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makepointdata.py
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makepointdata.py
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#!/usr/bin/env python
import os, sys, csv, time, math
from optparse import OptionParser
import numpy
import netcdf4_functions as nffun
from netCDF4 import Dataset
parser = OptionParser()
parser.add_option("--site", dest="site", default='', \
help = '6-character FLUXNET code to run (required)')
parser.add_option("--sitegroup", dest="sitegroup", default="AmeriFlux", \
help = "site group to use (default AmeriFlux)")
parser.add_option("--lat_bounds", dest="lat_bounds", default='-999,-999', \
help = 'latitude range for regional run')
parser.add_option("--lon_bounds", dest="lon_bounds", default='-999,-999', \
help = 'longitude range for regional run')
parser.add_option("--crop", dest="crop", default=False, \
help = 'Crop compset specified', action="store_true")
parser.add_option("--lai", dest="lai", default=-999, \
help = 'Set constant LAI (SP mode only)')
parser.add_option("--model", dest="mymodel", default='', \
help = 'Model to use (CLM5 or ELM)')
parser.add_option("--mask", dest="mymask", default='', \
help = 'Mask file to use (regional only)')
parser.add_option("--pft", dest="mypft", default=-1, \
help = 'Replace all gridcell PFT with this value')
parser.add_option("--point_list", dest="point_list", default='', \
help = 'File containing list of points to run (unstructured)')
parser.add_option("--point_area_kmxkm", dest="point_area_km2", default=None, \
help = 'user-specific area in km2 of each point in point list (unstructured')
parser.add_option("--point_area_degxdeg", dest="point_area_deg2", default=None, \
help = 'user-specific area in degreeXdegree of each point in point list (unstructured')
parser.add_option("--keep_duplicates", dest="keep_duplicates", default=False, \
help = 'Keep duplicate points', action='store_true')
parser.add_option("--ccsm_input", dest="ccsm_input", \
default='../../../../ccsm_inputdata', \
help = "input data directory for CESM (required)")
parser.add_option("--metdir", dest="metdir", default="none", \
help = 'subdirectory for met data forcing')
parser.add_option("--makemetdata", dest="makemet", default=False, \
help = 'Generate meteorology', action="store_true")
parser.add_option("--surfdata_grid", dest="surfdata_grid", default=False, \
help = 'Use gridded soil data', action="store_true")
#parser.add_option("--include_nonveg", dest="include_nonveg", default=False, \
# help = "Include non-vegetated fractions from surface data file")
parser.add_option("--res", dest="res", default="hcru_hcru", \
help = 'Resolution of global files')
parser.add_option("--nopftdyn", dest="nopftdyn", default=False, \
action='store_true', help='Do not make transient PFT file')
parser.add_option("--mysimyr", dest="mysimyr", default=1850, \
help = 'Simulation year (1850 or 2000)')
parser.add_option("--humhol", dest="humhol", default=False, \
help = 'Use hummock/hollow microtopography', action="store_true")
parser.add_option("--marsh", dest="marsh", default=False, \
help = 'Use marsh hydrology/elevation', action="store_true")
parser.add_option("--usersurfnc", dest="usersurfnc", default="none", \
help = 'User-provided surface data nc file, with one or more variable(s) as defined')
parser.add_option("--usersurfvar", dest="usersurfvar", default="none", \
help = 'variable name(s) in User-provided surface data nc file, separated by ","')
(options, args) = parser.parse_args()
ccsm_input = os.path.abspath(options.ccsm_input)
#------------------- get site information ----------------------------------
#Remove existing temp files
os.system('find ./temp/ -name "*.nc*" -exec rm {} \; ')
lat_bounds = options.lat_bounds.split(',')
lon_bounds = options.lon_bounds.split(',')
lat_bounds = [float(l) for l in lat_bounds]
lon_bounds = [float(l) for l in lon_bounds]
mysimyr=int(options.mysimyr)
if ('hcru' in options.res):
resx = 0.5
resy = 0.5
domainfile_orig = ccsm_input+'/share/domains/domain.clm/domain.lnd.360x720_cruncep.100429.nc'
if (options.mymodel == 'CLM5'):
surffile_orig = ccsm_input+'/lnd/clm2/surfdata_map/surfdata_360x720cru_16pfts_Irrig_CMIP6_simyr1850_c170824.nc'
elif (options.crop):
surffile_orig = ccsm_input+'/lnd/clm2/surfdata_map/surfdata_360x720cru_24pfts_simyr2000_c150227.nc'
else:
if (mysimyr == 2000):
surffile_orig = ccsm_input+'/lnd/clm2/surfdata_map/surfdata_360x720cru_simyr2000_c180216.nc'
else:
#CMIP6 stype (Hurtt v2)
surffile_orig = ccsm_input+'/lnd/clm2/surfdata_map/surfdata_360x720cru_simyr1850_c180216.nc'
pftdyn_orig = ccsm_input+'/lnd/clm2/surfdata_map/landuse.timeseries_360x720cru_hist_simyr1850-2015_c180220.nc'
nyears_landuse=166
elif ('f19' in options.res):
domainfile_orig = ccsm_input+'/share/domains/domain.lnd.fv1.9x2.5_gx1v6.090206.nc'
surffile_orig = ccsm_input+'/lnd/clm2/surfdata_map/surfdata_1.9x2.5_simyr1850_c180306.nc'
pftdyn_orig = ccsm_input+'/lnd/clm2/surfdata_map/landuse.timeseries_1.9x2.5_rcp8.5_simyr1850-2100_c141219.nc'
nyears_landuse=251
resx = 2.5
resy = 1.9
elif ('f09' in options.res):
domainfile_orig = ccsm_input+'/share/domains/domain.lnd.fv0.9x1.25_gx1v6.090309.nc'
surffile_orig = ccsm_input+'/lnd/clm2/surfdata_map/surfdata_0.9x1.25_simyr1850_c180306.nc'
pftdyn_orig = ccsm_input+'/lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_rcp8.5_simyr1850-2100_c141219.nc'
nyears_landuse=251
resx = 1.25
resy = 0.9
elif ('ne30' in options.res):
#domainfile_orig = ccsm_input+'/share/domains/domain.lnd.ne30np4_oEC60to30.20151214.nc'
#water cycle experiment
domainfile_orig = ccsm_input+'/share/domains/domain.lnd.ne30np4_oEC60to30v3.161222.nc'
#surffile_orig = ccsm_input+'/lnd/clm2/surfdata_map/surfdata_ne30np4_simyr1850_2015_c171018.nc'
surffile_orig = ccsm_input+'/lnd/clm2/surfdata_map/surfdata_ne30np4_simyr1850_c180306.nc'
pftdyn_orig = ccsm_input+'/lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_simyr1850_2015_c20171018.nc'
nyears_landuse = 166
n_grids=1
issite = False
isglobal = False
lat=[]
lon=[]
if (lat_bounds[0] > -90 and lon_bounds[0] > -180):
print( '\nCreating regional datasets using '+options.res+ 'resolution')
if (lon_bounds[0] < 0):
lon_bounds[0] = lon_bounds[0]+360.
if (lon_bounds[1] < 0):
lon_bounds[1] = lon_bounds[1]+360.
elif (options.point_list != ''):
issite=True
input_file = open(options.point_list,'r')
n_grids=0
point_pfts=[]
# if providing a user-defined nc file for extracting surface data other than standard inputs
if (options.usersurfnc!='none'):
if (options.usersurfvar=='none'):
print('must provide variable name(s) for extracting data from : ',options.usersurfnc)
sys.exit()
else:
mysurfvar = options.usersurfvar.split(',')
mysurfnc = Dataset(options.usersurfnc,'r') # must provide the full path and file name
mysurf_lat = numpy.asarray(mysurfnc['LATIXY'])
mysurf_lon = numpy.asarray(mysurfnc['LONGXY'])
ix=numpy.where(mysurf_lon<0.0)
if(ix[0].size>0): mysurf_lon[ix]=mysurf_lon[ix]+360.0
point_mysurf = {}
point_ij = []
for isurfvar in mysurfvar:
point_mysurf[isurfvar] = []
for s in input_file:
if (n_grids == 0):
header = s.split()
else:
data = s.split()
dnum=0
point_pfts.append(-1)
for d in data:
if ('lon' in header[dnum]):
mylon = float(d)
if (mylon < 0):
mylon = mylon+360
lon.append(mylon)
elif ('lat' in header[dnum]):
mylat = float(d)
lat.append(float(d))
elif ('pft' in header[dnum]):
point_pfts[n_grids-1] = int(d)
if (int(options.mypft) >= 0): #overrides info in file
point_pfts[n_grids-1] = options.mypft
dnum=dnum+1
#
#overrides data from a PCT_PFT nc input file (TIP: only index here to speed-up loop)
if(options.usersurfnc!='none' and options.usersurfvar!='none'):
dx=numpy.abs(mysurf_lon-mylon)
dy=numpy.abs(mysurf_lat-mylat)
dxy = numpy.sqrt(dx*dx+dy*dy)
ixy = numpy.unravel_index(numpy.argmin(dxy, axis=None), dxy.shape)
if (n_grids==1):
point_ij=[ixy[0],ixy[1]]
else:
point_ij=numpy.vstack((point_ij,[ixy[0],ixy[1]]))
n_grids=n_grids+1
if(divmod(n_grids, 100)[1]==0): print("grid counting: \n",n_grids)
#overrides data from a PCT_PFT nc input file, after all index are assembled
if(options.usersurfnc!='none' and options.usersurfvar!='none'):
for isurfvar in mysurfvar:
isurfvar_vals = numpy.asarray(mysurfnc[isurfvar])[:,point_ij[:,0],point_ij[:,1]]
point_mysurf[isurfvar] = numpy.transpose(isurfvar_vals)
input_file.close()
n_grids = n_grids-1
elif (options.site != ''):
print('\nCreating datasets for '+options.site+' using '+options.res+' resolution')
issite = True
AFdatareader = csv.reader(open(ccsm_input+'/lnd/clm2/PTCLM/'+options.sitegroup+'_sitedata.txt',"r"))
for row in AFdatareader:
if row[0] == options.site:
mylon=float(row[3])
if (mylon < 0):
mylon=360.0+float(row[3])
lon.append(mylon)
lat.append(float(row[4]))
if ('US-SPR' in options.site or
(options.marsh or options.humhol)):
lon.append(mylon)
lat.append(float(row[4]))
n_grids = 2
startyear=int(row[6])
endyear=int(row[7])
alignyear = int(row[8])
else:
isglobal=True
#get corresponding 0.5x0.5 and 1.9x2.5 degree grid cells
if (options.res == 'hcru_hcru'):
longxy = (numpy.cumsum(numpy.ones([721]))-1)*0.5
latixy = (numpy.cumsum(numpy.ones([361]))-1)*0.5 -90.0
elif ('f19' in options.res):
longxy = (numpy.cumsum(numpy.ones([145]))-1)*2.5-1.25
latixy_centers = (numpy.cumsum(numpy.ones([96]))-1)*(180.0/95) - 90.0
latixy = numpy.zeros([97], float)
longxy[0] = 0
latixy[0] = -90
latixy[96] = 90
for i in range(1,96):
latixy[i] = (latixy_centers[i-1]+latixy_centers[i])/2.0
elif ('f09' in options.res):
longxy = (numpy.cumsum(numpy.ones([289]))-1)*1.25-0.625
latixy_centers = (numpy.cumsum(numpy.ones([192]))-1)*(180.0/191) - 90.0
latixy = numpy.zeros([193], float)
longxy[0] = 0
latixy[0] = -90
latixy[192] = 90
for i in range(1,192):
latixy[i] = (latixy_centers[i-1]+latixy_centers[i])/2.0
else:
longxy = nffun.getvar(surffile_orig, 'LONGXY')
latixy = nffun.getvar(surffile_orig, 'LATIXY')
xgrid_min=[]
xgrid_max=[]
ygrid_min=[]
ygrid_max=[]
for n in range(0,n_grids):
if (issite):
lon_bounds = [lon[n],lon[n]]
lat_bounds = [lat[n],lat[n]]
xgrid_min.append(-1)
xgrid_max.append(-1)
ygrid_min.append(-1)
ygrid_max.append(-1)
if ('ne' in options.res):
if (lon_bounds[0] != lon_bounds[1] or lat_bounds[0] != lat_bounds[1]):
print('Regional subsets not allowed for ne resolutions. Use point lists instead')
sys.exit()
ygrid_min[n] = 0
ygrid_max[n] = 0
mindist=99999
for i in range(0,longxy.shape[0]-1):
thisdist = (lon_bounds[0]-longxy[i])**2 + (lat_bounds[0]-latixy[i])**2
if (thisdist < mindist):
xgrid_min[n] = i
xgrid_max[n] = i
mindist=thisdist
else:
for i in range(0,longxy.shape[0]-1):
if (lon_bounds[0] >= longxy[i]):
xgrid_min[n] = i
xgrid_max[n] = i
elif (lon_bounds[1] >= longxy[i+1]):
xgrid_max[n] = i
if (lon_bounds[0] == 180 and lon_bounds[1] == 180): #global
xgrid_min[n] = 0
xgrid_max[n] = longxy.shape[0]-2
for i in range(0,latixy.shape[0]-1):
if (lat_bounds[0] >= latixy[i]):
ygrid_min[n] = i
ygrid_max[n] = i
elif (lat_bounds[1] >= latixy[i+1]):
ygrid_max[n] = i
#print n, lat[n], lon[n], xgrid_max[n], ygrid_max[n]
if (n_grids > 1 and options.site == ''): #remove duplicate points
n_grids_uniq = 1
n_dups = 0
xgrid_min_uniq = [xgrid_min[0]]
ygrid_min_uniq = [ygrid_min[0]]
lon_uniq = [lon[0]]
lat_uniq = [lat[0]]
point_pfts_uniq = [point_pfts[0]]
point_index = [1]
myoutput = open('point_list_output.txt','w')
#myoutput.write(str(lon[0])+','+str(lat[0])+','+str(point_index[0])+'\n')
myoutput.write(str(lon[0])+','+str(lat[0])+','+str(point_index[0])+','+ \
str(xgrid_min_uniq[0])+','+str(ygrid_min_uniq[0])+'\n')
print('Total grids', n_grids)
for n in range (1,n_grids):
is_unique = True
#for m in range(0,n_grids_uniq):
# if (xgrid_min[n] == xgrid_min_uniq[m] and ygrid_min[n] == ygrid_min_uniq[m] \
# and point_pfts[n] == point_pfts_uniq[m]):
# n_dups = n_dups+1
# is_unique = False
# #point_index.append(m+1)
# the above is time-costing
if not options.keep_duplicates:
xidx = numpy.where(numpy.asarray(xgrid_min_uniq) == xgrid_min[n])
if len(xidx[0])>0: # more than 0 indicates duplicated 'x'
# search 'y indx' in same positions of 'ygrid_min_uniq'
yidx = numpy.where(numpy.asarray(ygrid_min_uniq)[xidx] == ygrid_min[n])
if len(yidx[0])>0: # both 'x','y' have duplicated points
pidx = numpy.where(numpy.asarray(point_pfts_uniq)[xidx[0][yidx]] == point_pfts[n])
if len(pidx[0])>0:
n_dups = n_dups + 1
is_unique = False
if (is_unique):
#if (is_unique or options.keep_duplicates):
xgrid_min_uniq.append(xgrid_min[n])
ygrid_min_uniq.append(ygrid_min[n])
point_pfts_uniq.append(point_pfts[n])
lon_uniq.append(lon[n])
lat_uniq.append(lat[n])
n_grids_uniq = n_grids_uniq+1
point_index.append(n_grids_uniq)
myoutput.write(str(lon[n])+','+str(lat[n])+','+str(point_index[n_grids_uniq-1])+','+ \
str(xgrid_min_uniq[n_grids_uniq-1])+','+str(ygrid_min_uniq[n_grids_uniq-1])+'\n')
#myoutput.write(str(lon[n])+','+str(lat[n])+','+str(point_index[n])+'\n')
myoutput.close()
xgrid_min = xgrid_min_uniq
xgrid_max = xgrid_min_uniq
ygrid_min = ygrid_min_uniq
ygrid_max = ygrid_min_uniq
lon = lon_uniq
lat = lat_uniq
point_pfts = point_pfts_uniq
n_grids = n_grids_uniq
if (not options.keep_duplicates):
print(n_grids, ' Unique points')
print(n_dups, ' duplicate points removed')
#print(len(point_index))
#print(point_index)
#---------------------Create domain data --------------------------------------------------
print('Creating domain data')
os.system('mkdir -p ./temp')
# 'AREA' in surfdata.nc is in KM2, which later used for scaling a point
area_orig = nffun.getvar(surffile_orig, 'AREA')
# in case NCO bin path not in $PATH
os.environ["PATH"] += ':/usr/local/nco/bin'
os.environ["PATH"] += ':/Users/f9y/ATS_ROOT/amanzi_tpls-install-master-Debug/bin'
domainfile_tmp = 'domain??????.nc' # filename pattern of 'domainfile_new'
for n in range(0,n_grids):
nst = str(1000000+n)[1:]
domainfile_new = './temp/domain'+nst+'.nc'
if (not os.path.exists(domainfile_orig)):
print('Error: '+domainfile_orig+' does not exist. Aborting')
sys.exit(1)
if (isglobal):
os.system('cp '+domainfile_orig+' '+domainfile_new)
else:
os.system('ncks -h -O -d ni,'+str(xgrid_min[n])+','+str(xgrid_max[n])+' -d nj,'+str(ygrid_min[n])+ \
','+str(ygrid_max[n])+' '+domainfile_orig+' '+domainfile_new)
# scaling x/y length for original grid
if (options.point_area_km2 != None):
area_n = area_orig[ygrid_min[n],xgrid_min[n]]
if(float(area_n)>0.0):
# asssuming a square of area (km2) in projected flat surface system
# its longitude/latitude range not square anymore
# (note: this is very coarse estimation)
side_km = math.sqrt(float(options.point_area_km2))
if(lat[n]==90.0): lat[n]=lat[n]-0.00001
if(lat[n]==-90.0): lat[n]=lat[n]+0.00001
kmratio_lon2lat = math.cos(math.radians(lat[n]))
re_km = 6371.22
yscalar = side_km/(math.pi*re_km/180.0*resy)
xscalar = side_km/(math.pi*re_km/180.0*resx*kmratio_lon2lat)
if (options.point_area_deg2 != None):
area_n = area_orig[ygrid_min[n],xgrid_min[n]]
if(float(area_n)>0.0):
side_deg = math.sqrt(float(options.point_area_deg2)) # degx X degy, NOT square radians
yscalar = side_deg/resy
xscalar = side_deg/resx
if (issite):
frac = nffun.getvar(domainfile_new, 'frac')
mask = nffun.getvar(domainfile_new, 'mask')
xc = nffun.getvar(domainfile_new, 'xc')
yc = nffun.getvar(domainfile_new, 'yc')
xv = nffun.getvar(domainfile_new, 'xv')
yv = nffun.getvar(domainfile_new, 'yv')
area = nffun.getvar(domainfile_new, 'area')
frac[0] = 1.0
mask[0] = 1
if (options.site != ''):
xc[0] = lon[n]
yc[0] = lat[n]
xv[0][0][0] = lon[n]-resx/2
xv[0][0][1] = lon[n]+resx/2
xv[0][0][2] = lon[n]-resx/2
xv[0][0][3] = lon[n]+resx/2
yv[0][0][0] = lat[n]-resy/2
yv[0][0][1] = lat[n]-resy/2
yv[0][0][2] = lat[n]+resy/2
yv[0][0][3] = lat[n]+resy/2
area[0] = resx*resy*math.pi/180*math.pi/180
ierr = nffun.putvar(domainfile_new, 'xc', xc)
ierr = nffun.putvar(domainfile_new, 'yc', yc)
ierr = nffun.putvar(domainfile_new, 'xv', xv)
ierr = nffun.putvar(domainfile_new, 'yv', yv)
ierr = nffun.putvar(domainfile_new, 'area', area)
elif (options.point_area_km2 != None or options.point_area_deg2 != None):
xc[0] = lon[n]
yc[0] = lat[n]
xv[0][0][0] = lon[n]-resx*xscalar
xv[0][0][1] = lon[n]+resx*xscalar
xv[0][0][2] = lon[n]-resx*xscalar
xv[0][0][3] = lon[n]+resx*xscalar
yv[0][0][0] = lat[n]-resy*yscalar
yv[0][0][1] = lat[n]-resy*yscalar
yv[0][0][2] = lat[n]+resy*yscalar
yv[0][0][3] = lat[n]+resy*yscalar
area[0] = area[0]*xscalar*yscalar
if(options.point_area_km2 != None):
area[0] = float(options.point_area_km2)/re_km/re_km # there is about 0.3% error with calculation above
ierr = nffun.putvar(domainfile_new, 'xc', xc)
ierr = nffun.putvar(domainfile_new, 'yc', yc)
ierr = nffun.putvar(domainfile_new, 'xv', xv)
ierr = nffun.putvar(domainfile_new, 'yv', yv)
ierr = nffun.putvar(domainfile_new, 'area', area)
ierr = nffun.putvar(domainfile_new, 'frac', frac)
ierr = nffun.putvar(domainfile_new, 'mask', mask)
os.system('ncks -h -O --mk_rec_dim nj '+domainfile_new+' '+domainfile_new)
elif (options.mymask != ''):
print('Applying mask from '+options.mymask)
os.system('ncks -h -O -d lon,'+str(xgrid_min[n])+','+str(xgrid_max[n])+' -d lat,'+str(ygrid_min[n])+ \
','+str(ygrid_max[n])+' '+options.mymask+' mask_temp.nc')
newmask = nffun.getvar('mask_temp.nc', 'PNW_mask')
ierr = nffun.putvar(domainfile_new, 'mask', newmask)
os.system('rm mask_temp.nc')
domainfile_old = domainfile_new
domainfile_new = './temp/domain.nc'
if (n_grids > 1):
#ierr = os.system('ncrcat -h '+domainfile_list+' '+domainfile_new) # OS error if '_list' too long
ierr = os.system('find ./temp/ -name "'+domainfile_tmp+ \
'" | xargs ls | sort | ncrcat -O -h -o'+domainfile_new)
if(ierr!=0): raise RuntimeError('Error: ncrcat -', ierr); #os.sys.exit()
ierr = os.system('nccopy -6 -u '+domainfile_new+' '+domainfile_new+'.tmp') #NC-3 with large dataset support due to 64bit offset
if(ierr!=0): raise RuntimeError('Error: nccopy -6 -u ', ierr); #os.sys.exit()
ierr = os.system('ncpdq -h -O -a ni,nj '+domainfile_new+'.tmp '+domainfile_new)
if(ierr!=0): raise RuntimeError('Error: ncpdq', ierr); #os.sys.exit()
ierr = os.system('ncrename -h -O -d ni,ni_temp '+domainfile_new+' '+domainfile_new+' ')
if(ierr!=0): raise RuntimeError('Error: ncrename', ierr); #os.sys.exit()
ierr = os.system('ncrename -h -O -d nj,ni '+domainfile_new+' '+domainfile_new+' ')
if(ierr!=0): raise RuntimeError('Error: ncrename', ierr); #os.sys.exit()
ierr = os.system('ncrename -h -O -d ni_temp,nj '+domainfile_new+' '+domainfile_new+' ')
if(ierr!=0): raise RuntimeError('Error: ncrename', ierr); #os.sys.exit()
os.system('find ./temp/ -name '+domainfile_tmp+' -exec rm {} \;')
os.system('rm '+domainfile_new+'.tmp*')
else:
ierr = os.system('mv '+domainfile_old+' '+domainfile_new)
#
if(ierr==0):
# NC-4 classic better for either NC-4 or NC-3 tools,
# but 'ncrename' not good with NC-4
ierr = os.system('nccopy -7 -u '+domainfile_new+' '+domainfile_new+'.tmp')
if(ierr!=0):
print('nccopy -7 -u '+domainfile_new+' '+domainfile_new+'.tmp')
raise RuntimeError('Error: nccopy -7 -u ');# os.sys.exit()
else:
ierr = os.system('mv '+domainfile_new+'.tmp '+domainfile_new)
print("INFO: Extracted and Compiled '"+ domainfile_new + "' FROM: '" + domainfile_orig+"'! \n")
else:
raise RuntimeError("FAILED: Extracted and Compiled '"+ domainfile_new + "' FROM: '" + domainfile_orig+"'! \n")
os.sys.exit(-1)
#-------------------- create surface data ----------------------------------
print('Creating surface data')
surffile_tmp = 'surfdata??????.nc' # filename pattern of 'surffile_new'
for n in range(0,n_grids):
nst = str(1000000+n)[1:]
surffile_new = './temp/surfdata'+nst+'.nc'
if (not os.path.exists(surffile_orig)):
print('Error: '+surffile_orig+' does not exist. Aborting')
sys.exit(1)
if (isglobal):
os.system('cp '+surffile_orig+' '+surffile_new)
else:
if ('ne' in options.res):
os.system('ncks -h -O --fix_rec_dmn time -d gridcell,'+str(xgrid_min[n])+','+str(xgrid_max[n])+ \
' '+surffile_orig+' '+surffile_new)
else:
os.system('ncks -h -O --fix_rec_dmn time -d lsmlon,'+str(xgrid_min[n])+','+str(xgrid_max[n])+ \
' -d lsmlat,'+str(ygrid_min[n])+','+str(ygrid_max[n])+' '+surffile_orig+' '+surffile_new)
if (issite):
landfrac_pft = nffun.getvar(surffile_new, 'LANDFRAC_PFT')
pftdata_mask = nffun.getvar(surffile_new, 'PFTDATA_MASK')
longxy = nffun.getvar(surffile_new, 'LONGXY')
latixy = nffun.getvar(surffile_new, 'LATIXY')
area = nffun.getvar(surffile_new, 'AREA')
pct_wetland = nffun.getvar(surffile_new, 'PCT_WETLAND')
pct_lake = nffun.getvar(surffile_new, 'PCT_LAKE')
pct_glacier = nffun.getvar(surffile_new, 'PCT_GLACIER')
pct_urban = nffun.getvar(surffile_new, 'PCT_URBAN')
if (options.mymodel == 'CLM5' or options.crop):
pct_crop = nffun.getvar(surffile_new, 'PCT_CROP')
pct_cft = nffun.getvar(surffile_new, 'PCT_CFT')
#put fake P data in this datset
vars_in = ['LABILE_P','APATITE_P','SECONDARY_P','OCCLUDED_P']
soil_order = 1
labilep = 1.0
primp = 1.0
secondp = 1.0
occlp = 1.0
tempdata = Dataset(surffile_new, 'a')
for v in vars_in:
tempvar = tempdata.createVariable(v, 'f4',('lsmlat','lsmlon',))
tempvar = tempdata.createVariable('SOIL_ORDER', 'i4',('lsmlat','lsmlon',))
tempdata.close()
else:
soil_order = nffun.getvar(surffile_new, 'SOIL_ORDER')
labilep = nffun.getvar(surffile_new, 'LABILE_P')
primp = nffun.getvar(surffile_new, 'APATITE_P')
secondp = nffun.getvar(surffile_new, 'SECONDARY_P')
occlp = nffun.getvar(surffile_new, 'OCCLUDED_P')
#input from site-specific information
soil_color = nffun.getvar(surffile_new, 'SOIL_COLOR')
pct_sand = nffun.getvar(surffile_new, 'PCT_SAND')
pct_clay = nffun.getvar(surffile_new, 'PCT_CLAY')
organic = nffun.getvar(surffile_new, 'ORGANIC')
fmax = nffun.getvar(surffile_new, 'FMAX')
pct_nat_veg = nffun.getvar(surffile_new, 'PCT_NATVEG')
pct_pft = nffun.getvar(surffile_new, 'PCT_NAT_PFT')
monthly_lai = nffun.getvar(surffile_new, 'MONTHLY_LAI')
monthly_sai = nffun.getvar(surffile_new, 'MONTHLY_SAI')
monthly_height_top = nffun.getvar(surffile_new, 'MONTHLY_HEIGHT_TOP')
monthly_height_bot = nffun.getvar(surffile_new, 'MONTHLY_HEIGHT_BOT')
npft = 17
npft_crop = 0
if (options.crop or options.mymodel == 'CLM5'):
npft = 15
npft_crop = 10
#read file for site-specific PFT information
mypft_frac = numpy.zeros([npft+npft_crop], float)
mypct_sand = 0.0
mypct_clay = 0.0
if (options.surfdata_grid == False and options.site != ''):
#read file for site-specific PFT information
AFdatareader = csv.reader(open(ccsm_input+'/lnd/clm2/PTCLM/'+options.sitegroup+'_pftdata.txt','r'))
for row in AFdatareader:
if row[0] == options.site:
for thispft in range(0,5):
mypft_frac[int(row[2+2*thispft])]=float(row[1+2*thispft])
if (sum(mypft_frac[0:npft+npft_crop]) == 0.0):
print('*** Warning: PFT data NOT found. Using gridded data ***')
#read file for site-specific soil information
AFdatareader = csv.reader(open(ccsm_input+'/lnd/clm2/PTCLM/'+options.sitegroup+'_soildata.txt','r'))
for row in AFdatareader:
if row[0] == options.site:
mypct_sand = row[4]
mypct_clay = row[5]
if (mypct_sand == 0.0 and mypct_clay == 0.0):
print('*** Warning: Soil data NOT found. Using gridded data ***')
else:
try:
#mypft_frac[point_pfts[n]] = 100.0
if(point_pfts[n]!=-1):
# a single PFT of 100% indicated by input option
mypft_frac[point_pfts[n]] = 100.0
else:
mypft_frac = pct_pft
# multiple PFTs' pct are read-in from a nc file
if('PCT_PFT' in mysurfvar or 'PCT_NAT_PFT' in mysurfvar):
sum_nat=numpy.sum(pct_pft)
if ('PCT_PFT' in point_mysurf.keys()):
if(numpy.sum(point_mysurf['PCT_PFT'][n])>0.0):
pct_pft[:,0,0] = point_mysurf['PCT_PFT'][n]
elif('PCT_NAT_PFT' in point_mysurf.keys()):
if(numpy.sum(point_mysurf['PCT_NAT_PFT'][n])>0.0):
pct_pft[:,0,0] = point_mysurf['PCT_NAT_PFT'][n]
else:
print('Error: PCT_PFT or PCT_NAT_PFT is used variable name for PFT fraction in surface data')
sys.exit()
# in case PCT not summed to 100.0
sum_nat2=numpy.sum(pct_pft[:,0,0])
if (sum_nat2!=100.0):
adj=100.0/sum_nat2
pct_pft[:,0,0] = pct_pft[:,0,0] * adj
if (sum_nat<100.0):
pct_pft[:,0,0] = pct_pft[:,0,0]*sum_nat/100.0
if(numpy.sum(pct_pft[:,0,0])!=sum_nat):
# this is rare to occur, after TWO corrections above,
# seems due to numerical error relevant to machine
# have to fix it if any (will throw error when used by ELM)
err=sum_nat - numpy.sum(pct_pft[:,0,0])
err_ix=numpy.argmax(pct_pft[:,0,0])
pct_pft[err_ix,0,0]=pct_pft[err_ix,0,0]+err
print('Error correction - ', err,numpy.sum(pct_pft[:,0,0]))
except NameError:
print('using PFT information from surface data')
#landfrac_pft[0][0] = 1.0
#pftdata_mask[0][0] = 1
if (options.site != ''):
longxy[0][0] = lon[n]
latixy[0][0] = lat[n]
area[0] = 111.2*resy*111.321*math.cos((lat[n]*resx)*math.pi/180)*resx
elif (options.point_area_km2 != None):
longxy[0][0] = lon[n]
latixy[0][0] = lat[n]
area[0] = float(options.point_area_km2)
elif (options.point_area_deg2 != None): # degx X degy (NOT square radians of area)
longxy[0][0] = lon[n]
latixy[0][0] = lat[n]
side_deg = math.sqrt(float(options.point_area_deg2)) # a square of lat/lon degrees assummed
area[0][0] = 111.2*side_deg*111.321*math.cos((lat[n]*side_deg)*math.pi/180)*side_deg
if (not options.surfdata_grid or sum(mypft_frac[0:npft+npft_crop]) > 0.0):
pct_wetland[0][0] = 0.0
pct_lake[0][0] = 0.0
pct_glacier[0][0] = 0.0
if (options.crop or options.mymodel == 'CLM5'):
if sum(mypft_frac[0:npft]) > 0.0:
pct_nat_veg[0][0] = 100.0
pct_crop[0][0] = 0.0
else:
pct_nat_veg[0][0] = 0.0
pct_crop[0][0] = 100.0
else:
pct_nat_veg[0][0] = 100.0
if ('US-SPR' in options.site and mysimyr !=2000):
#SPRUCE P initial data
soil_order[0][0] = 3
labilep[0][0] = 1.0
primp[0][0] = 0.1
secondp[0][0] = 1.0
occlp[0][0] = 1.0
for k in range(0,3):
pct_urban[k][0][0] = 0.0
for k in range(0,10):
if (float(mypct_sand) > 0.0 or float(mypct_clay) > 0.0):
if (k == 0):
print('Setting %sand to '+str(mypct_sand))
print('Setting %clay to '+str(mypct_clay))
pct_sand[k][0][0] = mypct_sand
pct_clay[k][0][0] = mypct_clay
if ('US-SPR' in options.site):
if (k < 8):
organic[k][0][0] = 130.0
elif (k == 8):
organic[k][0][0] = 65.0
# APW: this assumes that PFT labels do not change in the PFT file, consider reading from param file
pft_names=['Bare ground','ENF Temperate','ENF Boreal','DNF Boreal','EBF Tropical', \
'EBF Temperate', 'DBF Tropical', 'DBF Temperate', 'DBF Boreal', 'EB Shrub' \
, 'DB Shrub Temperate', 'BD Shrub Boreal', 'C3 arctic grass', \
'C3 non-arctic grass', 'C4 grass', 'Crop','xxx','xxx']
if options.marsh and n==1: # Set tidal channel column in marsh mode to zero PFT area
print('Setting PFT area in tidal column to zero')
mypft_frac = numpy.zeros([npft+npft_crop], float)
mypft_frac[0]=100.0
if (options.mypft >= 0 and not (options.marsh and n==1)):
print('Setting PFT '+str(options.mypft)+'('+pft_names[int(options.mypft)]+') to 100%')
pct_pft[:,0,0] = 0.0
pct_pft[int(options.mypft),0,0] = 100.0
else:
for p in range(0,npft+npft_crop):
#if (sum(mypft_frac[0:npft]) > 0.0):
#if (mypft_frac[p] > 0.0):
if (p < npft):
#if (mypft_frac[p] > 0.0): # too long print for long-list points
# print('Setting Natural PFT '+str(p)+'('+pft_names[p]+') to '+str(mypft_frac[p])+'%')
pct_pft[p][0][0] = mypft_frac[p]
else:
#if (mypft_frac[p] > 0.0):
# print('Setting Crop PFT '+str(p)+' to '+str(mypft_frac[p])+'%')
pct_cft[p-npft][0][0] = mypft_frac[p]
pct_pft[0][0][0] = 100.0
#maxlai = (monthly_lai).max(axis=0)
for t in range(0,12):
if (float(options.lai) > 0):
monthly_lai[t][p][0][0] = float(options.lai)
#monthly_lai[t][p][j][i] = monthly_lai[t][p][0][0]
#monthly_sai[t][p][j][i] = monthly_sai[t][p][0][0]
#monthly_height_top[t][p][j][i] = monthly_height_top[t][p][0][0]
#monthly_height_bot[t][p][j][i] = monthly_height_bot[t][p][0][0]
ierr = nffun.putvar(surffile_new, 'LANDFRAC_PFT', landfrac_pft)
ierr = nffun.putvar(surffile_new, 'PFTDATA_MASK', pftdata_mask)
ierr = nffun.putvar(surffile_new, 'LONGXY', longxy)
ierr = nffun.putvar(surffile_new, 'LATIXY', latixy)
ierr = nffun.putvar(surffile_new, 'AREA', area)
ierr = nffun.putvar(surffile_new, 'PCT_WETLAND', pct_wetland)
ierr = nffun.putvar(surffile_new, 'PCT_LAKE', pct_lake)
ierr = nffun.putvar(surffile_new, 'PCT_GLACIER',pct_glacier)
ierr = nffun.putvar(surffile_new, 'PCT_URBAN', pct_urban)
if (options.mymodel == 'CLM5' or options.crop):
ierr = nffun.putvar(surffile_new, 'PCT_CROP', pct_crop)
ierr = nffun.putvar(surffile_new, 'PCT_CFT', pct_cft)
ierr = nffun.putvar(surffile_new, 'SOIL_ORDER', soil_order)
ierr = nffun.putvar(surffile_new, 'LABILE_P', labilep)
ierr = nffun.putvar(surffile_new, 'APATITE_P', primp)
ierr = nffun.putvar(surffile_new, 'SECONDARY_P', secondp)
ierr = nffun.putvar(surffile_new, 'OCCLUDED_P', occlp)
ierr = nffun.putvar(surffile_new, 'SOIL_COLOR', soil_color)
ierr = nffun.putvar(surffile_new, 'FMAX', fmax)
ierr = nffun.putvar(surffile_new, 'ORGANIC', organic)
ierr = nffun.putvar(surffile_new, 'PCT_SAND', pct_sand)
ierr = nffun.putvar(surffile_new, 'PCT_CLAY', pct_clay)
ierr = nffun.putvar(surffile_new, 'PCT_NATVEG', pct_nat_veg)
ierr = nffun.putvar(surffile_new, 'PCT_NAT_PFT', pct_pft)
ierr = nffun.putvar(surffile_new, 'MONTHLY_HEIGHT_TOP', monthly_height_top)
ierr = nffun.putvar(surffile_new, 'MONTHLY_HEIGHT_BOT', monthly_height_bot)
ierr = nffun.putvar(surffile_new, 'MONTHLY_LAI', monthly_lai)
else: # not if(issite)
if (int(options.mypft) >= 0):
pct_pft = nffun.getvar(surffile_new, 'PCT_NAT_PFT')
pct_pft[:,:,:] = 0.0
pct_pft[int(options.mypft),:,:] = 100.0
ierr = nffun.putvar(surffile_new, 'PCT_NAT_PFT', pct_pft)
surffile_old = surffile_new
surffile_new = './temp/surfdata.nc'
if (n_grids > 1):
#os.system('ncecat '+surffile_list+' '+surffile_new) # not works with too long '_list'
ierr = os.system('find ./temp/ -name "'+surffile_tmp+ \
'" | xargs ls | sort | ncecat -O -h -o'+surffile_new)
if(ierr!=0): raise RuntimeError('Error: ncecat '); #os.sys.exit()
#os.system('rm ./temp/surfdata?????.nc*') # not works with too many files
os.system('find ./temp/ -name "'+surffile_tmp+'" -exec rm {} \;')
#remove ni dimension
ierr = os.system('ncwa -h -O -a lsmlat -d lsmlat,0,0 '+surffile_new+' '+surffile_new+'.tmp')
if(ierr!=0): raise RuntimeError('Error: ncwa '); #os.sys.exit()
ierr = os.system('nccopy -6 -u '+surffile_new+'.tmp'+' '+surffile_new+'.tmp2') #NC-3 with large dataset support (64bit offset)
if(ierr!=0): raise RuntimeError('Error: nccopy -6 -u '); #os.sys.exit()
ierr = os.system('ncpdq -h -a lsmlon,record '+surffile_new+'.tmp2 '+surffile_new+'.tmp3')
if(ierr!=0): raise RuntimeError('Error: ncpdq '); #os.sys.exit()
ierr = os.system('ncwa -h -O -a lsmlon -d lsmlon,0,0 '+surffile_new+'.tmp3 '+surffile_new+'.tmp4')
if(ierr!=0): raise RuntimeError('Error: ncwa '); #os.sys.exit()
ierr = os.system('ncrename -h -O -d record,gridcell '+surffile_new+'.tmp4 '+surffile_new+'.tmp5')
if(ierr!=0): raise RuntimeError('Error: ncrename '); #os.sys.exit()
os.system('mv '+surffile_new+'.tmp5 '+surffile_new)
os.system('rm '+surffile_new+'.tmp*')
else:
os.system('mv '+surffile_old+' '+surffile_new)
# NC-4 classic better for either NC-4 or NC-3 tools (though not writable as NC-4),
# but 'ncrename' used above may not works with NC-4
ierr = os.system('nccopy -7 -u '+surffile_new+' '+surffile_new+'.tmp')
if(ierr!=0):
raise RuntimeError('Error: nccopy -7 -u ');# os.sys.exit()
else:
ierr = os.system('mv '+surffile_new+'.tmp '+surffile_new)
print("INFO: Extracted and Compiled '"+ surffile_new + "' FROM: '" + surffile_orig+"'! \n")
#-------------------- create pftdyn surface data ----------------------------------
if (options.nopftdyn == False):
print('Creating dynpft data')
pftdyn_tmp = 'surfdata.pftdyn??????.nc' # filename pattern of 'pftdyn_new'
for n in range(0,n_grids):
nst = str(1000000+n)[1:]
pftdyn_new = './temp/surfdata.pftdyn'+nst+'.nc'
if (not os.path.exists(pftdyn_orig)):
print('Error: '+pftdyn_orig+' does not exist. Aborting')
sys.exit(1)
if (isglobal):
os.system('cp '+pftdyn_orig+' '+pftdyn_new)
else:
if ('ne' in options.res):
os.system('ncks -h -O --fix_rec_dmn time -d gridcell,'+str(xgrid_min[n])+','+str(xgrid_max[n])+ \
' '+pftdyn_orig+' '+pftdyn_new)
else:
os.system('ncks -h -O --fix_rec_dmn time -d lsmlon,'+str(xgrid_min[n])+','+str(xgrid_max[n])+ \
' -d lsmlat,'+str(ygrid_min[n])+','+str(ygrid_max[n])+' '+pftdyn_orig+' '+pftdyn_new)
if (issite):
landfrac = nffun.getvar(pftdyn_new, 'LANDFRAC_PFT')
pftdata_mask = nffun.getvar(pftdyn_new, 'PFTDATA_MASK')
longxy = nffun.getvar(pftdyn_new, 'LONGXY')
latixy = nffun.getvar(pftdyn_new, 'LATIXY')
area = nffun.getvar(pftdyn_new, 'AREA')
pct_pft = nffun.getvar(pftdyn_new, 'PCT_NAT_PFT')
pct_lake_1850 = nffun.getvar(surffile_new, 'PCT_LAKE')
pct_glacier_1850 = nffun.getvar(surffile_new, 'PCT_GLACIER')
pct_wetland_1850 = nffun.getvar(surffile_new, 'PCT_WETLAND')
pct_urban_1850 = nffun.getvar(surffile_new, 'PCT_URBAN')
pct_pft_1850 = nffun.getvar(surffile_new, 'PCT_NAT_PFT')
if (options.mymodel == 'CLM5'):
pct_crop_1850 = nffun.getvar(surffile_new, 'PCT_CROP')
grazing = nffun.getvar(pftdyn_new, 'GRAZING')
harvest_sh1 = nffun.getvar(pftdyn_new, 'HARVEST_SH1')
harvest_sh2 = nffun.getvar(pftdyn_new, 'HARVEST_SH2')
harvest_sh3 = nffun.getvar(pftdyn_new, 'HARVEST_SH3')
harvest_vh1 = nffun.getvar(pftdyn_new, 'HARVEST_VH1')
harvest_vh2 = nffun.getvar(pftdyn_new, 'HARVEST_VH2')
#read file for site-specific PFT information
dynexist = False
mypft_frac=[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
if (options.surfdata_grid == False and options.site != ''):
AFdatareader = csv.reader(open(ccsm_input+'/lnd/clm2/PTCLM/'+options.sitegroup+'_pftdata.txt','r'))
for row in AFdatareader:
#print(row[0], row[1], options.site)
if row[0] == options.site:
for thispft in range(0,5):
mypft_frac[int(row[2+2*thispft])]=float(row[1+2*thispft])
if (os.path.exists(ccsm_input+'/lnd/clm2/PTCLM/'+options.site+'_dynpftdata.txt')):
dynexist = True
DYdatareader = csv.reader(open(ccsm_input+'/lnd/clm2/PTCLM/'+options.site+'_dynpftdata.txt','r'))
dim = (19,200)
pftdata = numpy.zeros(dim)
for row in DYdatareader:
if row[0] == '1850':
nrows=1
for i in range(0,19):
pftdata[i][0] = float(row[i])
elif row[0] != 'trans_year':
nrows += 1
for i in range(0,19):
pftdata[i][nrows-1] = float(row[i])
else:
print('Warning: Dynamic pft file for site '+options.site+' does not exist')
print('Using constant 1850 values')
landfrac_pft[0][0] = 1.0
pftdata_mask[0][0] = 1
if (options.site != ''):
longxy[0][0] = lon[n]
latixy[0][0] = lat[n]
area[0][0] = 111.2*resy*111.321*math.cos((lat[n]*resx)*math.pi/180)*resx
elif (options.point_area_km2 != None):
longxy[0][0] = lon[n]
latixy[0][0] = lat[n]
area[0] = float(options.point_area_km2)
elif (options.point_area_deg2 != None): # degx X degy (NOT square radians of area)
longxy[0][0] = lon[n]
latixy[0][0] = lat[n]
side_deg = math.sqrt(float(options.point_area_deg2)) # a square of lat/lon degrees assummed
area[0][0] = 111.2*side_deg*111.321*math.cos((lat[n]*side_deg)*math.pi/180)*side_deg
thisrow = 0
for t in range(0,nyears_landuse):
if (options.surfdata_grid == False):
if (dynexist):
for p in range(0,npft):
pct_pft[t][p][0][0] = 0.
harvest_thisyear = False
if pftdata[0][thisrow+1] == 1850+t:
thisrow = thisrow+1
harvest_thisyear = True
if (t == 0 or pftdata[16][thisrow] == 1):
harvest_thisyear = True
for k in range(0,5):
pct_pft[t][int(pftdata[k*2+2][thisrow])][0][0] = \
pftdata[k*2+1][thisrow]
grazing[t][0][0] = pftdata[17][thisrow]
if (harvest_thisyear):
harvest_sh1[t][0][0] = pftdata[13][thisrow]
harvest_sh2[t][0][0] = pftdata[14][thisrow]
harvest_sh3[t][0][0] = pftdata[15][thisrow]
harvest_vh1[t][0][0] = pftdata[11][thisrow]
harvest_vh2[t][0][0] = pftdata[12][thisrow]
else:
harvest_sh1[t][0][0] = 0.
harvest_sh2[t][0][0] = 0.
harvest_sh3[t][0][0] = 0.
harvest_vh1[t][0][0] = 0.
harvest_vh2[t][0][0] = 0.
else:
for p in range(0,npft):
if (sum(mypft_frac[0:16]) == 0.0):
#No dyn file - use 1850 values from gridded file
pct_pft[t][p][0][0] = pct_pft_1850[p][n]
else:
#Use specified 1850 values
pct_pft[t][p][0][0] = mypft_frac[p]
grazing[t][0][0] = 0.
harvest_sh1[t][0][0] = 0.
harvest_sh2[t][0][0] = 0.
harvest_sh3[t][0][0] = 0.
harvest_vh1[t][0][0] = 0.
harvest_vh2[t][0][0] = 0.
#
# multiple natural PFTs' pct are read-in from a nc file
if(options.usersurfnc!='none' and ('PCT_PFT' in mysurfvar or 'PCT_NAT_PFT' in mysurfvar)):
print('Message: PCT_NAT_PFT is extracted from a non-dynamical surface data FOR surfdata.pftdyn.nc')
sum_nat=numpy.sum(pct_pft[t,:,0,0]) # this is the original, saved for use later
if ('PCT_PFT' in point_mysurf.keys()):
if(numpy.sum(point_mysurf['PCT_PFT'][n])>0.0):
pct_pft[t,:,0,0] = point_mysurf['PCT_PFT'][n]
elif('PCT_NAT_PFT' in point_mysurf.keys()):
if(numpy.sum(point_mysurf['PCT_NAT_PFT'][n])>0.0):
pct_pft[t,:,0,0] = point_mysurf['PCT_NAT_PFT'][n]
else:
print('Error: PCT_PFT or PCT_NAT_PFT is used variable name for PFT fraction in non-dynamical surface data')
sys.exit()
# in case new PCT not summed to 100.0
sum_nat2=numpy.sum(pct_pft[t,:,0,0]) # this is the updated above
if (sum_nat2!=100.0):
adj=100.0/sum_nat2
pct_pft[t,:,0,0] = pct_pft[t,:,0,0] * adj
if (sum_nat<100.0):
pct_pft[t,:,0,0] = pct_pft[t,:,0,0]*sum_nat/100.0
if(numpy.sum(pct_pft[t,:,0,0])!=sum_nat):
# this is rare to occur, after TWO corrections above,
# seems due to numerical error relevant to machine
# have to fix it if any (will throw error when used by ELM)
err=sum_nat - numpy.sum(pct_pft[t,:,0,0])
err_ix=numpy.argmax(pct_pft[t,:,0,0])
pct_pft[t,err_ix,0,0]=pct_pft[t,err_ix,0,0]+err
else:
#use time-varying files from gridded file
#print('using '+surffile_new+' for 1850 information') # too much printing if long list points
nonpft = float(pct_lake_1850[n]+pct_glacier_1850[n]+ \
pct_wetland_1850[n]+sum(pct_urban_1850[0:3,n]))
if (options.mymodel == 'CLM5'):
nonpft = nonpft+float(pct_crop_1850[n])
sumpft = 0.0
pct_pft_temp = pct_pft
for p in range(0,npft):
sumpft = sumpft + pct_pft_temp[t][p][0][0]
for p in range(0,npft):
if (t == 0):
#Force 1850 values to surface data file
pct_pft[t][p][0][0] = pct_pft_1850[p][n]
else:
#Scale time-varying values to non-pft fraction
#which might not agree with 1850 values
#WARNING: - large errors may result if files are inconsistent
pct_pft[t][p][0][0] = pct_pft[t][p][0][0]/sumpft*(100.0) #-nonpft)
ierr = nffun.putvar(pftdyn_new, 'LANDFRAC_PFT', landfrac)
ierr = nffun.putvar(pftdyn_new, 'PFTDATA_MASK', pftdata_mask)
ierr = nffun.putvar(pftdyn_new, 'LONGXY', longxy)
ierr = nffun.putvar(pftdyn_new, 'LATIXY', latixy)
ierr = nffun.putvar(pftdyn_new, 'AREA', area)
ierr = nffun.putvar(pftdyn_new, 'PCT_NAT_PFT', pct_pft)
ierr = nffun.putvar(pftdyn_new, 'GRAZING', grazing)
ierr = nffun.putvar(pftdyn_new, 'HARVEST_SH1', harvest_sh1)
ierr = nffun.putvar(pftdyn_new, 'HARVEST_SH2', harvest_sh2)
ierr = nffun.putvar(pftdyn_new, 'HARVEST_SH3', harvest_sh3)
ierr = nffun.putvar(pftdyn_new, 'HARVEST_VH1', harvest_vh1)
ierr = nffun.putvar(pftdyn_new, 'HARVEST_VH2', harvest_vh2)
pftdyn_old = pftdyn_new
pftdyn_new = './temp/surfdata.pftdyn.nc'
if (os.path.isfile(pftdyn_new)):
print('Warning: Removing existing pftdyn data file')
os.system('rm -rf '+pftdyn_new)
if (n_grids > 1):
#ios.system('ncecat -h '+pftdyn_list+' '+pftdyn_new) # not works with too long '_list'
ierr = os.system('find ./temp/ -name "'+pftdyn_tmp+ \
'" | xargs ls | sort | ncecat -O -h -o'+pftdyn_new)
if(ierr!=0): raise RuntimeError('Error: ncecat '); #os.sys.exit()
#os.system('rm ./temp/surfdata.pftdyn?????.nc*') # 'rm' not works for too long file list
os.system('find ./temp/ -name "'+pftdyn_tmp+'" -exec rm {} \;')