def gen_frc(fname,grd,tag='_ccmp'):
nc=netcdf.Pync(fname,'t',version=3)
# dims:
grd_dims=netcdf.fdim(grd)
gdims='xi_rho','xi_u','xi_v','eta_rho','eta_u','eta_v'
for name in gdims: nc.add_dim(name,grd_dims[name])
# time dim:
nc.add_dim('wind_time',0)
v=nc.add_var('wind_time',np.dtype('d'),('wind_time',))
v.add_att('long_name','wind forcing time')
tunits='days since 1970-01-01'
v.add_att('units',tunits)
v=nc.add_var('Uwind'+tag,np.dtype('d'),('wind_time','eta_rho', 'xi_rho'))
v.add_att('long_name','u-wind')
v.add_att('units','metre second-1')
v.add_att('time','time')
v=nc.add_var('Vwind'+tag,np.dtype('d'),('wind_time','eta_rho', 'xi_rho'))
v.add_att('long_name','v-wind')
v.add_att('units','metre second-1')
v.add_att('time','time')
# Global Attributes:
nc.add_att('type','Wind forcing file')
nc.add_att('title','CCMP wind')
nc.add_att('grd_file',os.path.realpath(grd))
from time import ctime
nc.add_att('history','ROMS wind file, '+ctime())
nc.add_att('author',cb.username()[1]+', '+cb.machinename())
nc.close()
def fill(self, data, tind='next', quiet=1):
'''
Fills model netcdf climatology file (data can be provided by
prognostic.data2roms
'''
nc = netcdf.Pync(self.filename, 'w')
if tind == 'next': tind = nc.dims['time']
if not quiet: print('filling clm file %s' % self.filename)
# about time:
try:
date = dts.parse_date(data['date'])
time = netcdf.date2num(date, self.tunits)
except:
time = data['date'] # date as number!
for i in nc.varnames:
if i.endswith('time'):
if not quiet: print(' -- %s tind=%d %f' % (i, tind, time))
nc.vars[i][tind] = time
names = 'temp', 'salt', 'u', 'v', 'ubar', 'vbar', 'zeta'
for i in names:
if not quiet: print(' %s' % i)
nc.vars[i][tind, ...] = data[i]
nc.close()
def fill_frc(fname, time, u, v):
nc = netcdf.Pync(fname, 'w')
tunits = netcdf.vatt(nc, 'wind_time', 'units')
time = netcdf.date2num(time, tunits)
tind = nc.dims['wind_time']
nc.vars['wind_time'][tind] = time
nc.vars['Uwind_ascat24'][tind, ...] = u
nc.vars['Vwind_ascat24'][tind, ...] = v
nc.close()
def set_time(self, time=0, tunits=False):
'''
Set (force) time and date info to user defined.
'''
nc = netcdf.Pync(self.filename, 'w')
for v in nc.varnames:
if v.endswith('time'):
nc.vars[v][:] = time
if tunits: nc.vars[v].atts['units'].update(tunits)
nc.close()
def fill(self, data, quiet=1):
'''
Fills model netcdf initial file (data can be provided by
prognostic.data2roms
'''
nc = netcdf.Pync(self.filename, 'w')
names = 'temp', 'salt', 'u', 'v', 'ubar', 'vbar', 'zeta'
if not quiet: print('filling ini file %s' % self.filename)
for i in names:
if not quiet: print(' %s' % i)
nc.vars[i][:] = data[i]
nc.close()
def fill(self, data, quiet=1):
'''
Fills model netcdf river forcing file
The input data shoud have as keys the river names
(with river runoff, temp, salt, vshape, xi,eta and direction)
and time (datetime)
Example:
data['amazonas']=q,temp,salt,vshape,Xi,Eta,Dir
data['time']=np.arange(20)
'''
# convert time to tunits:
time = data['time']
for i in range(len(time)):
time[i] = netcdf.date2num(time[i], self.tunits)
nc = netcdf.Pync(self.fname, 'a')
if not quiet: print ' -- filling time...'
for i in range(len(time)):
nc.vars['river_time'][i] = time[i]
# better sync here:
nc._nc.sync()
cont = -1
for k in data.keys():
if k == 'time': continue
cont += 1
q, temp, salt, vshape, Xi, Eta, Dir = data[k]
if not quiet: print ' -- filling river', cont
nc.vars['river'][cont] = cont
nc.vars['river_Xposition'][cont] = Xi
nc.vars['river_Eposition'][cont] = Eta
nc.vars['river_direction'][cont] = Dir
nc.vars['river_Vshape'][:, cont] = vshape
nc.vars['river_transport'][:, cont] = q
nc.vars['river_temp'][:, :, cont] = temp
nc.vars['river_salt'][:, :, cont] = salt
nc.close()
def fill(self, data, tind='next', quiet=1):
'''
Fills model netcdf boundary conditions (data can be provided by
prognostic.data2romsbry
'''
nc = netcdf.Pync(self.filename, 'w')
if tind == 'next': tind = nc.dims['time']
if not quiet: print('filling bry file %s' % self.filename)
# about time:
try:
date = dts.parse_date(data['date'])
time = netcdf.date2num(date, self.tunits)
except:
time = data['date'] # date as number!
for i in nc.varnames:
if i.endswith('time'):
if not quiet: print(' -- %s tind=%d %f' % (i, tind, time))
nc.vars[i][tind] = time
names = 'temp', 'salt', 'u', 'v', 'ubar', 'vbar', 'zeta'
if self.addxz:
names = list(names) + [
'dist', 'distu', 'distv', 'depth', 'depthu', 'depthv'
]
for i in names:
for j in 'north', 'south', 'east', 'west':
vname = i + '_' + j
if vname in nc.varnames:
if vname.startswith('dist'):
if tind == 0:
if not quiet: print(' %s' % vname)
nc.vars[vname][:] = data[
vname] # not time dependent
else:
if not quiet: print(' %s' % vname)
nc.vars[vname][tind, ...] = data[vname]
nc.close()
def create(self):
'''
Creates model netcdf river forcing file
'''
nc=netcdf.Pync(self.fname,self.perm,version=self.ncversion)
nx=netcdf.fdim(self.grid,'xi_rho')
ny=netcdf.fdim(self.grid,'eta_rho')
# Dimensions:
nc.add_dim('s_rho',self.nz)
nc.add_dim('river',self.nrivers)
nc.add_dim('river_time',0)
# Variables:
v=nc.add_var('river',np.dtype('d'),('river',))
v.add_att('long_name','river runoff identification number')
v=nc.add_var('river_Xposition',np.dtype('d'),('river',))
v.add_att('long_name','river XI-position at RHO-points')
v.add_att('valid_min',1)
v.add_att('valid_max',nx-1)
v=nc.add_var('river_Eposition',np.dtype('d'),('river',))
v.add_att('long_name','river ETA-position at RHO-points')
v.add_att('valid_min',1)
v.add_att('valid_max',ny-1)
v=nc.add_var('river_direction',np.dtype('d'),('river',))
v.add_att('long_name','river runoff direction')
v=nc.add_var('river_Vshape',np.dtype('d'),('s_rho','river'))
v.add_att('long_name','river runoff mass transport vertical profile')
v=nc.add_var('river_time',np.dtype('d'),('river_time',))
v.add_att('long_name','river runoff time')
v.add_att('units',self.tunits)
v.add_att('add_offset',0)
v=nc.add_var('river_transport',np.dtype('d'),('river_time','river'))
v.add_att('long_name','river runoff vertically integrated mass transport')
v.add_att('units','metre3 second-1')
v.add_att('time','river_time')
v=nc.add_var('river_temp',np.dtype('d'),('river_time','s_rho','river'))
v.add_att('long_name','river runoff potential temperature')
v.add_att('units','Celsius')
v.add_att('time','river_time')
v=nc.add_var('river_salt',np.dtype('d'),('river_time','s_rho','river'))
v.add_att('long_name','river runoff salinity')
v.add_att('units','Celsius')
v.add_att('time','river_time')
# Global Attributes:
nc.add_att('type',self.type)
nc.add_att('title',self.title)
nc.add_att('grd_file',os.path.realpath(self.grid))
nc.add_att('date',dts.currday().isoformat(' '))
nc.add_att('author',cb.username()[1]+', '+cb.username()[0]+'@'+cb.machinename())
# extra attrs:
for i in self.attr.keys(): nc.add_att(i,self.attr[i])
nc.close()
def create(self, model='roms', original=False):
'''
Creates netcdf bulk forcing file
for model 'roms' or 'roms-agrif'
'''
nc = netcdf.Pync(self.filename, 't', version=self.ncversion)
# Dimensions:
# horizontal dims:
self.add_horiz_dims(nc)
# time dim:
nc.add_dim('time', 0)
# original data dims:
addOriginal = not original is False
if addOriginal:
nc.add_dim('x_original', original[1])
nc.add_dim('y_original', original[0])
# Variables:
if model == 'roms': vname = 'time'
elif model == 'roms-agrif': vname = 'bulk_time'
v = nc.add_var(vname, np.dtype('d'), ('time', ))
v.add_att('long_name', 'bulk formulation atmospheric forcing time')
v.add_att('units', self.tunits)
if self.cycle: v.add_att('cycle_length', self.cycle)
if addOriginal:
nc.add_var('x_original', np.dtype('d'),
('y_original', 'x_original'))
nc.add_var('y_original', np.dtype('d'),
('y_original', 'x_original'))
if model == 'roms': vname = 'Tair'
elif model == 'roms-agrif': vname = 'tair'
v = nc.add_var(vname, np.dtype('d'), ('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'surface air temperature')
v.add_att('units', 'Celsius')
v.add_att('time', 'time')
if addOriginal:
v = nc.add_var('tair_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'Celsius')
if model == 'roms': vname, vunits = 'Pair', 'millibar'
elif model == 'roms-agrif': vname, vunits = 'pres', 'Pascal'
v = nc.add_var(vname, np.dtype('d'), ('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'surface pressure')
v.add_att('units', vunits)
v.add_att('time', 'time')
if addOriginal:
v = nc.add_var('pres_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'Pascal')
if model == 'roms': vname, vunits = 'Qair', 'percentage'
elif model == 'roms-agrif': vname, vunits = 'rhum', 'fraction'
v = nc.add_var(vname, np.dtype('d'), ('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'relative humidity')
v.add_att('units', vunits)
v.add_att('time', 'time')
if addOriginal:
v = nc.add_var('rhum_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'fraction')
if model == 'roms': vname, vunits = 'rain', 'kg m-2 s-1'
elif model == 'roms-agrif': vname, vunits = 'prate', 'cm day-1'
v = nc.add_var(vname, np.dtype('d'), ('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'precipitation rate')
v.add_att('units', vunits)
v.add_att('time', 'time')
if addOriginal:
v = nc.add_var('prate_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'cm day-1')
if model == 'roms':
vname, vlname = 'lwrad', 'net longwave radiation flux'
elif model == 'roms-agrif':
vname, vlname = 'radlw', 'outgoing longwave radiation'
v = nc.add_var(vname, np.dtype('d'), ('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', vlname)
v.add_att('units', 'Watts metre-2')
v.add_att('time', 'time')
if model == 'roms':
v.add_att('positive_value', 'downward flux, heating')
v.add_att('negative_value', 'upward flux, cooling')
elif model == 'roms-agrif': # opposite to ROMS !!!
v.add_att('positive', 'upward flux, cooling water')
if addOriginal:
v = nc.add_var('radlw_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'Watts metre-2')
if model == 'roms':
v.add_att('negative_value', 'upward flux, cooling')
elif model == 'roms-agrif':
v.add_att('positive', 'upward flux, cooling water')
if model == 'roms': vname = 'lwrad_down'
elif model == 'roms-agrif': vname = 'dlwrf'
v = nc.add_var(vname, np.dtype('d'), ('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'downward longwave radiation')
v.add_att('units', 'Watts metre-2')
v.add_att('time', 'time')
if model == 'roms':
v.add_att('positive_value', 'downward flux, heating')
v.add_att('negative_value', 'upward flux, cooling')
elif model == 'roms-agrif': # opposite to ROMS !!!
v.add_att('positive', 'upward flux, cooling water')
if addOriginal:
v = nc.add_var('dlwrf_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'Watts metre-2')
if model == 'roms':
v.add_att('negative_value', 'upward flux, cooling')
elif model == 'roms-agrif':
v.add_att('positive', 'upward flux, cooling water')
if model == 'roms': vname = 'swrad'
elif model == 'roms-agrif': vname = 'radsw'
v = nc.add_var(vname, np.dtype('d'), ('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'shortwave radiation')
v.add_att('units', 'Watts metre-2')
v.add_att('time', 'time')
v.add_att('positive_value', 'downward flux, heating')
v.add_att('negative_value', 'upward flux, cooling')
if addOriginal:
v = nc.add_var('radsw_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'Watts metre-2')
if model == 'roms': vname = 'Uwind'
elif model == 'roms-agrif': vname = 'uwnd'
v = nc.add_var(vname, np.dtype('d'), ('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'u-wind')
v.add_att('units', 'metre second-1')
v.add_att('time', 'time')
if model == 'roms': vname = 'Vwind'
elif model == 'roms-agrif': vname = 'vwnd'
v = nc.add_var(vname, np.dtype('d'), ('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'v-wind')
v.add_att('units', 'metre second-1')
v.add_att('time', 'time')
if addOriginal:
v = nc.add_var('uwnd_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'metre second-1')
v = nc.add_var('vwnd_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'metre second-1')
# cloud cover (for roms):
if model == 'roms' or 1: # add it anyway...
v = nc.add_var('cloud', np.dtype('d'),
('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'cloud fraction')
v.add_att('units', 'nondimensional')
v.add_att('time', 'time')
if addOriginal:
v = nc.add_var('cloud_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'cloud fraction')
# next only required by roms-agrif (wspd,sustr,svstr)
v = nc.add_var('wspd', np.dtype('d'), ('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'wind speed 10m')
v.add_att('units', 'metre second-1')
v.add_att('time', 'time')
v = nc.add_var('sustr', np.dtype('d'), ('time', 'eta_u', 'xi_u'))
v.add_att('long_name', 'surface u-momentum stress')
v.add_att('units', 'Newton metre-2')
v.add_att('time', 'time')
v = nc.add_var('svstr', np.dtype('d'), ('time', 'eta_v', 'xi_v'))
v.add_att('long_name', 'surface v-momentum stress')
v.add_att('units', 'Newton metre-2')
v.add_att('time', 'time')
if addOriginal:
v = nc.add_var('wspd_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'metre second-1')
v = nc.add_var('sustr_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'Newton metre-2')
v = nc.add_var('svstr_original', np.dtype('d'),
('time', 'y_original', 'x_original'))
v.add_att('units', 'Newton metre-2')
# Global Attributes:
nc.add_att('type', self.type)
nc.add_att('title', self.title)
nc.add_att('grd_file', realpath(self.grid))
nc.add_att('history', 'ROMS blk file, ' + ctime())
nc.add_att('author', cb.username()[1] + ', ' + cb.machinename())
# extra attrs:
for i in self.attr.keys():
nc.add_att(i, self.attr[i])
nc.close()
def create(self):
'''
Creates model netcdf boundary conditions file
'''
nc = netcdf.Pync(self.filename, 't', version=self.ncversion)
# Dimensions:
# horizontal and vertical dims:
self.add_horiz_dims(nc)
self.add_vert_dims(nc)
# time dim:
nc.add_dim('time', 0)
# Variables:
v = nc.add_var('bry_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'open boundary conditions time')
v.add_att('units', self.tunits)
v.add_att('field', 'bry_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
v = nc.add_var('temp_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'potential temperature time')
v.add_att('units', self.tunits)
v.add_att('field', 'temp_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
v = nc.add_var('salt_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'salinity time')
v.add_att('units', self.tunits)
v.add_att('field', 'salt_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
v = nc.add_var('u3d_time', np.dtype('d'), ('time', ))
v.add_att('long_name', '3D momentum time')
v.add_att('units', self.tunits)
v.add_att('field', 'u3d_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
#v=nc.add_var('v3d_time',np.dtype('d'),('time',))
#v.add_att('long_name','3D V-momentum time')
#v.add_att('units',self.tunits)
#v.add_att('field','v3d_time, scalar, series')
#if self.cycle: v.add_att('cycle_length',self.cycle)
v = nc.add_var('u2d_time', np.dtype('d'), ('time', ))
v.add_att('long_name', '2D momentum time')
v.add_att('units', self.tunits)
v.add_att('field', 'u2d_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
#v=nc.add_var('v2d_time',np.dtype('d'),('time',))
#v.add_att('long_name','2D V-momentum time')
#v.add_att('units',self.tunits)
#v.add_att('field','v2d_time, scalar, series')
#if self.cycle: v.add_att('cycle_length',self.cycle)
v = nc.add_var('zeta_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'free surface time')
v.add_att('units', self.tunits)
v.add_att('field', 'zeta_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
names = {'n': 'north', 's': 'south', 'e': 'east', 'w': 'west'}
Names = {
'n': 'northern',
's': 'southern',
'e': 'eastern',
'w': 'western'
}
Tdims = {
'n': ('time', 's_rho', 'xi_rho'),
's': ('time', 's_rho', 'xi_rho'),
'e': ('time', 's_rho', 'eta_rho'),
'w': ('time', 's_rho', 'eta_rho')
}
Udims = {
'n': ('time', 's_rho', 'xi_u'),
's': ('time', 's_rho', 'xi_u'),
'e': ('time', 's_rho', 'eta_u'),
'w': ('time', 's_rho', 'eta_u')
}
Vdims = {
'n': ('time', 's_rho', 'xi_v'),
's': ('time', 's_rho', 'xi_v'),
'e': ('time', 's_rho', 'eta_v'),
'w': ('time', 's_rho', 'eta_v')
}
for o in 'nsew':
if o in self.obc:
v = nc.add_var('temp_' + names[o], np.dtype('d'), Tdims[o])
v.add_att(
'long_name', 'potential temperature ' + Names[o] +
' boundary condition')
v.add_att('units', 'Celsius')
v.add_att('time', 'temp_time')
v.add_att('field', 'temp_' + names[o] + ', scalar, series')
v = nc.add_var('salt_' + names[o], np.dtype('d'), Tdims[o])
v.add_att('long_name',
'salinity ' + Names[o] + ' boundary condition')
v.add_att('units', 'Celsius')
v.add_att('time', 'salt_time')
v.add_att('field', 'salt_' + names[o] + ', scalar, series')
v = nc.add_var('u_' + names[o], np.dtype('d'), Udims[o])
v.add_att('long_name',
'3D u-momentum ' + Names[o] + ' boundary condition')
v.add_att('units', 'metre second-1')
v.add_att('time', 'u3d_time')
v.add_att('field', 'u_' + names[o] + ', scalar, series')
v = nc.add_var('v_' + names[o], np.dtype('d'), Vdims[o])
v.add_att('long_name',
'3D v-momentum ' + Names[o] + ' boundary condition')
v.add_att('units', 'metre second-1')
v.add_att('time', 'u3d_time')
v.add_att('field', 'v_' + names[o] + ', scalar, series')
v = nc.add_var('ubar_' + names[o], np.dtype('d'),
Udims[o][::2])
v.add_att('long_name',
'2D u-momentum ' + Names[o] + ' boundary condition')
v.add_att('units', 'metre second-1')
v.add_att('time', 'u2d_time')
v.add_att('field', 'ubar_' + names[o] + ', scalar, series')
v = nc.add_var('vbar_' + names[o], np.dtype('d'),
Vdims[o][::2])
v.add_att('long_name',
'2D v-momentum ' + Names[o] + ' boundary condition')
v.add_att('units', 'metre second-1')
v.add_att('time', 'u2d_time')
v.add_att('field', 'vbar_' + names[o] + ', scalar, series')
v = nc.add_var('zeta_' + names[o], np.dtype('d'),
Tdims[o][::2])
v.add_att('long_name',
'free surface ' + Names[o] + ' boundary condition')
v.add_att('units', 'metre')
v.add_att('time', 'zeta_time')
v.add_att('field', 'zeta_' + names[o] + ', scalar, series')
if self.addxz:
v = nc.add_var('dist_' + names[o], np.dtype('f'),
Tdims[o][1:])
v.add_att(
'long_name',
'distance of ' + Names[o] + ' boundary at rho points')
v.add_att('units', 'metre')
v.add_att('field', 'dist_' + names[o] + ', scalar, series')
v = nc.add_var('distu_' + names[o], np.dtype('f'),
Udims[o][1:])
v.add_att(
'long_name',
'distance of ' + Names[o] + ' boundary at u points')
v.add_att('units', 'metre')
v.add_att('field',
'distu_' + names[o] + ', scalar, series')
v = nc.add_var('distv_' + names[o], np.dtype('f'),
Vdims[o][1:])
v.add_att(
'long_name',
'distance of ' + Names[o] + ' boundary at v points')
v.add_att('units', 'metre')
v.add_att('field',
'distv_' + names[o] + ', scalar, series')
v = nc.add_var('depth_' + names[o], np.dtype('f'),
Tdims[o])
v.add_att(
'long_name',
'depths of ' + Names[o] + ' boundary at rho points')
v.add_att('units', 'metre')
v.add_att('field',
'depth_' + names[o] + ', scalar, series')
v = nc.add_var('depthu_' + names[o], np.dtype('f'),
Udims[o])
v.add_att(
'long_name',
'depths of ' + Names[o] + ' boundary at u points')
v.add_att('units', 'metre')
v.add_att('field',
'depthu_' + names[o] + ', scalar, series')
v = nc.add_var('depthv_' + names[o], np.dtype('f'),
Vdims[o])
v.add_att(
'long_name',
'depths of ' + Names[o] + ' boundary at v points')
v.add_att('units', 'metre')
v.add_att('field',
'depthv_' + names[o] + ', scalar, series')
# sparams vars:
v = nc.add_var('theta_s', np.dtype('d'), ())
v.add_att('long_name', 'S-coordinate surface control parameter')
v = nc.add_var('theta_b', np.dtype('d'), ())
v.add_att('long_name', 'S-coordinate bottom control parameter')
v = nc.add_var('Tcline', np.dtype('d'), ())
v.add_att('long_name', 'S-coordinate surface/bottom layer width')
v.add_att('units', 'metre')
v = nc.add_var('hc', np.dtype('d'), ())
v.add_att('long_name', 'S-coordinate parameter, critical depth')
v.add_att('units', 'metre')
v = nc.add_var('Vtransform', np.dtype('i'), ())
v.add_att('long_name',
'vertical terrain-following transformation equation')
v = nc.add_var('Vstretching', np.dtype('i'), ())
v.add_att('long_name',
'vertical terrain-following stretching function')
# Global Attributes:
nc.add_att('type', self.type)
nc.add_att('title', self.title)
nc.add_att('grd_file', realpath(self.grid))
nc.add_att('history', 'ROMS bry file, ' + ctime())
nc.add_att('obc', self.obc)
nc.add_att('author', cb.username()[1] + ', ' + cb.machinename())
# extra attrs:
for i in self.attr.keys():
nc.add_att(i, self.attr[i])
# fill sparams:
nc.vars['theta_s'][:] = self.sparams[0]
nc.vars['theta_b'][:] = self.sparams[1]
nc.vars['Tcline'][:] = self.sparams[2]
nc.vars['hc'][:] = self.sparams[2]
nc.vars['Vtransform'][:] = self.sparams[4]
nc.vars['Vstretching'][:] = self.sparams[5]
nc.close()
def create(self):
'''
Creates model netcdf climatology file
'''
nc = netcdf.Pync(self.filename, 't', version=self.ncversion)
# Dimensions:
# horizontal and vertical dims:
self.add_horiz_dims(nc)
self.add_vert_dims(nc)
# time dim:
nc.add_dim('time', 0)
# Variables:
v = nc.add_var('clim_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'time for climatology')
v.add_att('units', self.tunits)
v.add_att('field', 'clim_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
if not self.one_time:
v = nc.add_var('temp_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'time for temperature climatology')
v.add_att('units', self.tunits)
v.add_att('field', 'temp_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
if not self.one_time:
v = nc.add_var('salt_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'time for salinity climatology')
v.add_att('units', self.tunits)
v.add_att('field', 'salt_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
if not self.one_time:
v = nc.add_var('u3d_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'time for 3D U-momentum climatology')
v.add_att('units', self.tunits)
v.add_att('field', 'u3d_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
if not self.one_time:
v = nc.add_var('v3d_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'time for 3D V-momentum climatology')
v.add_att('units', self.tunits)
v.add_att('field', 'v3d_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
if not self.one_time:
v = nc.add_var('u2d_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'time for 2D U-momentum climatology')
v.add_att('units', self.tunits)
v.add_att('field', 'u2d_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
if not self.one_time:
v = nc.add_var('v2d_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'time for 2D V-momentum climatology')
v.add_att('units', self.tunits)
v.add_att('field', 'v2d_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
if not self.one_time:
v = nc.add_var('zeta_time', np.dtype('d'), ('time', ))
v.add_att('long_name', 'time for free surface climatology')
v.add_att('units', self.tunits)
v.add_att('field', 'zeta_time, scalar, series')
if self.cycle: v.add_att('cycle_length', self.cycle)
v = nc.add_var('temp', np.dtype('d'),
('time', 's_rho', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'potential temperature climatology')
v.add_att('units', 'Celsius')
if self.one_time: v.add_att('time', 'clim_time')
else: v.add_att('time', 'temp_time')
v.add_att('coordinates', 'lon_rho lat_rho s_rho temp_time')
v.add_att('field', 'temperature, scalar, series')
v = nc.add_var('salt', np.dtype('d'),
('time', 's_rho', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'salinity climatology')
v.add_att('units', 'PSU')
if self.one_time: v.add_att('time', 'clim_time')
else: v.add_att('time', 'salt_time')
v.add_att('coordinates', 'lon_rho lat_rho s_rho salt_time')
v.add_att('field', 'salinity, scalar, series')
v = nc.add_var('u', np.dtype('d'), ('time', 's_rho', 'eta_u', 'xi_u'))
v.add_att('long_name', 'u-momentum component climatology')
v.add_att('units', 'metre second-1')
if self.one_time: v.add_att('time', 'clim_time')
else: v.add_att('time', 'u3d_time')
v.add_att('coordinates', 'lon_u lat_u s_rho u3d_time')
v.add_att('field', 'u-velocity, scalar, series')
v = nc.add_var('v', np.dtype('d'), ('time', 's_rho', 'eta_v', 'xi_v'))
v.add_att('long_name', 'v-momentum component climatology')
v.add_att('units', 'metre second-1')
if self.one_time: v.add_att('time', 'clim_time')
else: v.add_att('time', 'v3d_time')
v.add_att('coordinates', 'lon_v lat_v s_rho v3d_time')
v.add_att('field', 'v-velocity, scalar, series')
v = nc.add_var('ubar', np.dtype('d'), ('time', 'eta_u', 'xi_u'))
v.add_att('long_name',
'vertically integrated u-momentum component climatology')
v.add_att('units', 'metre second-1')
if self.one_time: v.add_att('time', 'clim_time')
else: v.add_att('time', 'u2d_time')
v.add_att('coordinates', 'lon_u lat_u u2d_time')
v.add_att('field', 'ubar-velocity, scalar, series')
v = nc.add_var('vbar', np.dtype('d'), ('time', 'eta_v', 'xi_v'))
v.add_att('long_name',
'vertically integrated v-momentum component climatology')
v.add_att('units', 'metre second-1')
if self.one_time: v.add_att('time', 'clim_time')
else: v.add_att('time', 'v2d_time')
v.add_att('coordinates', 'lon_v lat_v v2d_time')
v.add_att('field', 'vbar-velocity, scalar, series')
v = nc.add_var('zeta', np.dtype('d'), ('time', 'eta_rho', 'xi_rho'))
v.add_att('long_name', 'free-surface climatology')
v.add_att('units', 'metre')
if self.one_time: v.add_att('time', 'clim_time')
else: v.add_att('time', 'zeta_time')
v.add_att('coordinates', 'lon_rho lat_rho zeta_time')
v.add_att('field', 'free-surface, scalar, series')
# sparams vars:
v = nc.add_var('theta_s', np.dtype('d'), ())
v.add_att('long_name', 'S-coordinate surface control parameter')
v = nc.add_var('theta_b', np.dtype('d'), ())
v.add_att('long_name', 'S-coordinate bottom control parameter')
v = nc.add_var('Tcline', np.dtype('d'), ())
v.add_att('long_name', 'S-coordinate surface/bottom layer width')
v.add_att('units', 'metre')
v = nc.add_var('hc', np.dtype('d'), ())
v.add_att('long_name', 'S-coordinate parameter, critical depth')
v.add_att('units', 'metre')
v = nc.add_var('Vtransform', np.dtype('i'), ())
v.add_att('long_name',
'vertical terrain-following transformation equation')
v = nc.add_var('Vstretching', np.dtype('i'), ())
v.add_att('long_name',
'vertical terrain-following stretching function')
# Global Attributes:
nc.add_att('type', self.type)
nc.add_att('title', self.title)
nc.add_att('grd_file', realpath(self.grid))
nc.add_att('history', 'ROMS clm file, ' + ctime())
nc.add_att('author', cb.username()[1] + ', ' + cb.machinename())
# extra attrs:
for i in self.attr.keys():
nc.add_att(i, self.attr[i])
# fill sparams:
nc.vars['theta_s'][:] = self.sparams[0]
nc.vars['theta_b'][:] = self.sparams[1]
nc.vars['Tcline'][:] = self.sparams[2]
nc.vars['hc'][:] = self.sparams[2]
nc.vars['Vtransform'][:] = self.sparams[4]
nc.vars['Vstretching'][:] = self.sparams[5]
nc.close()
def update_wind(self, data, keepOld=True, quiet=0):
# store old at first iteration
nc = netcdf.Pync(self.filename, 'w')
time = netcdf.nctime(self.filename, 'time')
tind, = np.where(time == data['date'])
if tind.size: tind = tind[0]
else:
if not quiet:
print('cannot find time=%s' % data['date'].isoformat(' '))
return
if 'Uwind' in nc.varnames: # roms
names = ('Uwind', 'uwnd'), ('Vwind',
'vwnd'), 'sustr', 'svstr', 'wspd'
else: # roms-agrif
names = 'uwnd', 'vwnd', 'sustr', 'svstr', 'wspd'
# store old wind data:
if False and tind == 0: # not using for now.... too slow!
# TODO: remove keepOld form argument !?
if 'x_wind' in data.keys():
if not quiet: print('adding x_wind, y_wind')
nc.add_dim('x_wind_original', data['x_wind'].shape[1])
nc.add_dim('y_wind_original', data['x_wind'].shape[0])
nc.add_var('x_wind_original', data['x_wind'].dtype,
('y_wind_original', 'x_wind_original'))
nc.add_var('y_wind_original', data['y_wind'].dtype,
('y_wind_original', 'x_wind_original'))
nc.vars['x_wind_original'][...] = data['x_wind']
nc.vars['y_wind_original'][...] = data['y_wind']
for i in names:
if isinstance(i, basestring): filev, datav = i, i
else: filev, datav = i
newName = filev + '_old'
newType = nc.vars[filev].dtype()
newDims = nc.vars[filev].dims.keys()
if not quiet: print(' creating var %s' % newName)
nc.add_var(newName, newType, newDims)
if not quiet: print(' filling var %s' % newName)
nc.vars[newName][...] = nc.vars[filev][...]
# also store old original data, if present:
orig = datav + '_original'
if orig in nc.varnames:
newName = orig + '_old'
newType = nc.vars[orig].dtype()
newDims = nc.vars[orig].dims.keys()
if not quiet: print(' creating var %s' % newName)
nc.add_var(newName, newType, newDims)
if not quiet: print(' filling var %s' % newName)
nc.vars[newName][...] = nc.vars[orig][...]
# store new wind data:
for i in names:
if isinstance(i, basestring): filev, datav = i, i
else: filev, datav = i
if not quiet:
print(' %s (%s) min=%8.3f max=%8.3f' %
(filev.ljust(7), datav.ljust(7), data[datav].min(),
data[datav].max()))
nc.vars[filev][tind, ...] = data[datav]
# also store new wind original data, if present:
orig = datav + '_original'
if not orig in data.keys(): continue
if not quiet:
print(' %s min=%8.3f max=%8.3f' %
(orig.ljust(7 + 9), data[orig].min(), data[orig].max()))
nc.vars[orig][tind, ...] = data[datav]
# adding global atts:
if 'attr' in data.keys():
for i in data['attr'].keys():
nc.add_att(i, data['attr'][i])
nc.close()
def fill(self, data, tind='next', quiet=1):
'''
Fills model netcdf bulk forcing file
'''
nc = netcdf.Pync(self.filename, 'w')
if tind == 'next': tind = nc.dims['time']
if not quiet: print('filling blk file %s' % self.filename)
# about time:
try:
date = dts.parse_date(data['date'])
time = netcdf.date2num(date, self.tunits)
except:
time = data['date'] # date as number!
for i in nc.varnames:
if i.endswith('time'):
if not quiet: print(' -- %s tind=%d %f' % (i, tind, time))
nc.vars[i][tind] = time
if 'Tair' in nc.varnames: # roms
names=('Tair','tair'),('Pair','pres'),('Qair','rhum'),('rain','prate'),\
('swrad','radsw'),('lwrad','radlw'),('Uwind','uwnd'),('Vwind','vwnd'),\
'sustr','svstr','wspd','cloud',('lwrad_down','dlwrf')
if not 'tair' in data.keys(
): # assuming data has roms (not agrif) varnames:
names = 'Tair', 'Pair', 'Qair', 'rain', 'swrad', 'lwrad', 'Uwind', 'Vwind', 'sustr', 'svstr', 'wspd', 'cloud', 'lwrad_down'
elif 'tair' in nc.varnames: # roms-agrif
names='tair','pres','rhum','prate','radlw','radsw','dlwrf','uwnd',\
'vwnd','wspd','sustr','svstr',\
'cloud' # not used, but add it anyway
for i in names:
if isinstance(i, basestring): filev, datav = i, i
else: filev, datav = i
if datav not in data.keys():
if not quiet:
print(' Warning: data key %s not present' % datav)
else:
if not quiet:
print(' %s (%s) min=%8.3f max=%8.3f' %
(filev.ljust(7), datav.ljust(7), data[datav].min(),
data[datav].max()))
nc.vars[filev][tind, ...] = data[datav]
# fill original data:
orig = datav + '_original'
if orig in data.keys() and not orig in nc.varnames:
if not quiet:
print(' Warning: original data will not be written %s' %
orig)
elif not orig in data.keys() and orig in nc.varnames:
if not quiet:
print(' Warning: original data not present %s' % orig)
elif orig in data.keys() and orig in nc.varnames:
if not quiet:
print(' %s min=%8.3f max=%8.3f' %
(orig.ljust(7 + 9), data[orig].min(),
data[orig].max()))
nc.vars[orig][tind, ...] = data[orig]
# fill original x,y:
if tind == 0 and 'x_original' in data.keys(
) and 'x_original' in nc.varnames:
if not quiet: print(' filling x,y original')
nc.vars['x_original'][:] = data['x_original']
nc.vars['y_original'][:] = data['y_original']
nc.close()
