From e5850dfbfeca361cb6b19d10f36db81b349477b8 Mon Sep 17 00:00:00 2001
From: lkugler <lukas.kugler@gmail.com>
Date: Tue, 23 Nov 2021 21:08:37 +0100
Subject: [PATCH] new initialconditions routines
---
scripts/prep_IC_prior.py | 60 ++++++++++++++++
scripts/prepare_namelist.py | 9 +--
scripts/prepare_wrf_initials.py | 118 --------------------------------
scripts/update_IC.py | 58 ++++++++++++++++
4 files changed, 120 insertions(+), 125 deletions(-)
create mode 100755 scripts/prep_IC_prior.py
delete mode 100755 scripts/prepare_wrf_initials.py
create mode 100755 scripts/update_IC.py
diff --git a/scripts/prep_IC_prior.py b/scripts/prep_IC_prior.py
new file mode 100755
index 0000000..a4d2a73
--- /dev/null
+++ b/scripts/prep_IC_prior.py
@@ -0,0 +1,60 @@
+import os, sys, warnings, glob
+import datetime as dt
+
+from config.cfg import exp, cluster
+from utils import copy, clean_wrfdir, try_remove
+
+"""
+Sets initial condition data (wrfinput/wrfrst file) in the run_WRF directory for each ensemble member
+
+You have 2 options to restart:
+1) using wrfout files (function create_wrfinput_from_wrfout)
+2) using wrfrst files (function create_wrfrst_in_WRF_rundir)
+
+Ad 1: copy wrfout from prior to archivedir
+
+Ad 2: copies wrfrst to run_WRF directory
+
+"""
+
+def create_wrfrst_in_WRF_rundir(time, prior_init_time, prior_path_exp):
+ """copies wrfrst to run_WRF directory (for next WRF run)
+ """
+ for iens in range(1, exp.n_ens+1):
+ clean_wrfdir(cluster.wrf_rundir(iens))
+
+ prior_wrfrst = prior_path_exp + prior_init_time.strftime('/%Y-%m-%d_%H:%M/') \
+ +str(iens)+time.strftime('/wrfrst_d01_%Y-%m-%d_%H:%M:%S')
+ wrfrst = cluster.wrf_rundir(iens) + time.strftime('/wrfrst_d01_%Y-%m-%d_%H:%M:%S')
+ print('copy prior (wrfrst)', prior_wrfrst, 'to', wrfrst)
+ copy(prior_wrfrst, wrfrst)
+
+ # remove all wrfrst (but not the one used)
+ files_rst = glob.glob(prior_path_exp + prior_init_time.strftime('/%Y-%m-%d_%H:%M/'+str(iens)+'/wrfrst_*'))
+ files_rst.remove(prior_wrfrst)
+ for f in files_rst:
+ print('removing', f)
+ try_remove(f)
+
+def create_updated_wrfinput_from_wrfout(time, prior_init_time, prior_path_exp):
+ """Same as create_wrfout_in_archivedir, but output is `wrfinput` in WRF run directory"""
+
+ print('writing updated wrfout to WRF run directory as wrfinput')
+ for iens in range(1, exp.n_ens+1):
+ prior_wrfout = prior_path_exp + prior_init_time.strftime('/%Y-%m-%d_%H:%M/') \
+ +str(iens)+time.strftime('/wrfout_d01_%Y-%m-%d_%H:%M:%S')
+ post_wrfout = cluster.wrf_rundir(iens) + '/wrfinput_d01'
+ copy(prior_wrfout, post_wrfout)
+ print(post_wrfout, 'created.')
+
+
+if __name__ == '__main__':
+ prior_path_exp = sys.argv[1]
+ prior_init_time = dt.datetime.strptime(sys.argv[2], '%Y-%m-%d_%H:%M')
+ prior_valid_time = dt.datetime.strptime(sys.argv[3], '%Y-%m-%d_%H:%M')
+
+ use_wrfout_as_wrfinput = False
+ if use_wrfout_as_wrfinput:
+ create_updated_wrfinput_from_wrfout(prior_valid_time, prior_init_time, prior_path_exp)
+ else:
+ create_wrfrst_in_WRF_rundir(prior_valid_time, prior_init_time, prior_path_exp)
diff --git a/scripts/prepare_namelist.py b/scripts/prepare_namelist.py
index 716c079..c71cd9b 100755
--- a/scripts/prepare_namelist.py
+++ b/scripts/prepare_namelist.py
@@ -42,15 +42,8 @@ def run(iens, begin, end, hist_interval=5, radt=5, archive=True,
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)
- if rst_inname: # rst_inname did not work -> link file to directory
- # sed_inplace(rundir+'/namelist.input', '<initdir>', rst_inname)
- fname = begin.strftime('/wrfrst_d01_%Y-%m-%d_%H:%M:%S')
- symlink(rst_inname+fname, rundir+fname)
- print('linked', rst_inname+fname, 'to rundir')
-
# set times
for k, v in {'<y1>': '%Y', '<m1>': '%m', '<d1>': '%d',
'<HH1>': '%H', '<MM1>': '%M'}.items():
@@ -59,6 +52,8 @@ def run(iens, begin, end, hist_interval=5, radt=5, archive=True,
'<HH2>': '%H', '<MM2>': '%M'}.items():
sed_inplace(rundir+'/namelist.input', k, end.strftime(v))
+ print(rundir+'/namelist.input created')
+ print('runtime:', begin, end, 'output to', archdir)
#########################
if archive:
diff --git a/scripts/prepare_wrf_initials.py b/scripts/prepare_wrf_initials.py
deleted file mode 100755
index 3c00abc..0000000
--- a/scripts/prepare_wrf_initials.py
+++ /dev/null
@@ -1,118 +0,0 @@
-print('loading modules')
-import os, sys, warnings, glob
-import datetime as dt
-import netCDF4 as nc
-
-from config.cfg import exp, cluster
-from utils import symlink, copy, mkdir, clean_wrfdir, try_remove
-
-"""
-Sets initial condition data (wrfinput/wrrst file) in the run_WRF directory for each ensemble member
-
-You have 2 options to restart:
-1) using wrfout files (function create_updated_wrfinput_from_wrfout)
-2) using wrfrst files (function create_wrfrst_in_WRF_rundir)
-
-Ad 1: copy wrfout from prior to archivedir
- overwrite DA-updated variables with DART output
-
-Ad 2: copies wrfrst to run_WRF directory
- overwrites DA-updated variables with DART output fields
-
-# assumes T = THM (dry potential temperature as prognostic variable)
-"""
-update_vars = ['Times',]
-update_vars.extend(exp.update_vars) # 'U', 'V', 'T', 'PH', 'MU', 'QVAPOR', 'QCLOUD', 'QICE', 'TSK', 'CLDFRA']
-updates = ','.join(update_vars)
-
-def create_wrfrst_in_WRF_rundir(time, prior_init_time, exppath_firstguess):
- """copies wrfrst to run_WRF directory (for next WRF run)
- """
- for iens in range(1, exp.n_ens+1):
- clean_wrfdir(cluster.wrf_rundir(iens))
-
- prior_wrfrst = exppath_firstguess + prior_init_time.strftime('/%Y-%m-%d_%H:%M/') \
- +str(iens)+time.strftime('/wrfrst_d01_%Y-%m-%d_%H:%M:%S')
- wrfrst = cluster.wrf_rundir(iens) + time.strftime('/wrfrst_d01_%Y-%m-%d_%H:%M:%S')
- print('copy prior (wrfrst)', prior_wrfrst, 'to', wrfrst)
- copy(prior_wrfrst, wrfrst)
-
- filter_out = cluster.dartrundir+'/filter_restart_d01.'+str(iens).zfill(4)
- print('update assimilated variables => overwrite', updates, 'in', wrfrst, 'from', filter_out)
- os.system(cluster.ncks+' -A -v '+updates+' '+filter_out+' '+wrfrst)
-
- print('writing T into THM of wrfrst') # assumes T = THM (dry potential temperature as prognostic variable)
- with nc.Dataset(filter_out, 'r') as ds_filter:
- with nc.Dataset(wrfrst, 'r+') as ds_wrfrst:
- ds_wrfrst.variables['THM_1'][:] = ds_filter.variables['T'][:]
- ds_wrfrst.variables['THM_2'][:] = ds_filter.variables['T'][:]
- print(wrfrst, 'created.')
-
- # remove all wrfrst (but not the one used)
- files_rst = glob.glob(exppath_firstguess + prior_init_time.strftime('/%Y-%m-%d_%H:%M/'+str(iens)+'/wrfrst_*'))
- files_rst.remove(prior_wrfrst)
- for f in files_rst:
- try_remove(f)
-
-def create_updated_wrfinput_from_wrfout(time, prior_init_time, exppath_firstguess):
- """Same as create_wrfout_in_archivedir, but output is `wrfinput` in WRF run directory"""
-
- print('writing updated wrfout to WRF run directory as wrfinput')
- for iens in range(1, exp.n_ens+1):
- prior_wrfout = exppath_firstguess + prior_init_time.strftime('/%Y-%m-%d_%H:%M/') \
- +str(iens)+time.strftime('/wrfout_d01_%Y-%m-%d_%H:%M:%S')
- post_wrfout = cluster.wrf_rundir(iens) + '/wrfinput_d01'
- copy(prior_wrfout, post_wrfout)
-
- if True: # overwrite DA updated variables
- filter_out = cluster.dartrundir+'/filter_restart_d01.'+str(iens).zfill(4)
- os.system(cluster.ncks+' -A -v '+updates+' '+filter_out+' '+post_wrfout)
-
- # need to overwrite THM manually
- with nc.Dataset(filter_out, 'r') as ds_filter:
- with nc.Dataset(post_wrfout, 'r+') as ds_wrfout:
- ds_wrfout.variables['THM'][:] = ds_filter.variables['T'][:]
- print(post_wrfout, 'created.')
-
-def create_wrfout_in_archivedir(time, prior_init_time, exppath_firstguess):
- """Put updated wrfout in archive dir (because wrf restart writes no 0 minute wrfout)
-
- probably not necessary, if using the wrf namelist option `write_hist_at_0h_rst`
- """
- print('writing updated wrfout to archive (for verification)')
- for iens in range(1, exp.n_ens+1):
- prior_wrfout = exppath_firstguess + prior_init_time.strftime('/%Y-%m-%d_%H:%M/') \
- +str(iens)+time.strftime('/wrfout_d01_%Y-%m-%d_%H:%M:%S')
- post_wrfout_archive = cluster.archivedir +time.strftime('/%Y-%m-%d_%H:%M/') \
- +str(iens)+time.strftime('/wrfout_d01_%Y-%m-%d_%H:%M:%S')
- # copy template wrfout (including cycled variables)
- os.makedirs(os.path.dirname(post_wrfout_archive), exist_ok=True)
- copy(prior_wrfout, post_wrfout_archive)
-
- # overwrite DA updated variables
- filter_out = cluster.dartrundir+'/filter_restart_d01.'+str(iens).zfill(4)
- #filter_out = cluster.archivedir +time.strftime('/%Y-%m-%d_%H:%M/assim_stage0/filter_restart_d01.'+str(iens).zfill(4))
- os.system(cluster.ncks+' -A -v '+updates+' '+filter_out+' '+post_wrfout_archive)
-
- # need to overwrite THM manually
- with nc.Dataset(filter_out, 'r') as ds_filter:
- with nc.Dataset(post_wrfout_archive, 'r+') as ds_wrfout:
- ds_wrfout.variables['THM'][:] = ds_filter.variables['T'][:]
- print(post_wrfout_archive, 'created.')
-
-if __name__ == '__main__':
- time = dt.datetime.strptime(sys.argv[1], '%Y-%m-%d_%H:%M')
- prior_init_time = dt.datetime.strptime(sys.argv[2], '%Y-%m-%d_%H:%M')
- exppath_firstguess = str(sys.argv[3])
-
-
- use_wrfout_as_wrfinput = False
- if use_wrfout_as_wrfinput:
- create_updated_wrfinput_from_wrfout(time, prior_init_time, exppath_firstguess)
- else:
- create_wrfrst_in_WRF_rundir(time, prior_init_time, exppath_firstguess)
-
- # this is done with the right WRF namelist entry (write first wrfout)
- #create_wrfout_in_archivedir(time, prior_init_time, exppath_firstguess)
-
-
diff --git a/scripts/update_IC.py b/scripts/update_IC.py
new file mode 100755
index 0000000..8158cc9
--- /dev/null
+++ b/scripts/update_IC.py
@@ -0,0 +1,58 @@
+import os, sys, warnings
+import datetime as dt
+import netCDF4 as nc
+
+from config.cfg import exp, cluster
+"""
+Updates initial condition (wrfinput/wrfrst files) in the run_WRF directories with ./filter output
+
+# assumes T = THM (dry potential temperature as prognostic variable)
+"""
+
+use_wrfrst = True # recommended to be True
+if use_wrfrst:
+ initials_fmt = '/wrfrst_d01_%Y-%m-%d_%H:%M:%S'
+else:
+ initials_fmt = '/wrfinput_d01'
+
+
+def update_initials_in_WRF_rundir(time):
+ """updates wrfrst in run_WRF directory with posterior state from ./filter
+
+ Args:
+ time (dt.datetime): time of assimilation (directory preceeding ./assim_stage0/...)
+ """
+
+ # which WRF variables will be updated?
+ update_vars = ['Times',]
+ update_vars.extend(exp.update_vars)
+ updates = ','.join(update_vars)
+
+ for iens in range(1, exp.n_ens+1):
+ ic_file = cluster.wrf_rundir(iens) + time.strftime(initials_fmt)
+ if not os.path.isfile(ic_file):
+ raise IOError(ic_file+' does not exist, updating impossible!')
+ else:
+ # overwrite DA updated variables
+ filter_out = cluster.archivedir+time.strftime('/%Y-%m-%d_%H:%M/assim_stage0/filter_restart_d01.'+str(iens).zfill(4))
+ print('update assimilated variables => overwrite', updates, 'from', filter_out)
+ os.system(cluster.ncks+' -A -v '+updates+' '+filter_out+' '+ic_file)
+
+ # assumes T = THM (dry potential temperature as prognostic variable)
+ print('writing T into THM')
+ with nc.Dataset(filter_out, 'r') as ds_filter:
+
+ if use_wrfrst:
+ with nc.Dataset(ic_file, 'r+') as ds_wrfrst:
+ ds_wrfrst.variables['THM_1'][:] = ds_filter.variables['T'][:]
+ ds_wrfrst.variables['THM_2'][:] = ds_filter.variables['T'][:]
+ else:
+ with nc.Dataset(ic_file, 'r+') as ds_wrfout:
+ ds_wrfout.variables['THM'][:] = ds_filter.variables['T'][:]
+
+ print(ic_file, 'updated.')
+
+
+if __name__ == '__main__':
+ time = dt.datetime.strptime(sys.argv[1], '%Y-%m-%d_%H:%M')
+ update_initials_in_WRF_rundir(time)
--
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