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pft_inversion.R
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##################################################
#-- Inversion script for PFT-based Harmonic scheme
##################################################
read.input.geos <- function(filename) {
return(readLines(filename))
}
write.input.geos <- function(input.geos.data,
filename) {
writeLines(input.geos.data,con=filename)
}
# remove trailing white space
trim <- function(x) {
return(gsub("[ \t]*$","",x))
}
rtrim <- trim
# remove leading white space
ltrim <- function(x) {
return(gsub("^[ \t]*","",x))
}
locate.key.input.geos <- function(input.geos.data,key,domain=NULL) {
# "domain" is a synonym for "menu". To look for "Output file name"
# within the ObsPack menu (which is capitalized within the
# input.geos file), you should use domain="OBSPACK MENU".
# parentheses cause problems for grep, we need to escape them
key <- gsub('\\(','\\\\(',gsub('\\)','\\\\)',key))
if(is.null(domain)) {
#lx <- grep(sprintf("^%s[[:blank:]]*:",key),input.geos.data)
lx < - grep(paste("*",key,"*",sep=""),input.geos.data)
} else {
lx.dstart <- grep(sprintf('^%%%%%%[[:blank:]]*%s[[:blank:]]*%%%%%%[[:blank:]]:',domain),input.geos.data)
if(length(lx.dstart) == 0) {
stop(sprintf("No such domain \"%s\" in input.geos data (\"input.geos.data\" here).",domain))
}
if(length(lx.dstart) > 1) {
stop(sprintf("%d matches to domain \"%s\" in input.geos data (\"input.geos.data\" here).",length(lx.dstart),domain))
}
# Now we have the location of the domain start. Search forward
# for domain end (the next "%%% * MENU %%%:" text or end-of-file)
nlines.tot <- length(input.geos.data)
lx.dend <- lx.dstart+1
while(TRUE) {
#print(grepl("^%%% .* MENU %%%.*:$",input.geos.data[lx.dend:lx.dend]))
#if(grepl("^%%% .* MENU %%%.*:.*$",input.geos.data[lx.dend:lx.dend])) {
if(grepl("*MENU*:*",input.geos.data[lx.dend:lx.dend])) {
break
}
lx.dend <- lx.dend+1
}
#lx <- lx.dstart-1+grep(sprintf("^%s[[:blank:]]*:",key),input.geos.data[lx.dstart:lx.dend])
lx <- lx.dstart-1+grep(paste("*",key,"*",sep=""),input.geos.data[lx.dstart:lx.dend])
}
if(length(lx)==0) {
stop(sprintf("No such key \"%s\" in input.geos data (\"input.geos.data\" here).",key))
}
if(length(lx)>1) {
stop(sprintf("%d matches to key \"%s\" in input.geos data (\"input.geos.data\" here).",
length(lx),key))
}
return(lx)
}
set.value.input.geos <- function(input.geos.data,key,val) {
lx <- locate.key.input.geos(input.geos.data,key)
# parentheses cause problems for grep, we need to escape them
key <- gsub('\\(','\\\\(',gsub('\\)','\\\\)',key))
# this is fancier that it needs to be, to preserve spacing before colons in input.geos
input.geos.data[lx] <- paste(gsub(sprintf("(^%s[[:blank:]]*:).*",key),"\\1",input.geos.data[lx]),val)
return(input.geos.data)
}
set.value.input.geos2 <- function(input.geos.data,key,val) {
# parentheses cause problems for grep, we need to escape them
key <- gsub('\\(','\\\\(',gsub('\\)','\\\\)',key))
#lx <- grep(input.geos.data,key)
matches = sum(grepl(glob2rx(key),input.geos.data))
if(matches==1)
{
lx = grep(glob2rx(key),input.geos.data)
}else{
print(paste("problem w/ keyword ",matches," matches",sep=""))
stop()
}
input.geos.data[lx] <- paste(strsplit(input.geos.data[lx],":")[[1]][1],": ",val,sep="")
return(input.geos.data)
}
get.value.input.geos <- function(input.geos.data,key,domain=NULL) {
lx <- locate.key.input.geos(input.geos.data,key,domain=domain)
# parentheses cause problems for grep, we need to escape them
key <- gsub('\\(','\\\\(',gsub('\\)','\\\\)',key))
return(trim(ltrim(gsub(sprintf("^%s[[:blank:]]*:",key),"",input.geos.data[lx]))))
}
dir.exists2 = function (paths)
{
x = base::file.info(paths)$isdir
!is.na(x) & x
}
create_dirs = function(baserundir,baseoutdir)
{
mk_subdir=function(dir,x){
if(!dir.exists2(paste(dir,x,sep="/"))){dir.create(paste(dir,x,sep="/"))}
}
mk_subdir(baserundir,"")
mk_subdir(baserundir,"land")
mk_subdir(baserundir,"ocean")
mk_subdir(baserundir,"fossil")
mk_subdir(baserundir,"bg")
mk_subdir(baserundir,"fires")
subdirs = apply(expand.grid(c("land","ocean","fossil","fires","bg"),
c("CO2","oco2","obspack","input.geoses","hemco.configs","restarts","logs","betas")),
1,FUN=function(x){paste(x,collapse="/")})
sapply(subdirs,FUN=function(x){mk_subdir(baserundir,x)})
}
replace_file_string = function(text_vector,line_num,file)
{
text_vector[line_num]= paste(strsplit(singles_file[line_num],":")[[1]][1],": ",file,sep="")
}
fill.pft.input.hemco=function(gppresp=0,sincos=0,harmonic=0,pft=1,tr=1,dates,input.hemco.file)
{
input.data = read.input.geos(input.hemco.file)
input.data = set.value.input.geos2(input.geos.data=input.data,key="GPPRESP",val=gppresp)
input.data = set.value.input.geos2(input.geos.data=input.data,key="SINCOS",val=sincos)
set.value.input.geos2(input.data,key="PFT",val=pft)
set.value.input.geos2(input.data,key="TR",val=tr)
set.value.input.geos2(input.data,key="HARMONIC",val=harmonic)
return(input.data)
}
fill.pft.input.geos=function(gppresp=0,sincos=0,harmonic=0,pft=1,tr=1,input.geos.file)
{
input.data = read.input.geos(input.hemco.file)
input.data =set.value.input.geos2(input.data,key="Start YYYYMMDD, HHMMSS",gppresp)
input.data =set.value.input.geos2(input.data,key="End YYYYMMDD, HHMMSS",sincos)
input.data =set.value.input.geos2(input.data,key="Input restart file",pft)
input.data =set.value.input.geos2(input.data,key="MERRA2",tr)
input.data =set.value.input.geos2(input.data,key="Run directory",harmonic)
return(input.data)
}
create_input_geoses = function(baserundir="/discover/nobackup/aschuh/run.v11_oco2_080117",
baseoutdir = "/discover/nobackup/aschuh/run.v11_oco2_080117/",
template_input_geos="/discover/nobackup/aschuh/inversion_template_files/input.geoses/input.geos.template")
{
#-- FOR LAND
combos.grid = expand.grid(gppresp=0:1,sincos=0:1,harmonic=0:3,pft=1:25,tr=1:11,year=2014:2016)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
input.data.orig = readLines(template_input_geos)
fluxtype = "land"
input.data =set.value.input.geos2(input.geos.data=input.data.orig,key="*Run*directory*",paste(baserundir,"/",fluxtype,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*=>*GEOS-FP*","../MERRA/MERRA.output/GEOS_4x5.d/GEOS_FP/YYYY/MM/")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Transport*Timestep*","30")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Convect*Timestep*","30")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Sat*track*info*","/discover/nobackup/aschuh/run/lite_wbias_20170815_standardized/inv_weight_insitu/oco2.MMDDYYYY.4x5.nc")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*OBSPACK*infile*","/discover/nobackup/aschuh/run/obspack_co2_1_NRT_v3.3_prepped_inputs_2017-04-26_links/flask_input.YYYYMMDD00.nc")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Avg*timeser*file*",paste(baseoutdir,fluxtype,"/CO2/ts_1h_avg.YYYYMMDDhh",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Input*restart*file*","/discover/nobackup/aschuh/inversion_template_files/CO2/restart.2014090600.nc")
#-- Going to need to add options for 4x5 vs 2x25 including i/j/l indicies out ND50
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep="")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Sat*output*file*name*",paste(baseoutdir,fluxtype,"/oco2/oco2.YYYYMMDD_",combo_tag,".nc",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*OBSPACK*outfile*",paste(baseoutdir,fluxtype,"/obspack/obspack.YYYYMMDD00_",combo_tag,".nc",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Start*YYYYMMDD*HHMMSS*","20140901 000000")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*End*YYYYMMDD*HHMMSS*","20170101 000000")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*HEMCO*Input*file*",
paste(baserundir,"/",fluxtype,"/hemco.configs/HEMCO_Config_",combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Output*restart*file*",paste(baseoutdir,fluxtype,"/restarts/GEOSChem_restart.",combo_tag,sep=""))
print(paste("writing ",i," of ",dim(combos.grid)[1]," input.geoses for land..."))
write.input.geos(input.geos.data=input.data,
paste(baserundir,"/",fluxtype,"/input.geoses/input.geos_",combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep=""))
}
#-- FOR OCEAN
combos.grid = expand.grid(gppresp=0,sincos=0:1,harmonic=0:2,pft=1,tr=1:30,year=2014:2016)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
input.data.orig = readLines(template_input_geos)
fluxtype = "ocean"
input.data =set.value.input.geos2(input.geos.data=input.data.orig,key="*Run*directory*",paste(baserundir,"/",fluxtype,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*=>*GEOS-FP*","../MERRA/MERRA.output/GEOS_4x5.d/GEOS_FP/YYYY/MM/")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Transport*Timestep*","30")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Convect*Timestep*","30")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Sat*track*info*","/discover/nobackup/aschuh/run/lite_wbias_20170815_standardized/inv_weight_insitu/oco2.MMDDYYYY.4x5.nc")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*OBSPACK*infile*","/discover/nobackup/aschuh/run/obspack_co2_1_NRT_v3.3_prepped_inputs_2017-04-26_links/flask_input.YYYYMMDD00.nc")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Avg*timeser*file*",paste(baseoutdir,fluxtype,"/CO2/ts_1h_avg.YYYYMMDDhh",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Input*restart*file*","/discover/nobackup/aschuh/inversion_template_files/CO2/restart.2014090600.nc")
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep="")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Sat*output*file*name*",paste(baseoutdir,fluxtype,"/oco2/oco2.YYYYMMDD_",combo_tag,".nc",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*OBSPACK*outfile*",paste(baseoutdir,fluxtype,"/obspack/obspack.YYYYMMDD00_",combo_tag,".nc",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*HEMCO*Input*file*",
paste(baserundir,"/",fluxtype,"/hemco.configs/HEMCO_Config_",combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Start*YYYYMMDD*HHMMSS*","20140901 000000")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*End*YYYYMMDD*HHMMSS*","20170101 000000")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Output*restart*file*",paste(baseoutdir,fluxtype,"/restarts/GEOSChem_restart.",combo_tag,sep=""))
print(paste("writing ",i," of ",dim(combos.grid)[1]," input.geoses for ocean..."))
write.input.geos(input.geos.data=input.data,
paste(baserundir,"/",fluxtype,"/input.geoses/input.geos_",combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep=""))
}
#-- FOR FIRES
combos.grid = expand.grid(gppresp=0,sincos=0:1,harmonic=0:2,pft=1,tr=1:30,year=2014:2016)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
input.data.orig = readLines(template_input_geos)
fluxtype = "fires"
input.data =set.value.input.geos2(input.geos.data=input.data.orig,key="*Run*directory*",paste(baserundir,"/",fluxtype,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*=>*GEOS-FP*","../MERRA/MERRA.output/GEOS_4x5.d/GEOS_FP/YYYY/MM/")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Transport*Timestep*","30")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Convect*Timestep*","30")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Sat*track*info*","/discover/nobackup/aschuh/run/lite_wbias_20170815_standardized/inv_weight_insitu/oco2.MMDDYYYY.4x5.nc")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*OBSPACK*infile*","/discover/nobackup/aschuh/run/obspack_co2_1_NRT_v3.3_prepped_inputs_2017-04-26_links/flask_input.YYYYMMDD00.nc")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Avg*timeser*file*",paste(baseoutdir,fluxtype,"/CO2/ts_1h_avg.YYYYMMDDhh",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Input*restart*file*","/discover/nobackup/aschuh/inversion_template_files/CO2/restart.2014090600.nc")
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep="")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Sat*output*file*name*",paste(baseoutdir,fluxtype,"/oco2/oco2.YYYYMMDD_",combo_tag,".nc",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*OBSPACK*outfile*",paste(baseoutdir,fluxtype,"/obspack/obspack.YYYYMMDD00_",combo_tag,".nc",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*HEMCO*Input*file*",
paste(baserundir,"/",fluxtype,"/hemco.configs/HEMCO_Config_",combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Start*YYYYMMDD*HHMMSS*","20140901 000000")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*End*YYYYMMDD*HHMMSS*","20170101 000000")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Output*restart*file*",paste(baseoutdir,fluxtype,"/restarts/GEOSChem_restart.",combo_tag,sep=""))
print(paste("writing ",i," of ",dim(combos.grid)[1]," input.geoses for ocean..."))
write.input.geos(input.geos.data=input.data,
paste(baserundir,"/",fluxtype,"/input.geoses/input.geos_",combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep=""))
}
#-- FOR FOSSIL
combos.grid = expand.grid(gppresp=0,sincos=0,harmonic=0,pft=0,tr=0,year=0)
input.data.orig = readLines(template_input_geos)
fluxtype = "fossil"
input.data =set.value.input.geos2(input.geos.data=input.data.orig,key="*Run*directory*",paste(baserundir,"/",fluxtype,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*=>*GEOS-FP*","../MERRA/MERRA.output/GEOS_4x5.d/GEOS_FP/YYYY/MM/")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Transport*Timestep*","30")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Convect*Timestep*","30")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Sat*track*info*","/discover/nobackup/aschuh/run/lite_wbias_20170815_standardized/inv_weight_insitu/oco2.MMDDYYYY.4x5.nc")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*OBSPACK*infile*","/discover/nobackup/aschuh/run/obspack_co2_1_NRT_v3.3_prepped_inputs_2017-04-26_links/flask_input.YYYYMMDD00.nc")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Avg*timeser*file*",paste(baseoutdir,fluxtype,"/CO2/ts_1h_avg.YYYYMMDDhh",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Input*restart*file*","/discover/nobackup/aschuh/inversion_template_files/CO2/restart.2014090600.nc")
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep="")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Sat*output*file*name*",paste(baseoutdir,fluxtype,"/oco2/oco2.YYYYMMDD_",combo_tag,".nc",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*OBSPACK*outfile*",paste(baseoutdir,fluxtype,"/obspack/obspack.YYYYMMDD00_",combo_tag,".nc",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*HEMCO*Input*file*",
paste(baserundir,"/",fluxtype,"/hemco.configs/HEMCO_Config_",combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Start*YYYYMMDD*HHMMSS*","20140901 000000")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*End*YYYYMMDD*HHMMSS*","20170101 000000")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Output*restart*file*",paste(baseoutdir,fluxtype,"/restarts/GEOSChem_restart.",combo_tag,sep=""))
print(paste("writing ",i," of ",dim(combos.grid)[1]," input.geoses for fossil..."))
write.input.geos(input.geos.data=input.data,
paste(baserundir,"/",fluxtype,"/input.geoses/input.geos_",combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep=""))
}
#-- FOR BG
combos.grid = expand.grid(gppresp=0,sincos=0,harmonic=0,pft=0,tr=0,year=0)
input.data.orig = readLines(template_input_geos)
fluxtype = "bg"
input.data =set.value.input.geos2(input.geos.data=input.data.orig,key="*Run*directory*",paste(baserundir,"/",fluxtype,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*=>*GEOS-FP*","../MERRA/MERRA.output/GEOS_4x5.d/GEOS_FP/YYYY/MM/")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Transport*Timestep*","30")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Convect*Timestep*","30")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Sat*track*info*","/discover/nobackup/aschuh/run/lite_wbias_20170815_standardized/inv_weight_insitu/oco2.MMDDYYYY.4x5.nc")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*OBSPACK*infile*","/discover/nobackup/aschuh/run/obspack_co2_1_NRT_v3.3_prepped_inputs_2017-04-26_links/flask_input.YYYYMMDD00.nc")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Avg*timeser*file*",paste(baseoutdir,fluxtype,"/CO2/ts_1h_avg.YYYYMMDDhh",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Input*restart*file*","/discover/nobackup/aschuh/inversion_template_files/CO2/restart.2014090600.nc.REAL")
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep="")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Sat*output*file*name*",paste(baseoutdir,fluxtype,"/oco2/oco2.YYYYMMDD_",combo_tag,".nc",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*OBSPACK*outfile*",paste(baseoutdir,fluxtype,"/obspack/obspack.YYYYMMDD00_",combo_tag,".nc",sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*HEMCO*Input*file*",
paste(baserundir,"/",fluxtype,"/hemco.configs/HEMCO_Config_",combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Start*YYYYMMDD*HHMMSS*","20140901 000000")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*End*YYYYMMDD*HHMMSS*","20170101 000000")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Output*restart*file*",paste(baseoutdir,fluxtype,"/restarts/GEOSChem_restart.",combo_tag,sep=""))
print(paste("writing ",i," of ",dim(combos.grid)[1]," input.geoses for fossil..."))
write.input.geos(input.geos.data=input.data,
paste(baserundir,"/",fluxtype,"/input.geoses/input.geos_",combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep=""))
}
}
create_hemco_configs = function(baserundir,template_hemco_config="/discover/nobackup/aschuh/inversion_template_files/hemco.configs/HEMCO_Config.rc_template")
{
#-- FOR LAND
combos.grid = expand.grid(gppresp=0:1,sincos=0:1,harmonic=0:3,pft=1:25,tr=1:11,year=2014:2016)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
input.data.orig = readLines(template_hemco_config)
fluxtype = "land"
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep="")
input.data =set.value.input.geos2(input.geos.data=input.data.orig,key="*TR:*",combos.grid[i,5])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*PFT:*",combos.grid[i,4])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*SINCOS:*",combos.grid[i,2])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*HARMONIC:*",combos.grid[i,3])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*GPPRESP:*",combos.grid[i,1])
RESP_TF = combos.grid[i,1] == 0
GPP_TF = ! RESP_TF
#-- If HARMONIC ARG is >= 1, then we modulate, otherwise we run base prior
HARMONIC_TF = combos.grid[i,3] != 0
if(HARMONIC_TF == TRUE)
{
harm_arg_gpp = "200"
harm_arg_resp = "100"
}else{
harm_arg_gpp = "-"
harm_arg_resp = "-"
}
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*SIB4_RESP_CO2*",tolower(as.character(RESP_TF)))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*SIB4_GPP_CO2*",tolower(as.character(GPP_TF)))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*CT_OCN_2016*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*CT_FIRE_2016*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*BASU_FOSSIL_2016*","false")
yr_run = combos.grid[i,6]
input.data[grep(glob2rx("*sib4_fluxes*ASSIM*"),input.data)] = paste("0 CO2 /discover/nobackup/aschuh/data/sib_harmonic/hemco_sib4/"
,yr_run,"/sib4_fluxes_TR_$TR_$YYYY$MM$DD.nc ASSIM ",(yr_run-1),"-",(yr_run),"/1-12/1-31/0-23 R xy+\"PFT=$PFT\" umol/m2/s CO2 ",harm_arg_gpp," 1 1",sep="")
input.data[grep(glob2rx("*sib4_fluxes*RESP.BAL*"),input.data)] = paste("0 CO2 /discover/nobackup/aschuh/data/sib_harmonic/hemco_sib4/"
,yr_run,"/sib4_fluxes_TR_$TR_$YYYY$MM$DD.nc RESP.BAL ",(yr_run-1),"-",(yr_run),"/1-12/1-31/0-23 R xy+\"PFT=$PFT\" umol/m2/s CO2 ",harm_arg_resp," 1 1",sep="")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Logfile:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO.log',combo_tag,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*DiagnPrefix:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO_diagnostics',combo_tag,sep=""))
print(paste("writing ",i," of ",dim(combos.grid)[1]," hemco.configs for land..."))
write.input.geos(input.geos.data=input.data,
paste(baserundir,"/",fluxtype,"/hemco.configs/HEMCO_Config_",combo_tag,sep=""))
}
#-- FOR OCEAN
combos.grid = expand.grid(gppresp=0,sincos=0:1,harmonic=0:2,pft=1,tr=1:30,year=2014:2016)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
input.data.orig = readLines(template_hemco_config)
fluxtype = "ocean"
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep="")
input.data =set.value.input.geos2(input.geos.data=input.data.orig,key="*TR:*",combos.grid[i,5])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*PFT:*",combos.grid[i,4])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*SINCOS:*",combos.grid[i,2])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*HARMONIC:*",combos.grid[i,3])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*GPPRESP:*",combos.grid[i,1])
#-- If HARMONIC ARG is >= 1, then we modulate, otherwise we run base prior
HARMONIC_TF = combos.grid[i,3] != 0
if(HARMONIC_TF == TRUE)
{
harm_arg_ocn = "300"
}else{
harm_arg_ocn = "-"
}
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*SIB4_RESP_CO2*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*SIB4_GPP_CO2*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*CT_OCN_2016*","true")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*CT_FIRE_2016*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*BASU_FOSSIL_2016*","false")
yr_run = combos.grid[i,6]
ocn_mask_ext = as.character(2000+combos.grid[i,5])
input.data[grep(glob2rx("*ocn_flux_opt*"),input.data)] = paste("0 CO2 /discover/nobackup/aschuh/data/ct2016_optimized/hemco_data/climate/",yr_run,"/CT2016.flux1x1.climate_oceansub.$YYYY$MM$DD.nc ocean_fluxes ",(yr_run-1),"-",(yr_run),"/1-12/1-31/0-23/+90minutes R xy+\"ocean_region=$TR\" mol/m2/s CO2 ",harm_arg_ocn," 1 1",sep="")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Logfile:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO.log',combo_tag,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*DiagnPrefix:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO_diagnostics',combo_tag,sep=""))
print(paste("writing ",i," of ",dim(combos.grid)[1]," hemco.configs for ocean..."))
write.input.geos(input.geos.data=input.data,
paste(baserundir,"/",fluxtype,"/hemco.configs/HEMCO_Config_",combo_tag,sep=""))
}
#-- FOR FIRES
combos.grid = expand.grid(gppresp=0,sincos=0,harmonic=0,pft=0,tr=0,year=0)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
input.data.orig = readLines(template_hemco_config)
fluxtype = "fires"
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep="")
input.data =set.value.input.geos2(input.geos.data=input.data.orig,key="*TR:*",combos.grid[i,5])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*PFT:*",combos.grid[i,4])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*SINCOS:*",combos.grid[i,2])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*HARMONIC:*",combos.grid[i,3])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*GPPRESP:*",combos.grid[i,1])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*SIB4_RESP_CO2*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*SIB4_GPP_CO2*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*CT_OCN_2016*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*CT_FIRE_2016*","true")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*BASU_FOSSIL_2016*","false")
input.data[grep(glob2rx("*ocn_flux_opt*"),input.data)] = paste("0 CO2 /discover/nobackup/aschuh/data/ct2016_optimized/hemco_data/CT2016.flux1x1.$YYYY$MM$DD.nc ocn_flux_opt ",combos.grid[i,6],"/1-12/1-31/0-23/+90minutes C xy mol/m2/s CO2 - 1 1",sep="")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Logfile:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO.log',combo_tag,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*DiagnPrefix:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO_diagnostics',combo_tag,sep=""))
print(paste("writing ",i," of ",dim(combos.grid)[1]," hemco.configs for fires..."))
write.input.geos(input.geos.data=input.data,
paste(baserundir,"/",fluxtype,"/hemco.configs/HEMCO_Config_",combo_tag,sep=""))
}
#-- FOR FOSSIL
combos.grid = expand.grid(gppresp=0,sincos=0,harmonic=0,pft=0,tr=0,year=0)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
input.data.orig = readLines(template_hemco_config)
fluxtype = "fossil"
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep="")
input.data =set.value.input.geos2(input.geos.data=input.data.orig,key="*TR:*",combos.grid[i,5])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*PFT:*",combos.grid[i,4])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*SINCOS:*",combos.grid[i,2])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*HARMONIC:*",combos.grid[i,3])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*GPPRESP:*",combos.grid[i,1])
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*SIB4_RESP_CO2*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*SIB4_GPP_CO2*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*CT_OCN_2016*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*CT_FIRE_2016*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*BASU_FOSSIL_2016*","true")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Logfile:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO.log',combo_tag,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Logfile:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO.log',combo_tag,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*DiagnPrefix:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO_diagnostics',combo_tag,sep=""))
print(paste("writing ",i," of ",dim(combos.grid)[1]," hemco.configs for fossil..."))
write.input.geos(input.geos.data=input.data,
paste(baserundir,"/",fluxtype,"/hemco.configs/HEMCO_Config_",combo_tag,sep=""))
}
#-- FOR BG
combos.grid = expand.grid(gppresp=0,sincos=0,harmonic=0,pft=0,tr=0,year=0)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
input.data.orig = readLines(template_hemco_config)
fluxtype = "bg"
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6],"_",combos.grid[i,1],"_",combos.grid[i,2],"_",combos.grid[i,3],"_",combos.grid[i,4],"_",combos.grid[i,5],sep="")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*SIB4_RESP_CO2*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*SIB4_GPP_CO2*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*CT_OCN_2016*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*CT_FIRE_2016*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*-->*BASU_FOSSIL_2016*","false")
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Logfile:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO.log',combo_tag,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*Logfile:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO.log',combo_tag,sep=""))
input.data =set.value.input.geos2(input.geos.data=input.data,key="*DiagnPrefix:*",
paste(baserundir,'/',fluxtype,'/logs/HEMCO_diagnostics',combo_tag,sep=""))
print(paste("writing ",i," of ",dim(combos.grid)[1]," hemco.configs for fossil..."))
write.input.geos(input.geos.data=input.data,
paste(baserundir,"/",fluxtype,"/hemco.configs/HEMCO_Config_",combo_tag,sep=""))
}
}
create_launch_scripts = function(baserundir,run.pulse.file="/discover/nobackup/aschuh/inversion_template_files/run.pulse")
{
pulse = readLines(run.pulse.file)
lx = grep(glob2rx("*basedir=*"),pulse)
pulse[lx] = paste("basedir='",baserundir,"'",sep="")
writeLines(pulse,paste(baserundir,"/run.pulse",sep=""))
system(paste("ln -s /discover/nobackup/aschuh/Code.v11-01/bin/geos ",baserundir,"/",sep=""))
#/discover/nobackup/aschuh/run.v9-02_oco2_111716/land/run.pulse 20140906 1 365 0 0 0 01 01 > out_0_0_0_01_01.txt
line_vector1 = vector()
line_vector2 = vector()
line_vector3 = vector()
line_vector4 = vector()
line_vector5 = vector()
#-- FOR LAND
combos.grid = expand.grid(gppresp=0:1,sincos=0:1,harmonic=0:3,pft=1:25,tr=1:11,year=2014:2016)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
fluxtype = "land"
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6]," ",combos.grid[i,1]," ",combos.grid[i,2]," ",combos.grid[i,3],
" ",combos.grid[i,4]," ",combos.grid[i,5],sep="")
line_vector1[i] = paste(baserundir,"/run.pulse ",fluxtype," ",combo_tag," > out_",gsub(" ","_",combo_tag),"_txt",sep="")
}
#-- FOR OCEAN
combos.grid = expand.grid(gppresp=0,sincos=0:1,harmonic=0:2,pft=1,tr=1:30,year=2014:2016)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
fluxtype = "ocean"
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6]," ",combos.grid[i,1]," ",combos.grid[i,2]," ",combos.grid[i,3],
" ",combos.grid[i,4]," ",combos.grid[i,5],sep="")
line_vector2[i] = paste(baserundir,"/run.pulse ",fluxtype," ",combo_tag," > out_",gsub(" ","_",combo_tag),"_txt",sep="")
}
#-- FOR FOSSIL
combos.grid = expand.grid(gppresp=0,sincos=0,harmonic=0,pft=0,tr=0,year=0)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
fluxtype = "fossil"
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6]," ",combos.grid[i,1]," ",combos.grid[i,2]," ",combos.grid[i,3],
" ",combos.grid[i,4]," ",combos.grid[i,5],sep="")
line_vector3[i] = paste(baserundir,"/run.pulse ",fluxtype," ",combo_tag," > out_",gsub(" ","_",combo_tag),"_txt",sep="")
}
#-- FOR FIRES
combos.grid = expand.grid(gppresp=0,sincos=0,harmonic=0,pft=0,tr=0,year=0)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
fluxtype = "fires"
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6]," ",combos.grid[i,1]," ",combos.grid[i,2]," ",combos.grid[i,3],
" ",combos.grid[i,4]," ",combos.grid[i,5],sep="")
line_vector4[i] = paste(baserundir,"/run.pulse ",fluxtype," ",combo_tag," > out_",gsub(" ","_",combo_tag),"_txt",sep="")
}
#-- FOR BG
combos.grid = expand.grid(gppresp=0,sincos=0,harmonic=0,pft=0,tr=0,year=0)
combos.grid = combos.grid[!(combos.grid[,3] == 0 & combos.grid[,2]==1),]
fluxtype = "bg"
for(i in 1:(dim(combos.grid)[1]))
{
combo_tag = paste(combos.grid[i,6]," ",combos.grid[i,1]," ",combos.grid[i,2]," ",combos.grid[i,3],
" ",combos.grid[i,4]," ",combos.grid[i,5],sep="")
line_vector5[i] = paste(baserundir,"/run.pulse ",fluxtype," ",combo_tag," > out_",gsub(" ","_",combo_tag),"_txt",sep="")
}
writeLines(c(line_vector1,line_vector2,line_vector3,line_vector4,line_vector5),con=paste(baserundir,"/exec.script",sep=""))
}
#-- CREATE RERUN FOR LOST SIMS
create_reruns = function(dir,filename_out){
fls.inputgeos = list.files(dir,pattern="new.exec.script_",full.names=TRUE)
for(i in 1:length(fls.inputgeos))
{
if(i==1) { indat = readLines(fls.inputgeos[i]) }else{
indat = c(indat,readLines(fls.inputgeos[i]))
}
}
ens.attemptrun = sapply(indat,FUN=function(x){gsub("_txt","",gsub("out_","",strsplit(x," > ")[[1]][2]))})
type_attempt = sapply(indat,FUN=function(x){strsplit(x," ")[[1]][2]})
ran = paste(type_attempt,ens.attemptrun,sep="_")
fls.output.land = list.files(paste(dir,"/land/oco2/",sep=""),pattern="oco2_total_")
fls.output.ocean = list.files(paste(dir,"/ocean/oco2/",sep=""),pattern="oco2_total_")
fls.output.fossil = list.files(paste(dir,"/fossil/oco2/",sep=""),pattern="oco2_total_")
fls.output.fires = list.files(paste(dir,"/fires/oco2/",sep=""),pattern="oco2_total_")
fls.output.bg = list.files(paste(dir,"/bg/oco2/",sep=""),pattern="oco2_total_")
fls.output = c(fls.output.land,fls.output.ocean,fls.output.fossil,
fls.output.fires,fls.output.bg)
type_ran = c(rep("land",length(fls.output.land)),
rep("ocean",length(fls.output.ocean)),
rep("fossil",length(fls.output.fossil)),
rep("fires",length(fls.output.fires)),
rep("bg",length(fls.output.bg)))
ens.run = sapply(fls.output,FUN=function(x){gsub(".nc","",gsub("oco2_total_","",x))})
ran.done = paste(type_ran,ens.run,sep="_")
needtorun = ran[!(ran %in% ran.done)]
linestowrite = indat[!(ran %in% ran.done)]
write(linestowrite,file=filename_out)
}
#-- Running
create_dirs(baserundir="/discover/nobackup/aschuh/run.v11_oco2_080117",baseoutdir="/discover/nobackup/aschuh/run.v11_oco2_080117")
create_input_geoses(baserundir="/discover/nobackup/aschuh/run.v11_oco2_080117",
baseoutdir = "/discover/nobackup/aschuh/run.v11_oco2_080117/",
template_input_geos="/discover/nobackup/aschuh/inversion_template_files/input.geoses/input.geos.template")
create_hemco_configs("/discover/nobackup/aschuh/run.v11_oco2_080117","/discover/nobackup/aschuh/inversion_template_files/hemco.configs/HEMCO_Config.rc_template")
create_launch_scripts(baserundir="/discover/nobackup/aschuh/run.v11_oco2_080117/",run.pulse.file="/discover/nobackup/aschuh/inversion_template_files/run.pulse")
create_reruns(dir="/discover/nobackup/aschuh/run.v11_oco2_080117",filename="/discover/nobackup/aschuh/run.v11_oco2_080117/dropped_runs")