Merge branch 'master' of https://github.com/lkugler/DART-WRF

docs/source/.readthedocs.yaml → .readthedocs.yaml

-version: 1
+version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-22.04"
   tools:
-    python: "3.10"
+    python: "3.11"
 
 sphinx:
-  fail_on_warning: true
+  configuration: docs/source/conf.py
+  fail_on_warning: false
   
 formats:
   - pdf
-  - epub
   
 python:
-  # Install our python package before building the docs
   install:
+    - requirements: docs/requirements.txt
     - method: pip
       path: .

config/cluster.py

@@ -42,35 +42,38 @@ slurm_cfg               python dictionary, containing options of SLURM
                             'cfg_update = {"nodes": "2"}'
 """
 
+
 cluster = utils.ClusterConfig(exp)
-cluster.name = 'srvx1'
-cluster.max_nproc = 6
-cluster.use_slurm = False
+cluster.name = 'jet'
+cluster.max_nproc = 12
+cluster.use_slurm = True
+cluster.size_jobarray = 40
 
 # binaries
-cluster.python = '/users/staff/lkugler/miniconda3/bin/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.python = '/jetfs/home/lkugler/miniconda3/envs/DART/bin/python'
+cluster.python_verif = '/jetfs/home/lkugler/miniconda3/envs/enstools/bin/python'
+cluster.ncks = '/jetfs/spack/opt/spack/linux-rhel8-skylake_avx512/intel-20.0.2/nco-4.9.3-dhlqiyog7howjmaleyfhm6lkt7ra37xf/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.container = ''
 
 # paths for data output
-cluster.wrf_rundir_base = '/users/staff/lkugler/AdvDA23/run_WRF/'  # path for temporary files
-cluster.dart_rundir_base = '/users/staff/lkugler/AdvDA23/run_DART/'  # path for temporary files
-cluster.archive_base = '/mnt/jetfs/scratch/lkugler/data/sim_archive/'
+cluster.wrf_rundir_base = '/jetfs/home/lkugler/data/run_WRF/'  # path for temporary files
+cluster.dart_rundir_base = '/jetfs/home/lkugler/data/run_DART/'  # path for temporary files
+cluster.archive_base = '/jetfs/home/lkugler/data/sim_archive/'
 
 # paths used as input
-cluster.srcdir = '/users/staff/lkugler/AdvDA23/DART/WRF-4.3/run'
-cluster.dart_srcdir = '/users/staff/lkugler/AdvDA23/DART/models/wrf/work'
-cluster.rttov_srcdir = '/users/staff/lkugler/AdvDA23/RTTOV13/rtcoef_rttov13/'
-cluster.scriptsdir = '/users/staff/lkugler/AdvDA23/DART-WRF/dartwrf/'
-cluster.geo_em = '/mnt/jetfs/scratch/lkugler/data/geo_em.d01.nc'
+cluster.srcdir = '/jetfs/home/lkugler/data/compile/WRF-4.3/run'
+cluster.dart_srcdir = '/jetfs/home/lkugler/data/compile/DART/DART-10.5.3/models/wrf/work'
+cluster.rttov_srcdir = '/jetfs/home/lkugler/data/compile/RTTOV13/rtcoef_rttov13/'
+cluster.scriptsdir = '/jetfs/home/lkugler/DART-WRF/dartwrf/'
 
-# templates/run scripts
+# other inputs
+cluster.geo_em = '/jetfs/home/lkugler/data/geo_em.d01.nc'
+cluster.obs_impact_filename = cluster.scriptsdir+'/../templates/impactfactor_T.txt'
 cluster.namelist = cluster.scriptsdir+'/../templates/namelist.input'
-cluster.run_WRF = cluster.scriptsdir+'/run_ens.jet.sh'
+cluster.run_WRF = '/jetfs/home/lkugler/DART-WRF/dartwrf/run_ens.jet.sh'
 
-cluster.slurm_cfg = {"account": "lkugler", "partition": "compute",
+cluster.slurm_cfg = {"account": "lkugler", "partition": "compute", #"nodelist": "jet07",
                  "ntasks": "1", "ntasks-per-core": "1", "mem": "50G",
                  "mail-type": "FAIL", "mail-user": "lukas.kugler@univie.ac.at"}

cycled_exp.py

@@ -74,7 +74,7 @@ if __name__ == "__main__":
                     depends_on=id)
         
         # as we have WRF output, we can use own exp path as prior
-        prior_path_exp = cluster.archivedir       
+        prior_path_exp = w.cluster.archivedir       
 
         id_sat = w.create_satimages(time, depends_on=id)
         

dartwrf/assim_synth_obs.py

@@ -3,7 +3,7 @@ import time as time_module
 import datetime as dt
 import numpy as np
 
-from dartwrf.utils import symlink, copy, sed_inplace, append_file, mkdir, try_remove, print, shell
+from dartwrf.utils import symlink, copy, sed_inplace, append_file, mkdir, try_remove, print, shell, write_txt
 from dartwrf.obs import error_models as err
 import dartwrf.create_obsseq as osq
 from dartwrf import wrfout_add_geo
@@ -141,13 +141,6 @@ def prepare_prior_ensemble(assim_time, prior_init_time, prior_valid_time, prior_
     os.system("rm -rf " + cluster.dartrundir + "/perfect_output_*")
     os.system("rm -rf " + cluster.dartrundir + "/obs_seq.fina*")
 
-
-def write_txt(lines, fpath):
-    try_remove(fpath)
-    with open(fpath, "w") as file:
-        for line in lines:
-            file.write(line+'\n')
-
 def write_list_of_inputfiles_prior():
      files = []
      for iens in range(1, exp.n_ens+1):
@@ -236,13 +229,13 @@ def archive_filteroutput(time):
 def get_parametrized_error(obscfg, osf_prior):
     """Calculate the parametrized error for an ObsConfig (one obs type)
 
-    Args
-        obscfg (object):                configuration of observations
-        osf_prior (obsseq.ObsRecord):   contains truth and prior values from obs_seq.final
+    Args:
+        obscfg (object): Configuration of observations
+        osf_prior (obsseq.ObsRecord): Contains truth and prior values from obs_seq.final
                                         (output of ./final in evaluate-mode (no posterior))
 
-    Returns
-        np.array            observation error std-dev for assimilation
+    Returns:
+        np.array: observation error std-dev for assimilation
     """
     Hx_prior = osf_prior.get_prior_Hx().T
     Hx_truth = osf_prior.get_truth_Hx()
@@ -263,8 +256,7 @@ def set_obserr_assimilate_in_obsseqout(oso, osf_prior, outfile="./obs_seq.out"):
     """"Overwrite existing variance values in obs_seq.out files
     
     Args:
-        oso (ObsSeq) :  python representation of obs_seq.out file, 
-                        will be modified and written to file
+        oso (ObsSeq): python representation of obs_seq.out file, will be modified and written to file
         osf_prior (ObsSeq): python representation of obs_seq.final (output of filter in evaluate-mode without posterior)
                             contains prior values; used for parameterized errors
 

dartwrf/config

+../config/
\ No newline at end of file

dartwrf/create_obsseq.py

@@ -180,15 +180,15 @@ def create_obs_seq_in(time_dt, list_obscfg,
     Args:
         time_dt (dt.datetime): time of observation
         list_obscfg (list of dict): configuration for observation types
-            must have keys: 
+
+    Note:
+        `list_obscfg` must have these keys: 
             - n_obs (int) : number of observations (must be a square of an integer: 4, 9, 1000, ...)
             - obs_locations (str or tuple) in ['square_array_from_domaincenter', 'square_array_evenly_on_grid', ] 
                                             or list of (lat, lon) coordinate tuples, in degrees north/east
-                - error_generate (float)
-                - error_assimilate (float or False) : False -> parameterized
+            - error_generate (np.array)
+            - error_assimilate (np.array or False) : False -> parameterized
             - cov_loc_radius_km (float)
-
-        obs_errors (np.array): contains observation errors, one for each observation
     """
     print('creating obs_seq.in:')
     time_dt = add_timezone_UTC(time_dt)

docs/requirements.txt

+sphinx>=6
+pysolar==0.10.0
+docopt
+nbsphinx

docs/source/conf.py

@@ -11,7 +11,10 @@ author = 'Lukas Kugler'
 release = '2023.2.21'
 
 # -- General configuration
-sys.path.insert(0, os.path.abspath('../../'))
+sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('../'))
+
+master_doc = 'index'
 
 extensions = [
     'sphinx.ext.duration',

docs/source/index.rst

@@ -18,7 +18,7 @@ DART-WRF is available at `github.com/lkugler/DART-WRF <https://github.com/lkugle
 Other helpful resources
 -----------------------
 
-**DART documentation** `[docs.ucar.edu] <https://docs.dart.ucar.edu/en/latest/README.html>`_
+**DART documentation** `[here] <https://docs.dart.ucar.edu/en/latest/README.html>`_
 **WRF user guide** `[here] <http://www2.mmm.ucar.edu/wrf/users/docs/user_guide_v4/v4.2/WRFUsersGuide_v42.pdf>`_
 
 
@@ -31,9 +31,10 @@ Other helpful resources
    :maxdepth: 2
    :caption: Tutorials:
 
-   tutorial1
-   tutorial2
-   tutorial3
+   notebooks/tutorial1
+   notebooks/tutorial2
+   notebooks/tutorial3
+
 
 API
 ===

requirements.txt

-pysolar==1.10.0
-docopt
-nbsphinx>=0.8.6