R/wrf_create.R
In ibarraespinosa/eixport: Export Emissions to Atmospheric Models
Defines functions
wrf_create
Documented in
wrf_create
#' Create emission files for the WRF-Chem model
#'
#' @description Create WRF-chem emission files using information from the WRF initial condictions (wrfinput) file(s). The wrfinput file of the corresponding domain is read from the current folder or from the wrfinput_dir.
#'
#' There are two emission styles available: the 12 hour pair of emissions (that will be recycled by the model) using io_style_emissions = 1 and the date_hour format using io_style_emissions = 2 (default), see notes for more detail.
#'
#' The initial time is the original (wrfinput file) adjusted by the day_offset argument, this argument can be useful for split the emissions into several files or for a restarted simulation. The emissions are recorded at the interval of 60 minutes (or the auxinput5_interval_m argument) for 1 time (or frames_per_auxinput5 argument times).
#'
#' The variables created on output file is based on emis_opt data or a character vector contains the species, any change in variables need to be followed by a change in the n_aero for the correspondent number of aerosol species in the emission file (the n_aero last variables).
#'
#' Title argument will be written on global attribute TITLE, from the version 4.0 the model checks if the TITLE version contains "V4.", this can be disabled setting 'force_use_old_data = .true.' on WRF namelist.input.
#'
#' @param wrfinput_dir input folder with the wrfinput file(s)
#' @param wrfchemi_dir output folder
#' @param domains domain / domains to be process
#' @param frames_per_auxinput5 value from wrf &time_control namelist.input,
#' number of times (frames) in a single emission file
#' @param auxinput5_interval_m value from wrf &time_control namelist.input,
#' interval in minutes between different times (frames) see Details
#' @param day_offset number of days (can be a fraction) see Details
#' @param io_style_emissions from wrf &chem namelist.input, 1 for 12z/00z style and 2 to date_hour style, see Details
#' @param kemit from wrf &chem namelist.input number of vertical levels of the emission file
#' @param variables emission species, can be used `emis_opt`
#' @param n_aero number of aerosol species
#' @param COMPRESS integer between 1 (least comp.) and 9 (most comp.) or NA for
#' no compression
#' @param force_ncdf4 force NetCDF4 format
#' @param title TITLE attribute for the NetCDF
#' @param separator filename alternative separator for hour:minutes:seconds with io_style_emission=2
#' @param prefix file name prefix, default is wrfchemi (wrf default)
#' @param overwrite logical, defoult is true, if FALSE check if the file exist
#' @param return_fn logical, return the name of the last file created
#' @param verbose print file info
#'
#' @note Using io_style_emissions = 1, the wrfchemi_00z will be generated with day_offset = 0 and
#' wrfchemi_12z with day_offset = 0.5 (frames_per_auxinput5 and auxinput5_interval_m will have no effect).
#'
#' @note Windows users may need to rename the emission files or change in namelist the defoult filename before run wrf.exe with these emission files.
#'
#' @note The separator argument can be useful for write in NTSF format discs on linux systems, for 'default' the separator is ':' for linux-like systems and '%3A' for windowns.
#'
#' @author Daniel Schuch
#'
#' @importFrom ncdf4 nc_open nc_close ncvar_get ncvar_put ncdim_def ncvar_def ncatt_put
#'
#' @export
#'
#' @seealso \code{\link{to_wrf}} and \code{\link{emis_opt}}
#'
#' @examples \dontrun{
#' # Do not run
#'
#' # emissions for a 1 day forecast for domains 1 and 2
#'
#' dir.create(file.path(tempdir(), "EMISS"))
#'
#' # emissions on date_hour style
#' wrf_create(wrfinput_dir = system.file("extdata", package = "eixport"),
#' wrfchemi_dir = file.path(tempdir(), "EMISS"),
#' domains = 1:2,
#' frames_per_auxinput5 = 25,
#' auxinput5_interval_m = 60,
#' verbose = TRUE)
#'
#' # emissions on 00z / 12z style, create the 00z
#' wrf_create(wrfinput_dir = system.file("extdata", package = "eixport"),
#' wrfchemi_dir = file.path(tempdir(), "EMISS"),
#' domains = 1:2,
#' io_style_emissions = 1,
#' day_offset = 0,
#' verbose = TRUE,
#' )
#' # emissions on 00z / 12z style, create the 12z
#' wrf_create(wrfinput_dir = system.file("extdata", package = "eixport"),
#' wrfchemi_dir = file.path(tempdir(), "EMISS"),
#' domains = 1:2,
#' io_style_emissions = 1,
#' day_offset = 0.5,
#' verbose = TRUE)
#'}
wrf_create <- function(wrfinput_dir = getwd(),
wrfchemi_dir = wrfinput_dir,
domains = 1,
frames_per_auxinput5 = 1,
auxinput5_interval_m = 60,
day_offset = 0,
io_style_emissions = 2,
kemit = 1,
variables = "ecb05_opt2",
n_aero = 15,
COMPRESS = NA,
force_ncdf4 = FALSE,
title = "Anthropogenic emissions for WRF V4.0",
separator = 'default',
prefix = 'wrfchemi',
overwrite = TRUE,
return_fn = FALSE,
verbose = FALSE)
{
a <- Sys.info()["sysname"]
# to avoid special chacacteres in the filename
if(a[[1]] == "Windows") linux = FALSE else linux = TRUE # nocov
if(a[[1]] == "Windows")
if(io_style_emissions == 2) # nocov
cat("NOTE: see wrf_create domumentation notes before run\n") # nocov
if(length(variables) == 1 & !is.na(variables)[1]){
emis_opt <- sysdata$emis_opt
if(variables %in% names(emis_opt)){
variables <- emis_opt[[variables]]
}else{
cat(paste(variables,"is not valid, use one of:\n")) # nocov
cat(names(emis_opt)) # nocov
stop("name, numeric value or a set of variable names") # nocov
}
}
if(is.na(variables)[1]){
cat("writing the emission file without emission variables\n") # nocov
}else{
if(n_aero > length(variables)){
stop("n_aero cannot be greater than the number of variables ") # nocov
}
}
for(domain in domains){
# basic information from wrfinput
wrfinput <- paste(wrfinput_dir, "/wrfinput_d0", domain, sep = "")
wrfinput <- ncdf4::nc_open(wrfinput,write = F)
input_time <- ncdf4::ncvar_get(wrfinput,"Times")
date <- as.character(paste(substr(input_time, 1, 10),
substr(input_time, 12, 19)))
date <- as.POSIXct(strptime(date, "%Y-%m-%d %H:%M:%S"))
if(io_style_emissions == 1){
if(day_offset != 0){ # nocov
day_offset <- 0.5 # nocov
}
}
date <- date + 86400 * day_offset
hora <- format(date,"%H")
minuto <- format(date,"%M")
segundo <- format(date,"%S")
hora <- paste(formatC(hora, width = 2, format = "d", flag = "0"))
minuto <- paste(formatC(minuto, width = 2, format = "d", flag = "0"))
segundo <- paste(formatC(segundo, width = 2, format = "d", flag = "0"))
if(separator == 'default'){
separator <- "%3A" # nocov
}else{
linux <- FALSE # nocov
}
if(io_style_emissions == 1){
frames_per_auxinput5 <- 12 # nocov start
if(day_offset == 0){
h <- "00z"
}else{
h <- "12z"
}
file_name <- paste(wrfchemi_dir, "/",prefix,"_", h, "_", "d0",domain, sep = "") # nocov end
}
if(io_style_emissions ==2){ # nocov start
if(linux){
file_name <- paste(wrfchemi_dir, "/",prefix,"_d0", domain, "_",
format(date,"%Y-%m-%d"),
"_",hora,":", minuto,":", segundo, sep = "")
} else file_name <- paste(wrfchemi_dir, "/",prefix,"_d0", domain, "_",
format(date,"%Y-%m-%d"),
"_", hora, separator, minuto, separator, segundo, sep = "")# nocov end
}
if(!overwrite & file.exists(file_name)){
cat('using current file for domain',domain,'...\n') # nocov
next # nocov
}else{
cat('creating emission for domain',domain,'...\n')
}
if(frames_per_auxinput5 == 1){
file_time <- paste(format(date,"%Y-%m-%d"),
"_", hora, ":", minuto, ":", segundo, sep = "")
}
else{ # nocov start
file_time <- character(frames_per_auxinput5)
for(i in 1:frames_per_auxinput5){
file_time[i] <- paste(format(date,"%Y-%m-%d"),
"_", hora, ":", minuto, ":", segundo, sep = "")
date <- date + 60 * auxinput5_interval_m
hora <- format(date,"%H")
minuto <- format(date,"%M")
segundo <- format(date,"%S")
hora <- paste(formatC(hora,
width = 2,
format = "d",
flag = "0"))
minuto <- paste(formatC(minuto,
width = 2,
format = "d",
flag = "0"))
segundo <- paste(formatC(segundo,
width = 2,
format = "d",
flag = "0"))
} # nocov end
}
input_lat <- ncdf4::ncvar_get(wrfinput, "XLAT")
input_lon <- ncdf4::ncvar_get(wrfinput, "XLONG")
g_atributos <- ncdf4::ncatt_get(wrfinput, 0)
g_atributos <- c( list(TITLE = title,
History = paste("created on",
format(Sys.time(),
"%Y-%m-%d at %H:%M")),
Author = paste0("R package eixport v",
utils::packageVersion("eixport"))),
g_atributos[4:length(g_atributos)])
# definition of dimensions
west_east <- ncdf4::ncdim_def("west_east",
units = "",
longname = "",
vals = 1:g_atributos$`WEST-EAST_PATCH_END_UNSTAG`)
south_north <- ncdf4::ncdim_def("south_north",
units = "",
longname = "",
vals = 1:g_atributos$`SOUTH-NORTH_PATCH_END_UNSTAG`)
emissions_zdim_stag <- ncdf4::ncdim_def("emissions_zdim_stag",
units = "",
longname = "",
vals = 1:kemit)
DateStrLen <- ncdf4::ncdim_def("DateStrLen",
units = "",
longname = "",
vals = 1:19)
Time <- ncdf4::ncdim_def("Time",
units = "",
longname = "",
vals = 1:frames_per_auxinput5,
unlim = TRUE)
# definition of variables
Times <- ncdf4::ncvar_def(name = "Times",
dim = list(DateStrLen,Time),
units = "",
prec = "char",
compression = COMPRESS)
XLONG <- ncdf4::ncvar_def(name = "XLONG",
units = "",
dim = list(west_east,south_north),
prec = "float",
compression = COMPRESS)
XLAT <- ncdf4::ncvar_def(name = "XLAT" ,
units = "",
dim = list(west_east, south_north),
prec = "float",
compression = COMPRESS)
if(!is.na(variables)[1]){
# GAS phase emissions
if(n_aero != length(variables)){
for(i in 1:(length(variables) - n_aero)){
assign(variables[i],
ncdf4::ncvar_def(name = variables[i],
units = "",
dim = list(west_east,
south_north,
emissions_zdim_stag,
Time),
prec="float",
compression = COMPRESS))
}
}
# AEROSOLS emissions
if(n_aero > 0){
for(i in (1+length(variables) - n_aero):length(variables)){
assign(variables[i],
ncdf4::ncvar_def(name = variables[i],
units = "",
dim = list(west_east,
south_north,
emissions_zdim_stag,
Time),prec="float",
compression = COMPRESS))
}
}
}
emiss_file <- nc_create(filename = file_name,
vars = c(list('Times' = Times,
'XLAT' = XLAT,
'XLONG' = XLONG),
mget(ls(pattern = "E_"))),
force_v4 = force_ncdf4)
for(i in 1:length(g_atributos)){
ncdf4::ncatt_put(emiss_file,
varid = 0,
attname = names(g_atributos)[i],
attval = g_atributos[[i]])
}
# values for the basic variables
ncdf4::ncvar_put(emiss_file,
"Times",
file_time)
ncdf4::ncvar_put(emiss_file,
"XLONG",
input_lon)
ncdf4::ncatt_put(emiss_file,
varid = "XLONG",
attname = "MemoryOrder",
attval = "XY")
ncdf4::ncatt_put(emiss_file,
varid = "XLONG",
attname = "description",
attval = "LONGITUDE, WEST IS NEGATIVE")
ncdf4::ncatt_put(emiss_file,
varid = "XLONG",
attname = "units",
attval = "degree east")
ncdf4::ncatt_put(emiss_file,
varid = "XLONG",
attname = "stagger",
attval = "")
ncdf4::ncatt_put(emiss_file,
varid = "XLONG",
attname = "FieldType",
attval = 104)
ncdf4::ncvar_put(emiss_file,
"XLAT",
input_lat)
ncdf4::ncatt_put(emiss_file,
varid = "XLAT",
attname = "MemoryOrder",
attval = "XY")
ncdf4::ncatt_put(emiss_file,
varid = "XLAT",
attname = "description",
attval = "LATITUDE, SOUTH IS NEGATIVE")
ncdf4::ncatt_put(emiss_file,
varid = "XLAT",
attname = "units",
attval = "degree north")
ncdf4::ncatt_put(emiss_file,
varid = "XLAT",
attname = "stagger",
attval = "")
ncdf4::ncatt_put(emiss_file,
varid = "XLAT",
attname = "FieldType",
attval = 104)
# vetor of zeros
zero <- array(0, c(west_east$len,
south_north$len,
emissions_zdim_stag$len,
Time$len))
if(!is.na(variables)[1]){
# GASES initialization with zeros
if(n_aero != length(variables)){
for(i in 1:(length(variables) - n_aero)){
ncdf4::ncvar_put(emiss_file,
varid = variables[i],
zero)
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "MemoryOrder",
attval = "XYZ")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "description",
attval = "EMISSIONS")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "units",
attval = "mol km^-2 hr^-1")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "stagger",
attval = "Z")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "FieldType",
attval = 104)
}
}
# AEROSOIS initialization with zeros
if(n_aero > 0){
for(i in (1 + length(variables) - n_aero):length(variables)){
ncdf4::ncvar_put(emiss_file,
varid = variables[i],
zero)
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "MemoryOrder",
attval = "XYZ")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "description",
attval = "EMISSIONS")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "units",
attval = "ug m^-2 s^-1")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "stagger",
attval = "Z")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "FieldType",
attval = 104)
}
}
}
if(verbose){
print(emiss_file, "\n")
}
cat('output file:',emiss_file$filename,'\n')
ncdf4::nc_close(emiss_file)
ncdf4::nc_close(wrfinput)
}
if(return_fn){
return(emiss_file$filename) # nocov
}
}
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Defines functions wrf_create
Documented in wrf_create
#' Create emission files for the WRF-Chem model
#'
#' @description Create WRF-chem emission files using information from the WRF initial condictions (wrfinput) file(s). The wrfinput file of the corresponding domain is read from the current folder or from the wrfinput_dir.
#'
#' There are two emission styles available: the 12 hour pair of emissions (that will be recycled by the model) using io_style_emissions = 1 and the date_hour format using io_style_emissions = 2 (default), see notes for more detail.
#'
#' The initial time is the original (wrfinput file) adjusted by the day_offset argument, this argument can be useful for split the emissions into several files or for a restarted simulation. The emissions are recorded at the interval of 60 minutes (or the auxinput5_interval_m argument) for 1 time (or frames_per_auxinput5 argument times).
#'
#' The variables created on output file is based on emis_opt data or a character vector contains the species, any change in variables need to be followed by a change in the n_aero for the correspondent number of aerosol species in the emission file (the n_aero last variables).
#'
#' Title argument will be written on global attribute TITLE, from the version 4.0 the model checks if the TITLE version contains "V4.", this can be disabled setting 'force_use_old_data = .true.' on WRF namelist.input.
#'
#' @param wrfinput_dir input folder with the wrfinput file(s)
#' @param wrfchemi_dir output folder
#' @param domains domain / domains to be process
#' @param frames_per_auxinput5 value from wrf &time_control namelist.input,
#' number of times (frames) in a single emission file
#' @param auxinput5_interval_m value from wrf &time_control namelist.input,
#' interval in minutes between different times (frames) see Details
#' @param day_offset number of days (can be a fraction) see Details
#' @param io_style_emissions from wrf &chem namelist.input, 1 for 12z/00z style and 2 to date_hour style, see Details
#' @param kemit from wrf &chem namelist.input number of vertical levels of the emission file
#' @param variables emission species, can be used `emis_opt`
#' @param n_aero number of aerosol species
#' @param COMPRESS integer between 1 (least comp.) and 9 (most comp.) or NA for
#' no compression
#' @param force_ncdf4 force NetCDF4 format
#' @param title TITLE attribute for the NetCDF
#' @param separator filename alternative separator for hour:minutes:seconds with io_style_emission=2
#' @param prefix file name prefix, default is wrfchemi (wrf default)
#' @param overwrite logical, defoult is true, if FALSE check if the file exist
#' @param return_fn logical, return the name of the last file created
#' @param verbose print file info
#'
#' @note Using io_style_emissions = 1, the wrfchemi_00z will be generated with day_offset = 0 and
#' wrfchemi_12z with day_offset = 0.5 (frames_per_auxinput5 and auxinput5_interval_m will have no effect).
#'
#' @note Windows users may need to rename the emission files or change in namelist the defoult filename before run wrf.exe with these emission files.
#'
#' @note The separator argument can be useful for write in NTSF format discs on linux systems, for 'default' the separator is ':' for linux-like systems and '%3A' for windowns.
#'
#' @author Daniel Schuch
#'
#' @importFrom ncdf4 nc_open nc_close ncvar_get ncvar_put ncdim_def ncvar_def ncatt_put
#'
#' @export
#'
#' @seealso \code{\link{to_wrf}} and \code{\link{emis_opt}}
#'
#' @examples \dontrun{
#' # Do not run
#'
#' # emissions for a 1 day forecast for domains 1 and 2
#'
#' dir.create(file.path(tempdir(), "EMISS"))
#'
#' # emissions on date_hour style
#' wrf_create(wrfinput_dir = system.file("extdata", package = "eixport"),
#' wrfchemi_dir = file.path(tempdir(), "EMISS"),
#' domains = 1:2,
#' frames_per_auxinput5 = 25,
#' auxinput5_interval_m = 60,
#' verbose = TRUE)
#'
#' # emissions on 00z / 12z style, create the 00z
#' wrf_create(wrfinput_dir = system.file("extdata", package = "eixport"),
#' wrfchemi_dir = file.path(tempdir(), "EMISS"),
#' domains = 1:2,
#' io_style_emissions = 1,
#' day_offset = 0,
#' verbose = TRUE,
#' )
#' # emissions on 00z / 12z style, create the 12z
#' wrf_create(wrfinput_dir = system.file("extdata", package = "eixport"),
#' wrfchemi_dir = file.path(tempdir(), "EMISS"),
#' domains = 1:2,
#' io_style_emissions = 1,
#' day_offset = 0.5,
#' verbose = TRUE)
#'}
wrf_create <- function(wrfinput_dir = getwd(),
wrfchemi_dir = wrfinput_dir,
domains = 1,
frames_per_auxinput5 = 1,
auxinput5_interval_m = 60,
day_offset = 0,
io_style_emissions = 2,
kemit = 1,
variables = "ecb05_opt2",
n_aero = 15,
COMPRESS = NA,
force_ncdf4 = FALSE,
title = "Anthropogenic emissions for WRF V4.0",
separator = 'default',
prefix = 'wrfchemi',
overwrite = TRUE,
return_fn = FALSE,
verbose = FALSE)
{
a <- Sys.info()["sysname"]
# to avoid special chacacteres in the filename
if(a[[1]] == "Windows") linux = FALSE else linux = TRUE # nocov
if(a[[1]] == "Windows")
if(io_style_emissions == 2) # nocov
cat("NOTE: see wrf_create domumentation notes before run\n") # nocov
if(length(variables) == 1 & !is.na(variables)[1]){
emis_opt <- sysdata$emis_opt
if(variables %in% names(emis_opt)){
variables <- emis_opt[[variables]]
}else{
cat(paste(variables,"is not valid, use one of:\n")) # nocov
cat(names(emis_opt)) # nocov
stop("name, numeric value or a set of variable names") # nocov
}
}
if(is.na(variables)[1]){
cat("writing the emission file without emission variables\n") # nocov
}else{
if(n_aero > length(variables)){
stop("n_aero cannot be greater than the number of variables ") # nocov
}
}
for(domain in domains){
# basic information from wrfinput
wrfinput <- paste(wrfinput_dir, "/wrfinput_d0", domain, sep = "")
wrfinput <- ncdf4::nc_open(wrfinput,write = F)
input_time <- ncdf4::ncvar_get(wrfinput,"Times")
date <- as.character(paste(substr(input_time, 1, 10),
substr(input_time, 12, 19)))
date <- as.POSIXct(strptime(date, "%Y-%m-%d %H:%M:%S"))
if(io_style_emissions == 1){
if(day_offset != 0){ # nocov
day_offset <- 0.5 # nocov
}
}
date <- date + 86400 * day_offset
hora <- format(date,"%H")
minuto <- format(date,"%M")
segundo <- format(date,"%S")
hora <- paste(formatC(hora, width = 2, format = "d", flag = "0"))
minuto <- paste(formatC(minuto, width = 2, format = "d", flag = "0"))
segundo <- paste(formatC(segundo, width = 2, format = "d", flag = "0"))
if(separator == 'default'){
separator <- "%3A" # nocov
}else{
linux <- FALSE # nocov
}
if(io_style_emissions == 1){
frames_per_auxinput5 <- 12 # nocov start
if(day_offset == 0){
h <- "00z"
}else{
h <- "12z"
}
file_name <- paste(wrfchemi_dir, "/",prefix,"_", h, "_", "d0",domain, sep = "") # nocov end
}
if(io_style_emissions ==2){ # nocov start
if(linux){
file_name <- paste(wrfchemi_dir, "/",prefix,"_d0", domain, "_",
format(date,"%Y-%m-%d"),
"_",hora,":", minuto,":", segundo, sep = "")
} else file_name <- paste(wrfchemi_dir, "/",prefix,"_d0", domain, "_",
format(date,"%Y-%m-%d"),
"_", hora, separator, minuto, separator, segundo, sep = "")# nocov end
}
if(!overwrite & file.exists(file_name)){
cat('using current file for domain',domain,'...\n') # nocov
next # nocov
}else{
cat('creating emission for domain',domain,'...\n')
}
if(frames_per_auxinput5 == 1){
file_time <- paste(format(date,"%Y-%m-%d"),
"_", hora, ":", minuto, ":", segundo, sep = "")
}
else{ # nocov start
file_time <- character(frames_per_auxinput5)
for(i in 1:frames_per_auxinput5){
file_time[i] <- paste(format(date,"%Y-%m-%d"),
"_", hora, ":", minuto, ":", segundo, sep = "")
date <- date + 60 * auxinput5_interval_m
hora <- format(date,"%H")
minuto <- format(date,"%M")
segundo <- format(date,"%S")
hora <- paste(formatC(hora,
width = 2,
format = "d",
flag = "0"))
minuto <- paste(formatC(minuto,
width = 2,
format = "d",
flag = "0"))
segundo <- paste(formatC(segundo,
width = 2,
format = "d",
flag = "0"))
} # nocov end
}
input_lat <- ncdf4::ncvar_get(wrfinput, "XLAT")
input_lon <- ncdf4::ncvar_get(wrfinput, "XLONG")
g_atributos <- ncdf4::ncatt_get(wrfinput, 0)
g_atributos <- c( list(TITLE = title,
History = paste("created on",
format(Sys.time(),
"%Y-%m-%d at %H:%M")),
Author = paste0("R package eixport v",
utils::packageVersion("eixport"))),
g_atributos[4:length(g_atributos)])
# definition of dimensions
west_east <- ncdf4::ncdim_def("west_east",
units = "",
longname = "",
vals = 1:g_atributos$`WEST-EAST_PATCH_END_UNSTAG`)
south_north <- ncdf4::ncdim_def("south_north",
units = "",
longname = "",
vals = 1:g_atributos$`SOUTH-NORTH_PATCH_END_UNSTAG`)
emissions_zdim_stag <- ncdf4::ncdim_def("emissions_zdim_stag",
units = "",
longname = "",
vals = 1:kemit)
DateStrLen <- ncdf4::ncdim_def("DateStrLen",
units = "",
longname = "",
vals = 1:19)
Time <- ncdf4::ncdim_def("Time",
units = "",
longname = "",
vals = 1:frames_per_auxinput5,
unlim = TRUE)
# definition of variables
Times <- ncdf4::ncvar_def(name = "Times",
dim = list(DateStrLen,Time),
units = "",
prec = "char",
compression = COMPRESS)
XLONG <- ncdf4::ncvar_def(name = "XLONG",
units = "",
dim = list(west_east,south_north),
prec = "float",
compression = COMPRESS)
XLAT <- ncdf4::ncvar_def(name = "XLAT" ,
units = "",
dim = list(west_east, south_north),
prec = "float",
compression = COMPRESS)
if(!is.na(variables)[1]){
# GAS phase emissions
if(n_aero != length(variables)){
for(i in 1:(length(variables) - n_aero)){
assign(variables[i],
ncdf4::ncvar_def(name = variables[i],
units = "",
dim = list(west_east,
south_north,
emissions_zdim_stag,
Time),
prec="float",
compression = COMPRESS))
}
}
# AEROSOLS emissions
if(n_aero > 0){
for(i in (1+length(variables) - n_aero):length(variables)){
assign(variables[i],
ncdf4::ncvar_def(name = variables[i],
units = "",
dim = list(west_east,
south_north,
emissions_zdim_stag,
Time),prec="float",
compression = COMPRESS))
}
}
}
emiss_file <- nc_create(filename = file_name,
vars = c(list('Times' = Times,
'XLAT' = XLAT,
'XLONG' = XLONG),
mget(ls(pattern = "E_"))),
force_v4 = force_ncdf4)
for(i in 1:length(g_atributos)){
ncdf4::ncatt_put(emiss_file,
varid = 0,
attname = names(g_atributos)[i],
attval = g_atributos[[i]])
}
# values for the basic variables
ncdf4::ncvar_put(emiss_file,
"Times",
file_time)
ncdf4::ncvar_put(emiss_file,
"XLONG",
input_lon)
ncdf4::ncatt_put(emiss_file,
varid = "XLONG",
attname = "MemoryOrder",
attval = "XY")
ncdf4::ncatt_put(emiss_file,
varid = "XLONG",
attname = "description",
attval = "LONGITUDE, WEST IS NEGATIVE")
ncdf4::ncatt_put(emiss_file,
varid = "XLONG",
attname = "units",
attval = "degree east")
ncdf4::ncatt_put(emiss_file,
varid = "XLONG",
attname = "stagger",
attval = "")
ncdf4::ncatt_put(emiss_file,
varid = "XLONG",
attname = "FieldType",
attval = 104)
ncdf4::ncvar_put(emiss_file,
"XLAT",
input_lat)
ncdf4::ncatt_put(emiss_file,
varid = "XLAT",
attname = "MemoryOrder",
attval = "XY")
ncdf4::ncatt_put(emiss_file,
varid = "XLAT",
attname = "description",
attval = "LATITUDE, SOUTH IS NEGATIVE")
ncdf4::ncatt_put(emiss_file,
varid = "XLAT",
attname = "units",
attval = "degree north")
ncdf4::ncatt_put(emiss_file,
varid = "XLAT",
attname = "stagger",
attval = "")
ncdf4::ncatt_put(emiss_file,
varid = "XLAT",
attname = "FieldType",
attval = 104)
# vetor of zeros
zero <- array(0, c(west_east$len,
south_north$len,
emissions_zdim_stag$len,
Time$len))
if(!is.na(variables)[1]){
# GASES initialization with zeros
if(n_aero != length(variables)){
for(i in 1:(length(variables) - n_aero)){
ncdf4::ncvar_put(emiss_file,
varid = variables[i],
zero)
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "MemoryOrder",
attval = "XYZ")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "description",
attval = "EMISSIONS")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "units",
attval = "mol km^-2 hr^-1")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "stagger",
attval = "Z")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "FieldType",
attval = 104)
}
}
# AEROSOIS initialization with zeros
if(n_aero > 0){
for(i in (1 + length(variables) - n_aero):length(variables)){
ncdf4::ncvar_put(emiss_file,
varid = variables[i],
zero)
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "MemoryOrder",
attval = "XYZ")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "description",
attval = "EMISSIONS")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "units",
attval = "ug m^-2 s^-1")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "stagger",
attval = "Z")
ncdf4::ncatt_put(emiss_file,
varid = variables[i],
attname = "FieldType",
attval = 104)
}
}
}
if(verbose){
print(emiss_file, "\n")
}
cat('output file:',emiss_file$filename,'\n')
ncdf4::nc_close(emiss_file)
ncdf4::nc_close(wrfinput)
}
if(return_fn){
return(emiss_file$filename) # nocov
}
}
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