Initial commit of existing rose setup

.gitignore

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+*.nc

app/archive_output/rose-app.conf

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+[command]
+default =	dst=${ARCHIVE_DIR};
+			src=${ROSE_DATAC}/wrfout_*
+			ssh ceto6 -t "rsync -aph --no-o --no-g $src $dst"
+

app/copy_common_to_remote/rose-app.conf

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+[command]
+default = cp /pml${COMMON_FILES_PATH:1}/* ${ROSE_DATA};

app/generate_CMEMS_nest/file/make_nest_bound.py

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+import numpy as np
+import netCDF4 as nc
+import datetime as dt
+import glob as gb
+import sys
+
+import PyFVCOM as pf
+
+#"""
+cmems_data_dir = '/data/sthenno1/backup/mbe/Data/CMEMS'
+start_date = dt.datetime(2018,9,19)
+end_date = dt.datetime(2018,9,20)
+grid = 'tamar_v2_grd.dat'
+sigma_file = 'sigma_gen.dat'
+native_coordinates = 'cartesian'
+fvcom_harmonics = '/data/sthenno1/backup/mbe/Data/harmonics_files/tamar_2006_harmonics.nc'
+interval = 1/24 
+
+#"""
+
+"""
+cmems_data_dir = sys.argv[1]
+start_date = dt.datetime.strptime(sys.argv[2], '%Y-%m-%d')
+end_date = dt.datetime.strptime(sys.argv[3], '%Y-%m-%d')
+grid = sys.argv[4]
+sigma_file = sys.argv[5]
+native_coordinates = sys.argv[6]
+fvcom_harmonics = sys.argv[7]
+interval = 1/float(sys.argv[8])
+"""
+
+
+constituents = ['M2', 'S2']
+output_file = 'boundary_nest.nc'.format(grid)
+cmems_time_res = 'hi'
+
+
+##############################################################################################
+# Setup preproc Model object
+aqua_prep = pf.preproc.Model(start_date, end_date, grid, native_coordinates, zone='30N', sampling=interval)
+aqua_prep.add_sigma_coordinates(sigma_file)
+
+# Make the nested boundary object
+aqua_prep.add_nests(4)
+aqua_prep.add_nests_harmonics(fvcom_harmonics, harmonics_vars=['u', 'v', 'ua', 'va', 'zeta'], constituents=constituents, pool_size=20)
+
+# Make the regular readers for the CMEMS data
+fvcom_cmems_names = {'salinity':['SAL', 'vosaline'], 'temp':['TEM', 'votemper'],
+					'v':['CUR', 'vomecrty'], 'u':['CUR', 'vozocrtx'],
+					'zeta':['SSH', 'sossheig']}
+
+dt_list = [start_date + dt.timedelta(days = int(i)) for i in np.arange(-1, (end_date - start_date).days + 2)]
+datestr_list = [this_date.strftime('%Y%m%d') for this_date in dt_list]
+
+for this_fvcom, this_var in fvcom_cmems_names.items():
+	cmems_file_list = []
+	for this_date in datestr_list:
+		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]])
+
+	aqua_prep.add_nests_regular(this_fvcom, this_data_reader, this_var[1], constrain_coordinates=False)
+
+# Depth avg the velocities
+aqua_prep.avg_nest_force_vel()
+
+# Write the forcing file 
+
+aqua_prep.write_nested_forcing(output_file, adjust_tides=['zeta', 'u', 'v', 'ua', 'va'])
+

app/generate_CMEMS_nest/file/sigma_gen.dat

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+NUMBER OF SIGMA LEVELS = 25
+SIGMA COORDINATE TYPE = GENERALIZED
+DU = 35.0
+DL = 15.0
+MIN CONSTANT DEPTH =      120.0
+KU = 7
+KL = 3
+ZKU =  5.0 5.0 5.0 5.0 5.0 5.0 5.0
+ZKL =  5.0 5.0 5.0