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ensemble_copy.py
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ensemble_copy.py
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#!/usr/bin/env python
import netcdf4_functions as nffun
import os, sys, csv, time, math, numpy
from optparse import OptionParser
#Create, run and process a CLM/ALM model ensemble member
# given specified case and parameters (see parm_list and parm_data files)
# Parent case must be pre-built and all namelists in run directory.
# Post-processing calcuates normalized sum of squared errors (SSE) given
# data constraints specified in "constraints" directory"
# DMRicciuto 12/1/2015
#
# Note: This will only work for single-point CLM/ALM compiled with MPI_SERIAL
#-------------------Parse options-----------------------------------------------
parser = OptionParser()
parser.add_option("--runroot", dest="runroot", default="../../run", \
help="Directory where the run would be created")
parser.add_option("--ens_num", dest="ens_num", default=1, \
help="Ensemble member number")
parser.add_option("--case", dest="casename", default="", \
help="Name of case")
parser.add_option("--ens_file", dest="ens_file", default="", \
help="Name of samples file")
parser.add_option("--parm_list", dest="parm_list", default='parm_list', \
help = 'File containing list of parameters to vary')
parser.add_option("--cnp", dest="cnp", default = False, action="store_true", \
help = 'CNP mode - initialize P pools')
parser.add_option("--site", dest="site", default='parm_list', \
help = 'Site name')
parser.add_option('--model_name', dest='model_name', default="clm2", \
help='Model name used in restart file (clm2 or elm)')
(options, args) = parser.parse_args()
parm_names=[]
parm_indices=[]
parm_values=[]
myinput = open(options.parm_list, 'r')
casename = options.casename
# get parameter names and PFT information
pnum=0
for s in myinput:
pdata = s.split()
parm_names.append(pdata[0])
if (pdata[0] == 'co2'):
pnum_co2 = pnum
if (len(pdata) == 3):
parm_indices.append(-1)
else:
parm_indices.append(int(pdata[1]))
pnum=pnum+1
myinput.close()
# get parameter values
if (options.ens_file == ''):
myinput = open('./parm_data', 'r')
for s in myinput:
parm_values.append(float(s))
myinput.close()
os.system('rm ./parm_data')
else:
myinput = open(options.ens_file, 'r')
linenum = 1
for s in myinput:
if (int(options.ens_num) == linenum):
parm_values_str = s.split()
for v in parm_values_str:
parm_values.append(float(v))
linenum = linenum+1
myinput.close()
n_parameters = len(parm_names)
gst=str(100000+int(options.ens_num))
# create ensemble directory from original case
est = str(100000+int(options.ens_num))
orig_dir = str(os.path.abspath(options.runroot)+'/'+casename+'/run')
ens_dir = os.path.abspath(options.runroot)+'/UQ/'+casename+'/g'+gst[1:]
os.system('mkdir -p '+options.runroot+'/UQ/'+casename+'/g'+gst[1:]+'/timing/checkpoints')
os.system('cp '+orig_dir+'/*_in* '+ens_dir)
os.system('cp '+orig_dir+'/*nml '+ens_dir)
if (not ('CB' in casename)):
os.system('cp '+orig_dir+'/*stream* '+ens_dir)
os.system('cp '+orig_dir+'/*.rc '+ens_dir)
os.system('cp '+orig_dir+'/surf*.nc '+ens_dir)
os.system('cp '+orig_dir+'/domain*.nc '+ens_dir)
os.system('cp '+orig_dir+'/*para*.nc '+ens_dir)
# loop through all filenames, change directories in namelists, change parameter values
for f in os.listdir(ens_dir):
if (os.path.isfile(ens_dir+'/'+f) and (f[-2:] == 'in' or f[-3:] == 'nml' or 'streams' in f)):
myinput=open(ens_dir+'/'+f)
myoutput=open(ens_dir+'/'+f+'.tmp','w')
for s in myinput:
if ('fates_paramfile' in s):
paramfile_orig = ((s.split()[2]).strip("'"))
if (paramfile_orig[0:2] == './'):
paramfile_orig = orig_dir+'/'+paramfile_orig[2:]
paramfile_new = ens_dir+'/fates_params_'+est[1:]+'.nc'
os.system('cp '+paramfile_orig+' '+paramfile_new)
os.system('nccopy -3 '+paramfile_new+' '+paramfile_new+'_tmp')
os.system('mv '+paramfile_new+'_tmp '+paramfile_new)
myoutput.write(" fates_paramfile = '"+paramfile_new+"'\n")
fates_paramfile = ens_dir+'/fates_params_'+est[1:]+'.nc'
elif ('paramfile' in s):
paramfile_orig = ((s.split()[2]).strip("'"))
if (paramfile_orig[0:2] == './'):
paramfile_orig = orig_dir+'/'+paramfile_orig[2:]
paramfile_new = ens_dir+'/clm_params_'+est[1:]+'.nc'
os.system('cp '+paramfile_orig+' '+paramfile_new)
os.system('nccopy -3 '+paramfile_new+' '+paramfile_new+'_tmp')
os.system('mv '+paramfile_new+'_tmp '+paramfile_new)
myoutput.write(" paramfile = '"+paramfile_new+"'\n")
pftfile = ens_dir+'/clm_params_'+est[1:]+'.nc'
elif ('ppmv' in s and 'co2' in parm_names):
myoutput.write(" co2_ppmv = "+str(parm_values[pnum_co2])+'\n')
elif ('fsoilordercon' in s):
CNPfile_orig = ((s.split()[2]).strip("'"))
if (CNPfile_orig[0:2] == './'):
CNPfile_orig = orig_dir+'/'+CNPfile_orig[2:]
CNPfile_new = ens_dir+'/CNP_parameters_'+est[1:]+'.nc'
os.system('cp '+CNPfile_orig+' '+CNPfile_new)
os.system('nccopy -3 '+CNPfile_new+' '+CNPfile_new+'_tmp')
os.system('mv '+CNPfile_new+'_tmp '+CNPfile_new)
myoutput.write(" fsoilordercon = '"+CNPfile_new+"'\n")
CNPfile = ens_dir+'/CNP_parameters_'+est[1:]+'.nc'
elif ('fsurdat =' in s):
surffile_orig = ((s.split()[2]).strip("'"))
if (surffile_orig[0:2] == './'):
surffile_orig = orig_dir+'/'+surffile_orig[2:]
surffile_new = ens_dir+'/surfdata_'+est[1:]+'.nc'
os.system('cp '+surffile_orig+' '+surffile_new)
os.system('nccopy -3 '+surffile_new+' '+surffile_new+'_tmp')
os.system('mv '+surffile_new+'_tmp '+surffile_new)
myoutput.write(" fsurdat = '"+surffile_new+"'\n")
surffile = ens_dir+'/surfdata_'+est[1:]+'.nc'
elif ('finidat = ' in s):
finidat_file_orig = ((s.split()[2]).strip("'"))
if (finidat_file_orig.strip() != ''):
finidat_file_new = ens_dir+'/'+(finidat_file_orig.split('/')[-1:])[0]
if (finidat_file_orig[0:2] == './'):
finidat_file_orig = orig_dir+'/'+finidat_file_orig[2:]
#get finidat files from previous ensemble cases if available
if (('1850' in casename or 'CROP' in casename) and not ('ad_spinup' in casename) and not \
('trans' in casename or '20TR' in casename)):
finidat_file_path = os.path.abspath(options.runroot)+'/UQ/'+casename.replace('1850CNP','1850CN')+'_ad_spinup/g'+gst[1:]
if (os.path.exists(finidat_file_path)):
finidat_file_orig = finidat_file_path+'/*.'+options.model_name+'.r.*.nc'
os.system('python adjust_restart.py --rundir '+finidat_file_path+' --casename '+ \
casename.replace('1850CNP','1850CN')+'_ad_spinup')
if ('20TR' in casename):
if ( not ('CO2' in casename)):
finidat_file_path = os.path.abspath(options.runroot)+'/UQ/'+casename.replace('20TR','1850')+ \
'/g'+gst[1:]
if (os.path.exists(finidat_file_path)):
finidat_file_orig = finidat_file_path+'/*.'+options.model_name+'.r.*.nc'
os.system('rm '+finidat_file_path+'/*ad_spinup*.'+options.model_name+'.r.*.nc')
else:
finidat_file_path = os.path.abspath(options.runroot)+'/UQ/'+casename[:-5]+ \
'/g'+gst[1:]
if (os.path.exists(finidat_file_path)):
finidat_file_orig = finidat_file_path+'/*.'+options.model_name+'.r.*.nc'
os.system('rm '+finidat_file_path+'/*1850*.'+options.model_name+'.r.*.nc')
if ('trans' in casename):
finidat_file_path = os.path.abspath(options.runroot)+'/UQ/'+casename.replace('_trans','')+ \
'/g'+gst[1:]
if (os.path.exists(finidat_file_path)):
finidat_file_orig = finidat_file_path+'/*.'+options.model_name+'.r.*.nc'
os.system('rm '+finidat_file_path+'/*ad_spinup*.'+options.model_name+'.r.*.nc')
os.system('cp '+finidat_file_orig+' '+finidat_file_new)
myoutput.write(" finidat = '"+finidat_file_new+"'\n")
else:
myoutput.write(s)
elif ('logfile =' in s):
os.system('date +%y%m%d-%H%M%S > mytime'+str(options.ens_num))
mytinput=open('./mytime'+str(options.ens_num),'r')
for st in mytinput:
timestr = st.strip()
mytinput.close()
os.system('rm mytime'+str(options.ens_num))
myoutput.write(s.replace('`date +%y%m%d-%H%M%S`',timestr))
else:
myoutput.write(s.replace(orig_dir,ens_dir))
myoutput.close()
myinput.close()
os.system(' mv '+ens_dir+'/'+f+'.tmp '+ens_dir+'/'+f)
pnum = 0
CNP_parms = ['ks_sorption', 'r_desorp', 'r_weather', 'r_adsorp', 'k_s1_biochem', 'smax', 'k_s3_biochem', \
'r_occlude', 'k_s4_biochem', 'k_s2_biochem']
fates_seed_zeroed=[False,False]
for p in parm_names:
if ('INI' in p):
if ('BGC' in casename):
scalevars = ['soil3c_vr','soil3n_vr','soil3p_vr']
else:
scalevars = ['soil4c_vr','soil4n_vr','soil4p_vr']
sumvars = ['totsomc','totsomp','totcolc','totcoln','totcolp']
for v in scalevars:
myvar = nffun.getvar(finidat_file_new, v)
myvar = parm_values[pnum] * myvar
ierr = nffun.putvar(finidat_file_new, v, myvar)
elif (p == 'lai'):
myfile = surffile
param = nffun.getvar(myfile, 'MONTHLY_LAI')
param[:,:,:,:] = parm_values[pnum]
ierr = nffun.putvar(myfile, 'MONTHLY_LAI', param)
elif (p != 'co2'):
if (p in CNP_parms):
myfile= CNPfile
elif ('fates' in p):
myfile = fates_paramfile
else:
myfile = pftfile
param = nffun.getvar(myfile,p)
if (('fates_prt' in p and 'stoich' in p) or ('fates_turnover' in p and 'retrans' in p)):
#this is a 2D parameter.
param[parm_indices[pnum] % 12 , parm_indices[pnum] / 12] = parm_values[pnum]
param[parm_indices[pnum] % 12 , parm_indices[pnum] / 12] = parm_values[pnum]
elif ('fates_hydr_p50_node' in p or 'fates_hydr_avuln_node' in p or 'fates_hydr_kmax_node' in p or \
'fates_hydr_pitlp_node' in p or 'fates_hydr_thetas_node' in p):
param[parm_indices[pnum] / 12 , parm_indices[pnum] % 12] = parm_values[pnum]
param[parm_indices[pnum] / 12 , parm_indices[pnum] % 12] = parm_values[pnum]
elif ('fates_leaf_long' in p or 'fates_leaf_vcmax25top' in p):
param[0,parm_indices[pnum]] = parm_values[pnum]
#elif (p == 'fates_seed_alloc'):
# if (not fates_seed_zeroed[0]):
# param[:]=0.
# fates_seed_zeroed[0]=True
# param[parm_indices[pnum]] = parm_values[pnum]
#elif (p == 'fates_seed_alloc_mature'):
# if (not fates_seed_zeroed[1]):
# param[:]=0.
# fates_seed_zeroed[1]=True
# param[parm_indices[pnum]] = parm_values[pnum]
elif (p == 'dayl_scaling' or p == 'vcmaxse'):
os.system('ncap2 -O -s "'+p+' = flnr" '+myfile+' '+myfile)
print('Creting netcdf variable for '+p)
param = nffun.getvar(myfile,'flnr')
param[:] = parm_values[pnum]
elif (p == 'psi50'):
param[:,parm_indices[pnum]] = parm_values[pnum]
elif (parm_indices[pnum] > 0):
param[parm_indices[pnum]] = parm_values[pnum]
elif (parm_indices[pnum] == 0):
try:
param[:] = parm_values[pnum]
except:
param = parm_values[pnum]
ierr = nffun.putvar(myfile, p, param)
#if ('fr_flig' in p):
# param=nffun.getvar(myfile, 'fr_fcel')
# param[parm_indices[pnum]]=1.0-parm_values[pnum]-parm_values[pnum-1]
# ierr = nffun.putvar(myfile, 'fr_fcel', param)
pnum = pnum+1
#ensure FATES seed allocation paramters sum to one
#if (fates_seed_zeroed[0]):
# param = nffun.getvar(myfile,'fates_seed_alloc')
# param2 = nffun.getvar(myfile,'fates_seed_alloc_mature')
# for i in range(0,12):
# if (param[i] + param2[i] > 1.0):
# sumparam= param[i]+param2[i]
# param[i] = param[i]/sumparam
# param2[i] = param2[i]/sumparam
# ierr = nffun.putvar(myfile, 'fates_seed_alloc', param)
# ierr = nffun.putvar(myfile, 'fates_seed_alloc_mature', param2)
### END ###