print zmax
# Set up the vertical coordinates
dz = grd.calcVertSpace(Nkmax,r,zmax) # Default version
#def calcvertspace(Nkmax,r,depth):
# ktop=15
# dztop=2.0
grd.setDepth(dz)
# Save vertspace.dat
grd.saveVertspace(suntanspath+'/vertspace.dat')
# Save cells.dat to ensure that is in the right format
grd.saveCells(suntanspath+'/cells.dat')
###################################################################
# Modify the boundary markers and create the boundary condition file
###################################################################
if makebnd:
####
# Open boundary options
####
# Shapefile with boundary condition types (set to None to skip)
bcpolygonfile = 'gis/sfbay_boundary_poly.shp'
bcfile = 'SFBay3D_BC.nc' # output boundary netcdf file name
hamp = 0.5 # tidal range
"""
Updates suntans grid text files to the quad format
Edges.dat has an extra column for the 'edge_id' variable
"""
from sunpy import Grid
import os
#
grdfolder = 'grids/quad/'
outfolder = 'rundata/'
maxfaces = 4
grd = Grid(grdfolder, MAXFACES=maxfaces)
try:
os.mkdir(outfolder)
except:
pass
os.system('cp %s/*.dat %s' % (grdfolder, outfolder))
grd.saveEdges(outfolder + '/edges.dat')
grd.saveCells(outfolder + '/cells.dat')
print 'Saved new grid in: %s' % outfolder
class sundriver(object):
"""
Driver class for generating SUNTANS input files
"""
# Switches to generate bathymetry, boundary, meteorology and initial condition input files
makebathy=False
makebnd=False
makewinds=False
makeinitial=False
###
# General options
###
# Grid projection variables
convert2utm=False
CS='NAD83'
utmzone=51
isnorth=False
vdatum = 'MSL'
# Verical grid options
Nkmax = 1 # number of layers
r = 1.01 # vertical stretching parameter
setconstantdepth=False # Option to set constant depth
H0 = 10.0 # Constant depth
###
# Bathymetry interpolation options
###
depthfile = None
depthmax=0.1
interpmethod='idw' # Interpolation method: 'nn', 'idw', 'kriging', 'griddata'
plottype='mpl' # Type of plot: 'mpl', 'vtk2' or 'vtk3'
shapefieldname='contour' # name of shapefile attribute with contour data
scalefac = 1.0
# Interpolation options
NNear=3
# Interpolate to nodes then take maximum depth for cell
interpnodes=False
# IF interpmethod = 'idw'
p = 1.0 # power for inverse distance weighting
# IF interpmethod = 'kriging'
varmodel = 'spherical'
nugget = 0.1
sill = 0.8
vrange = 250.0
# Smoothing options
smooth=True
smoothmethod='kriging' # USe kriging or idw for smoothing
smoothnear=4 # No. of points to use for smoothing
# Option to adjust channel depths using a shapefile
adjust_depths=False
channel_shpfile='channel.shp'
####
# Open boundary options
####
opt_bcseg = 'constant' # Segment boundary condition option: 'constant' or 'file'
opt_bctype2 = 'constant' # Type 2 boundary condition option: 'constant' or 'file'
opt_bctype3 = 'constant' # Type 3 boundary condition option: 'constant', ,'file','OTIS', 'ROMS', 'ROMSOTIS','ROMSFILE', 'OTISFILE', 'ROMSOTISFILE'
modifyedges = False # Option to modify the boundary edges
bcpolygonfile = None # Shape file with fields 'marker' and 'edge_id'
bcfile = 'SUNTANS_BC.nc' # Input boundary condition file
# IF opt_bcseg = 'consant
Q0 = 100.0 # m3/s
# IF opt_bctype2/opt_bctype3 = 'constant'
T0 = 0 # Open boundary background temperature
S0 = 0 # Open boundary background salinity
# IF opt_bctype3 = 'file' or 'ROMSFILE'
waterlevelstationID = None
# IF opt_bctype3 = 'harmonic'
amp = 0.25
omega = 2*PI/(24.0*3600.0)
# IF opt_bctype2 = 'file'
TairstatationID = None
# Filter type (waterlevel)
filttype='low'
cutoff=3600.0
# Air temp cuttoff (bctype2 = file)
tairfilttype = 'low'
taircutoff = 14.0*24.0*3600.0
####
# Atmospheric input options
####
opt_met = 'constant' # Met file creation options: 'constant'
metfile = 'SUNTANS_MetForcing.nc'
# IF opt_met = 'consant'
Uwind = 0.0
Vwind = 5.0
RH = 50.0
Tair = 30.0
Pair = 1010.0
rain = 0.0
cloud = 0.0
####
# Initial condition options
####
opt_ic = 'constant', 'depth_profile', 'ROMS' , 'SUNTANS'
icfile = 'SUNTANS_IC.nc'
icfilterdx = 0.0 # Filtering length scale
# Age source term polygon
agesourcepoly = None
# Initial condition temperature and salinity
T0ic = 0
S0ic = 0
###
# Input file names
###
romsfile = None
suntansicfile = None
otisfile = None
dbasefile = None
# Use ROMS u,v and eta
useROMSuv=False
useROMSeta=False
# Use OTIS u & v
useOTISuv=False
############################
def __init__(self,**kwargs):
self.__dict__.update(kwargs)
def __call__(self,suntanspath,starttime,endtime,dt):
self.suntanspath = suntanspath
self.starttime = starttime
self.endtime = endtime
self.dt = dt
# Step through and perform each step
self._makebathy()
if self.makebnd:
self._makebnd()
if self.makeinitial:
self._makeinitial()
if self.makewinds:
self._makewinds()
print '###########\n Completed generating input files. Check text for errors!!!!\n##########'
def _makebathy(self):
"""
Loads the grid object and interpolates the depths
"""
# Interpolate the depths onto the grid
if self.makebathy:
if self.depthfile == None:
raise Exception, 'need to set "depthfile" parameter'
else:
print 'Interpolation depths onto grid from file:\n%s'%self.depthfile
D = DepthDriver(self.depthfile,interpmethod=self.interpmethod,\
plottype=self.plottype,NNear=self.NNear,\
p=self.p,varmodel=self.varmodel,nugget=self.nugget,sill=self.sill,vrange=self.vrange,\
convert2utm=self.convert2utm,utmzone=self.utmzone,isnorth=self.isnorth,vdatum=self.vdatum,\
shapefieldname=self.shapefieldname,\
smooth=self.smooth,smoothmethod=self.smoothmethod,smoothnear=self.smoothnear)
D(self.suntanspath,depthmax=self.depthmax,interpnodes=self.interpnodes,\
scalefac=self.scalefac)
self.grd = D.grd
# Now go through and adjust the channel depths from a shapefile
if self.adjust_depths:
self.grd = adjust_channel_depth(self.grd,self.channel_shpfile)
# Write the depths to file
print 'Writing depths.dat (again)...'
self.grd.saveBathy(self.suntanspath+'/depths.dat-voro')
print 'Data (re-)saved to %s.'%self.suntanspath+'/depths.dat-voro'
print 'SUNTANS depths saved to: %s'%(self.suntanspath+'/depths.dat-voro')
elif self.setconstantdepth:
print 'Using constant depth (%6.2f m)...'%self.H0
self.grd = Grid(self.suntanspath)
self.grd.dv = np.zeros_like(self.grd.xv)
self.grd.dv[:] = self.H0
else:
print 'Loading grid from folder:\n%s'%self.suntanspath
# Load the grid
self.grd = Grid(self.suntanspath)
# Load the depth data into the grid object
self.grd.loadBathy(self.suntanspath+'/depths.dat-voro')
zmax = np.abs(self.grd.dv.max())
print 'Calculating vertical grid spacing for Nk = %d, r = %1.3f, %6.3f...'%(self.Nkmax,self.r,zmax)
# Set up the vertical coordinates
dz = self.grd.calcVertSpace(self.Nkmax,self.r,zmax)
self.grd.setDepth(dz)
# Save vertspace.dat
self.grd.saveVertspace(self.suntanspath+'/vertspace.dat')
# Write cells.dat and edges.dat to ensure they are in the right format
print 'Overwriting cells.dat and edges.dat to ensure format consistency.'
self.grd.saveCells(self.suntanspath+'/cells.dat')
self.grd.saveEdges(self.suntanspath+'/edges.dat')
def _makebnd(self):
"""
Generate boundary condition files
"""
if self.modifyedges:
modifyBCmarker(self.suntanspath,self.bcpolygonfile)
#Load the boundary object from the grid
bnd = Boundary(self.suntanspath,(self.starttime,self.endtime,self.dt))
###
# Segment (flux) boundaries
###
if self.opt_bcseg == 'constant':
print 'Setting %d boundary segments to discharge of %6.3f m3/s'%(bnd.Nseg,self.Q0)
bnd.boundary_Q[:]=self.Q0
elif self.opt_bcseg == 'file':
print 'Loading river segment data from file...\n'
for ii, ID in enumerate(bnd.segp):
print 'Loading discahrge data for boundary segment (%d) StationID: %d...'%(ii,ID)
ts = timeseries.loadDBstation(self.dbasefile,ID,'discharge',timeinfo=(self.starttime,self.endtime,self.dt),\
filttype=self.filttype,cutoff=self.cutoff)
bnd.boundary_Q[:,ii]=ts.y.copy()
else:
print 'Unknown option: opt_bcseg = %s. Not setting boundary segment data.'%self.opt_bcseg
###
# Type-3 boundaries
###
self.useROMS = False
self.useOTIS = False
self.useFILE = False
self.useOTISFILE = False
if self.opt_bctype3=='constant':
print 'Setting constant type-3 boundary conditions...'
print 'Setting salinity = %f, temperature = %f'%(self.S0,self.T0)
bnd.S[:]=self.S0
bnd.T[:]=self.T0
elif self.opt_bctype3=='depth_profile':
print 'Setting type-3 boundary T/S from profile...'
self.loadTSprofile()
for ii in range(0,bnd.N3):
bnd.T[0,:,ii] = self.Tz
bnd.S[0,:,ii] = self.Sz
elif self.opt_bctype3 in ('ROMS'):
self.useROMS = True
elif self.opt_bctype3 in ('OTIS'):
self.useOTIS = True
elif self.opt_bctype3 in ('file'):
self.useFILE = True
elif self.opt_bctype3 in ('ROMSOTIS'):
self.useROMS = True
self.useOTIS = True
elif self.opt_bctype3 in ('ROMSFILE'):
self.useROMS = True
self.useFILE = True
elif self.opt_bctype3 in ('OTISFILE'):
self.useOTISFILE = True
elif self.opt_bctype3 in ('ROMSOTISFILE'):
self.useOTISFILE = True
self.useROMS = True
else:
print 'Unknown option: opt_bctype3 = %s. Not setting type-3 boundaries.'%self.opt_bctype3
if self.useROMS:
bnd.roms2boundary(self.romsfile,setUV=self.useROMSuv,seth=self.useROMSeta)
if self.useOTIS:
bnd.otis2boundary(self.otisfile,setUV=self.useOTISuv)
if self.useOTISFILE:
bnd.otisfile2boundary(self.otisfile,self.dbasefile,self.waterlevelstationID,setUV=self.useOTISuv)
if self.useFILE:
ID = self.waterlevelstationID
print 'Loading waterlevel onto all type-3 points from stationID: %d...'%(ID)
ts = timeseries.loadDBstation(self.dbasefile,ID,'waterlevel',timeinfo=(self.starttime,self.endtime,self.dt),\
filttype=self.filttype,cutoff=self.cutoff)
for ii in range(bnd.N3):
bnd.h[:,ii] += ts.y.copy()
###
# Type-2 boundaries
###
self.useFILE2 = False
if self.opt_bctype2 == 'constant':
print 'Setting constant type-2 boundary conditions...'
print 'Setting salinity = %f, temperature = %f'%(self.S0,self.T0)
bnd.boundary_S[:]=self.S0
bnd.boundary_T[:]=self.T0
elif self.opt_bctype2 == 'file':
print 'Using file for type-2 boundary condition (temperature only)'
print 'Setting salinity = %f'%(self.S0)
bnd.boundary_S[:]=self.S0
self.useFILE2 = True
else:
print 'Unknown option: opt_bctype2 = %s. Not setting type-2 boundaries.'%self.opt_bctype3
if self.useFILE2:
ID = self.TairstationID
print 'Loading air temperature onto all type-2 points from stationID: %s...'%(ID)
ts = timeseries.loadDBstation(self.dbasefile,ID,'Tair',timeinfo=(self.starttime,self.endtime,self.dt),\
filttype=self.tairfilttype,cutoff=self.taircutoff)
for ii in range(bnd.N2):
for kk in range(bnd.Nk):
bnd.boundary_T[:,kk,ii] += ts.y.copy()
# Write to netcdf
bnd.write2NC(self.suntanspath+'/'+self.bcfile)
def _makeinitial(self):
"""
Generate initial conditions
"""
# Initialise the class
IC = InitialCond(self.suntanspath,self.starttime)
if self.opt_ic=='constant':
print 'Setting constant initial conditions...'
print 'Setting salinity = %f, temperature = %f'%(self.S0ic,self.T0ic)
IC.T[:]=self.T0ic
IC.S[:]=self.S0ic
elif self.opt_ic=='depth_profile':
print 'Setting depth-varying initial conditions...'
self.loadTSprofile()
for ii in range(0,IC.Nc):
IC.T[0,:,ii] = self.Tz
IC.S[0,:,ii] = self.Sz
elif self.opt_ic=='ROMS':
print 'Setting initial conditions from ROMS model output...'
IC.roms2ic(self.romsfile,setUV=self.useROMSuv,seth=self.useROMSeta,interpmethod='idw',NNear=5,p=2)
#interpmethod=self.interpmethod,NNear=self.NNear,p=self.p,\
#varmodel=self.varmodel,nugget=self.nugget,sill=self.sill,\
#vrange=self.vrange)
elif self.opt_ic=='SUNTANS':
IC.suntans2ic(self.suntansicfile,setUV=self.useROMSuv,seth=self.useROMSeta)
else:
print 'Unknown option: opt_ic = %s. Not setting initial conditions.'%self.opt_ic
# Filter the variables in space
if self.icfilterdx>0:
IC.filteric(self.icfilterdx)
# Set the age source term from a polygon
if not self.agesourcepoly==None:
print 'Setting age source term with shapefile: %s...'%self.agesourcepoly
IC.setAgeSource(self.agesourcepoly)
# Write the initial condition file
IC.writeNC(self.suntanspath+'/'+self.icfile,dv=self.grd.dv)
def _makewinds(self):
"""
Generate a metfile
"""
if self.opt_met=='constant':
print 'Setting constant met forcing with: Uwind = %6.2f\nVwind = %6.2f\nTair = %6.2f\nPair = %6.2f\nRH = %6.2f\nrain = %6.2f\ncloud = %6.2f\n'\
%(self.Uwind,self.Vwind,self.Tair,self.Pair,self.RH,self.cloud,self.rain)
xpt = self.grd.xv.mean()
ypt = self.grd.yv.mean()
zpt = 10.0
# Load the met object
met = SunMet(xpt,ypt,zpt,(self.starttime,self.endtime,self.dt))
# Fill the arrays
met.Uwind.data[:] = self.Uwind
met.Vwind.data[:] = self.Vwind
met.Tair.data[:] = self.Tair
met.Pair.data[:] = self.Pair
met.RH.data[:] = self.RH
met.cloud.data[:] = self.cloud
met.rain.data[:] = self.rain
met.write2NC(self.suntanspath+'/'+self.metfile)
else:
print 'Unknown option: opt_met=%s. Failed to generate a metfile'%self.opt_met
def loadTSprofile(self):
"""
Loads a temperature salinity profile from a matfile and interpolates onto the grid depths
"""
try:
data=io.loadmat(self.TSprofilefile)
z = data['depth'].ravel()
temp = data['temp_profile'].ravel()
salt = data['salt_profile'].ravel()
FT = interp1d(z,temp,kind=3)
self.Tz=FT(self.grd.z_r)
FS = interp1d(z,salt,kind=3)
self.Sz=FS(self.grd.z_r)
except:
print 'Warning could not find variables: "depth", "temp_profile" or "salt_profile" in file:\n%s'%self.TSprofilefile
self.Tz = self.T0
self.Sz = self.S0
class sundriver(object):
"""
Driver class for generating SUNTANS input files
"""
# Switches to generate bathymetry, boundary, meteorology and initial condition input files
makebathy = False
makebnd = False
makewinds = False
makeinitial = False
###
# General options
###
# Grid projection variables
convert2utm = False
CS = 'NAD83'
utmzone = 51
isnorth = False
vdatum = 'MSL'
# Verical grid options
Nkmax = 1 # number of layers
r = 1.01 # vertical stretching parameter
setconstantdepth = False # Option to set constant depth
H0 = 10.0 # Constant depth
###
# Bathymetry interpolation options
###
depthfile = None
depthmax = 0.1
interpmethod = 'idw' # Interpolation method: 'nn', 'idw', 'kriging', 'griddata'
plottype = 'mpl' # Type of plot: 'mpl', 'vtk2' or 'vtk3'
shapefieldname = 'contour' # name of shapefile attribute with contour data
scalefac = 1.0
# Interpolation options
NNear = 3
# Interpolate to nodes then take maximum depth for cell
interpnodes = False
# IF interpmethod = 'idw'
p = 1.0 # power for inverse distance weighting
# IF interpmethod = 'kriging'
varmodel = 'spherical'
nugget = 0.1
sill = 0.8
vrange = 250.0
# Smoothing options
smooth = True
smoothmethod = 'kriging' # USe kriging or idw for smoothing
smoothnear = 4 # No. of points to use for smoothing
# Option to adjust channel depths using a shapefile
adjust_depths = False
channel_shpfile = 'channel.shp'
####
# Open boundary options
####
opt_bcseg = 'constant' # Segment boundary condition option: 'constant' or 'file'
opt_bctype2 = 'constant' # Type 2 boundary condition option: 'constant' or 'file'
opt_bctype3 = 'constant' # Type 3 boundary condition option: 'constant', ,'file','OTIS', 'ROMS', 'ROMSOTIS','ROMSFILE', 'OTISFILE', 'ROMSOTISFILE'
modifyedges = False # Option to modify the boundary edges
bcpolygonfile = None # Shape file with fields 'marker' and 'edge_id'
bcfile = 'SUNTANS_BC.nc' # Input boundary condition file
# IF opt_bcseg = 'consant
Q0 = 100.0 # m3/s
# IF opt_bctype2/opt_bctype3 = 'constant'
T0 = 0 # Open boundary background temperature
S0 = 0 # Open boundary background salinity
# IF opt_bctype3 = 'file' or 'ROMSFILE'
waterlevelstationID = None
# IF opt_bctype3 = 'harmonic'
amp = 0.25
omega = 2 * PI / (24.0 * 3600.0)
# IF opt_bctype2 = 'file'
TairstatationID = None
# Filter type (waterlevel)
filttype = 'low'
cutoff = 3600.0
# Air temp cuttoff (bctype2 = file)
tairfilttype = 'low'
taircutoff = 14.0 * 24.0 * 3600.0
####
# Atmospheric input options
####
opt_met = 'constant' # Met file creation options: 'constant'
metfile = 'SUNTANS_MetForcing.nc'
# IF opt_met = 'consant'
Uwind = 0.0
Vwind = 5.0
RH = 50.0
Tair = 30.0
Pair = 1010.0
rain = 0.0
cloud = 0.0
####
# Initial condition options
####
opt_ic = 'constant', 'depth_profile', 'ROMS', 'SUNTANS'
icfile = 'SUNTANS_IC.nc'
icfilterdx = 0.0 # Filtering length scale
# Age source term polygon
agesourcepoly = None
# Initial condition temperature and salinity
T0ic = 0
S0ic = 0
###
# Input file names
###
romsfile = None
suntansicfile = None
otisfile = None
dbasefile = None
# Use ROMS u,v and eta
useROMSuv = False
useROMSeta = False
# Use OTIS u & v
useOTISuv = False
############################
def __init__(self, **kwargs):
self.__dict__.update(kwargs)
def __call__(self, suntanspath, starttime, endtime, dt):
self.suntanspath = suntanspath
self.starttime = starttime
self.endtime = endtime
self.dt = dt
# Step through and perform each step
self._makebathy()
if self.makebnd:
self._makebnd()
if self.makeinitial:
self._makeinitial()
if self.makewinds:
self._makewinds()
print '###########\n Completed generating input files. Check text for errors!!!!\n##########'
def _makebathy(self):
"""
Loads the grid object and interpolates the depths
"""
# Interpolate the depths onto the grid
if self.makebathy:
if self.depthfile == None:
raise Exception, 'need to set "depthfile" parameter'
else:
print 'Interpolation depths onto grid from file:\n%s' % self.depthfile
D = DepthDriver(self.depthfile,interpmethod=self.interpmethod,\
plottype=self.plottype,NNear=self.NNear,\
p=self.p,varmodel=self.varmodel,nugget=self.nugget,sill=self.sill,vrange=self.vrange,\
convert2utm=self.convert2utm,utmzone=self.utmzone,isnorth=self.isnorth,vdatum=self.vdatum,\
shapefieldname=self.shapefieldname,\
smooth=self.smooth,smoothmethod=self.smoothmethod,smoothnear=self.smoothnear)
D(self.suntanspath,depthmax=self.depthmax,interpnodes=self.interpnodes,\
scalefac=self.scalefac)
self.grd = D.grd
# Now go through and adjust the channel depths from a shapefile
if self.adjust_depths:
self.grd = adjust_channel_depth(self.grd, self.channel_shpfile)
# Write the depths to file
print 'Writing depths.dat (again)...'
self.grd.saveBathy(self.suntanspath + '/depths.dat-voro')
print 'Data (re-)saved to %s.' % self.suntanspath + '/depths.dat-voro'
print 'SUNTANS depths saved to: %s' % (self.suntanspath +
'/depths.dat-voro')
elif self.setconstantdepth:
print 'Using constant depth (%6.2f m)...' % self.H0
self.grd = Grid(self.suntanspath)
self.grd.dv = np.zeros_like(self.grd.xv)
self.grd.dv[:] = self.H0
else:
print 'Loading grid from folder:\n%s' % self.suntanspath
# Load the grid
self.grd = Grid(self.suntanspath)
# Load the depth data into the grid object
self.grd.loadBathy(self.suntanspath + '/depths.dat-voro')
zmax = np.abs(self.grd.dv.max())
print 'Calculating vertical grid spacing for Nk = %d, r = %1.3f, %6.3f...' % (
self.Nkmax, self.r, zmax)
# Set up the vertical coordinates
dz = self.grd.calcVertSpace(self.Nkmax, self.r, zmax)
self.grd.setDepth(dz)
# Save vertspace.dat
self.grd.saveVertspace(self.suntanspath + '/vertspace.dat')
# Write cells.dat and edges.dat to ensure they are in the right format
print 'Overwriting cells.dat and edges.dat to ensure format consistency.'
self.grd.saveCells(self.suntanspath + '/cells.dat')
self.grd.saveEdges(self.suntanspath + '/edges.dat')
def _makebnd(self):
"""
Generate boundary condition files
"""
if self.modifyedges:
modifyBCmarker(self.suntanspath, self.bcpolygonfile)
#Load the boundary object from the grid
bnd = Boundary(self.suntanspath,
(self.starttime, self.endtime, self.dt))
###
# Segment (flux) boundaries
###
if self.opt_bcseg == 'constant':
print 'Setting %d boundary segments to discharge of %6.3f m3/s' % (
bnd.Nseg, self.Q0)
bnd.boundary_Q[:] = self.Q0
elif self.opt_bcseg == 'file':
print 'Loading river segment data from file...\n'
for ii, ID in enumerate(bnd.segp):
print 'Loading discahrge data for boundary segment (%d) StationID: %d...' % (
ii, ID)
ts = timeseries.loadDBstation(self.dbasefile,ID,'discharge',timeinfo=(self.starttime,self.endtime,self.dt),\
filttype=self.filttype,cutoff=self.cutoff)
bnd.boundary_Q[:, ii] = ts.y.copy()
else:
print 'Unknown option: opt_bcseg = %s. Not setting boundary segment data.' % self.opt_bcseg
###
# Type-3 boundaries
###
self.useROMS = False
self.useOTIS = False
self.useFILE = False
self.useOTISFILE = False
if self.opt_bctype3 == 'constant':
print 'Setting constant type-3 boundary conditions...'
print 'Setting salinity = %f, temperature = %f' % (self.S0,
self.T0)
bnd.S[:] = self.S0
bnd.T[:] = self.T0
elif self.opt_bctype3 == 'depth_profile':
print 'Setting type-3 boundary T/S from profile...'
self.loadTSprofile()
for ii in range(0, bnd.N3):
bnd.T[0, :, ii] = self.Tz
bnd.S[0, :, ii] = self.Sz
elif self.opt_bctype3 in ('ROMS'):
self.useROMS = True
elif self.opt_bctype3 in ('OTIS'):
self.useOTIS = True
elif self.opt_bctype3 in ('file'):
self.useFILE = True
elif self.opt_bctype3 in ('ROMSOTIS'):
self.useROMS = True
self.useOTIS = True
elif self.opt_bctype3 in ('ROMSFILE'):
self.useROMS = True
self.useFILE = True
elif self.opt_bctype3 in ('OTISFILE'):
self.useOTISFILE = True
elif self.opt_bctype3 in ('ROMSOTISFILE'):
self.useOTISFILE = True
self.useROMS = True
else:
print 'Unknown option: opt_bctype3 = %s. Not setting type-3 boundaries.' % self.opt_bctype3
if self.useROMS:
bnd.roms2boundary(self.romsfile,
setUV=self.useROMSuv,
seth=self.useROMSeta)
if self.useOTIS:
bnd.otis2boundary(self.otisfile, setUV=self.useOTISuv)
if self.useOTISFILE:
bnd.otisfile2boundary(self.otisfile,
self.dbasefile,
self.waterlevelstationID,
setUV=self.useOTISuv)
if self.useFILE:
ID = self.waterlevelstationID
print 'Loading waterlevel onto all type-3 points from stationID: %d...' % (
ID)
ts = timeseries.loadDBstation(self.dbasefile,ID,'waterlevel',timeinfo=(self.starttime,self.endtime,self.dt),\
filttype=self.filttype,cutoff=self.cutoff)
for ii in range(bnd.N3):
bnd.h[:, ii] += ts.y.copy()
###
# Type-2 boundaries
###
self.useFILE2 = False
if self.opt_bctype2 == 'constant':
print 'Setting constant type-2 boundary conditions...'
print 'Setting salinity = %f, temperature = %f' % (self.S0,
self.T0)
bnd.boundary_S[:] = self.S0
bnd.boundary_T[:] = self.T0
elif self.opt_bctype2 == 'file':
print 'Using file for type-2 boundary condition (temperature only)'
print 'Setting salinity = %f' % (self.S0)
bnd.boundary_S[:] = self.S0
self.useFILE2 = True
else:
print 'Unknown option: opt_bctype2 = %s. Not setting type-2 boundaries.' % self.opt_bctype3
if self.useFILE2:
ID = self.TairstationID
print 'Loading air temperature onto all type-2 points from stationID: %s...' % (
ID)
ts = timeseries.loadDBstation(self.dbasefile,ID,'Tair',timeinfo=(self.starttime,self.endtime,self.dt),\
filttype=self.tairfilttype,cutoff=self.taircutoff)
for ii in range(bnd.N2):
for kk in range(bnd.Nk):
bnd.boundary_T[:, kk, ii] += ts.y.copy()
# Write to netcdf
bnd.write2NC(self.suntanspath + '/' + self.bcfile)
def _makeinitial(self):
"""
Generate initial conditions
"""
# Initialise the class
IC = InitialCond(self.suntanspath, self.starttime)
if self.opt_ic == 'constant':
print 'Setting constant initial conditions...'
print 'Setting salinity = %f, temperature = %f' % (self.S0ic,
self.T0ic)
IC.T[:] = self.T0ic
IC.S[:] = self.S0ic
elif self.opt_ic == 'depth_profile':
print 'Setting depth-varying initial conditions...'
self.loadTSprofile()
for ii in range(0, IC.Nc):
IC.T[0, :, ii] = self.Tz
IC.S[0, :, ii] = self.Sz
elif self.opt_ic == 'ROMS':
print 'Setting initial conditions from ROMS model output...'
IC.roms2ic(self.romsfile,
setUV=self.useROMSuv,
seth=self.useROMSeta,
interpmethod='idw',
NNear=5,
p=2)
#interpmethod=self.interpmethod,NNear=self.NNear,p=self.p,\
#varmodel=self.varmodel,nugget=self.nugget,sill=self.sill,\
#vrange=self.vrange)
elif self.opt_ic == 'SUNTANS':
IC.suntans2ic(self.suntansicfile,
setUV=self.useROMSuv,
seth=self.useROMSeta)
else:
print 'Unknown option: opt_ic = %s. Not setting initial conditions.' % self.opt_ic
# Filter the variables in space
if self.icfilterdx > 0:
IC.filteric(self.icfilterdx)
# Set the age source term from a polygon
if not self.agesourcepoly == None:
print 'Setting age source term with shapefile: %s...' % self.agesourcepoly
IC.setAgeSource(self.agesourcepoly)
# Write the initial condition file
IC.writeNC(self.suntanspath + '/' + self.icfile, dv=self.grd.dv)
def _makewinds(self):
"""
Generate a metfile
"""
if self.opt_met == 'constant':
print 'Setting constant met forcing with: Uwind = %6.2f\nVwind = %6.2f\nTair = %6.2f\nPair = %6.2f\nRH = %6.2f\nrain = %6.2f\ncloud = %6.2f\n'\
%(self.Uwind,self.Vwind,self.Tair,self.Pair,self.RH,self.cloud,self.rain)
xpt = self.grd.xv.mean()
ypt = self.grd.yv.mean()
zpt = 10.0
# Load the met object
met = SunMet(xpt, ypt, zpt,
(self.starttime, self.endtime, self.dt))
# Fill the arrays
met.Uwind.data[:] = self.Uwind
met.Vwind.data[:] = self.Vwind
met.Tair.data[:] = self.Tair
met.Pair.data[:] = self.Pair
met.RH.data[:] = self.RH
met.cloud.data[:] = self.cloud
met.rain.data[:] = self.rain
met.write2NC(self.suntanspath + '/' + self.metfile)
else:
print 'Unknown option: opt_met=%s. Failed to generate a metfile' % self.opt_met
def loadTSprofile(self):
"""
Loads a temperature salinity profile from a matfile and interpolates onto the grid depths
"""
try:
data = io.loadmat(self.TSprofilefile)
z = data['depth'].ravel()
temp = data['temp_profile'].ravel()
salt = data['salt_profile'].ravel()
FT = interp1d(z, temp, kind=3)
self.Tz = FT(self.grd.z_r)
FS = interp1d(z, salt, kind=3)
self.Sz = FS(self.grd.z_r)
except:
print 'Warning could not find variables: "depth", "temp_profile" or "salt_profile" in file:\n%s' % self.TSprofilefile
self.Tz = self.T0
self.Sz = self.S0