Add apps to make a CMEMS warm start file instead of starting from constant T and S values

app/generate_CMEMS_start/file/make_restart.py

+import multiprocessing
+import numpy as np
+import datetime as dt
+import glob as gb
+from pathlib import Path
+
+import PyFVCOM as pf
+from PyFVCOM.utilities.time import date_range
+
+cmems_data_dir = sys.argv[1]
+start_date = dt.datetime.strptime(sys.argv[2], '%Y-%m-%d')
+grid = sys.argv[3]
+donor_filepath = sys.argv[4]
+
+"""
+cmems_data_dir = '/data/sthenno1/scratch/modop/Data/CMEMS'
+start_date = dt.datetime(2019,1,15)
+grid = 'tamar_v2'
+"""
+
+cmems_time_res = 'hi'
+
+
+fvcom_cmems_names = {'salinity':['SAL', 'vosaline'], 'temp':['TEM', 'votemper'],
+                                        'v':['CUR', 'vomecrty'], 'u':['CUR', 'vozocrtx'],
+                                        'zeta':['SSH', 'sossheig']}
+
+
+# Modify a donor restart file.
+restart = pf.preproc.Restart(donor_filepath,
+                          variables=['siglay', 'siglev'])
+
+# and alter the time variable
+restart.time.datetime = np.asarray([start_date])
+ref_date = dt.datetime(1858,11,17,0,0,0)
+restart.time.time = np.asarray([(start_date - ref_date).days])
+restart.time.Itime = np.asarray([(start_date - ref_date).days])
+restart.time.Times = np.asarray(['{}T00:00:00.0000000'.format(start_date.strftime('%Y-%m-%d'))])
+
+# We need to bracket the restart data in time with CMEMS data to ensure it interpolates properly.
+for this_fvcom, this_var in fvcom_cmems_names.items():
+    cmems_file_list = []
+    offset = dt.timedelta(days=1)
+    for this_date_dt in date_range(start_date - offset, start_date + offset):
+        this_date = this_date_dt.strftime('%Y%m%d')
+        if this_var[0] == 'SSH':
+                poss_files = gb.glob('{}/*{}*{}*/*{}.nc'.format(cmems_data_dir, 'hi', this_var[0], this_date))
+        else:
+                poss_files = gb.glob('{}/*{}*{}*/*{}.nc'.format(cmems_data_dir, cmems_time_res, this_var[0], this_date))
+        # Handle that sometimes theres multiple files for one day from different forecast runs
+        if len(poss_files) > 1:
+                chosen_file = poss_files[0]
+                for this_file in poss_files[1:]:
+                        if this_file > chosen_file:
+                                chosen_file = this_file
+                cmems_file_list.append(chosen_file)
+        elif len(poss_files) == 1:
+                cmems_file_list.append(poss_files[0])
+
+    if this_var[0] =='SSH':
+        reg_reader = pf.preproc.Regular2DReader
+    else:
+        reg_reader = pf.preproc.RegularReader
+
+    this_data_reader = reg_reader(cmems_file_list[0], [this_var[1]])
+
+    if len(cmems_file_list) > 1:
+        for this_file in cmems_file_list[1:]:
+            this_data_reader += reg_reader(this_file, [this_var[1]])
+
+    # Interpolate onto the FVCOM grid.
+    if this_fvcom in ['u', 'v']:
+        this_mode = 'elements'
+    elif this_fvcom == 'zeta':
+        this_mode = 'surface'
+    else:
+        this_mode = 'nodes'
+
+    restart.replace_variable_with_regular(this_fvcom, this_var[1], this_data_reader, constrain_coordinates=True, mode=this_mode)
+
+restart.write_restart('{}_restart_0001.nc'.format(grid))
+

app/generate_CMEMS_start/rose-app.conf

+[command]
+default = python3 make_restart.py ${CMEMS_DATA_DIR} ${START_DAY} ${GRID_NAME} ${DONOR_RESTART_FILE_PATH}; cp ${GRID_NAME}_restart_0001.nc /${REMOTE_TRANSFER_DIR}/

app/mv_start_file/rose-app.conf

+[command]
+default = cp /pml${REMOTE_TRANSFER_DIR}/${GRID_NAME}_restart_0001.nc ${ROSE_DATAC};

rose-suite_TAMAR.conf

@@ -48,6 +48,8 @@ BOUNDARY_FORCING='CMEMS'
 HARMONICS_FILE_PATH='/users/modellers/modop/Models/FVCOM_tamar_harmonics/tamar_2006_harmonics.nc'
 ## Required for CMEMS
 CMEMS_DATA_DIR='/data/sthenno1/scratch/modop/Data/CMEMS'
+## Required for CMEMS warm start
+DONOR_RESTART_FILE_PATH='/users/modellers/modop/Models/FVCOM_tamar_restart/tamar_v2_donor_restart.nc'
 ## Required for NEST_FILE
 NEST_RUN_SUITE='fvcom-rosa'
 # The time resolution of the nest output, as divisions of 1 day (i.e. 24 would be hourly, 48 every half hour)

suite.rc

@@ -14,7 +14,12 @@
 		[[[R1]]]
 			graph = """
 					copy_common_to_remote => softlink_forcing_remote
-					write_run_namelist => hot_cold_start => run_fvcom
+{%- if COLD_START and BOUNDARY_FORCING == 'CMEMS' %}
+					write_run_namelist => adjust_namelist & generate_CMEMS_start => mv_start_file => run_fvcom
+{% elif COLD_START and BOUNDARY_FORCING == 'NEST_FILE' %}
+					write_run_namelist => adjust_namelist & generate_nest_start => mv_start_file => run_fvcom
+{%- if COLD_START %}
+
 					"""
 		[[[P1D]]]
 			graph = """
@@ -95,6 +100,7 @@
 			ARCHIVE_DIR={{ARCHIVE_DIR}}
 
 			HARMONICS_FILE_PATH={{HARMONICS_FILE_PATH}}
+			DONOR_RESTART_FILE_PATH={{DONOR_RESTART_FILE_PATH}}
 			CMEMS_DATA_DIR={{CMEMS_DATA_DIR}}
 			NEST_RUN_SUITE={{NEST_RUN_SUITE}}
 			NEST_INTERVAL={{NEST_INTERVAL}}
@@ -263,20 +269,18 @@
 
 	[[run_fvcom]]
 		inherit = slurm_job
-	[[hot_cold_start]]
+	[[adjust_namelist]]
 		inherit = remote_job
-{%- if COLD_START %}
 		script = """
-			sed -i "s|.*STARTUP_TYPE.*|STARTUP_TYPE = 'coldstart',|" ${ROSE_DATAC}/${GRID_NAME}_run.nml
-			sed -i "s|.*STARTUP_FILE.*|STARTUP_FILE = 'none',|" ${ROSE_DATAC}/${GRID_NAME}_run.nml
 			sed -i "s|.*STARTUP_UV_TYPE.*|STARTUP_UV_TYPE   = 'default',|" ${ROSE_DATAC}/${GRID_NAME}_run.nml
 			sed -i "s|.*STARTUP_TURB_TYPE.*|STARTUP_TURB_TYPE = 'default',|" ${ROSE_DATAC}/${GRID_NAME}_run.nml
-			sed -i "s|.*STARTUP_TS_TYPE.*|STARTUP_TS_TYPE   = 'constant',|" ${ROSE_DATAC}/${GRID_NAME}_run.nml
+			sed -i "s|.*STARTUP_TS_TYPE.*|STARTUP_TS_TYPE   = 'set values',|" ${ROSE_DATAC}/${GRID_NAME}_run.nml
 	{%- if SEDIMENT %}
 			sed -i "s|.*SED_HOT_START.*|SED_HOT_START = F|" ${ROSE_DATAC}/cstms_sediment.inp
 	{%- endif %}
 			"""
-{%- endif %}
+	[[generate_CMEMS_start]]
+	[[mv_start_file]]
 	[[transfer_data]]
 		inherit = slurm_job_1
 	[[transfer_data_today]]