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Testing4 #5

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7f6ae9b
Update met2model.FATES.R
rahul799 Apr 23, 2020
acde392
Update write.configs.FATES.R
rahul799 Apr 23, 2020
529405a
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Apr 23, 2020
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147 changes: 78 additions & 69 deletions models/fates/R/met2model.FATES.R
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#-------------------------------------------------------------------------------
# Copyright (c) 2016 NCSA.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the
# are made available under the terms of the
# University of Illinois/NCSA Open Source License
# which accompanies this distribution, and is available at
# http://opensource.ncsa.illinois.edu/license.html
Expand All @@ -10,7 +10,7 @@
# R Code to convert NetCDF CF met files into NetCDF FATES met files.

##' met2model wrapper for FATES
##'
##'
##' @title met2model for FATES
##' @export
##' @param in.path location on disk where inputs are stored
Expand All @@ -22,143 +22,152 @@
##' @param overwrite should existing files be overwritten
##' @param verbose should the function be very verbosefor(year in start_year:end_year)
##' @importFrom ncdf4 ncvar_get ncdim_def ncatt_get ncvar_put
met2model.FATES <- function(in.path, in.prefix, outfolder, start_date, end_date, lst = 0, lat, lon,
met2model.FATES <- function(in.path, in.prefix, outfolder, start_date, end_date, lst = 0, lat, lon,
overwrite = FALSE, verbose = FALSE, ...) {

# General Structure- FATES Uses Netcdf so we need to rename vars, split files from years into months, and generate the header file
# Get Met file from inpath.
# Loop over years (Open nc.file,rename vars,change dimensions as needed,close/save .nc file)
# close
# defining temporal dimension needs to be figured out. If we configure FATES to use same tstep then we may not need to change dimensions
# defining temporal dimension needs to be figured out. If we configure FATES to use same tstep then we may not need to change dimensions

library(PEcAn.utils)

insert <- function(ncout, name, unit, data) {
var <- ncdf4::ncvar_def(name = name, units = unit, dim = dim, missval = -6999, verbose = verbose)
var <- ncdf4::ncvar_def(name = name, units = unit, dim = dim, missval = -6999, verbose = verbose)
ncout <- ncdf4::ncvar_add(nc = ncout, v = var, verbose = verbose)
ncvar_put(nc = ncout, varid = name, vals = data)
return(invisible(ncout))
}
sm <- c(0, 31, 59, 90, 120, 151, 181, 212, 243, 273, 304, 334, 365) * 86400 ## day of year thresholds
sm <- c(0, 31, 59, 90, 120, 151, 181, 212, 243, 273, 304, 334, 365) * 86400 ## day of year thresholds

## Create output directory
dir.create(outfolder)

# Process start and end dates
start_date <- as.POSIXlt(start_date, tz = "UTC")
end_date <- as.POSIXlt(end_date, tz = "UTC")
end_date <- as.POSIXlt(end_date, tz = "UTC")
start_year <- lubridate::year(start_date)
end_year <- lubridate::year(end_date)
end_year <- lubridate::year(end_date)

## Build met
for (year in start_year:end_year) {

in.file <- file.path(in.path, paste(in.prefix, year, "nc", sep = "."))

if (file.exists(in.file)) {

## Open netcdf file
nc <- ncdf4::nc_open(in.file)

## extract variables. These need to be read in and converted to CLM names (all units are correct)
time <- ncvar_get(nc, "time")
latitude <- ncvar_get(nc, "latitude")
time <- ncvar_get(nc, "time")
latitude <- ncvar_get(nc, "latitude")
longitude <- ncvar_get(nc, "longitude")
FLDS <- ncvar_get(nc, "surface_downwelling_longwave_flux_in_air") ## W/m2
FSDS <- ncvar_get(nc, "surface_downwelling_shortwave_flux_in_air") ## W/m2
PRECTmms <- ncvar_get(nc, "precipitation_flux") ## kg/m2/s -> mm/s (same val, diff name)
PSRF <- ncvar_get(nc, "air_pressure") ## Pa
SHUM <- ncvar_get(nc, "specific_humidity") ## g/g -> kg/kg
TBOT <- ncvar_get(nc, "air_temperature") ## K
WIND <- sqrt(ncvar_get(nc, "eastward_wind") ^ 2 + ncvar_get(nc, "northward_wind") ^ 2) ## m/s
FLDS <- ncvar_get(nc, "surface_downwelling_longwave_flux_in_air") ## W/m2
FSDS <- ncvar_get(nc, "surface_downwelling_shortwave_flux_in_air") ## W/m2
PRECTmms <- ncvar_get(nc, "precipitation_flux") ## kg/m2/s -> mm/s (same val, diff name)
PSRF <- ncvar_get(nc, "air_pressure") ## Pa
SHUM <- ncvar_get(nc, "specific_humidity") ## g/g -> kg/kg
TBOT <- ncvar_get(nc, "air_temperature") ## K
WIND <- sqrt(ncvar_get(nc, "eastward_wind")^2 + ncvar_get(nc, "northward_wind")^2) ## m/s

## CREATE MONTHLY FILES
for (mo in 1:12) {
tsel <- which(time > sm[mo] & time <= sm[mo + 1])
outfile <- file.path(outfolder, paste0(formatC(year, width = 4, flag = "0"), "-",
formatC(mo, width = 2, flag = "0"), ".nc"))
outfile <- file.path(outfolder, paste0(
formatC(year, width = 4, flag = "0"), "-",
formatC(mo, width = 2, flag = "0"), ".nc"
))
if (file.exists(outfile) & overwrite == FALSE) {
next
}

lat.dim <- ncdim_def(name = "latitude", units = "", vals = 1:1, create_dimvar = FALSE)
lon.dim <- ncdim_def(name = "longitude", units = "", vals = 1:1, create_dimvar = FALSE)
time.dim <- ncdim_def(name = "time", units = "seconds", vals = time,
create_dimvar = TRUE, unlim = TRUE)
dim <- list(lat.dim, lon.dim, time.dim) ## docs say this should be time,lat,lon but get error writing unlimited first

lat.dim <- ncdim_def(name = "latitude", units = "", vals = 1:1, create_dimvar = FALSE)
lon.dim <- ncdim_def(name = "longitude", units = "", vals = 1:1, create_dimvar = FALSE)
time.dim <- ncdim_def(
name = "time", units = "seconds", vals = time,
create_dimvar = TRUE, unlim = TRUE
)
dim <- list(lat.dim, lon.dim, time.dim) ## docs say this should be time,lat,lon but get error writing unlimited first
## http://www.cesm.ucar.edu/models/cesm1.2/clm/models/lnd/clm/doc/UsersGuide/x12979.html

# LATITUDE
var <- ncdf4::ncvar_def(name = "latitude", units = "degree_north",
dim = list(lat.dim, lon.dim), missval = as.numeric(-9999))
var <- ncdf4::ncvar_def(
name = "latitude", units = "degree_north",
dim = list(lat.dim, lon.dim), missval = as.numeric(-9999)
)
ncout <- ncdf4::nc_create(outfile, vars = var, verbose = verbose)
ncvar_put(nc = ncout, varid = "latitude", vals = latitude)

# LONGITUDE
var <- ncdf4::ncvar_def(name = "longitude", units = "degree_east",
dim = list(lat.dim, lon.dim), missval = as.numeric(-9999))
var <- ncdf4::ncvar_def(
name = "longitude", units = "degree_east",
dim = list(lat.dim, lon.dim), missval = as.numeric(-9999)
)
ncout <- ncdf4::ncvar_add(nc = ncout, v = var, verbose = verbose)
ncvar_put(nc = ncout, varid = "longitude", vals = longitude)

## surface_downwelling_longwave_flux_in_air
ncout <- insert(ncout, "FLDS", "W m-2", FLDS)

## surface_downwelling_shortwave_flux_in_air
ncout <- insert(ncout, "FSDS", "W m-2", FSDS)

## precipitation_flux
ncout <- insert(ncout, "PRECTmms", "mm/s", PRECTmms)

## air_pressure
ncout <- insert(ncout, "PSRF", "Pa", PSRF)

## specific_humidity
ncout <- insert(ncout, "SHUM", "kg/kg", SHUM)

## air_temperature
ncout <- insert(ncout, "TBOT", "K", TBOT)

## eastward_wind & northward_wind
ncout <- insert(ncout, "WIND", "m/s", WIND)

ncdf4::nc_close(ncout)

# ncvar_rename(ncfile,varid="LONGXY")
# ncvar_rename(ncfile,varid="LATIXY")
# #
# #
# # double EDGEW(scalar) ;
# # EDGEW:long_name = "western edge in atmospheric data" ;
# # EDGEW:units = "degrees E" ;
# EDGEW = ncvar_rename(ncfile,"EDGEW","EDGEW")
#
#
# # double EDGEE(scalar) ;
# # EDGEE:long_name = "eastern edge in atmospheric data" ;
# # EDGEE:units = "degrees E" ;
# EDGEE = ncvar_rename(ncfile,"EDGEE","EDGEE")
#
#
# # double EDGES(scalar) ;
# # EDGES:long_name = "southern edge in atmospheric data" ;
# # EDGES:units = "degrees N" ;
# EDGES = ncvar_rename(ncfile,"EDGES","EDGES")
# #
# EDGES = ncvar_rename(ncfile,"EDGES","EDGES")
# #
# # double EDGEN(scalar) ;
# # EDGEN:long_name = "northern edge in atmospheric data" ;
# # EDGEN:units = "degrees N" ;
# EDGEN = ncvar_rename(ncfile,"EDGEN","EDGEN")
}

ncdf4::nc_close(nc)
} ## end file exists
} ### end loop over met files
} ## end file exists
} ### end loop over met files

PEcAn.logger::logger.info("Done with met2model.FATES")

return(data.frame(file = paste0(outfolder, "/"),
host = c(PEcAn.remote::fqdn()),
mimetype = c("application/x-netcdf"),
formatname = c("CLM met"),
startdate = c(start_date),
enddate = c(end_date),
dbfile.name = "",
stringsAsFactors = FALSE))

return(data.frame(
file = paste0(outfolder, "/"),
host = c(PEcAn.remote::fqdn()),
mimetype = c("application/x-netcdf"),
formatname = c("CLM met"),
startdate = c(start_date),
enddate = c(end_date),
dbfile.name = "",
stringsAsFactors = FALSE
))
} # met2model.FATES
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