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Commit 262b4c9c authored by brunner's avatar brunner
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da/cosmo/observationoperator.py
View file @ 262b4c9c
......@@ -55,8 +55,8 @@ class ObservationOperator(object):
self.simulated_file = os.path.join(self.outputdir, 'samples_simulated.%s.nc' % self.dacycle['time.sample.stamp'])
self.forecast_nmembers = int(self.dacycle['da.optimizer.nmembers'])
def run(self,lag,dacycle):
def run(self,lag,dacycle,statevector):
members = statevector.ensemble_members[lag]
absolute_start_time = str((to_datetime(dacycle['abs.time.start'])).strftime('%Y-%m-%d'))
starth = abs((to_datetime(dacycle['abs.time.start'])-dacycle['time.start']).days)*24
endh = abs((to_datetime(dacycle['abs.time.start'])-dacycle['time.finish']).days)*24
......@@ -126,11 +126,18 @@ class ObservationOperator(object):
for dt in rrule.rrule(rrule.HOURLY, dtstart=dacycle['time.start']+timedelta(hours=24*lag*int(dacycle['time.cycle'])), until=dacycle['time.start']+timedelta(hours=(lag+1)*24*int(dacycle['time.cycle']))):
logging.info('Multiplying emissions with parameters for lag %d, date %s' % (lag, dt.strftime('%Y%m%d%H')))
for ens in range(0,self.forecast_nmembers):
dthh = dt.strftime('%H')
co2_bg=str((members[ens].param_values[-1]))
ens = str(ens).zfill(3)
cdo.setunit("'kg m-2 s-1' -expr,GPP_"+ens+"_F=CO2_GPP_F*parametermap -merge "+os.path.join(dacycle['da.bio.input'], 'gpp_%s.nc' % dt.strftime('%Y%m%d%H')), input = os.path.join(dacycle['restartmap.dir'],"parameters_gpp_lag"+str(lag)+"."+ens+".nc"), output = os.path.join(dacycle['da.bio.input'], 'ensemble', "gpp_"+ens+"_%s.nc" % dt.strftime('%Y%m%d%H')))
cdo.setunit("'kg m-2 s-1' -expr,RESP_"+ens+"_F=CO2_RESP_F*parametermap -merge "+os.path.join(dacycle['da.bio.input'], 'ra_%s.nc' % dt.strftime('%Y%m%d%H')), input = os.path.join(dacycle['restartmap.dir'],"parameters_resp_lag"+str(lag)+"."+ens+".nc"), output = os.path.join(dacycle['da.bio.input'], 'ensemble', "ra_"+ens+"_%s.nc" % dt.strftime('%Y%m%d%H')))
if dthh=='00' or dthh=='03' or dthh=='06' or dthh=='09' or dthh=='12' or dthh=='15' or dthh=='18' or dthh=='21':
cdo.setunit("'kg m-2 s-1' -expr,BG_"+ens+"=CO2_BG*"+co2_bg+" -merge "+os.path.join(dacycle['da.bg.input'], 'ct_%s.nc' % dt.strftime('%Y%m%d%H')), output = os.path.join(dacycle['da.bg.input'], 'ensemble', "ct_"+ens+"_%s.nc" % dt.strftime('%Y%m%d%H')))
cdo.merge(input = os.path.join(dacycle['da.bio.input'], 'ensemble', "gpp_???_%s.nc" % dt.strftime('%Y%m%d%H')), output = os.path.join(dacycle['da.bio.input'], 'ensemble', "gpp_%s.nc" % dt.strftime('%Y%m%d%H')))
cdo.merge(input = os.path.join(dacycle['da.bio.input'], 'ensemble', "ra_???_%s.nc" % dt.strftime('%Y%m%d%H')), output = os.path.join(dacycle['da.bio.input'], 'ensemble', "ra_%s.nc" % dt.strftime('%Y%m%d%H')))
if dthh=='00' or dthh=='03' or dthh=='06' or dthh=='09' or dthh=='12' or dthh=='15' or dthh=='18' or dthh=='21':
cdo.merge(input = os.path.join(dacycle['da.bg.input'], 'ensemble', "ct_???_%s.nc" % dt.strftime('%Y%m%d%H')), output = os.path.join(dacycle['da.bg.input'], 'ensemble', "ct_%s.nc" % dt.strftime('%Y%m%d%H')))
os.chdir(dacycle['da.obsoperator.home'])
......@@ -167,9 +174,9 @@ class ObservationOperator(object):
logging.info('ObservationOperator finished successfully, output file written (%s)' % self.simulated_file)
def run_forecast_model(self, lag, dacycle):
def run_forecast_model(self, lag, dacycle, statevector):
self.prepare_run()
self.run(lag, dacycle)
self.run(lag, dacycle, statevector)
def extract_model_data(self,dacycle,hstart,hstop,ensnum):
......@@ -192,7 +199,7 @@ class ObservationOperator(object):
logging.info('Extracting output for ens %s, time %s' % (str(ens),str(dt)))
co2_in_fn = cosmo_out+'lffd'+dt+'.nc'
co2_out_fn = cosmo_out+'CO2_'+ens+'_'+dt+'.nc'
cdo.expr("'CO2=(CO2_BG-GPP_"+ens+"+RESP_"+ens+"+CO2_A_CH+CO2_A)/(1.-QV)'", input = "-selname,QV,CO2_BG,GPP_"+ens+",RESP_"+ens+",CO2_A_CH,CO2_A "+co2_in_fn, output = co2_out_fn)
cdo.expr("'CO2=(BG_"+ens+"-GPP_"+ens+"+RESP_"+ens+"+CO2_A_CH+CO2_A)/(1.-QV)'", input = "-selname,QV,BG_"+ens+",GPP_"+ens+",RESP_"+ens+",CO2_A_CH,CO2_A "+co2_in_fn, output = co2_out_fn)
files2cat.append(co2_out_fn)
cdo.cat(input = files2cat, output = cosmo_out+"CO2_"+ens+"_"+time_stamp+".nc")
......
da/cosmo/pipeline.py
View file @ 262b4c9c
......@@ -336,7 +336,7 @@ def sample_step(dacycle, samples, statevector, obsoperator, lag, advance=False):
# Run the observation operator
obsoperator.run_forecast_model(lag, dacycle)
obsoperator.run_forecast_model(lag, dacycle, statevector)
# Read forecast model samples that were written to NetCDF files by each member. Add them to the exisiting
......
da/cosmo/statevector.py
View file @ 262b4c9c
......@@ -150,7 +150,7 @@ class StateVector(object):
self.nlag = int(dacycle['time.nlag'])
self.nmembers = int(dacycle['da.optimizer.nmembers'])
# self.nparams = int(dacycle.dasystem['nparameters'])
self.nparams = 22
self.nparams = 23
self.nobs = 0
self.obs_to_assimilate = () # empty containter to hold observations to assimilate later on
......@@ -182,7 +182,7 @@ class StateVector(object):
# Create a dictionary for state <-> gridded map conversions
nparams = 22
nparams = 23
#nparams = self.gridmap.max()
self.griddict = {}
for r in range(1, 11):
......@@ -267,7 +267,7 @@ class StateVector(object):
except:
s = np.linalg.svd(covariancematrix, full_matrices=1, compute_uv=0) #Cartesius fix
dof = np.sum(s) ** 2 / sum(s ** 2)
# covariancematrix = np.identity(self.nparams) # pavle - for testing, final matrix will be 22x22
# covariancematrix = np.identity(self.nparams) # pavle - for testing, final matrix will be 23x23
C = np.linalg.cholesky(covariancematrix)
logging.debug('Cholesky decomposition has succeeded ')
......@@ -291,9 +291,9 @@ class StateVector(object):
self.ensemble_members[lag].append(newmember)
# Create members 1:nmembers and add to ensemble_members list
for member in range(1, self.nmembers):
rands = np.random.uniform(low=-1., high=1., size=self.nparams)
rands = np.random.uniform(low=-1., high=1., size=self.nparams-1)
rands_bg = np.random.uniform(low=-0.05., high=0.05., size=1)
# if (member==1):
# rands = np.array([1.836451,1.91572,1.719371,1.947495,1.788597,1.109507,0.9401712,2,0.003201536,1.2276,0])-1.
# elif (member==2):
......@@ -303,11 +303,9 @@ class StateVector(object):
newmember = EnsembleMember(member)
# newmember.param_values = np.concatenate([np.dot(C, rands[0:self.nparams/2]),np.dot(C, rands[self.nparams/2:self.nparams])]) + newmean
newmember.param_values = np.concatenate([np.dot(C, rands[0:11]),np.dot(C, rands[11:22])]) + newmean
#newmember.param_values = np.dot(C, rands) + newmean
newmember.param_values = (np.hstack((np.dot(C, rands[0:11]),np.dot(C, rands[11:22]), rands_bg)) + newmean).ravel()
newmember.param_values[10] = 0.
newmember.param_values[21] = 0.
# newmember.param_values[-1] = 0
newmember.param_values[newmember.param_values<0.] = 0.
self.ensemble_members[lag].append(newmember)
......@@ -501,11 +499,12 @@ class StateVector(object):
# GPP
filename_gpp = os.path.join(outdir, 'parameters_gpp_lag'+str(lag)+'.%03d%s' % (mem.membernumber, endswith))
ncf = io.CT_CDF(filename_gpp, method='create')
dimparams = ncf.add_params_dim(self.nparams//2)
#dimparams = ncf.add_params_dim(self.nparams)
dimparams = ncf.add_params_dim(11)
#dimparams = ncf.add_params_dim((self.nparams-1)//2)
dimgrid = ncf.add_latlon_dim()
data = mem.param_values[0:self.nparams//2]
data = mem.param_values[0:11]
#data = mem.param_values[0:(self.nparams-1)//2]
savedict = io.std_savedict.copy()
savedict['name'] = "parametervalues"
......@@ -531,10 +530,12 @@ class StateVector(object):
# RESP
filename_resp = os.path.join(outdir, 'parameters_resp_lag'+str(lag)+'.%03d%s' % (mem.membernumber, endswith))
ncf = io.CT_CDF(filename_resp, method='create')
dimparams = ncf.add_params_dim(self.nparams//2)
dimparams = ncf.add_params_dim(11)
#dimparams = ncf.add_params_dim((self.nparams-1)//2)
dimgrid = ncf.add_latlon_dim()
data = mem.param_values[self.nparams//2:self.nparams]
data = mem.param_values[11:22]
#data = mem.param_values[(self.nparams-1)//2:self.nparams-1]
savedict = io.std_savedict.copy()
savedict['name'] = "parametervalues"
......@@ -558,6 +559,38 @@ class StateVector(object):
ncf.close()
# BACKGROUND CO2
# filename_bg = os.path.join(outdir, 'parameters_bg_lag'+str(lag)+'.%03d%s' % (mem.membernumber, endswith))
# ncf = io.CT_CDF(filename_bg, method='create')
# dimparams = ncf.add_params_dim(11)
# dimgrid = ncf.add_latlon_dim()
#
# data = mem.param_values[-1]
# data = np.hstack((data, data, data, data, data, data, data, data, data, data, data)).ravel()
#
# savedict = io.std_savedict.copy()
# savedict['name'] = "parametervalues"
# savedict['long_name'] = "parameter_values_for_member_%d" % mem.membernumber
# savedict['units'] = "unitless"
# savedict['dims'] = dimparams
# savedict['values'] = data
# savedict['comment'] = 'These are parameter values to use for member %d' % mem.membernumber
# ncf.add_data(savedict)
#
# griddata = self.vector2grid(vectordata=data)
#
# savedict = io.std_savedict.copy()
# savedict['name'] = "parametermap"
# savedict['long_name'] = "parametermap_for_member_%d" % mem.membernumber
# savedict['units'] = "unitless"
# savedict['dims'] = dimgrid
# savedict['values'] = griddata.tolist()
# savedict['comment'] = 'These are gridded parameter values to use for member %d' % mem.membernumber
# ncf.add_data(savedict)
#
# ncf.close()
#
#
def grid2vector(self, griddata=None, method='avg'):
# not used --pavle
"""
......
template.rc
View file @ 262b4c9c
......@@ -29,19 +29,19 @@
! The time for which to start and end the data assimilation experiment in format YYYY-MM-DD HH:MM:SS
! the following 3 lines are for initial start
!time.start : 2013-04-01 00:00:00
!time.finish : 2013-04-07 23:00:00
!time.end : 2013-04-07 23:00:00
time.start : 2013-04-01 00:00:00
time.finish : 2013-04-07 23:00:00
time.end : 2013-04-07 23:00:00
time.start : 2013-04-08 00:00:00
time.finish : 2013-04-14 23:00:00
time.end : 2013-04-14 23:00:00
!time.start : 2013-04-08 00:00:00
!time.finish : 2013-04-14 23:00:00
!time.end : 2013-04-14 23:00:00
abs.time.start : 2013-04-01 00:00:00
! Whether to restart the CTDAS system from a previous cycle, or to start the sequence fresh. Valid entries are T/F/True/False/TRUE/FALSE
time.restart : T
time.restart : F
da.restart.tstamp : 2013-04-01 00:00:00
! The length of a cycle is given in days, such that the integer 7 denotes the typically used weekly cycle. Valid entries are integers > 1
......@@ -104,6 +104,7 @@ da.obsoperator : cosmo
da.obsoperator.home : /store/empa/em05/parsenov/cosmo_processing_chain
da.bio.input : /store/empa/em05/parsenov/cosmo_input/vprm/processed
da.bg.input : /store/empa/em05/parsenov/cosmo_input/icbc/processed
da.obsoperator.rc : ${da.obsoperator.home}/tm5-ctdas-ei-zoom.rc
!forward.savestate.exceptsam : TRUE
......
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