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commented out daily cohort-level output
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@stineb
stineb committed May 17, 2024
1 parent 22f03f7 commit b177d49
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Showing 5 changed files with 474 additions and 370 deletions.
258 changes: 181 additions & 77 deletions R/run_biomee_f_bysite.R
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Original file line number Diff line number Diff line change
Expand Up @@ -610,44 +610,108 @@ run_biomee_f_bysite <- function(
if (size_of_object_gb < 5){
output_daily_tile <- as.data.frame(biomeeout[[1]], stringAsFactor = FALSE)
colnames(output_daily_tile) <- c(
"year", "doy", "Tc",
"Prcp", "totWs", "Trsp",
"Evap", "Runoff", "ws1",
"ws2", "ws3", "LAI",
"GPP", "Rauto", "Rh",
"NSC", "seedC", "leafC",
"rootC", "SW_C", "HW_C",
"NSN", "seedN", "leafN",
"rootN", "SW_N", "HW_N",
"McrbC", "fastSOM", "slowSOM",
"McrbN", "fastSoilN", "slowSoilN",
"mineralN", "N_uptk")
"year",
"doy",
"Tc",
"Prcp",
"totWs",
"Trsp",
"Evap",
"Runoff",
"ws1",
"ws2",
"ws3",
"LAI",
"GPP",
"Rauto",
"Rh",
"NSC",
"seedC",
"leafC",
"rootC",
"SW_C",
"HW_C",
"NSN",
"seedN",
"leafN",
"rootN",
"SW_N",
"HW_N",
"McrbC",
"fastSOM",
"slowSOM",
"McrbN",
"fastSoilN",
"slowSoilN",
"mineralN",
"N_uptk")
} else {
output_daily_tile <- NA
}

# annual tile
output_annual_tile <- as.data.frame(biomeeout[[29]], stringAsFactor = FALSE)
colnames(output_annual_tile) <- c("year", "CAI", "LAI",
"Density", "DBH", "Density12",
"DBH12", "QMD", "NPP",
"GPP", "Rauto", "Rh",
"rain", "SoilWater","Transp",
"Evap", "Runoff", "plantC",
"soilC", "plantN", "soilN",
"totN", "NSC", "SeedC", "leafC",
"rootC", "SapwoodC", "WoodC",
"NSN", "SeedN", "leafN",
"rootN", "SapwoodN", "WoodN",
"McrbC", "fastSOM", "SlowSOM",
"McrbN", "fastSoilN", "slowSoilN",
"mineralN", "N_fxed", "N_uptk",
"N_yrMin", "N_P2S", "N_loss",
"totseedC", "totseedN", "Seedling_C",
"Seedling_N", "MaxAge", "MaxVolume",
"MaxDBH", "NPPL", "NPPW",
"n_deadtrees", "c_deadtrees", "m_turnover",
"c_turnover_time")
output_annual_tile <- as.data.frame(biomeeout[[2]], stringAsFactor = FALSE)
colnames(output_annual_tile) <- c(
"year",
"CAI",
"LAI",
"Density",
"DBH",
"Density12",
"DBH12",
"QMD",
"NPP",
"GPP",
"Rauto",
"Rh",
"rain",
"SoilWater","
Transp",
"Evap",
"Runoff",
"plantC",
"soilC",
"plantN",
"soilN",
"totN",
"NSC",
"SeedC",
"leafC",
"rootC",
"SapwoodC",
"WoodC",
"NSN",
"SeedN",
"leafN",
"rootN",
"SapwoodN",
"WoodN",
"McrbC",
"fastSOM",
"SlowSOM",
"McrbN",
"fastSoilN",
"slowSoilN",
"mineralN",
"N_fxed",
"N_uptk",
"N_yrMin",
"N_P2S",
"N_loss",
"totseedC",
"totseedN",
"Seedling_C",
"Seedling_N",
"MaxAge",
"MaxVolume",
"MaxDBH",
"NPPL",
"NPPW",
"n_deadtrees",
"c_deadtrees",
"m_turnover",
"c_turnover_time"
)

#---- Multi-level output, multiple matrices to be combined ----

Expand All @@ -661,57 +725,97 @@ run_biomee_f_bysite <- function(
# as vector()

#---- daily cohorts ----
if (size_of_object_gb < 5){
daily_values <- c(
"year","doy","hour",
"cID", "PFT", "layer",
"density","f_layer", "LAI",
"gpp","resp","transp",
"NPPleaf","NPProot", "NPPwood", "NSC",
"seedC", "leafC", "rootC",
"SW_C", "HW_C", "NSN",
"seedN", "leafN", "rootN",
"SW_N", "HW_N"
)
output_daily_cohorts <- lapply(1:length(daily_values), function(x){
loc <- 1 + x
v <- data.frame(
as.vector(biomeeout[[loc]]),
stringsAsFactors = FALSE)
names(v) <- daily_values[x]
return(v)
})
# if (size_of_object_gb < 5){
# daily_values <- c(
# "year","
# doy","
# hour"
# "cID",
# "PFT",
# "layer"
# "density","
# f_layer",
# "LAI"
# "gpp","
# resp","
# transp"
# "NPPleaf","
# NPProot",
# "NPPwood",
# "NSC"
# "seedC",
# "leafC",
# "rootC"
# "SW_C",
# "HW_C",
# "NSN"
# "seedN",
# "leafN",
# "rootN"
# "SW_N",
# "HW_N"
# )
# output_daily_cohorts <- lapply(1:length(daily_values), function(x){
# loc <- 1 + x
# v <- data.frame(
# as.vector(biomeeout[[loc]]),
# stringsAsFactors = FALSE)
# names(v) <- daily_values[x]
# return(v)
# })

output_daily_cohorts <- do.call("cbind", output_daily_cohorts)
# output_daily_cohorts <- do.call("cbind", output_daily_cohorts)

cohort <- sort(rep(1:ncol(biomeeout[[3]]),nrow(biomeeout[[3]])))
output_daily_cohorts <- cbind(cohort, output_daily_cohorts)
# cohort <- sort(rep(1:ncol(biomeeout[[3]]),nrow(biomeeout[[3]])))
# output_daily_cohorts <- cbind(cohort, output_daily_cohorts)

# drop rows (cohorts) with no values
output_daily_cohorts$year[output_daily_cohorts$year == -9999 |
output_daily_cohorts$year == 0] <- NA
output_daily_cohorts <-
output_daily_cohorts[!is.na(output_daily_cohorts$year),]
} else {
output_daily_cohorts <- NA
}
# # drop rows (cohorts) with no values
# output_daily_cohorts$year[output_daily_cohorts$year == -9999 |
# output_daily_cohorts$year == 0] <- NA
# output_daily_cohorts <- output_daily_cohorts[!is.na(output_daily_cohorts$year),]
# } else {
# output_daily_cohorts <- NA
# }

#--- annual cohorts ----
annual_values <- c(
"year","cID",
"PFT","layer","density",
"flayer","DBH","dDBH","height",
"age","BA","dBA","Acrown","Aleaf",
"nsc","seedC","leafC","rootC",
"sapwC","woodC","nsn","treeG",
"fseed","fleaf","froot","fwood",
"GPP","NPP","Rauto",
"Nupt","Nfix","n_deadtrees",
"c_deadtrees","deathrate"
"year",
"cID",
"PFT",
"layer",
"density",
"flayer",
"DBH",
"dDBH",
"height",
"age",
"BA",
"dBA",
"Acrown",
"Aleaf",
"nsc",
"seedC",
"leafC",
"rootC",
"sapwC",
"woodC",
"nsn",
"treeG",
"fseed",
"fleaf",
"froot",
"fwood",
"GPP",
"NPP",
"Rauto",
"Nupt",
"Nfix",
"n_deadtrees",
"c_deadtrees",
"deathrate"
)

output_annual_cohorts <- lapply(1:length(annual_values), function(x){
loc <- 29 + x
loc <- 2 + x
v <- data.frame(
as.vector(biomeeout[[loc]]),
stringsAsFactors = FALSE)
Expand All @@ -735,7 +839,7 @@ run_biomee_f_bysite <- function(
out <- list(
# output_hourly_tile = output_hourly_tile,
output_daily_tile = output_daily_tile,
output_daily_cohorts = output_daily_cohorts,
# output_daily_cohorts = output_daily_cohorts,
output_annual_tile = output_annual_tile,
output_annual_cohorts = output_annual_cohorts)

Expand Down
8 changes: 4 additions & 4 deletions src/biosphere_biomee.mod.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ module md_biosphere_biomee

subroutine biosphere_annual( &
out_biosphere_daily_tile, &
out_biosphere_daily_cohorts, &
! out_biosphere_daily_cohorts, &
out_biosphere_annual_tile, &
out_biosphere_annual_cohorts &
)
Expand All @@ -31,14 +31,14 @@ subroutine biosphere_annual( &
!----------------------------------------------------------------
use md_interface_biomee, only: myinterface, &
outtype_daily_tile, &
outtype_daily_cohorts, &
! outtype_daily_cohorts, &
outtype_annual_tile, &
outtype_annual_cohorts
use md_gpp_biomee, only: getpar_modl_gpp

! return variables
type(outtype_daily_tile), dimension(ndayyear) , intent(out) :: out_biosphere_daily_tile
type(outtype_daily_cohorts), dimension(ndayyear,out_max_cohorts), intent(out) :: out_biosphere_daily_cohorts
! type(outtype_daily_cohorts), dimension(ndayyear,out_max_cohorts), intent(out) :: out_biosphere_daily_cohorts
type(outtype_annual_tile) , intent(out) :: out_biosphere_annual_tile
type(outtype_annual_cohorts), dimension(out_max_cohorts) , intent(out) :: out_biosphere_annual_cohorts

Expand Down Expand Up @@ -144,7 +144,7 @@ subroutine biosphere_annual( &
soil_theta = vegn%thetaS

! sum over fast time steps and cohorts
call daily_diagnostics( vegn, iyears, idoy, out_biosphere_daily_cohorts(doy,:), out_biosphere_daily_tile(doy) )
call daily_diagnostics( vegn, iyears, idoy, out_biosphere_daily_tile(doy) ) ! , out_biosphere_daily_cohorts(doy,:)

! Determine start and end of season and maximum leaf (root) mass
call vegn_phenology( vegn )
Expand Down
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