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IOwrite.py
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IOwrite.py
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from datetime import datetime
from netCDF4 import Dataset
from netCDF4 import num2date
import numpy as np
import time
import os
__author__ = 'Trond Kristiansen'
__email__ = 'trond.kristiansen@imr.no'
__created__ = datetime(2009, 3, 2)
__modified__ = datetime(2014, 10, 23)
__version__ = "1.1"
__status__ = "Development"
def help():
"""
This function generates a CLIM file from scratch. The variables created 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
(also see: https://www.myroms.org/forum/viewtopic.php?f=30&t=1450&p=5209&hilit=cf+compliant#p5209)
This function is called from model2roms.py.
"""
def writeClimFile(grdROMS, ntime, outfilename, myvar, isClimatology, writeIce, mytype, myformat, data1=None, data2=None, data3=None, data4=None):
if (myformat=='NETCDF4'):
myzlib = True
else:
myzlib = False
if grdROMS.ioClimInitialized is False:
grdROMS.ioClimInitialized = True
if os.path.exists(outfilename):
os.remove(outfilename)
f1 = Dataset(outfilename, mode='w', format=myformat)
f1.title = "Climatology forcing file (CLIM) used for forcing the ROMS model"
f1.description = "Created for grid file: %s" % (grdROMS.grdName)
f1.grd_file = "Gridfile: %s" % (grdROMS.grdfilename)
f1.history = "Created " + time.ctime(time.time())
f1.source = "Trond Kristiansen (trond.kristiansen@imr.no)"
f1.type = "File in %s format created using MODEL2ROMS"%(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('s_rho', len(grdROMS.s_rho))
f1.createDimension('s_w', len(grdROMS.s_w))
if isClimatology is False:
f1.createDimension('ocean_time', None)
if isClimatology is True:
f1.createDimension('clim_time', 12)
vnc = f1.createVariable('lon_rho', 'd', ('eta_rho', 'xi_rho',), zlib=myzlib, fill_value=grdROMS.fill_value)
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.fill_value)
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.fill_value)
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.fill_value)
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.fill_value)
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.fill_value)
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.fill_value)
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.fill_value)
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.fill_value)
vnc.long_name = 'Bathymetry at RHO-points'
vnc.units = 'meter'
vnc.field = "bath, scalar"
vnc[:, :] = grdROMS.h
vnc = f1.createVariable('f', 'd', ('eta_rho', 'xi_rho',), zlib=myzlib, fill_value=grdROMS.fill_value)
vnc.long_name = 'Coriolis parameter at RHO-points'
vnc.units = 'second-1'
vnc.field = "Coriolis, scalar"
vnc[:, :] = grdROMS.f
vnc = f1.createVariable('pm', 'd', ('eta_rho', 'xi_rho',), zlib=myzlib, fill_value=grdROMS.fill_value)
vnc.long_name = 'curvilinear coordinate metric in XI'
vnc.units = 'meter-1'
vnc.field = "pm, scalar"
vnc[:, :] = grdROMS.pm
vnc = f1.createVariable('pn', 'd', ('eta_rho', 'xi_rho',), zlib=myzlib, fill_value=grdROMS.fill_value)
vnc.long_name = 'curvilinear coordinate metric in ETA'
vnc.units = 'meter-1'
vnc.field = "pn, scalar"
vnc[:, :] = grdROMS.pn
vnc = f1.createVariable('s_rho', 'd', ('s_rho',), zlib=myzlib, fill_value=grdROMS.fill_value)
vnc.long_name = "S-coordinate at RHO-points"
vnc.valid_min = -1.
vnc.valid_max = 0.
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.fill_value)
vnc.long_name = "S-coordinate at W-points"
vnc.valid_min = -1.
vnc.valid_max = 0.
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_r', 'd', ('s_rho',), zlib=myzlib, fill_value=grdROMS.fill_value)
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('Cs_w', 'd', ('s_w',), zlib=myzlib, fill_value=grdROMS.fill_value)
vnc.long_name = "S-coordinate stretching curves at W-points"
vnc.valid_min = -1.
vnc.valid_max = 0.
vnc.field = "s_w, scalar"
vnc[:] = grdROMS.Cs_w
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.fill_value)
vnc.long_name = "Sigma layer to depth matrix";
vnc.units = "meter"
vnc[:, :, :] = grdROMS.z_r
vnc = f1.createVariable('z_w', 'd', ('s_w', 'eta_rho', 'xi_rho',), zlib=myzlib, fill_value=grdROMS.fill_value)
vnc.long_name = "Sigma layer to depth matrix";
vnc.units = "meter"
vnc[:, :, :] = grdROMS.z_w
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.fill_value)
vnc.long_name = "angle between xi axis and east"
vnc.units = "radian"
vnc[:, :] = grdROMS.angle
# Now start creating variables for regular climatology/bry/init creations
if isClimatology is False:
v_time = f1.createVariable('ocean_time', 'd', ('ocean_time',), zlib=myzlib, fill_value=grdROMS.fill_value)
if (mytype=="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_u = f1.createVariable('u', 'f', ('ocean_time', 's_rho', 'eta_u', 'xi_u',), zlib=myzlib,
fill_value=grdROMS.fill_value)
v_u.long_name = "u-momentum component"
v_u.units = "meter second-1"
v_u.time = "ocean_time"
v_u.field = "u-velocity, scalar, series"
v_u.missing_value = grdROMS.fill_value
v_v = f1.createVariable('v', 'f', ('ocean_time', 's_rho', 'eta_v', 'xi_v',), zlib=myzlib,
fill_value=grdROMS.fill_value)
v_v.long_name = "v-momentum component"
v_v.units = "meter second-1"
v_v.time = "ocean_time"
v_v.field = "v-velocity, scalar, series"
v_v.missing_value = grdROMS.fill_value
v_salt = f1.createVariable('salt', 'f', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
v_salt.long_name = "salinity"
v_salt.time = "ocean_time"
v_salt.field = "salinity, scalar, series"
v_salt.missing_value = grdROMS.fill_value
v_temp = f1.createVariable('temp', 'f', ('ocean_time', 's_rho', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
v_temp.long_name = "potential temperature"
v_temp.units = "Celsius"
v_temp.time = "ocean_time"
v_temp.field = "temperature, scalar, series"
v_temp.missing_value = grdROMS.fill_value
v_ssh = f1.createVariable('zeta', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
v_ssh.long_name = "sea level"
v_ssh.units = "meter"
v_ssh.time = "ocean_time"
v_ssh.field = "sea level, scalar, series"
v_ssh.missing_value = grdROMS.fill_value
v_ubar = f1.createVariable('ubar', 'f', ('ocean_time', 'eta_u', 'xi_u',), zlib=myzlib,
fill_value=grdROMS.fill_value)
v_ubar.long_name = "u-2D momentum"
v_ubar.units = "meter second-1"
v_ubar.time = "ocean_time"
v_ubar.field = "u2-D velocity, scalar, series"
v_ubar.missing_value = grdROMS.fill_value
v_vbar = f1.createVariable('vbar', 'f', ('ocean_time', 'eta_v', 'xi_v',), zlib=myzlib,
fill_value=grdROMS.fill_value)
v_vbar.long_name = "v-2D momentum"
v_vbar.units = "meter second-1"
v_vbar.time = "ocean_time"
v_vbar.field = "v2-D velocity, scalar, series"
v_vbar.missing_value = grdROMS.fill_value
if writeIce:
ageice = f1.createVariable('ageice', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
uice = f1.createVariable('uice', 'd', ('ocean_time', 'eta_u', 'xi_u',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
vice = f1.createVariable('vice', 'd', ('ocean_time', 'eta_v', 'xi_v',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
aice = f1.createVariable('aice', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
hice = f1.createVariable('hice', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
snow_thick = f1.createVariable('snow_thick', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
ti = f1.createVariable('ti', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
sfwat = f1.createVariable('sfwat', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
tisrf = f1.createVariable('tisrf', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
sig11 = f1.createVariable('sig11', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
sig12 = f1.createVariable('sig12', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
sig22 = f1.createVariable('sig22', 'f', ('ocean_time', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
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.fill_value
# If we are creating climatology files with loops every 360 days, then create these variables here
if isClimatology is True:
v_time = f1.createVariable('clim_time', 'd', ('clim_time',), zlib=myzlib, fill_value=grdROMS.fill_value)
v_time.units = 'day'
v_time.field = 'time, scalar, series'
v_time.calendar = 'standard'
v_time.cycle_length = 360.;
v_salt = f1.createVariable('salt', 'f', ('clim_time', 's_rho', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
v_salt.long_name = "salinity"
v_salt.time = "clim_time"
v_salt.field = "salinity, scalar, series"
v_salt.missing_value = grdROMS.fill_value
v_salt = f1.createVariable('SSS', 'f', ('clim_time', 's_rho', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
v_salt.long_name = "salinity"
v_salt.time = "clim_time"
v_salt.field = "salinity, scalar, series"
v_salt.missing_value = grdROMS.fill_value
v_temp = f1.createVariable('temp', 'f', ('clim_time', 's_rho', 'eta_rho', 'xi_rho',), zlib=myzlib,
fill_value=grdROMS.fill_value)
v_temp.long_name = "potential temperature"
v_temp.units = "Celsius"
v_temp.time = "clim_time"
v_temp.field = "temperature, scalar, series"
v_temp.missing_value = grdROMS.fill_value
else:
f1 = Dataset(outfilename, mode='a', format=myformat)
if isClimatology is False:
if myvar == grdROMS.myvars[0]:
if (grdROMS.timeunits[0:7]=="seconds"):
f1.variables['ocean_time'][ntime] = grdROMS.time
d = num2date(grdROMS.time, units=f1.variables['ocean_time'].long_name,
calendar=f1.variables['ocean_time'].calendar)
else:
f1.variables['ocean_time'][ntime] = grdROMS.time * 86400.0
d = num2date(grdROMS.time * 86400.0, units=f1.variables['ocean_time'].long_name,
calendar=f1.variables['ocean_time'].calendar)
grdROMS.message = d
if myvar == 'temperature':
f1.variables['temp'][ntime, :, :, :] = data1
if myvar == 'salinity':
f1.variables['salt'][ntime, :, :, :] = data1
if myvar == 'ssh':
f1.variables['zeta'][ntime, :, :] = data1
if myvar == 'vvel':
f1.variables['u'][ntime, :, :, :] = data1
f1.variables['v'][ntime, :, :, :] = data2
f1.variables['ubar'][ntime, :, :] = data3
f1.variables['vbar'][ntime, :, :] = data4
if myvar == "ageice":
#print "NOTE! Setting values of ageice to ZERO! (IOWrite.py)"
data1 = np.where(abs(data1)>100,0,data1)
print "AGEICE:",np.min(data1),np.max(data1),np.mean(data1),myvar
f1.variables['ageice'][ntime, :, :] = data1
if myvar=='uice':
data1 = np.where(abs(data1)>120,0,data1)
print "UICE:",np.min(data1*0.01),np.max(data1*0.01),np.mean(data1*0.01),myvar
f1.variables['uice'][ntime, :, :] = data1*0.01 # NorESM is cm/s divide by 100 to get m/s
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':
# Special care for GLORYS as dataset does not contain sea ice age and snow thickness
f1.variables['ageice'][ntime, :, :] = 0.
f1.variables['snow_thick'][ntime, :, :] = 0
if myvar=='vice':
data1 = np.where(abs(data1)>120,0,data1)
f1.variables['vice'][ntime, :, :] = data1*0.01 # NorESM is cm/s divide by 100 to get m/s
if myvar=='aice':
data1 = np.where(abs(data1)>120,0,data1)
f1.variables['aice'][ntime, :, :] = data1*0.01 #NorESM is % divide by 100 to get fraction
if myvar=='hice':
data1 = np.where(abs(data1)>10,0,data1)
#data1 = np.ma.masked_where(abs(data1) > 10, data1)
f1.variables['hice'][ntime, :, :] = data1
if myvar=='snow_thick':
#data1 = np.ma.masked_where(abs(data1) > 100, data1)
data1 = np.where(abs(data1)>10,0,data1)
f1.variables['snow_thick'][ntime, :, :] = data1
if isClimatology is True:
# Climatological time starts at the 15th of each month
d = datetime(2012, int(ntime) + 1, 1)
tt = d.timetuple()
if myvar == grdROMS.myvars[0]:
f1.variables['clim_time'][ntime] = tt.tm_yday + 15
grdROMS.message = tt.tm_yday + 15
if myvar == 'temperature':
f1.variables['temp'][ntime, :, :, :] = data1
if myvar == 'salinity':
f1.variables['salt'][ntime, :, :, :] = data1
f1.variables['SSS'][ntime, :, :, :] = data1
f1.close()