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IOinitial.py
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import time
from datetime import datetime, timedelta
import os, sys, string
from netCDF4 import Dataset
from netCDF4 import num2date
import numpy as np
__author__ = 'Trond Kristiansen'
__email__ = '[email protected]'
__created__ = datetime(2009, 3, 16)
__modified__ = datetime(2014, 10, 23)
__version__ = "1.0"
__status__ = "Development"
def help():
"""
This function generates an INIT file from scratch. Varibales include:
salt, temp, u, v, ubar, vbar, zeta, and time. Time dimension for each variable is ocean_time which is days
since 1948/1/1.
This file is netcdf CF compliant and to check the CLIM file for CF compliancy:
http://titania.badc.rl.ac.uk/cgi-bin/cf-checker.pl?cfversion=1.0
Edited by Trond Kristiansen, 16.3.2009, 11.11.2009, 20.11.2009
"""
def createinitfile(confM2R, ntime, var, data1=None, data2=None, data3=None, data4=None):
# Create initial file for use with ROMS. This is the same as extracting time 0 from
# the climatology file.
if (confM2R.myformat == 'NETCDF4'):
myzlib = True
else:
myzlib = False
grdROMS = confM2R.grdROMS
if not grdROMS.ioInitInitialized:
grdROMS.ioInitInitialized = True
if os.path.exists(confM2R.initname):
os.remove(confM2R.initname)
f1 = Dataset(confM2R.initname, mode='w', format=confM2R.myformat)
f1.title = "Initial forcing file (INIT) used for foring of the ROMS model"
f1.description = "Created for the %s grid file" % (confM2R.romsgridpath)
f1.grd_file = "Gridfile: %s" % (confM2R.romsgridpath)
f1.history = "Created " + time.ctime(time.time())
f1.source = "Trond Kristiansen ([email protected])"
f1.type = "File in %s format created using MODEL2ROMS" % (confM2R.myformat)
f1.link = "https://github.com/trondkr/model2roms"
f1.Conventions = "CF-1.0"
# Define dimensions
f1.createDimension('xi_rho', grdROMS.xi_rho)
f1.createDimension('eta_rho', grdROMS.eta_rho)
f1.createDimension('xi_u', grdROMS.xi_u)
f1.createDimension('eta_u', grdROMS.eta_u)
f1.createDimension('xi_v', grdROMS.xi_v)
f1.createDimension('eta_v', grdROMS.eta_v)
f1.createDimension('xi_psi', grdROMS.xi_psi)
f1.createDimension('eta_psi', grdROMS.eta_psi)
f1.createDimension('ocean_time', None)
f1.createDimension('s_rho', len(grdROMS.s_rho))
f1.createDimension('s_w', len(grdROMS.s_w))
vnc = f1.createVariable('lon_rho', 'd', ('eta_rho', 'xi_rho',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = 'Longitude of RHO-points'
vnc.units = 'degree_east'
vnc.standard_name = 'longitude'
vnc[:, :] = grdROMS.lon_rho
vnc = f1.createVariable('lat_rho', 'd', ('eta_rho', 'xi_rho',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = 'Latitude of RHO-points'
vnc.units = 'degree_north'
vnc.standard_name = 'latitude'
vnc[:, :] = grdROMS.lat_rho
vnc = f1.createVariable('lon_u', 'd', ('eta_u', 'xi_u',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = 'Longitude of U-points'
vnc.units = 'degree_east'
vnc.standard_name = 'longitude'
vnc[:, :] = grdROMS.lon_u
vnc = f1.createVariable('lat_u', 'd', ('eta_u', 'xi_u',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = 'Latitude of U-points'
vnc.units = 'degree_north'
vnc.standard_name = 'latitude'
vnc[:, :] = grdROMS.lat_u
vnc = f1.createVariable('lon_v', 'd', ('eta_v', 'xi_v',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = 'Longitude of V-points'
vnc.units = 'degree_east'
vnc.standard_name = 'longitude'
vnc[:, :] = grdROMS.lon_v
vnc = f1.createVariable('lat_v', 'd', ('eta_v', 'xi_v',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = 'Latitude of V-points'
vnc.units = 'degree_north'
vnc.standard_name = 'latitude'
vnc[:, :] = grdROMS.lat_v
vnc = f1.createVariable('lat_psi', 'd', ('eta_psi', 'xi_psi',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = 'Latitude of PSI-points'
vnc.units = 'degree_north'
vnc.standard_name = 'latitude'
vnc[:, :] = grdROMS.lat_psi
vnc = f1.createVariable('lon_psi', 'd', ('eta_psi', 'xi_psi',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = 'Longitude of PSI-points'
vnc.units = 'degree_east'
vnc.standard_name = 'longitude'
vnc[:, :] = grdROMS.lon_psi
vnc = f1.createVariable('h', 'd', ('eta_rho', 'xi_rho',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = 'Final bathymetry at RHO points'
vnc.units = 'meter'
vnc.field = "bath, scalar"
vnc[:, :] = grdROMS.h
vnc = f1.createVariable('s_rho', 'd', ('s_rho',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = "S-coordinate at RHO-points"
vnc.valid_min = -1.
vnc.valid_max = 0.
vnc.positive = "up"
if grdROMS.vtransform == 2:
vnc.standard_name = "ocean_s_coordinate_g2"
vnc.formula_terms = "s: s_rho C: Cs_r eta: zeta depth: h depth_c: hc"
if grdROMS.vtransform == 1:
vnc.standard_name = "ocean_s_coordinate_g1"
vnc.formula_terms = "s: s_rho C: Cs_r eta: zeta depth: h depth_c: hc"
vnc.field = "s_rho, scalar"
vnc[:] = grdROMS.s_rho
vnc = f1.createVariable('s_w', 'd', ('s_w',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = "S-coordinate at W-points"
vnc.valid_min = -1.
vnc.valid_max = 0.
vnc.positive = "up"
if grdROMS.vtransform == 2:
vnc.standard_name = "ocean_s_coordinate_g2"
vnc.formula_terms = "s: s_w C: Cs_w eta: zeta depth: h depth_c: hc"
if grdROMS.vtransform == 1:
vnc.standard_name = "ocean_s_coordinate_g1"
vnc.formula_terms = "s: s_w C: Cs_w eta: zeta depth: h depth_c: hc"
vnc.field = "s_w, scalar"
vnc[:] = grdROMS.s_w
vnc = f1.createVariable('Cs_rho', 'd', ('s_rho',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = "S-coordinate stretching curves at RHO-points"
vnc.valid_min = -1.
vnc.valid_max = 0.
vnc.field = "s_rho, scalar"
vnc[:] = grdROMS.Cs_rho
vnc = f1.createVariable('hc', 'd')
vnc.long_name = "S-coordinate parameter, critical depth";
vnc.units = "meter"
vnc[:] = grdROMS.hc
vnc = f1.createVariable('z_r', 'd', ('s_rho', 'eta_rho', 'xi_rho',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = "Sigma layer to depth matrix";
vnc.units = "meter"
vnc[:, :, :] = grdROMS.z_r
vnc = f1.createVariable('Tcline', 'd')
vnc.long_name = "S-coordinate surface/bottom layer width";
vnc.units = "meter"
vnc[:] = grdROMS.tcline
vnc = f1.createVariable('theta_s', 'd')
vnc.long_name = "S-coordinate surface control parameter"
vnc[:] = grdROMS.theta_s
vnc = f1.createVariable('theta_b', 'd')
vnc.long_name = "S-coordinate bottom control parameter"
vnc[:] = grdROMS.theta_b
vnc = f1.createVariable('angle', 'd', ('eta_rho', 'xi_rho',), zlib=myzlib, fill_value=grdROMS.fillval)
vnc.long_name = "angle between xi axis and east"
vnc.units = "radian"
v_time = f1.createVariable('ocean_time', 'd', ('ocean_time',), zlib=myzlib, fill_value=grdROMS.fillval)
if (confM2R.indatatype == "NORESM"):
v_time.long_name = 'seconds since 1800-01-01 00:00:00'
v_time.units = 'seconds since 1800-01-01 00:00:00'
v_time.field = 'time, scalar, series'
v_time.calendar = 'noleap'
else:
v_time.long_name = 'seconds since 1948-01-01 00:00:00'
v_time.units = 'seconds since 1948-01-01 00:00:00'
v_time.field = 'time, scalar, series'
v_time.calendar = 'standard'
v_temp = f1.createVariable('temp', 'f', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
v_temp.long_name = "potential temperature"
v_temp.units = "Celsius"
v_temp.time = "ocean_time"
#v_temp.missing_value = grdROMS.fillval
v_salt = f1.createVariable('salt', 'f', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
v_salt.long_name = "salinity"
v_salt.time = "ocean_time"
v_salt.field = "salinity, scalar, series"
#v_salt.missing_value = grdROMS.fillval
v_ssh = f1.createVariable('zeta', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
v_ssh.long_name = "sea level"
v_ssh.units = "meter"
v_ssh.time = "ocean_time"
#v_ssh.missing_value = grdROMS.fillval
v_u = f1.createVariable('u', 'f', ('ocean_time', 's_rho', 'eta_u', 'xi_u',), zlib=myzlib,
fill_value=grdROMS.fillval)
v_u.long_name = "U-velocity, scalar, series"
v_u.units = "meter second-1"
v_u.time = "ocean_time"
#v_u.missing_value = grdROMS.fillval
v_v = f1.createVariable('v', 'f', ('ocean_time', 's_rho', 'eta_v', 'xi_v',), zlib=myzlib,
fill_value=grdROMS.fillval)
v_v.long_name = "V-velocity, scalar, series"
v_v.units = "meter second-1"
v_v.time = "ocean_time"
#v_v.missing_value = grdROMS.fillval
v_vbar = f1.createVariable('vbar', 'f', ('ocean_time', 'eta_v', 'xi_v',), zlib=myzlib,
fill_value=grdROMS.fillval)
v_vbar.long_name = "Barotropic V-velocity, scalar, series"
v_vbar.units = "meter second-1"
v_vbar.time = "ocean_time"
#v_vbar.missing_value = grdROMS.fillval
v_ubar = f1.createVariable('ubar', 'f', ('ocean_time', 'eta_u', 'xi_u',), zlib=myzlib,
fill_value=grdROMS.fillval)
v_ubar.long_name = "Barotropic U-velocity, scalar, series"
v_ubar.units = "meter second-1"
v_ubar.time = "ocean_time"
#v_ubar.missing_value = grdROMS.fillval
if confM2R.writeice:
ageice = f1.createVariable('ageice', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
ageice.long_name = "time-averaged age of the ice"
ageice.units = "years"
ageice.time = "ocean_time"
ageice.field = "ice age, scalar, series"
# ageice.missing_value = grdROMS.fillval
uice = f1.createVariable('uice', 'f', ('ocean_time', 'eta_u', 'xi_u',), zlib=myzlib,
fill_value=grdROMS.fillval)
uice.long_name = "time-averaged u-component of ice velocity"
uice.units = "meter second-1"
uice.time = "ocean_time"
uice.field = "u-component of ice velocity, scalar, series"
# uice.missing_value = grdROMS.fillval
vice = f1.createVariable('vice', 'f', ('ocean_time', 'eta_v', 'xi_v',), zlib=myzlib,
fill_value=grdROMS.fillval)
vice.long_name = "time-averaged v-component of ice velocity"
vice.units = "meter second-1"
vice.time = "ocean_time"
vice.field = "v-component of ice velocity, scalar, series"
# vice.missing_value = grdROMS.fillval
aice = f1.createVariable('aice', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
aice.long_name = "time-averaged fraction of cell covered by ice"
aice.time = "ocean_time"
aice.field = "ice concentration, scalar, series"
#aice.missing_value = grdROMS.fillval
hice = f1.createVariable('hice', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
hice.long_name = "time-averaged average ice thickness in cell"
hice.units = "meter"
hice.time = "ocean_time"
hice.field = "ice thickness, scalar, series"
#hice.missing_value = grdROMS.fillval
snow_thick = f1.createVariable('snow_thick', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
snow_thick.long_name = "time-averaged thickness of snow cover"
snow_thick.units = "meter"
snow_thick.time = "ocean_time"
snow_thick.field = "snow thickness, scalar, series"
#snow_thick.missing_value = grdROMS.fillval
ti = f1.createVariable('ti', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
ti.long_name = "time-averaged interior ice temperature"
ti.units = "degrees Celcius"
ti.time = "ocean_time"
ti.field = "interior temperature, scalar, series"
#ti.missing_value = grdROMS.fillval
sfwat = f1.createVariable('sfwat', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
sfwat.long_name = "time-averaged surface melt water thickness on ice"
sfwat.units = "meter"
sfwat.time = "ocean_time"
sfwat.field = "melt water thickness, scalar, series"
#sfwat.missing_value = grdROMS.fillval
tisrf = f1.createVariable('tisrf', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
tisrf.long_name = "time-averaged temperature of ice surface"
tisrf.units = "degrees Celcius"
tisrf.time = "ocean_time"
tisrf.field = "surface temperature, scalar, series"
#tisrf.missing_value = grdROMS.fillval
sig11 = f1.createVariable('sig11', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
sig11.long_name = "time-averaged internal ice stress 11 component"
sig11.units = "Newton meter-1"
sig11.time = "ocean_time"
sig11.field = "ice stress 11, scalar, series"
#sig11.missing_value = grdROMS.fillval
sig12 = f1.createVariable('sig12', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
sig12.long_name = "time-averaged internal ice stress 12 component"
sig12.units = "Newton meter-1"
sig12.time = "ocean_time"
sig12.field = "ice stress 12, scalar, series"
#sig12.missing_value = grdROMS.fillval
sig22 = f1.createVariable('sig22', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
sig22.long_name = "time-averaged internal ice stress 22 component"
sig22.units = "Newton meter-1"
sig22.time = "ocean_time"
sig22.field = "ice stress 22, scalar, series"
#sig22.missing_value = grdROMS.fillval
vnc = f1.createVariable('tau_iw', 'd')
vnc.long_name = "Tau_iw";
vnc.units = "unknown"
vnc = f1.createVariable('chu_iw', 'd')
vnc.long_name = "Chu_iw";
vnc.units = "unknown"
v_tomk = f1.createVariable('t0mk', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
v_tomk.long_name = "t0mk potential temperature"
v_tomk.units = "Celsius"
v_tomk.time = "ocean_time"
#v_tomk.missing_value = grdROMS.fillval
v_somk = f1.createVariable('s0mk', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fillval)
v_somk.long_name = "s0mk salinity"
v_somk.time = "ocean_time"
v_somk.field = "salinity, scalar, series"
#v_somk.missing_value = grdROMS.fillval
print(("grdROMS.time: ", grdROMS.time))
if grdROMS.timeunits[0:7] == "seconds":
d = num2date(grdROMS.time, units=v_time.long_name, calendar=v_time.calendar)
else:
d = num2date(grdROMS.time * 86400.0, units=v_time.long_name, calendar=v_time.calendar)
print('\n')
print('=========================================================================')
print('Created INIT file')
print(('set inittime in grd.py for time-index to print (current=%s)' % (grdROMS.inittime)))
print(('The time stamp for ROMS .in file saved to initial file is=> %s' % (d)))
print(('DSTART = %s' % (grdROMS.time)))
print(('TIME_REF = %s' % (v_time.long_name)))
print('=========================================================================')
print('\n')
else:
f1 = Dataset(confM2R.initname, mode='a', format=confM2R.myformat)
ntime = 0
if (grdROMS.timeunits[0:7] == "seconds"):
f1.variables['ocean_time'][ntime] = grdROMS.time
else:
f1.variables['ocean_time'][ntime] = grdROMS.time * 86400.0
if var.lower() == 'temperature':
f1.variables['temp'][ntime, :, :, :] = data1
if confM2R.writeice:
f1.variables['t0mk'][ntime, :, :] = np.squeeze(data1[len(grdROMS.z_r) - 1, :, :])
if var.lower() == 'salinity':
f1.variables['salt'][ntime, :, :, :] = data1
if confM2R.writeice:
f1.variables['s0mk'][ntime, :, :] = np.squeeze(data1[len(grdROMS.z_r) - 1, :, :])
if var.lower() == 'ssh':
f1.variables['zeta'][ntime, :, :] = data1
if var in ['uvel', 'vvel', 'ubar', 'vbar']:
f1.variables['u'][ntime, :, :, :] = data1
f1.variables['v'][ntime, :, :, :] = data2
f1.variables['ubar'][ntime, :, :] = data3
f1.variables['vbar'][ntime, :, :] = data4
if confM2R.writeice:
if var.lower() == "ageice":
data1 = np.where(abs(data1) > 120, 0, data1)
f1.variables['ageice'][ntime, :, :] = data1
if var.lower() in ['uice', 'vice']:
data1 = np.where(abs(data1) > 120, 0, data1)
f1.variables[var.lower()][ntime, :, :] = data1 / 100.
if var.lower() == 'aice':
data1 = np.where(abs(data1) > 120, 0, data1)
f1.variables['aice'][ntime, :, :] = data1 / 100.
f1.variables['sfwat'][ntime, :, :] = 0.
f1.variables['tisrf'][ntime, :, :] = 0.
f1.variables['ti'][ntime, :, :] = 0.
f1.variables['sig11'][ntime, :, :] = 0.
f1.variables['sig12'][ntime, :, :] = 0.
f1.variables['sig22'][ntime, :, :] = 0.
if mytype == 'GLORYS':
f1.variables['snow_thick'][ntime, :, :] = 0.
f1.variables['ageice'][ntime, :, :] = 0.
if var.lower() == 'hice':
data1 = np.where(abs(data1) > 10, 0, data1)
f1.variables['hice'][ntime, :, :] = data1
if var.lower() == 'snow_thick':
data1 = np.where(abs(data1) > 100, 0, data1)
f1.variables['snow_thick'][ntime, :, :] = data1
f1.variables['tau_iw'] = 0.015
f1.variables['chu_iw'] = 0.0012
f1.close()