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Commit ead46230 authored by ivar's avatar ivar
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latest revisions from ivar. fixed scalefac alignment and added log statements

parent db708dbc
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da/stilt/stilt.co2.simu.2015.Sep.bc.r
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......@@ -24,7 +24,7 @@ procs= as.integer(args[1])
#inputs and outputs
stiltfile = paste("stilt_",procs,".rc", sep="")
curdir="/Storage/CO2/wei/ctdas-stilt-cofiltered-bioSiBCASA-bcCTNA-bcaircraft-fixedstilt/exec/da/stilt/"
curdir="TYPE PATH HERE/exec/da/stilt/"
fn=paste(curdir, stiltfile,sep="")
conf=as.matrix(read.table(fn,header=FALSE))
......@@ -166,10 +166,13 @@ for(yy in 1:length(uyr))
# read needed event ids from sample_coordinates files
ncf <- nc_open(paste(samdir,"sample_coordinates_",tb2,"00","_",tb3,"00","-",procs,".nc",sep=""))
eventidarr <- ncvar_get(ncf,"obs_num")
obs_id <- ncvar_get(ncf,"obs_id")
# filter before loop
pfbfns=NULL
fn=NULL
eventids=NULL
obsids=NULL
for(mm in 1:length(fns))
{
......@@ -179,6 +182,8 @@ for(mm in 1:length(fns))
if(eid==eventidarr[i])
{
pfbfns = c(pfbfns,fns[mm])
obsids = c(obsids,obs_id[i])
eventids = c(eventids,eventidarr[i])
break
}
}
......@@ -213,6 +218,8 @@ for(mm in 1:length(pfbfns))
#--------------------------------------------
# STEP 1: Read footprints
#--------------------------------------------
flog.info('obsids: %s',obsids[mm], name='logger.b')
flog.info('eventids: %s',eventids[mm], name='logger.b') #June 23
yr=substring(pfbfns[mm],6,9)
mo=substring(pfbfns[mm],11,12)
fn=paste(footpdir,yr,"/",mo,"/",pfbfns[mm],sep="")
......@@ -389,6 +396,7 @@ for(mm in 1:length(pfbfns))
gpp[d,,,]=biof$gpp
rec[d,,,]=biof$resp
remove(list=c("biof"))
flog.info('d: %s, yr: %s, mn: %s, dy: %s',d,yr,mn,dy,name='logger.b')
}
#flog.info("mean gpp= %f", mean(gpp[d,,,]), name='logger.b')
......@@ -478,6 +486,7 @@ for(mm in 1:length(pfbfns))
{
gppflux[,,ntimes-hh+1]=gpp[inxd,52:117,113:152,inxh]
recflux[,,ntimes-hh+1]=rec[inxd,52:117,113:152,inxh]
flog.info('gppflux: %s, gpp: %s, %s, %s, %s',gppflux[30,30,ntimes-hh+1],gpp[inxd,82,143,inxh],ntimes-hh+1,inxd,inxh,name='logger.b')
}
if(bioflux_flag == "CT_OPT")
......@@ -519,23 +528,50 @@ for(mm in 1:length(pfbfns))
#print("XXXdateall")
#print(dateall) #reversed order
# note: ixflux should not be from 1:ntimes, should be more accurate in hours
#dd=as.character(min(yy))
dd=as.character(xx)
#yrlist=substring(dd,1,4)
#monlist=substring(dd,6,7)
#daylist=substring(dd,9,10)
hr=substring(dd,12,13)
mi=substring(dd,15,16)
n = 24-floor(as.numeric(hr) + as.numeric(mi)/60)
print("XXXn")
print(n)
datevalid=dateall[1]+0.5*3600-(0:(ntimes-1))*3600
#ixflux=(1:ntimes)[(datevalid<=xx)][1:endtime] #time backward
ixflux=(1:ntimes)[(datevalid<=xx)][n:(endtime+n-1)]
print(ixflux)
# # note: ixflux should not be from 1:ntimes, should be more accurate in hours
# dd=as.character(min(yy))
# #yrlist=substring(dd,1,4)
# #monlist=substring(dd,6,7)
# #daylist=substring(dd,9,10)
# hr=substring(dd,12,13)
# mi=substring(dd,15,16)
# n = floor(as.numeric(hr) + as.numeric(mi)/60)
# n = 24-n
# print("XXXn")
# print(n)
# datevalid=dateall[1]+0.5*3600-(0:(ntimes-1))*3600
# #ixflux=(1:ntimes)[(datevalid<=xx)][1:endtime] #time backward
# #ixflux=(ntimes:1)[(datevalid<=xx)][(endtime+n-1):n]
# #ixflux=(ntimes:1)[(datevalid<=xx)][(endtime+n-1):(n)]
# ixflux<-c(n:endtime+n-1)
## ixflux=(1:ntimes)[(datevalid<=xx)][n:(endtime+n-1)]
#dd=as.character(min(yy))
dd=as.character(xx)
#yrlist=substring(dd,1,4)
#monlist=substring(dd,6,7)
#daylist=substring(dd,9,10)
hr=substring(dd,12,13)
mi=substring(dd,15,16)
n = 24-floor(as.numeric(hr) + as.numeric(mi)/60)
print("XXXn")
print(n)
datevalid=dateall[1]+0.5*3600-(0:(ntimes-1))*3600
#ixflux=(1:ntimes)[(datevalid<=xx)][1:endtime] #time backward
#ixflux=(1:ntimes)[(datevalid<=xx)][1:(endtime+n)]
ixflux <-array(n:(endtime+n-1),dim=c(240))
flog.info('ixflux endtime: %s,%s,%s',endtime,n,as.numeric(hr)+(as.numeric(hr)/60),name='logger.b')
for (ttt in 1:240)
flog.info('ixflux: %s,%s',ttt,ixflux[ttt],name='logger.b')
if(bioflux_flag == "SiB3") #footprint is backward
{
gpptmp=foot*gppflux[,,ixflux]
......@@ -571,30 +607,33 @@ for(mm in 1:length(pfbfns))
{
if(xxleft<b2) #flux with scaling factors located in first lag
{
diff=abs(as.numeric(difftime(b2,xxleft,units='hours')))
diff=abs(as.numeric(difftime(b2,xxleft,units='hours')))+24
#if(bioflux_flag == "SiBCASA" || bioflux_flag == "CT_OPT")
# diff = diff/3.0
diff=ceiling(diff)
align=24*ceiling((ntimes-diff)/24)#-(ntimes-diff)
if (i==1)
flog.info('diff: %s, align: %s',diff,align,name='logger.b')
#if(ident=="2010x01x22x19x27x40.0500Nx105.0040Wx00300")
# flog.info("after diff = %f", diff, name='logger.b')
for (hh in 1:(ntimes-diff))
if(hh<=ntimes-diff && hh>=1)
for (hh in 1:(align))
if(hh<=align && hh>=1)
{
#if(i==1 && ident=="2010x01x22x19x27x40.0500Nx105.0040Wx00300")
# flog.info("neeflux[,,hh]=%f, scalefacarr1 = %f ",neeflux[,,hh], scalefacarr1[,,i], name='logger.b')
if(i==1)
flog.info("hh: %s, neeflux[,,hh]=%f, scalefacarr2 = %f ",hh, neeflux[30,30,hh], scalefacarr2[30,30,i], name='logger.b')
neeflux1[,,hh] = neeflux[,,hh]*(scalefacarr2[,,i]) #delete "t" transform
bc1[hh] = scalefacarr_bc2[i]
}
for (hh in ( (ntimes-diff+1):ntimes ) )
if(hh<=ntimes && hh>=ntimes-diff+1)
for (hh in ( (align+1):ntimes ) )
if(hh<=ntimes && hh>=align+1)
{
#if(i==1 && ident=="2010x01x22x19x27x40.0500Nx105.0040Wx00300")
# flog.info("neeflux[,,hh]=%f, scalefacarr2 = %f",neeflux[,,hh], scalefacarr2[,,i],name='logger.b')
if(i==1)
flog.info("hh: %s, neeflux[,,hh]=%f, scalefacarr1 = %f",hh, neeflux[30,30,hh], scalefacarr1[30,30,i],name='logger.b')
neeflux1[,,hh] = neeflux[,,hh]*(scalefacarr1[,,i])
bc1[hh] = scalefacarr_bc1[i]
}
......@@ -630,8 +669,10 @@ for(mm in 1:length(pfbfns))
for(i in 1:nsam)
{
neetmp=foot*neefluxarr[,,ixflux,i]
#if(ident=="2010x01x22x19x27x40.0500Nx105.0040Wx00300")
# flog.info("neetmp = %f",neetmp, name='logger.b')
neetmp2=foot*neefluxarr[,,6:245,i]
if(i==1)
flog.info("neetmp = %f, %f",sum(neetmp,na.rm=TRUE), sum(neetmp2,na.rm=TRUE),name='logger.b')
neeout=sum(neetmp,na.rm=TRUE)
neeoutarr[i]=neeout
......@@ -673,6 +714,7 @@ for(mm in 1:length(pfbfns))
bioout=sum(biotmp,na.rm=TRUE)
}
foot2=foot
remove(list=c("ocnflux","fosflux","firflux","ocntmp","fostmp","firtmp","foot","dateall"))
gc()
......@@ -767,6 +809,9 @@ for(mm in 1:length(pfbfns))
print("hpos")
print(hpos)
flog.info('p3:, %s, pbou: %s, dy: %s, i: %s, j: %s, k: %s, hpos: %s',p,pbou,dy,i,j,k,hpos,name='logger.b')
tt=bouarr[dy,i,j,k,hpos] #notice bouarr not be reversed
if(length(tt)==1) #why sometimes we get a unnormal array?
......@@ -820,12 +865,46 @@ for(mm in 1:length(pfbfns))
fsimuarr[i]=(fbou+bcoutarr[i]+deltaco2)*1e-6
#fsimuarr[i]=(fbouarr[i]+deltaco2)*1e-6
#if(ident=="2010x01x22x19x27x40.0500Nx105.0040Wx00300")
# flog.info("fsimuarr[i] = %f",fsimuarr[i], name='logger.b')
if(i==1)
flog.info("fsimuarr[i] = %f, fbou = %f, neeoutarr[i] = %f, bcoutarr[i] = %f",fsimuarr[i]*1e6,fbou, neeoutarr[i],bcoutarr[i], name='logger.b')
outlist<-c(outlist, fsimuarr[i])
}
# if (eventids[mm] ==289997 || eventids[mm] ==300326)
# {
# output_fname=paste("/Storage/ivar/run_test_allsites_bcopt_stiltout_wei/exec","/","lefdata_",eventids[mm],".nc",sep="")
#
# if (file.exists(output_fname)== FALSE)
#
# {
#
# xdim <- ncdim_def( 'Lon', 'degree', 1:ncol2 )
# ydim <- ncdim_def( 'Lat', 'degree', 1:nrow2 )
# timedim <- ncdim_def( 'time', 'degree', 1:240 )
# ensdim <- ncdim_def( 'ensemble', 'degree', 1:100 )
#
#
#
# mv <- 0 # missing value
# var_nee <- ncvar_def( name="nee", units="-", dim=list(xdim,ydim,timedim,ensdim), longname="nee",missval=mv )
# var_neeco2 <- ncvar_def( name="neeco2", units="-", dim=list(ensdim), longname="neeco2",missval=mv )
# var_foot <- ncvar_def( name="foot", units="-", dim=list(xdim,ydim,timedim), longname="foot",missval=mv )
#
#
# ncid_new <- nc_create( output_fname, list(var_nee,var_neeco2,var_foot))
# ncvar_put( ncid_new,var_nee, neefluxarr, start=c(1,1,1,1), count=c(ncol2,nrow2,240,100))
# ncvar_put( ncid_new,var_neeco2, neeoutarr, start=c(1), count=c(100))
# ncvar_put( ncid_new,var_foot, foot2, start=c(1,1,1), count=c(ncol2,nrow2,240))
#
# nc_close( ncid_new )
#
# }
# }
#add component varibles:gpp,reco,ocn,fos,fir,boundary
#outlist<-c(outlist,gppout,recoout,ocnout,fosout,firout,fbou,bioout)
if(bioflux_flag == "SiB3" || bioflux_flag == "SiBCASA")
......
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