R/rpmodel.grid.R
In dsval/rpmodel-grid-dev: P-Model
Defines functions
rpmodel.grid
#' rpmodel.grid
#'
#' rpmodel looping through pixels in parallel and writing on the go
#' @param same as rpmodel, tc, vpd, fapar, ppfd, elev, soilm, meanalpha as grid type objects
#' @import raster
#' @keywords rpmodel
#' @export
#' @examples
#' rpmodel.grid()
rpmodel.grid<-function(tc, vpd, co2, fapar, ppfd, elev = NA,
kphio = ifelse(do_ftemp_kphio, ifelse(do_soilmstress, 0.0870, 0.0817), 0.0492),
beta = 146.0, soilm = 1.0, meanalpha = 1.0, apar_soilm = 0.0, bpar_soilm = 0.685,
c4 = FALSE, method_optci = "prentice14", method_jmaxlim = "wang17",
do_ftemp_kphio = TRUE, do_soilmstress = TRUE,inmem=FALSE,outdir=getwd()){
###############################################################################################
# 00. create array for results
###############################################################################################
rasterOptions(maxmemory=1e7, tmptime = 24, chunksize = 1e6,todisk = FALSE, overwrite=TRUE, tolerance = 0.5)
y<-as.numeric(unique(format(getZ(tc),'%Y')))
ny <- nlayers(tc)
# gpp gC/m2
gpp<-brick(nrows=nrow(elev), ncols=ncol(elev), crs=crs(elev), nl=ny)
extent(gpp)<-extent(elev)
gpp<-setZ(gpp,getZ(tc))
# lue g C / mol photons
lue<-brick(nrows=nrow(elev), ncols=ncol(elev), crs=crs(elev), nl=ny)
extent(lue)<-extent(elev)
gpp<-setZ(gpp,getZ(tc))
# transpiration mm
Tr<-brick(nrows=nrow(elev), ncols=ncol(elev), crs=crs(elev), nl=ny)
extent(Tr)<-extent(elev)
Tr<-setZ(Tr,getZ(tc))
# wue g C / mol H2O
wue<-brick(nrows=nrow(elev), ncols=ncol(elev), crs=crs(elev), nl=ny)
extent(wue)<-extent(elev)
wue<-setZ(wue,getZ(tc))
gc()
setwd(outdir)
if(inmem){
tc<-readAll(tc)
vap<-readAll(vap)
elev<-readAll(elev)
fapar<-readAll(fa)
ppfd<-readAll(ppfd)
soilm<-readAll(soilm)
meanalpha<-readAll(meanalpha)
}
# ************************************************************************
# Name: density_h2o
# Inputs: - double (tc), air temperature, degrees C
# - double (pa), atm pressure, Pa
# Returns: double, kg/m^3
# Features: This function calculates the temperature and pressure
# dependent density of pure water
# * Ref: Chen, C.T., R.A. Fine, and F.J. Millero (1977), The equation
# of state of pure water determined from sound speeds, The
# Journal of Chemical Physics 66, 2142;
# doi:10.1063/1.434179
# ************************************************************************
density_h2o <- function(tc, pa) {
# Calculate density of water at 1 atm, g/cm^3
po <- 0.99983952 +
(6.788260e-5)*tc +
-(9.08659e-6)*tc*tc +
(1.022130e-7)*tc*tc*tc +
-(1.35439e-9)*tc*tc*tc*tc +
(1.471150e-11)*tc*tc*tc*tc*tc +
-(1.11663e-13)*tc*tc*tc*tc*tc*tc +
(5.044070e-16)*tc*tc*tc*tc*tc*tc*tc +
-(1.00659e-18)*tc*tc*tc*tc*tc*tc*tc*tc
# Calculate the bulk modulus of water at 1 atm, atm
ko <- 19652.17 +
148.1830*tc +
-2.29995*tc*tc +
0.01281*tc*tc*tc +
-(4.91564e-5)*tc*tc*tc*tc +
(1.035530e-7)*tc*tc*tc*tc*tc
# Calculate temperature-dependend coefficients
ca <- 3.26138 +
(5.223e-4)*tc +
(1.324e-4)*tc*tc +
-(7.655e-7)*tc*tc*tc +
(8.584e-10)*tc*tc*tc*tc
cb <- (7.2061e-5) +
-(5.8948e-6)*tc +
(8.69900e-8)*tc*tc +
-(1.0100e-9)*tc*tc*tc +
(4.3220e-12)*tc*tc*tc*tc
# Convert pressure to bar (1 bar = 100000 Pa)
pbar <- (1e-5)*pa
pw <- (1e3)*po*(ko + ca*pbar + cb*pbar^2)/(ko + ca*pbar + cb*pbar^2 - pbar)
return(pw)
}
###############################################################################################
# 01. set the clusters for parallel computing
###############################################################################################
cl <- getCluster()
on.exit( returnCluster() )
nodes <- length(cl)
bs<- blockSize(tc, minblocks=nodes*10)
parallel::clusterEvalQ(cl, library("rpmodel"))
pmodel<-Vectorize(rpmodel,c("tc","vpd","co2","fapar","ppfd","meanalpha","soilm"))
parallel::clusterExport(cl, varlist=c("tc","vpd","co2",'elev','fapar',"ppfd","kphio",'beta','soilm','meanalpha','apar_soilm','bpar_soilm','c4','method_optci','method_jmaxlim','do_ftemp_kphio','do_soilmstress','pmodel','ny','density_h2o','y','bs'),envir=environment())
pb <- pbCreate(bs$n)
pb <- txtProgressBar(min=1,max = bs$n, style = 3)
###############################################################################################
# 02. create the functions to send to the workers, split the data in chunks
###############################################################################################
clFun <- function(i) {
tcrow<-split(getValues(tc,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
vpdrow<-split(getValues(vpd,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
elevrow<-split(getValues(elev,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
faparrow<-split(getValues(fapar,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
ppfdrow<-split(getValues(ppfd,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
soilmrow<-split(getValues(soilm,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
alpharow<-split(getValues(meanalpha,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
co2row<-lapply(1:(ncol(elev)*bs$nrows[i]),function(j) co2)
# define function to get transpiration
calc_transp<-function(mat,vpd,tc, elev){
gs_mol<-as.numeric(mat[12,])*calc_patm(elev)
gs_mol[gs_mol<0]<-NA
T_mol<-1.6*gs_mol*(vpd)/calc_patm(elev)
T_mm<-T_mol*(18/density_h2o(tc,calc_patm(elev)))
wue<-as.numeric(mat[10,])/T_mol
return(rbind(mat,T_mm,wue))
}
# apply vectorized rpmodel
result<-mapply(pmodel,
tc = tcrow, # temperature, deg C
vpd = vpdrow, # Pa,
co2 = co2row, # ppm,
elv = elevrow, # m.a.s.l.,
kphio = kphio, # quantum yield efficiency,
beta = beta, # unit cost ratio a/b,
fapar = faparrow, # fraction ,
ppfd = ppfdrow, # mol/m2/d month?,
method_optci = method_optci,
method_jmaxlim = method_jmaxlim,
soilm = soilmrow,
meanalpha=alpharow, SIMPLIFY = FALSE)
# calc transpiration and wue
result<-mapply(calc_transp,result,vpdrow,tcrow,elevrow, SIMPLIFY = FALSE)
gc()
return(result)
}
###############################################################################################
# 03. send tasks to the nodes
###############################################################################################
for (i in 1:nodes) {
parallel:::sendCall(cl[[i]], clFun, i, tag=i)
}
###############################################################################################
# 04. write to the disk on the go, or save to the ram
###############################################################################################
if(!inmem){
gpp<-writeStart(gpp,filename=paste0(outdir,"/",y[1],"_",y[length(y)],".",'gpp',".","nc"),
format="CDF",overwrite=TRUE,varname='gpp', varunit='gC/m2',longname='gross primary production',
xname="lon", yname="lat", zname="time", zunit=paste("months","since",paste0(y[1]-1,"-",12)))
Tr<-writeStart(Tr,filename=paste0(outdir,"/",y[1],"_",y[length(y)],".",'Tr',".","nc"),
format="CDF",overwrite=TRUE,varname='Tr', varunit='mm',longname='Transpiration',
xname="lon", yname="lat", zname="time", zunit=paste("months","since",paste0(y[1]-1,"-",12)))
wue<-writeStart(wue,filename=paste0(outdir,"/",y[1],"_",y[length(y)],".",'wue',".","nc"),
format="CDF",overwrite=TRUE,varname='wue', varunit='gC/mol',longname='water use efficiency',
xname="lon", yname="lat", zname="time", zunit=paste("months","since",paste0(y[1]-1,"-",12)))
lue<-writeStart(lue,filename=paste0(outdir,"/",y[1],"_",y[length(y)],".",'lue',".","nc"),
format="CDF",overwrite=TRUE,varname='wue', varunit='gC/mol',longname='light use efficiency',
xname="lon", yname="lat", zname="time", zunit=paste("months","since",paste0(y[1]-1,"-",12)))
}else {
matgpp <- matrix(ncol=nlayers(tc), nrow=ncell(tc))
matTr<- matrix(ncol=nlayers(tc), nrow=ncell(tc))
matwue <- matrix(ncol=nlayers(tc), nrow=ncell(tc))
matlue <- matrix(ncol=nlayers(tc), nrow=ncell(tc))
endind<-cumsum(bs$nrows*tc@ncols)
startind<-c(1,endind+1)
}
# mbl1<-do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[10,])}))
###############################################################################################
# 05. receive results from the nodes
###############################################################################################
for (i in 1:bs$n) {
d <- parallel:::recvOneData(cl)
# error?
if (! d$value$success) {
stop('error!! check the data...')
}
# which block is this?
b <- d$value$tag
# cat('received block: ',b,'\n'); flush.console();
if (!inmem) {
gpp <- writeValues(gpp,do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[10,])})), bs$row[b])
Tr <- writeValues(Tr, do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[16,])})), bs$row[b])
wue <- writeValues(wue, do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[17,])})), bs$row[b])
lue <- writeValues(lue, do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[9,])})), bs$row[b])
} else {
matgpp[startind[b]:endind[b],] <- do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[10,])}))
matTr[startind[b]:endind[b],] <- do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[16,])}))
matwue[startind[b]:endind[b],] <- do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[17,])}))
matlue[startind[b]:endind[b],] <- do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[9,])}))
}
# need to send more data?
ni <- nodes + i
if (ni <= bs$n) {
parallel:::sendCall(cl[[d$node]], clFun, ni, tag=ni)
}
gc()
setTxtProgressBar(pb,i)
}
###############################################################################################
# 06. close connection with the files, or assign valueas to the raster objects
###############################################################################################
if (!inmem) {
gpp <- writeStop(gpp)
Tr <- writeStop(Tr)
wue <- writeStop(wue)
lue <- writeStop(lue)
} else {
# gpp
gpp<-setValues(gpp,matgpp)
# transpiration
Tr<-setValues(Tr,matTr)
# water use efficiency
wue<-setValues(wue,matwue)
# light use efficiency
lue<-setValues(lue,matlue)
}
close(pb)
gc()
return(list(gpp=gpp,lue=lue,Tr=Tr,wue=wue))
}
dsval/rpmodel-grid-dev documentation built on March 11, 2021, 7:47 a.m.
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Defines functions rpmodel.grid
#' rpmodel.grid
#'
#' rpmodel looping through pixels in parallel and writing on the go
#' @param same as rpmodel, tc, vpd, fapar, ppfd, elev, soilm, meanalpha as grid type objects
#' @import raster
#' @keywords rpmodel
#' @export
#' @examples
#' rpmodel.grid()
rpmodel.grid<-function(tc, vpd, co2, fapar, ppfd, elev = NA,
kphio = ifelse(do_ftemp_kphio, ifelse(do_soilmstress, 0.0870, 0.0817), 0.0492),
beta = 146.0, soilm = 1.0, meanalpha = 1.0, apar_soilm = 0.0, bpar_soilm = 0.685,
c4 = FALSE, method_optci = "prentice14", method_jmaxlim = "wang17",
do_ftemp_kphio = TRUE, do_soilmstress = TRUE,inmem=FALSE,outdir=getwd()){
###############################################################################################
# 00. create array for results
###############################################################################################
rasterOptions(maxmemory=1e7, tmptime = 24, chunksize = 1e6,todisk = FALSE, overwrite=TRUE, tolerance = 0.5)
y<-as.numeric(unique(format(getZ(tc),'%Y')))
ny <- nlayers(tc)
# gpp gC/m2
gpp<-brick(nrows=nrow(elev), ncols=ncol(elev), crs=crs(elev), nl=ny)
extent(gpp)<-extent(elev)
gpp<-setZ(gpp,getZ(tc))
# lue g C / mol photons
lue<-brick(nrows=nrow(elev), ncols=ncol(elev), crs=crs(elev), nl=ny)
extent(lue)<-extent(elev)
gpp<-setZ(gpp,getZ(tc))
# transpiration mm
Tr<-brick(nrows=nrow(elev), ncols=ncol(elev), crs=crs(elev), nl=ny)
extent(Tr)<-extent(elev)
Tr<-setZ(Tr,getZ(tc))
# wue g C / mol H2O
wue<-brick(nrows=nrow(elev), ncols=ncol(elev), crs=crs(elev), nl=ny)
extent(wue)<-extent(elev)
wue<-setZ(wue,getZ(tc))
gc()
setwd(outdir)
if(inmem){
tc<-readAll(tc)
vap<-readAll(vap)
elev<-readAll(elev)
fapar<-readAll(fa)
ppfd<-readAll(ppfd)
soilm<-readAll(soilm)
meanalpha<-readAll(meanalpha)
}
# ************************************************************************
# Name: density_h2o
# Inputs: - double (tc), air temperature, degrees C
# - double (pa), atm pressure, Pa
# Returns: double, kg/m^3
# Features: This function calculates the temperature and pressure
# dependent density of pure water
# * Ref: Chen, C.T., R.A. Fine, and F.J. Millero (1977), The equation
# of state of pure water determined from sound speeds, The
# Journal of Chemical Physics 66, 2142;
# doi:10.1063/1.434179
# ************************************************************************
density_h2o <- function(tc, pa) {
# Calculate density of water at 1 atm, g/cm^3
po <- 0.99983952 +
(6.788260e-5)*tc +
-(9.08659e-6)*tc*tc +
(1.022130e-7)*tc*tc*tc +
-(1.35439e-9)*tc*tc*tc*tc +
(1.471150e-11)*tc*tc*tc*tc*tc +
-(1.11663e-13)*tc*tc*tc*tc*tc*tc +
(5.044070e-16)*tc*tc*tc*tc*tc*tc*tc +
-(1.00659e-18)*tc*tc*tc*tc*tc*tc*tc*tc
# Calculate the bulk modulus of water at 1 atm, atm
ko <- 19652.17 +
148.1830*tc +
-2.29995*tc*tc +
0.01281*tc*tc*tc +
-(4.91564e-5)*tc*tc*tc*tc +
(1.035530e-7)*tc*tc*tc*tc*tc
# Calculate temperature-dependend coefficients
ca <- 3.26138 +
(5.223e-4)*tc +
(1.324e-4)*tc*tc +
-(7.655e-7)*tc*tc*tc +
(8.584e-10)*tc*tc*tc*tc
cb <- (7.2061e-5) +
-(5.8948e-6)*tc +
(8.69900e-8)*tc*tc +
-(1.0100e-9)*tc*tc*tc +
(4.3220e-12)*tc*tc*tc*tc
# Convert pressure to bar (1 bar = 100000 Pa)
pbar <- (1e-5)*pa
pw <- (1e3)*po*(ko + ca*pbar + cb*pbar^2)/(ko + ca*pbar + cb*pbar^2 - pbar)
return(pw)
}
###############################################################################################
# 01. set the clusters for parallel computing
###############################################################################################
cl <- getCluster()
on.exit( returnCluster() )
nodes <- length(cl)
bs<- blockSize(tc, minblocks=nodes*10)
parallel::clusterEvalQ(cl, library("rpmodel"))
pmodel<-Vectorize(rpmodel,c("tc","vpd","co2","fapar","ppfd","meanalpha","soilm"))
parallel::clusterExport(cl, varlist=c("tc","vpd","co2",'elev','fapar',"ppfd","kphio",'beta','soilm','meanalpha','apar_soilm','bpar_soilm','c4','method_optci','method_jmaxlim','do_ftemp_kphio','do_soilmstress','pmodel','ny','density_h2o','y','bs'),envir=environment())
pb <- pbCreate(bs$n)
pb <- txtProgressBar(min=1,max = bs$n, style = 3)
###############################################################################################
# 02. create the functions to send to the workers, split the data in chunks
###############################################################################################
clFun <- function(i) {
tcrow<-split(getValues(tc,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
vpdrow<-split(getValues(vpd,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
elevrow<-split(getValues(elev,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
faparrow<-split(getValues(fapar,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
ppfdrow<-split(getValues(ppfd,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
soilmrow<-split(getValues(soilm,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
alpharow<-split(getValues(meanalpha,bs$row[i], bs$nrows[i]),1:(ncol(elev)*bs$nrows[i]))
co2row<-lapply(1:(ncol(elev)*bs$nrows[i]),function(j) co2)
# define function to get transpiration
calc_transp<-function(mat,vpd,tc, elev){
gs_mol<-as.numeric(mat[12,])*calc_patm(elev)
gs_mol[gs_mol<0]<-NA
T_mol<-1.6*gs_mol*(vpd)/calc_patm(elev)
T_mm<-T_mol*(18/density_h2o(tc,calc_patm(elev)))
wue<-as.numeric(mat[10,])/T_mol
return(rbind(mat,T_mm,wue))
}
# apply vectorized rpmodel
result<-mapply(pmodel,
tc = tcrow, # temperature, deg C
vpd = vpdrow, # Pa,
co2 = co2row, # ppm,
elv = elevrow, # m.a.s.l.,
kphio = kphio, # quantum yield efficiency,
beta = beta, # unit cost ratio a/b,
fapar = faparrow, # fraction ,
ppfd = ppfdrow, # mol/m2/d month?,
method_optci = method_optci,
method_jmaxlim = method_jmaxlim,
soilm = soilmrow,
meanalpha=alpharow, SIMPLIFY = FALSE)
# calc transpiration and wue
result<-mapply(calc_transp,result,vpdrow,tcrow,elevrow, SIMPLIFY = FALSE)
gc()
return(result)
}
###############################################################################################
# 03. send tasks to the nodes
###############################################################################################
for (i in 1:nodes) {
parallel:::sendCall(cl[[i]], clFun, i, tag=i)
}
###############################################################################################
# 04. write to the disk on the go, or save to the ram
###############################################################################################
if(!inmem){
gpp<-writeStart(gpp,filename=paste0(outdir,"/",y[1],"_",y[length(y)],".",'gpp',".","nc"),
format="CDF",overwrite=TRUE,varname='gpp', varunit='gC/m2',longname='gross primary production',
xname="lon", yname="lat", zname="time", zunit=paste("months","since",paste0(y[1]-1,"-",12)))
Tr<-writeStart(Tr,filename=paste0(outdir,"/",y[1],"_",y[length(y)],".",'Tr',".","nc"),
format="CDF",overwrite=TRUE,varname='Tr', varunit='mm',longname='Transpiration',
xname="lon", yname="lat", zname="time", zunit=paste("months","since",paste0(y[1]-1,"-",12)))
wue<-writeStart(wue,filename=paste0(outdir,"/",y[1],"_",y[length(y)],".",'wue',".","nc"),
format="CDF",overwrite=TRUE,varname='wue', varunit='gC/mol',longname='water use efficiency',
xname="lon", yname="lat", zname="time", zunit=paste("months","since",paste0(y[1]-1,"-",12)))
lue<-writeStart(lue,filename=paste0(outdir,"/",y[1],"_",y[length(y)],".",'lue',".","nc"),
format="CDF",overwrite=TRUE,varname='wue', varunit='gC/mol',longname='light use efficiency',
xname="lon", yname="lat", zname="time", zunit=paste("months","since",paste0(y[1]-1,"-",12)))
}else {
matgpp <- matrix(ncol=nlayers(tc), nrow=ncell(tc))
matTr<- matrix(ncol=nlayers(tc), nrow=ncell(tc))
matwue <- matrix(ncol=nlayers(tc), nrow=ncell(tc))
matlue <- matrix(ncol=nlayers(tc), nrow=ncell(tc))
endind<-cumsum(bs$nrows*tc@ncols)
startind<-c(1,endind+1)
}
# mbl1<-do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[10,])}))
###############################################################################################
# 05. receive results from the nodes
###############################################################################################
for (i in 1:bs$n) {
d <- parallel:::recvOneData(cl)
# error?
if (! d$value$success) {
stop('error!! check the data...')
}
# which block is this?
b <- d$value$tag
# cat('received block: ',b,'\n'); flush.console();
if (!inmem) {
gpp <- writeValues(gpp,do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[10,])})), bs$row[b])
Tr <- writeValues(Tr, do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[16,])})), bs$row[b])
wue <- writeValues(wue, do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[17,])})), bs$row[b])
lue <- writeValues(lue, do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[9,])})), bs$row[b])
} else {
matgpp[startind[b]:endind[b],] <- do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[10,])}))
matTr[startind[b]:endind[b],] <- do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[16,])}))
matwue[startind[b]:endind[b],] <- do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[17,])}))
matlue[startind[b]:endind[b],] <- do.call(rbind,lapply(d$value$value,function(mat){as.numeric(mat[9,])}))
}
# need to send more data?
ni <- nodes + i
if (ni <= bs$n) {
parallel:::sendCall(cl[[d$node]], clFun, ni, tag=ni)
}
gc()
setTxtProgressBar(pb,i)
}
###############################################################################################
# 06. close connection with the files, or assign valueas to the raster objects
###############################################################################################
if (!inmem) {
gpp <- writeStop(gpp)
Tr <- writeStop(Tr)
wue <- writeStop(wue)
lue <- writeStop(lue)
} else {
# gpp
gpp<-setValues(gpp,matgpp)
# transpiration
Tr<-setValues(Tr,matTr)
# water use efficiency
wue<-setValues(wue,matwue)
# light use efficiency
lue<-setValues(lue,matlue)
}
close(pb)
gc()
return(list(gpp=gpp,lue=lue,Tr=Tr,wue=wue))
}
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