various fixes

config/cfg.py

-
+import numpy as np
 from . import clusters
 cluster = clusters.vsc  # change cluster configuration here
 
@@ -31,7 +31,7 @@ radar = dict(kind='RADAR', n_obs=n_obs, err_std=5.,
 t2m = dict(kind='SYNOP_TEMPERATURE', n_obs=n_obs, err_std=1.0, 
            cov_loc_radius_km=32, cov_loc_vert_km=1)
 psfc = dict(kind='SYNOP_SURFACE_PRESSURE', n_obs=n_obs, err_std=50.,
-           cov_loc_radius_km=32)
+           cov_loc_radius_km=32, cov_loc_vert_km=5)
            
 
 exp.observations = [t2m, psfc, ]

scheduler.py

@@ -43,19 +43,25 @@ def backup_scripts():
     old_a = main_a+'/old/'
 
     os.makedirs(cluster.archivedir(), exist_ok=True)
-    os.makedirs main_a, exist_ok=True)
-    os.makedirs , exist_ok=True)
+    os.makedirs(main_a, exist_ok=True)
+    os.makedirs(old_a, exist_ok=True)
+
+    def func(a, b, method): # call method if not link or directory
+        if os.path.islink(a) or os.path.isdir(a):
+            pass
+        else:
+            method(a, b)
 
     # archive existing files
     for f in os.listdir(main_a):
-        shutil.move(os.path.join(main_a, f), old_a+'/')
+        func(os.path.join(main_a, f), old_a+'/'+f, shutil.move)
 
     # reproducibility
     for f in ['scheduler.py', 'config/clusters.py', 'config/cfg.py']:
-        shutil.copy(current+'/../'+f,  main_a+'/scheduler.py')
+        func(current+'/../'+f,  main_a+'/scheduler.py', shutil.copy)
         
     for f in os.listdir(current):
-        shutil.copy(os.path.join(current, f), main_a+'/')
+        func(os.path.join(current, f), main_a+'/', shutil.copy)
 
 def prepare_wrfinput():
     """Create WRF/run directories and wrfinput files
@@ -112,7 +118,7 @@ def run_ENS(begin, end, depends_on=None):
                cluster.scriptsdir+'/prepare_namelist.py',
                begin.strftime('%Y-%m-%d_%H:%M'),
                begin_plus1.strftime('%Y-%m-%d_%H:%M'),
-               str(hist_interval), str(radt),]) 
+               str(hist_interval), str(radt),]), 
              depends_on=[id])
 
     s = my_Slurm("runWRF1", cfg_update={"nodes": "1", "array": "1-"+str(exp.n_nodes),
@@ -135,7 +141,7 @@ def run_ENS(begin, end, depends_on=None):
                cluster.scriptsdir+'/prepare_namelist.py',
                begin.strftime('%Y-%m-%d_%H:%M'),
                begin_plus1.strftime('%Y-%m-%d_%H:%M'),
-               str(hist_interval), str(radt),])
+               str(hist_interval), str(radt),]), 
             depends_on=[id])
 
     time_in_simulation_hours = (end-begin).total_seconds()/3600
@@ -164,8 +170,8 @@ def assimilate(assim_time, prior_init_time,
             if False: use `archivedir` (defined in config) to get prior state
             if str: use this directory to get prior state
     """
-    if prior_path_exp == False:
-        prior_expdir = cluster.archivedir()
+    if not prior_path_exp:
+        prior_path_exp = cluster.archivedir()
     elif not isinstance(prior_path_exp, str):
         raise TypeError('prior_path_exp either str or False, is '+str(type(prior_path_exp)))
 
@@ -243,13 +249,13 @@ elif start_from_existing_state:
     
     # get initial conditions from archive
     init_time = dt.datetime(2008, 7, 30, 6)
-    valid_time = dt.datetime(2008, 7, 30, 10)
+    time = dt.datetime(2008, 7, 30, 10)
     exppath_arch = '/gpfs/data/fs71386/lkugler/sim_archive/exp_v1.11_LMU_filter'
     
-    id = update_wrfinput_from_archive(valid_time, init_time, exppath_arch, depends_on=id)
+    id = update_wrfinput_from_archive(time, init_time, exppath_arch, depends_on=id)
 
 # values for assimilation
-assim_time = valid_time
+assim_time = time
 prior_init_time = init_time
 prior_path_exp = exppath_arch
 

scripts/apply_obs_op_dart.py

@@ -9,23 +9,22 @@ import create_obsseq as osq
 from gen_synth_obs import read_prior_obs, set_input_nml
 import pre_assim
 
-def run_operator(time):
+def run_operator(obscfg, time):
     """
     time_for_dart (dt.datetime) : needs to be consistent with wrfout files!
     """
 
-    # assume only 1 obstype for now
-    obscfg = exp.observations[0]
-
     # get observation file (obs not important, but their locations)
     # this should correspond to configuration to have same locations as in real assim
     obs_seq_all_out = cluster.dartrundir + '/obs_seq_all.out'
     os.chdir(cluster.dartrundir)
+
     n_obs = obscfg['n_obs']
     error_var = (obscfg['err_std'])**2
     sat_channel = obscfg.get('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)
@@ -55,8 +54,10 @@ def run_operator(time):
     # copy output to archive
     savedir = cluster.archivedir()+'/obs_seq_final_1min/'
     mkdir(savedir)
-    copy(cluster.dartrundir+'/obs_seq.final', 
-         savedir+time.strftime('/%Y-%m-%d_%H:%M_obs_seq.final'))
+    obsname = obscfg.get('kind', 'satch'+str(obscfg['sat_channel']))
+    fout = time.strftime('/%Y-%m-%d_%H:%M_'+obsname+'_obs_seq.final')
+    copy(cluster.dartrundir+'/obs_seq.final', savedir+fout)
+    print('output of observation operator saved to', fout)
 
 
 if __name__ == '__main__':
@@ -69,4 +70,5 @@ if __name__ == '__main__':
     pre_assim.run(time_to_run_fw_op, prev_forecast_init, exppath_firstguess)
 
     # run fwd operator, save to archive
-    run_operator(time_to_run_fw_op)
+    for i_obs, obscfg in enumerate(exp.observations):
+        run_operator(obscfg, time_to_run_fw_op)

scripts/gen_synth_obs.py

@@ -115,13 +115,16 @@ def set_input_nml(sat_channel=False, just_prior_values=False,
 
     # input.nml for RTTOV
     if sat_channel > 0:
-        if sat_channel in [1, 2, 3, 12]:
+        if sat_channel in [1, 2, 3, 12]:  # VIS channels
             rttov_nml = cluster.scriptsdir+'/../templates/obs_def_rttov.VIS.nml'
+        else:  # IR channels
+            rttov_nml = cluster.scriptsdir+'/../templates/obs_def_rttov.IR.nml'
+        append_file(cluster.dartrundir+'/input.nml', rttov_nml)
     else:
+        # append any rttov segment, needs to exist anyway
         rttov_nml = cluster.scriptsdir+'/../templates/obs_def_rttov.IR.nml'
         append_file(cluster.dartrundir+'/input.nml', rttov_nml)
 
-
 def obs_operator_ensemble():
     os.chdir(cluster.dartrundir)
 
@@ -162,8 +165,9 @@ if __name__ == "__main__":
     time = dt.datetime.strptime(sys.argv[1], '%Y-%m-%d_%H:%M')
     fpath_obs_coords = cluster.archivedir()+time.strftime('/%Y-%m-%d_%H:%M/obs_coords.pkl')
 
-    # remove any existing observation files
-    os.chdir(cluster.dartrundir); os.system('rm -f obs_seq_*.out obs_seq.in obs_seq.final')
+    
+    os.chdir(cluster.dartrundir)
+    os.system('rm -f obs_seq_*.out obs_seq.in obs_seq.final')  # remove any existing observation files
 
     def prepare_nature_dart():
         # get wrfout_d01 from nature run