+ vert_normalization_pressure = 6666666.7,
+ vert_normalization_height = <vert_norm_hgt>,
+ vert_normalization_level = 2666.7,
+ vert_normalization_scale_height = 10.0,
+ approximate_distance = .false.,
+ nlon = 71,
+ nlat = 36,
+ output_box_info = .false.,
+ /
+
+&utilities_nml
+ TERMLEVEL = 1,
+ module_details = .false.,
+ logfilename = 'dart_log.out',
+ nmlfilename = 'dart_log.nml',
+ write_nml = 'file',
+ /
+
+&mpi_utilities_nml
+ /
+
+®_factor_nml
+ select_regression = 1,
+ input_reg_file = "time_mean_reg",
+ save_reg_diagnostics = .true.,
+ reg_diagnostics_file = "reg_diagnostics",
+ /
+
+# layout = 2 spreads the IO tasks across the nodes.
+# This can greatly improve the performance in IO if
+# tasks_per_node is set to match your hardware
+&ensemble_manager_nml
+ layout = 1,
+ tasks_per_node = 48
+ communication_configuration = 1
+ debug = .false.
+ /
+
+&obs_def_gps_nml
+ max_gpsro_obs = 100000,
+ /
+
+&obs_def_tpw_nml
+ /
+
+# The times in the namelist for the obs_diag program are vectors
+# that follow the following sequence:
+# year month day hour minute second
+# max_num_bins can be used to specify a fixed number of bins,
+# in which case last_bin_center should be safely in the future.
+#
+# Acceptable latitudes range from [-90, 90]
+# Acceptable longitudes range from [ 0, Inf]
+
+&obs_diag_nml
+ obs_sequence_name = '',
+ obs_sequence_list = 'obsdiag_inputlist.txt',
+ first_bin_center = 2008, 7,30,10, 0, 0 ,
+ last_bin_center = 2008, 7,30,18, 0, 0 ,
+ bin_separation = 0, 0, 0, 0, 1, 0 ,
+ bin_width = 0, 0, 0, 0, 1, 0 ,
+ time_to_skip = 0, 0, 0, 0, 0, 0 ,
+ max_num_bins = 1000,
+ trusted_obs = 'null',
+ Nregions = 1,
+ lonlim1 = 0.0, 0.0, 0.0, 235.0,
+ lonlim2 = 360.0, 360.0, 360.0, 295.0,
+ latlim1 = 20.0, -80.0, -20.0, 25.0,
+ latlim2 = 80.0, -20.0, 20.0, 55.0,
+ reg_names = 'all',
+ print_mismatched_locs = .false.,
+ create_rank_histogram = .true.,
+ outliers_in_histogram = .true.,
+ use_zero_error_obs = <zero_error_obs>,
+ verbose = .false.
+ /
+
+&schedule_nml
+ calendar = 'Gregorian',
+ first_bin_start = 1601, 1, 1, 0, 0, 0,
+ first_bin_end = 2999, 1, 1, 0, 0, 0,
+ last_bin_end = 2999, 1, 1, 0, 0, 0,
+ bin_interval_days = 1000000,
+ bin_interval_seconds = 0,
+ max_num_bins = 1000,
+ print_table = .true.,
+ /
+
+&obs_seq_to_netcdf_nml
+ obs_sequence_name = '',
+ obs_sequence_list = 'obsdiag_inputlist.txt',
+ append_to_netcdf = .true.,
+ lonlim1 = 0.0,
+ lonlim2 = 360.0,
+ latlim1 = -90.0,
+ latlim2 = 90.0,
+ verbose = .false.,
+ /
+
+# There is one GIGANTIC difference between the obsdef_mask.txt and .nc
+# The netCDF file intentionally ignores the effect of nTmin/nTmax.
+# The netCDF file has ALL matching stations, regardless of temporal coverage.
+
+&obs_seq_coverage_nml
+ obs_sequences = ''
+ obs_sequence_list = 'obs_coverage_list.txt'
+ obs_of_interest = 'METAR_U_10_METER_WIND'
+ textfile_out = 'METAR_U_10_METER_WIND_obsdef_mask.txt'
+ netcdf_out = 'METAR_U_10_METER_WIND_obsdef_mask.nc'
+ first_analysis = 2003, 1, 1, 0, 0, 0
+ last_analysis = 2003, 1, 2, 0, 0, 0
+ forecast_length_days = 1
+ forecast_length_seconds = 0
+ verification_interval_seconds = 21600
+ temporal_coverage_percent = 100.0
+ lonlim1 = 0.0
+ lonlim2 = 360.0
+ latlim1 = -90.0
+ latlim2 = 90.0
+ verbose = .true.
+ /
+
+# selections_file is a list of obs_defs output
+# from the obs_seq_coverage utility.
+
+&obs_selection_nml
+ filename_seq = 'obs_seq.out',
+ filename_seq_list = '',
+ filename_out = 'obs_seq.processed',
+ selections_file = 'obsdef_mask.txt',
+ selections_is_obs_seq = .false.,
+ print_only = .false.,
+ calendar = 'gregorian',
+ /
+
+&obs_seq_verify_nml
+ obs_sequences = ''
+ obs_sequence_list = 'obs_verify_list.txt'
+ input_template = 'obsdef_mask.nc'
+ netcdf_out = 'forecast.nc'
+ obtype_string = 'METAR_U_10_METER_WIND'
+ print_every = 10000
+ verbose = .true.
+ debug = .false.
+ /
+
+&obs_sequence_tool_nml
+ num_input_files = 1,
+ filename_seq = 'obs_seq.out',
+ filename_out = 'obs_seq.processed',
+ first_obs_days = -1,
+ first_obs_seconds = -1,
+ last_obs_days = -1,
+ last_obs_seconds = -1,
+ obs_types = '',
+ keep_types = .false.,
+ print_only = .false.,
+ min_lat = -90.0,
+ max_lat = 90.0,
+ min_lon = 0.0,
+ max_lon = 360.0,
+ /
+
+&replace_wrf_fields_nml
+ debug = .false.,
+ fail_on_missing_field = .false.,
+ fieldnames = "SNOWC",
+ "ALBBCK",
+ "TMN",
+ "TSK",
+ "SH2O",
+ "SMOIS",
+ "SEAICE",
+ "HGT_d01",
+ "TSLB",
+ "SST",
+ "SNOWH",
+ "SNOW",
+ fieldlist_file = '',
+ /
+
+&obs_common_subset_nml
+ num_to_compare_at_once = 2,
+ filename_seq = 'obs_seq1.final', 'obs_seq2.final',
+ filename_seq_list = '',
+ filename_out_suffix = '.common' ,
+ calendar = 'Gregorian',
+ print_every = 1000,
+ dart_qc_threshold = 3,
+ print_only = .false.,
+ /
+
+&wrf_dart_to_fields_nml
+ include_slp = .true.,
+ include_wind_components = .true.,
+ include_height_on_pres = .true.,
+ include_temperature = .true.,
+ include_rel_humidity = .true.,
+ include_surface_fields = .false.,
+ include_sat_ir_temp = .false.,
+ pres_levels = 70000.,
+ /
+
+&ncepobs_nml
+ year = 2010,
+ month = 06,
+ day = 00,
+ tot_days = 1,
+ max_num = 1000000,
+ ObsBase = 'temp_obs.',
+ select_obs = 0,
+ ADPUPA = .false.,
+ AIRCAR = .false.,
+ AIRCFT = .false.,
+ SATEMP = .false.,
+ SFCSHP = .false.,
+ ADPSFC = .false.,
+ SATWND = .true.,
+ obs_U = .false.,
+ obs_V = .false.,
+ obs_T = .false.,
+ obs_PS = .false.,
+ obs_QV = .false.,
+ daily_file = .true.,
+ obs_time = .false.,
+ lat1 = 10.00,
+ lat2 = 60.00,
+ lon1 = 210.0,
+ lon2 = 300.0
+ /
+
+&prep_bufr_nml
+ obs_window_upa = 1.0,
+ obs_window_air = 1.0,
+ obs_window_cw = 1.0,
+ otype_use = 242.0, 243.0, 245.0, 246.0, 251.0, 252.0, 253.0, 257.0, 259.0
+ qctype_use = 0, 1, 2, 3, 4, 9, 15
+ /
+
+&convert_cosmic_gps_nml
+ gpsro_netcdf_file = '',
+ gpsro_netcdf_filelist = 'flist',
+ gpsro_out_file = 'obs_seq.gpsro',
+ local_operator = .true.,
+ obs_levels = 0.22, 0.55, 1.1, 1.8, 2.7, 3.7, 4.9,
+ 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0, 13.0,
+ ray_ds = 5000.0,
+ ray_htop = 13000.1,
+ /
+
+&wrf_obs_preproc_nml
+
+ file_name_input = 'obs_seq20110901'
+ file_name_output = 'obs_seq.europe.prev'
+
+ overwrite_obs_time = .false.
+
+ obs_boundary = 0.0
+ increase_bdy_error = .false.
+ maxobsfac = 2.5
+ obsdistbdy = 1.0
+
+ sfc_elevation_check = .false.
+ sfc_elevation_tol = 3000.0
+ obs_pressure_top = 0.0
+ obs_height_top = 2.0e10
+
+ include_sig_data = .true.
+ tc_sonde_radii = -1.0
+
+ superob_aircraft = .true.
+ aircraft_horiz_int = 800.0
+ aircraft_pres_int = 25000.0
+
+ superob_sat_winds = .true.
+ sat_wind_horiz_int = 800.0
+ sat_wind_pres_int = 25000.0
+
+ overwrite_ncep_satwnd_qc = .false.
+ overwrite_ncep_sfc_qc = .false.
+ /
+
+! sonde_extra = 'obs_seq.rawin'
+! land_sfc_extra = 'obs_seq.land_sfc'
+! metar_extra = 'obs_seq.metar'
+! marine_sfc_extra = 'obs_seq.marine'
+! sat_wind_extra = 'obs_seq.satwnd'
+! profiler_extra = 'obs_seq.profiler'
+! gpsro_extra = 'obs_seq.gpsro'
+! acars_extra = 'obs_seq.acars'
+! trop_cyclone_extra = 'obs_seq.tc'
+
+&state_vector_io_nml
+ single_precision_output = .true.,
+ /
+
+&compare_states_nml
+ /
+
+&closest_member_tool_nml
+ input_restart_file_list = 'input_file_list_d01.txt',
+ output_file_name = 'closest_results.txt'
+ ens_size = 3,
+ single_restart_file_in = .false.,
+ difference_method = 4,
+ use_only_qtys = 'QTY_U_WIND_COMPONENT'
+ /
+
+# To test both domains, you must change 'model_nml:num_domains = 2'
+
+&model_mod_check_nml
+ input_state_files = 'wrfinput_d01', 'wrfinput_d02'
+ output_state_files = 'mmc_output1.nc', 'mmc_output2.nc'
+ test1thru = 0
+ run_tests = 1,2,3,4,5
+ x_ind = 87370
+ loc_of_interest = 231.0, 40.0, 10.0
+ quantity_of_interest = 'QTY_U_WIND_COMPONENT'
+ interp_test_dlon = 0.1
+ interp_test_dlat = 0.1
+ interp_test_dvert = 1000.0
+ interp_test_lonrange = 250.0, 260.0
+ interp_test_latrange = 30.0, 45.0
+ interp_test_vertrange = 2000.0, 4000.0
+ interp_test_vertcoord = 'VERTISHEIGHT'
+ verbose = .false.
+ /
diff --git a/templates/input.prioronly.nml b/templates/input.prioronly.nml
index 21d7de55e1ff8674e7f24fc0eff8633e007a3e9b..19471bb280abc0e238bc62657d674c5338aa5d10 100644
--- a/templates/input.prioronly.nml
+++ b/templates/input.prioronly.nml
@@ -31,7 +31,7 @@
async = 0,
adv_ens_command = "../shell_scripts/advance_model.csh",
ens_size = <n_ens>,
- obs_sequence_in_name = "obs_seq_all.out",
+ obs_sequence_in_name = "obs_seq.out",
obs_sequence_out_name = "obs_seq.final",
input_state_file_list = "input_list.txt"
output_state_file_list = "output_list.txt"
@@ -143,7 +143,8 @@
/
&obs_kind_nml
- assimilate_these_obs_types = 'RADIOSONDE_TEMPERATURE',
+ assimilate_these_obs_types = ,
+ evaluate_these_obs_types = 'RADIOSONDE_TEMPERATURE',
'RADIOSONDE_U_WIND_COMPONENT',
'RADIOSONDE_V_WIND_COMPONENT',
'SAT_U_WIND_COMPONENT',
@@ -156,11 +157,10 @@
'ACARS_TEMPERATURE',
'GPSRO_REFRACTIVITY',
'DOPPLER_RADIAL_VELOCITY',
- 'RADAR_REFLECTIVITY',
+ 'RADAR_REFLECTIVITY',
'MSG_4_SEVIRI_RADIANCE',
- 'MSG_4_SEVIRI_TB',
- 'MSG_4_SEVIRI_BDRF'
- evaluate_these_obs_types = 'RADIOSONDE_SPECIFIC_HUMIDITY',
+ 'MSG_4_SEVIRI_TB',
+ 'MSG_4_SEVIRI_BDRF'
/
# Notes for obs_def_radar_mod_nml:
@@ -246,7 +246,7 @@
&location_nml
horiz_dist_only = .false.,
vert_normalization_pressure = 6666666.7,
- vert_normalization_height = 5000000.0,
+ vert_normalization_height = 500.0,
vert_normalization_level = 2666.7,
vert_normalization_scale_height = 10.0,
approximate_distance = .false.,