project_workflows/workflow_calpuff_india-orissa.R
In energyandcleanair/creapuff: CREAPUFF: R package to work with CALMET and CALPUFF
# Set up the environment
# remotes::install_github("energyandcleanair/creapuff", dependencies=T, update=F)
# devtools::reload(pkgload::inst("creapuff"))
library(creapuff)
library(readxl)
library(writexl)
library(lubridate)
library(tidyverse)
library(magrittr)
library(pbapply)
# Parameters ###################################################################
# ============================= Project specific ===============================
expand_grids = '*' # All grids are expanded (for CALMET)
expand_ncells = -5 # Number of cells to expand met grid (e.g., WRF) in each direction (use negative values to crop)
# project_dir="Z:/" # network disk (wrf_data). If Z disk is not present: mount 10.58.186.210:/wrf_data Z:)
project_dir="G:/india-orissa" # calpuff_external_data-2 persistent disk (project data)
wrf_dir <- file.path(project_dir,"calwrf") # Where calwrf data are stored
output_dir <- file.path(project_dir,"calpuff_suite") ; if (!dir.exists(output_dir)) dir.create(output_dir) # Where to write all generated files
# emission_type = "varying"
emission_type = "constant"
if (emission_type == "constant"){
emissions_dir <- file.path(project_dir,"emissions") # Directory where arbitrary-varying emission files are stored
input_xls <- file.path(emissions_dir,"emissions.xlsx") # File where constant-emission data are specified
# Emission file # Plants Capacity[MW] Lat[deg] Long[deg] Status COD[year] SO2_tpa[t/y] NOx_tpa[t/y] PM_tpa[t/y] Hg_kgpa[kg/y] Exit temperature[C] Stack diameter[m] Stack height[m] Flue gas velocity[m/s] FGD[logical]
}
if (emission_type == "varying") {
emissions_dir <- file.path(project_dir,"emissions/2019") # Directory where arbitrary-varying emission files are stored
input_xls <- file.path(emissions_dir,"coordinates.xlsx") # Where plant positions are reported
}
# ================================ General =====================================
# BE CARREFULL : gis_dir/landcover/C3S-LC-L4-LCCS-Map-300m-P1Y-2018-v2.1.1.nc is CORRUPETED in the repository !! You should replace it with a good one
gis_dir <- "F:/gis" # The folder where we store general GIS data
bc_dir <- file.path(gis_dir, "background") # The folder with background atmospheric concentrations for O3, NH3, H2O2
exe_dir="C:/CALPUFF"
calmet_exe <- file.path(exe_dir,"CALMET_v6.5.0_L150223/calmet_v6.5.0.exe")
calpuff_exe <- file.path(exe_dir,"CALPUFF_v7.2.1_L150618/calpuff_v7.2.1.exe")
pu_exe <- file.path(exe_dir,"POSTUTIL_v7.0.0_L150207/postutil_v7.0.0.exe")
calpost_exe <- file.path(exe_dir,"CALPOST_v7.1.0_L141010/calpost_v7.1.0.exe")
template_dir="F:/templates"
calmet_templates <- list(noobs=file.path(template_dir,"CALMET_template.INP"),
surfobs=file.path(template_dir,"CALMET_surfObs_template.inp"))
# calpuff_template <- file.path(template_dir,"CALPUFF_7.0_template.INP") # No mercury in emission file
calpuff_template <- file.path(template_dir,"CALPUFF_7.0_template_Hg.INP") # Mercury (Hg) in emission file
pu_templates <- list (# repartition = file.path(template_dir, "Mintia_postutilRepartition_noHg.inp"), # No mercury in emission file
repartition = file.path(template_dir, "Mintia_postutilRepartition.inp"), # Mercury (Hg) in emission file
deposition = file.path(template_dir, "Mintia_postutil_depo.inp"),
# total_pm = file.path(template_dir, "Mintia_postutil_PM10_noHg.inp")) # No mercury in emission file
total_pm = file.path(template_dir, "Mintia_postutil_PM10.inp")) # Mercury (Hg) in emission file
calpost_templates <- list(concentration = file.path(template_dir, "Mintia_AllOutput_calpost.inp"),
deposition = file.path(template_dir, "Mintia_depo_calpost.inp"))
# CALMET #######################################################################
calmet_result <- creapuff::runCalmet(
input_xls = input_xls,
wrf_dir = wrf_dir,
expand_grids = expand_grids,
expand_ncells = expand_ncells,
output_dir = output_dir,
gis_dir = gis_dir,
calmet_exe = calmet_exe,
calmet_templates = calmet_templates,
only_make_additional_files=F,
run_calmet = T
)
browser()
calmet_result <- readRDS(file.path(output_dir,"calmet_result.RDS" ))
# INPUT DATA ###################################################################
# ============================== Emissions =====================================
# Define target_crs
calmet_result$params %>% lapply(data.frame) %>% bind_rows(.id='grid_name') %>% mutate(run_name=calmet_result$run_name) %>%
mutate_at(c('DGRIDKM', 'XORIGKM', 'YORIGKM', 'NX', 'NY'), as.numeric) %>%
rename(UTMZ=IUTMZN,
UTMH=UTMHEM,
GridD=DGRIDKM,
GridNX=NX,
GridNY=NY,
GridX=XORIGKM,
GridY=YORIGKM) %>%
mutate(StartDate=paste(IBYR, IBMO, IBDY) %>% ymd %>% format("%Y%m%d"),
EndDate=paste(IEYR, IEMO, IEDY) %>% ymd %>% format("%Y%m%d"),
TZ=ABTZ %>% gsub('UTC', '', .) %>% as.numeric %>% divide_by(100)) -> out_files
target_crs <- get_utm_proj(zone = unique(out_files$UTMZ), hem = unique(out_files$UTMH))
if (emission_type == "constant") {
# Read emission data from file
# read_xlsx(input_xls, sheet='CALPUFF input') -> emissions_data
read_xlsx(input_xls, sheet='CALPUFF input') -> emissions_data
# Filter Data. For example by COD = commercial operation date
# emissions_data$COD %>% substr(.,nchar(.)-3,nchar(.)) %>% as.numeric () <
# calmet_result$start_dates[[1]] %>% format("%Y") %>% as.numeric() ->
# emissions_data$existing
# emissions_data$status = ifelse(emissions_data$existing,'operating', 'future')
# Selection of operating/future plants
# emissions_data %<>% filter(status == "operating")
# Produce unique ascii names with 8 characters
emissions_data$Plants %>% gsub(' ', '', .) %>% substr(1,5) %>% stringi::stri_trans_general("Latin-ASCII") %>%
make.names %>% make.unique(sep='') %>%
paste0('_', substr(emissions_data$Status,1,1)) -> emissions_data$emission_names
if (emissions_data$emission_names %>% nchar %>% max > 8) stop("ERROR in plant-name length (too much plants with the same name?)")
# Ensure numeric values of lat and long
emissions_data$Lat %<>% as.numeric()
emissions_data$Long %<>% as.numeric()
emissions_data$FGD %<>% as.logical()
# Create polygons of grid boundaries
dom_pols = grids_to_domains(calmet_result$grids, target_crs)
# Exclude sources outside domain
emissions_data %<>% to_spdf %>% crop(spTransform(dom_pols, crs(.))) %>% '@'('data')
# Test with less data
# emissions_data %<>% head(1)
# emissions_data %<>% tail(1)
# emissions_data <- rbind(emissions_data %>% head(1), emissions_data %>% tail(1))
}
if (emission_type == "varying") {
# Find ptemarb.DAT files
emissions_file <- file.path(emissions_dir) %>% list.files(pattern='\\.DAT$', recursive = F, full.names=T)
# Read plant names and positions
read_xlsx(input_xls) -> emissions_data
# Emission names
emissions_data$Plants %>% gsub(' ', '', .) %>% substr(1,5) %>% stringi::stri_trans_general("Latin-ASCII") %>%
make.names %>% make.unique(sep='') -> emissions_data$emission_names
# Ensure numeric values of lat and long
emissions_data$Lat %<>% as.numeric()
emissions_data$Long %<>% as.numeric()
# Create polygons of grid boundaries
dom_pols = grids_to_domains(calmet_result$grids, target_crs)
# Exclude sources outside domain
emissions_data %<>% to_spdf %>% crop(spTransform(dom_pols, crs(.))) %>% '@'('data')
# Test with less data
# emissions_data %<>% head(1)
# emissions_data %<>% tail(1)
# emissions_data <- rbind(emissions_data %>% head(1), emissions_data %>% tail(1))
}
# browser()
# ============================== Receptors =====================================
# MESHDN parameter (in CALPUFF.INP) which defines the grid spacing
# (DGRIDKM/MECHDN) of each disk, wrt the grid spacing of the outer
# meteo grid (DGRIDKM). Higher factor: higher density of receptors.
nesting_factors = c(1,5,15) # c(1,2,5,15) # c(1,5,15) # c(1,2,5,15)
if(!exists('receptors')) receptors = list()
queue = unique(emissions_data$emission_names)
for(run in queue) {
emissions_data_run <- emissions_data %>% filter(emission_names == run) %>% head(1)
loc <- emissions_data_run %>% to_spdf %>% spTransform(target_crs)
# Get discrete receptors with 400x400 dim
get_recep(loc = loc,
run_name = calmet_result$run_name,
nesting_factors=nesting_factors,
files_met=out_files,
target_crs=target_crs) -> receptors [[run]]
print(run)
}
# Select discrete receptors around sources
nesfact_range = c(125,25,5) # c(150,75,25,10) # c(125,25,5) # c(125,25,10) # c(150,75,25,10) # Radius of receptor disks [km], from outer to inner disk
sources <- emissions_data %>% to_spdf %>% spTransform(target_crs)
receptors %<>% select_receptors(sources=sources,
run_name = calmet_result$run_name,
nesting_factors=nesting_factors,
nesfact_range=nesfact_range,
files_met=out_files)
# Discrete receptor background grid
receptors[receptors$Xkm %% 30 < 15 & receptors$Ykm %% 30 < 15 & receptors$nesfact==1, 'include'] <- T
# Receptor check
print(paste('Adding background grid:', calmet_result$run_name, sum(receptors$include), 'receptors'))
if(sum(receptors$include)>=10000) stop('too many receptors!') # LC
# Receptor plot
quickpng(file.path(output_dir, paste0(calmet_result$run_name, '_', 'receptors+background_grid.png')) )
receptors %>% subset(include==1) %>% plot(cex=.2)
plot(sources, col='blue', add=T)
get_adm(0, 'coarse') %>% cropProj(raster(receptors)) %>% plot(add=T, border='gray')
dev.off()
# ========================== Background concentrations =========================
# sources <- emissions_data %>% to_spdf %>% spTransform(target_crs)
bgconcs <- get_bg_concs(sources, mod_dir=bc_dir)
o3dat <- NULL # Hourly ozone data file (NULL: no ozone monitoring stations)
# CALPUFF ######################################################################
if (emission_type == "constant") {
queue = unique(emissions_data$emission_names)
for(run in queue) {
emissions_data_run <- emissions_data %>% filter(emission_names == run) %>% head(1)
run_name <- emissions_data_run$emission_names
print(paste0("CALPUFF run name: ", run_name))
calpuff_result <- creapuff::runCalpuff(
emissions_data = emissions_data_run, # For constant emission data
source_names = emissions_data_run$emission_names, # Optional. If not set: read from emissions_data (if not present, set automatically)
FGD = emissions_data_run$FGD, # Optional. If not set: read from emissions_data (if not present an error occurs)
receptors = receptors, # Optional. If not set: full domain grid
o3dat = o3dat, # Optional. If not set: no surface data
species_configuration = "so2_nox_pm_hg", # Two possible values: "so2_nox_pm" or "so2_nox_pm_hg"
bgconcs = bgconcs, # Optional. If not set: std values
# addparams = addparams, # Optional. If not set: std values
run_name = run_name,
output_dir = output_dir,
params_allgrids = calmet_result$params,
gis_dir = gis_dir,
calpuff_exe = calpuff_exe,
calpuff_template = calpuff_template,
)
}
# Execute each CALPUFF bat file
for(run in queue) {
emissions_data_run <- emissions_data %>% filter(emission_names == run) %>% head(1)
run_name <- emissions_data_run$emission_names
bat_file <- file.path(output_dir, paste0(run_name, '_1', '.bat'))
shell.exec(normalizePath(bat_file))
Sys.sleep(10)
}
# All-in-one solution: only one CALPUFF simulation for all sources
# calpuff_result <- creapuff::runCalpuff(
# emissions_data = emissions_data, # For constant emission data
# source_names = emissions_data$emission_names, # Optional. If not set: read from emissions_data (if not present, set automatically)
# FGD = emissions_data$FGD, # Optional. If not set: read from emissions_data (if not present an error occurs)
# receptors = receptors, # Optional. If not set: full domain grid
# o3dat = o3dat, # Optional. If not set: no surface data
# species_configuration = "so2_nox_pm_hg", # Two possible values: "so2_nox_pm" or "so2_nox_pm_hg"
# bgconcs = bgconcs, # Optional. If not set: std values
# # addparams = addparams, # Optional. If not set: std values
# run_name = calmet_result$run_name,
# output_dir = output_dir,
# params_allgrids = calmet_result$params,
# gis_dir = gis_dir,
# calpuff_exe = calpuff_exe,
# calpuff_template = calpuff_template)
}
if (emission_type == "varying") {
queue = unique(emissions_data$emission_names)
for(run in queue) {
emissions_data_run <- emissions_data %>% filter(emission_names == run) %>% head(1)
# run_name <- paste(calmet_result$run_name, emissions_data_run$emission_names,sep='_') # TO DO : delete calmet_result$run_name in run name !
run_name <- emissions_data_run$emission_names
NPT2 <- emissions_data_run$N_sources # Number of emission sources per file
print(paste0("CALPUFF run name: ", run_name, ", n_sources: ", NPT2))
calpuff_result <- creapuff::runCalpuff(
# emissions_data = emissions_data, # For constant emissions
# source_names = source_names, # Optional. If not set: read from emissions_data (if not present, set automatically)
# FGD = "T", # Optional. If not set: read from emissions_data (if not present, an error occurs)
receptors=receptors, # Optional. If not set: full domain grid
o3dat=o3dat, # Optional. If not set: no surface data
bgconcs=bgconcs, # Optional. If not set: std values
species_configuration = "so2_nox_pm_hg", # Two possible values: "so2_nox_pm", "so2_nox_pm_hg"
addparams = list(NPTDAT = 1, # For arbitrary-varying emissions
PTDAT = emissions_data_run$Path,
NPT2 = NPT2),
run_name=run_name,
output_dir = output_dir,
params_allgrids = calmet_result$params,
gis_dir = gis_dir,
calpuff_exe = calpuff_exe,
calpuff_template = calpuff_template
)
}
# Execute each CALPUFF bat file
for(run in queue) {
emissions_data_run <- emissions_data %>% filter(emission_names == run) %>% head(1)
run_name <- emissions_data_run$emission_names
bat_file <- file.path(output_dir, paste0(run_name, '_1', '.bat'))
# shell.exec(normalizePath(bat_file))
# Sys.sleep(10)
}
}
browser()
for (i_Sc in seq(1,2)) {
# POST-PROCESSING ##############################################################
# ============================ All clusters together ============================
# 1. Sum up all output CALPUFF concentrations (.CON), using POSTUTIL
# Load all CAPUFF results, from calpuff_result_*.RDS
calpuff_results_all <- file.path(output_dir, list.files(output_dir, pattern = 'calpuff_result.*\\.RDS')) %>% lapply(readRDS)
calpuff_results_all %>% lapply('[[', 'inpfiles_created') %>% unlist -> inpfiles_created
names(calpuff_results_all) <- gsub(paste0('.*/','|_CALPUFF.*\\.inp'), '', inpfiles_created) # TO DO : delete calmet_result$run_name in run name !
names(inpfiles_created) <- names(calpuff_results_all)
# ========================== Scenario definition ===============================
# # --- Scenario ScA : old limits (2008), from coal consumption
# scenario_prefix <- "ScA" # Max 8 char # included_stations = names(inpfiles_created)
# included_stations <- names(inpfiles_created)[grep("oCC", names(inpfiles_created) )]
# --- Two main scenarios :
if (i_Sc==1) {scenario_prefix <- "ScA"; included_stations <- emissions_data$emission_names[emissions_data$Scenario=='2008 standards, FGD']}
if (i_Sc==2) {scenario_prefix <- "ScB"; included_stations <- emissions_data$emission_names[emissions_data$Scenario=='2019 standards, FGD']}
# if (i_Sc==3) {scenario_prefix <- "ScS" ; included_stations <- emissions_data$emission_names[emissions_data$Scenario=='2008 standards, FGD, 130 degrees']}
# if (i_Sc==4) {scenario_prefix <- "ScW"; included_stations <- emissions_data$emission_names[emissions_data$Scenario=='2008 standards, no FGD']}
# ---
calpuff_results_all[names(calpuff_results_all) %in% included_stations == TRUE] -> calpuff_results_all
inpfiles_created[names(inpfiles_created) %in% included_stations == TRUE] -> inpfiles_created
emissions_data %>% filter(emissions_data$emission_names %in% names(inpfiles_created) == TRUE) -> emissions_data_scenario
write_xlsx(list("CALPUFF input"=emissions_data_scenario), file.path(emissions_dir, paste0("coordinates_",scenario_prefix,".xlsx")))
# ==============================================================================
# 1. Create "SUMRUNS" INP files for summing up all CALPUFF outputs for each station, for :
# - concentrations (.CON), no need for nitrate reparation (MNITRATE = 0), a further run will do the repartition
# - deposition (.DRY, .WET) (together with acid, mercury, dust species)
files_met <- out_files # or calpuff_results_all[[1]]$out_files # All clusters have the same meteo
first_cluster_inp <- inpfiles_created[1]
first_cluster_name <- names(inpfiles_created)[1]
calpuff_results_all %>% lapply('[[', 'pm10fraction') %>% unlist %>% mean() -> pm10fraction
# Generate "generic" PU and CP INP files (only for the first cluster, run_pu=F, run_calpost=F)
creapuff::runPostprocessing(
calpuff_inp=first_cluster_inp,
output_dir=output_dir,
files_met = files_met,
pm10fraction=pm10fraction,
METRUN = 0,
nper = NULL,
pu_start_hour = NULL,
cp_species = c('PM25', 'TPM10', 'SO2', 'NO2'), # c('PM25', 'TPM10', 'TSP', 'SO2', 'NO2'),
cp_period_function = get_cp_period,
run_discrete_receptors=T,
run_gridded_receptors=F,
run_concentrations=T,
run_deposition=T,
run_timeseries = T,
run_hourly = c('PM25', 'NO2', 'SO2'),
run_pu=F,
run_calpost=F,
pu_templates = pu_templates,
calpost_templates=calpost_templates
)
# Read generic inp files
pu_template_desinence <- pu_templates %>% lapply(function(x) gsub("^[^_]*", "", x))
pu_sumruns_template_generic=paste0(first_cluster_name, pu_template_desinence$repartition)
pu_sumruns_depo_template_generic=paste0(first_cluster_name, pu_template_desinence$depo)
readLines(file.path(output_dir,pu_sumruns_template_generic)) -> inp
readLines(file.path(output_dir,pu_sumruns_depo_template_generic)) -> inp_depo
# Define current input-data list
sumfiles = paste0(toupper(names(inpfiles_created)), '.CON')
sumfiles_depo = append (paste0(toupper(names(inpfiles_created)), '.DRY'), paste0(toupper(names(inpfiles_created)), '.WET'))
# Fill generic inp files with current parameters and output-data names
inp %<>% set_puff(list(NFILES = length(sumfiles), # Function to set parameters in a CALPUFF input file
MNITRATE = 0, # Recompute the HNO3/NO3 partition for concentrations, for all sources combined
UTLLST = file.path(output_dir,paste0(scenario_prefix,"_POSTUTIL_SUMRUNS.LST")), # Output LST file
UTLDAT = file.path(output_dir,paste0(scenario_prefix,".CON")))) # Output data file, for concentrations (.CON)
inp_depo %<>% set_puff(list(NFILES = length(sumfiles_depo), # Function to set parameters in a CALPUFF input file
UTLLST = file.path(output_dir,paste0(scenario_prefix,"_POSTUTIL_Depo.LST")), # Output LST file. Filename-format as ScAll_POSTUTIL_Depo.LST
UTLDAT = file.path(output_dir,paste0(scenario_prefix,"_Depo.FLX")))) # Output data file, for fluxes (.FLX). Filename-format as ScAll_Depo.FLX
# Fill the corresponding lines for with current input-data list (CALPUFF outputs)
con_line <- grep("!MODDAT=", gsub(" ", "", inp)) # Looking for input-data position index
inp <- c(inp[1:(con_line-1)],
paste(" ",1:length(sumfiles)," CALPUFF.DAT ! MODDAT =",file.path(output_dir, sumfiles),"! !END!"), # For concentrations (.CON)
inp[-1:-con_line])
con_line_depo <- grep("!MODDAT=", gsub(" ", "", inp_depo)) # Looking for input-data position index
inp_depo <- c(inp_depo[1:(con_line_depo-1)],
paste(" ",1:length(sumfiles_depo)," CALPUFF.DAT ! MODDAT =",file.path(output_dir, sumfiles_depo),"! !END!"), # For deposition (.DRY, .WET)
inp_depo[-1:-con_line_depo[2]])
# Write the _POSTUTIL_SUMRUNS.INP and _postutil_depo.inp files
pu_sumruns_template_all <- file.path(output_dir, paste0(scenario_prefix,"_POSTUTIL_SUMRUNS.INP"))
writeLines(inp, pu_sumruns_template_all)
pu_sumruns_depo_template_all <- file.path(output_dir, paste0(scenario_prefix,"_postutil_depo.inp")) # Filename-format for PU bat files (ex: pu_ScAll.bat)
writeLines(inp_depo, pu_sumruns_depo_template_all)
# Create the _SUMRUNS.bat bat file
pu_sumruns_bat <- file.path(output_dir, paste0("pu_",scenario_prefix,"_SUMRUNS.bat"))
writeLines(c(paste("cd", output_dir),
paste0(pu_exe, " ", normalizePath(pu_sumruns_template_all)),
"pause"),
pu_sumruns_bat) # shell.exec(normalizePath(pu_sumruns_bat))
# 2. Define PU and CP INP and bat files, for summed-up concentrations
name_generic=first_cluster_name
# PU INP: change names of input and output parameters, from generic "first_cluster_name" to selected scenario (ScAll, or ScB, ...)
file.path(output_dir, list.files(output_dir, pattern=paste0('^',first_cluster_name,'_postutil'))) -> pu_files_generic
pu_files_generic <- pu_files_generic[c(grep("Repartition", pu_files_generic),grep("PM10", pu_files_generic))] # No need for _postutil_depo.inp, already created
for(f in pu_files_generic) {
f %>% readLines %>% gsub(name_generic, scenario_prefix, .) %>%
writeLines(file.path (output_dir, gsub(paste0('^',first_cluster_name), scenario_prefix, basename(f))))
}
# CP INP: change names of input and output parameters, from generic "first_cluster_name" to selected scenario (ScAll, or ScB, ...)
file.path(output_dir, list.files(output_dir, pattern=paste0('^',first_cluster_name,'_.*calpost'))) -> cp_files_generic
for(f in cp_files_generic) {
f %>% readLines %>% gsub(name_generic, scenario_prefix, .) %>%
gsub(first_cluster_name, scenario_prefix, .) %>%
writeLines(file.path (output_dir, gsub(paste0('^',first_cluster_name), scenario_prefix, basename(f))))
}
# Bat files
file.path(output_dir,list.files(output_dir, pattern=paste0(first_cluster_name,'\\.bat'))) -> bat_files_generic
for(f in bat_files_generic) {
f %>% readLines %>% gsub(name_generic, scenario_prefix, .) %>%
gsub(first_cluster_name, scenario_prefix, .) %>%
writeLines(file.path (output_dir, gsub(paste0(first_cluster_name), scenario_prefix, basename(f))))
}
pu_bat <- file.path(output_dir, paste0("pu_", scenario_prefix, ".bat")) # shell.exec(normalizePath(pu_bat))
cp_bat <- file.path(output_dir, paste0("calpost_", scenario_prefix, ".bat")) # shell.exec(normalizePath(cp_bat))
# Remove generic INP and bat files
file.remove(pu_files_generic)
file.remove(cp_files_generic)
file.remove(bat_files_generic)
# 3. Run all bat files, in sequence
system2(pu_sumruns_bat) -> exit_code
if(exit_code != 0) stop("errors in POSTUTIL SUMRUNS execution")
system2(pu_bat) -> exit_code
if(exit_code != 0) stop("errors in POSTUTIL execution")
system2(cp_bat) -> exit_code
if(exit_code != 0) stop("errors in CALPOST execution")
}
energyandcleanair/creapuff documentation built on Feb. 8, 2025, 4:29 p.m.
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# Set up the environment
# remotes::install_github("energyandcleanair/creapuff", dependencies=T, update=F)
# devtools::reload(pkgload::inst("creapuff"))
library(creapuff)
library(readxl)
library(writexl)
library(lubridate)
library(tidyverse)
library(magrittr)
library(pbapply)
# Parameters ###################################################################
# ============================= Project specific ===============================
expand_grids = '*' # All grids are expanded (for CALMET)
expand_ncells = -5 # Number of cells to expand met grid (e.g., WRF) in each direction (use negative values to crop)
# project_dir="Z:/" # network disk (wrf_data). If Z disk is not present: mount 10.58.186.210:/wrf_data Z:)
project_dir="G:/india-orissa" # calpuff_external_data-2 persistent disk (project data)
wrf_dir <- file.path(project_dir,"calwrf") # Where calwrf data are stored
output_dir <- file.path(project_dir,"calpuff_suite") ; if (!dir.exists(output_dir)) dir.create(output_dir) # Where to write all generated files
# emission_type = "varying"
emission_type = "constant"
if (emission_type == "constant"){
emissions_dir <- file.path(project_dir,"emissions") # Directory where arbitrary-varying emission files are stored
input_xls <- file.path(emissions_dir,"emissions.xlsx") # File where constant-emission data are specified
# Emission file # Plants Capacity[MW] Lat[deg] Long[deg] Status COD[year] SO2_tpa[t/y] NOx_tpa[t/y] PM_tpa[t/y] Hg_kgpa[kg/y] Exit temperature[C] Stack diameter[m] Stack height[m] Flue gas velocity[m/s] FGD[logical]
}
if (emission_type == "varying") {
emissions_dir <- file.path(project_dir,"emissions/2019") # Directory where arbitrary-varying emission files are stored
input_xls <- file.path(emissions_dir,"coordinates.xlsx") # Where plant positions are reported
}
# ================================ General =====================================
# BE CARREFULL : gis_dir/landcover/C3S-LC-L4-LCCS-Map-300m-P1Y-2018-v2.1.1.nc is CORRUPETED in the repository !! You should replace it with a good one
gis_dir <- "F:/gis" # The folder where we store general GIS data
bc_dir <- file.path(gis_dir, "background") # The folder with background atmospheric concentrations for O3, NH3, H2O2
exe_dir="C:/CALPUFF"
calmet_exe <- file.path(exe_dir,"CALMET_v6.5.0_L150223/calmet_v6.5.0.exe")
calpuff_exe <- file.path(exe_dir,"CALPUFF_v7.2.1_L150618/calpuff_v7.2.1.exe")
pu_exe <- file.path(exe_dir,"POSTUTIL_v7.0.0_L150207/postutil_v7.0.0.exe")
calpost_exe <- file.path(exe_dir,"CALPOST_v7.1.0_L141010/calpost_v7.1.0.exe")
template_dir="F:/templates"
calmet_templates <- list(noobs=file.path(template_dir,"CALMET_template.INP"),
surfobs=file.path(template_dir,"CALMET_surfObs_template.inp"))
# calpuff_template <- file.path(template_dir,"CALPUFF_7.0_template.INP") # No mercury in emission file
calpuff_template <- file.path(template_dir,"CALPUFF_7.0_template_Hg.INP") # Mercury (Hg) in emission file
pu_templates <- list (# repartition = file.path(template_dir, "Mintia_postutilRepartition_noHg.inp"), # No mercury in emission file
repartition = file.path(template_dir, "Mintia_postutilRepartition.inp"), # Mercury (Hg) in emission file
deposition = file.path(template_dir, "Mintia_postutil_depo.inp"),
# total_pm = file.path(template_dir, "Mintia_postutil_PM10_noHg.inp")) # No mercury in emission file
total_pm = file.path(template_dir, "Mintia_postutil_PM10.inp")) # Mercury (Hg) in emission file
calpost_templates <- list(concentration = file.path(template_dir, "Mintia_AllOutput_calpost.inp"),
deposition = file.path(template_dir, "Mintia_depo_calpost.inp"))
# CALMET #######################################################################
calmet_result <- creapuff::runCalmet(
input_xls = input_xls,
wrf_dir = wrf_dir,
expand_grids = expand_grids,
expand_ncells = expand_ncells,
output_dir = output_dir,
gis_dir = gis_dir,
calmet_exe = calmet_exe,
calmet_templates = calmet_templates,
only_make_additional_files=F,
run_calmet = T
)
browser()
calmet_result <- readRDS(file.path(output_dir,"calmet_result.RDS" ))
# INPUT DATA ###################################################################
# ============================== Emissions =====================================
# Define target_crs
calmet_result$params %>% lapply(data.frame) %>% bind_rows(.id='grid_name') %>% mutate(run_name=calmet_result$run_name) %>%
mutate_at(c('DGRIDKM', 'XORIGKM', 'YORIGKM', 'NX', 'NY'), as.numeric) %>%
rename(UTMZ=IUTMZN,
UTMH=UTMHEM,
GridD=DGRIDKM,
GridNX=NX,
GridNY=NY,
GridX=XORIGKM,
GridY=YORIGKM) %>%
mutate(StartDate=paste(IBYR, IBMO, IBDY) %>% ymd %>% format("%Y%m%d"),
EndDate=paste(IEYR, IEMO, IEDY) %>% ymd %>% format("%Y%m%d"),
TZ=ABTZ %>% gsub('UTC', '', .) %>% as.numeric %>% divide_by(100)) -> out_files
target_crs <- get_utm_proj(zone = unique(out_files$UTMZ), hem = unique(out_files$UTMH))
if (emission_type == "constant") {
# Read emission data from file
# read_xlsx(input_xls, sheet='CALPUFF input') -> emissions_data
read_xlsx(input_xls, sheet='CALPUFF input') -> emissions_data
# Filter Data. For example by COD = commercial operation date
# emissions_data$COD %>% substr(.,nchar(.)-3,nchar(.)) %>% as.numeric () <
# calmet_result$start_dates[[1]] %>% format("%Y") %>% as.numeric() ->
# emissions_data$existing
# emissions_data$status = ifelse(emissions_data$existing,'operating', 'future')
# Selection of operating/future plants
# emissions_data %<>% filter(status == "operating")
# Produce unique ascii names with 8 characters
emissions_data$Plants %>% gsub(' ', '', .) %>% substr(1,5) %>% stringi::stri_trans_general("Latin-ASCII") %>%
make.names %>% make.unique(sep='') %>%
paste0('_', substr(emissions_data$Status,1,1)) -> emissions_data$emission_names
if (emissions_data$emission_names %>% nchar %>% max > 8) stop("ERROR in plant-name length (too much plants with the same name?)")
# Ensure numeric values of lat and long
emissions_data$Lat %<>% as.numeric()
emissions_data$Long %<>% as.numeric()
emissions_data$FGD %<>% as.logical()
# Create polygons of grid boundaries
dom_pols = grids_to_domains(calmet_result$grids, target_crs)
# Exclude sources outside domain
emissions_data %<>% to_spdf %>% crop(spTransform(dom_pols, crs(.))) %>% '@'('data')
# Test with less data
# emissions_data %<>% head(1)
# emissions_data %<>% tail(1)
# emissions_data <- rbind(emissions_data %>% head(1), emissions_data %>% tail(1))
}
if (emission_type == "varying") {
# Find ptemarb.DAT files
emissions_file <- file.path(emissions_dir) %>% list.files(pattern='\\.DAT$', recursive = F, full.names=T)
# Read plant names and positions
read_xlsx(input_xls) -> emissions_data
# Emission names
emissions_data$Plants %>% gsub(' ', '', .) %>% substr(1,5) %>% stringi::stri_trans_general("Latin-ASCII") %>%
make.names %>% make.unique(sep='') -> emissions_data$emission_names
# Ensure numeric values of lat and long
emissions_data$Lat %<>% as.numeric()
emissions_data$Long %<>% as.numeric()
# Create polygons of grid boundaries
dom_pols = grids_to_domains(calmet_result$grids, target_crs)
# Exclude sources outside domain
emissions_data %<>% to_spdf %>% crop(spTransform(dom_pols, crs(.))) %>% '@'('data')
# Test with less data
# emissions_data %<>% head(1)
# emissions_data %<>% tail(1)
# emissions_data <- rbind(emissions_data %>% head(1), emissions_data %>% tail(1))
}
# browser()
# ============================== Receptors =====================================
# MESHDN parameter (in CALPUFF.INP) which defines the grid spacing
# (DGRIDKM/MECHDN) of each disk, wrt the grid spacing of the outer
# meteo grid (DGRIDKM). Higher factor: higher density of receptors.
nesting_factors = c(1,5,15) # c(1,2,5,15) # c(1,5,15) # c(1,2,5,15)
if(!exists('receptors')) receptors = list()
queue = unique(emissions_data$emission_names)
for(run in queue) {
emissions_data_run <- emissions_data %>% filter(emission_names == run) %>% head(1)
loc <- emissions_data_run %>% to_spdf %>% spTransform(target_crs)
# Get discrete receptors with 400x400 dim
get_recep(loc = loc,
run_name = calmet_result$run_name,
nesting_factors=nesting_factors,
files_met=out_files,
target_crs=target_crs) -> receptors [[run]]
print(run)
}
# Select discrete receptors around sources
nesfact_range = c(125,25,5) # c(150,75,25,10) # c(125,25,5) # c(125,25,10) # c(150,75,25,10) # Radius of receptor disks [km], from outer to inner disk
sources <- emissions_data %>% to_spdf %>% spTransform(target_crs)
receptors %<>% select_receptors(sources=sources,
run_name = calmet_result$run_name,
nesting_factors=nesting_factors,
nesfact_range=nesfact_range,
files_met=out_files)
# Discrete receptor background grid
receptors[receptors$Xkm %% 30 < 15 & receptors$Ykm %% 30 < 15 & receptors$nesfact==1, 'include'] <- T
# Receptor check
print(paste('Adding background grid:', calmet_result$run_name, sum(receptors$include), 'receptors'))
if(sum(receptors$include)>=10000) stop('too many receptors!') # LC
# Receptor plot
quickpng(file.path(output_dir, paste0(calmet_result$run_name, '_', 'receptors+background_grid.png')) )
receptors %>% subset(include==1) %>% plot(cex=.2)
plot(sources, col='blue', add=T)
get_adm(0, 'coarse') %>% cropProj(raster(receptors)) %>% plot(add=T, border='gray')
dev.off()
# ========================== Background concentrations =========================
# sources <- emissions_data %>% to_spdf %>% spTransform(target_crs)
bgconcs <- get_bg_concs(sources, mod_dir=bc_dir)
o3dat <- NULL # Hourly ozone data file (NULL: no ozone monitoring stations)
# CALPUFF ######################################################################
if (emission_type == "constant") {
queue = unique(emissions_data$emission_names)
for(run in queue) {
emissions_data_run <- emissions_data %>% filter(emission_names == run) %>% head(1)
run_name <- emissions_data_run$emission_names
print(paste0("CALPUFF run name: ", run_name))
calpuff_result <- creapuff::runCalpuff(
emissions_data = emissions_data_run, # For constant emission data
source_names = emissions_data_run$emission_names, # Optional. If not set: read from emissions_data (if not present, set automatically)
FGD = emissions_data_run$FGD, # Optional. If not set: read from emissions_data (if not present an error occurs)
receptors = receptors, # Optional. If not set: full domain grid
o3dat = o3dat, # Optional. If not set: no surface data
species_configuration = "so2_nox_pm_hg", # Two possible values: "so2_nox_pm" or "so2_nox_pm_hg"
bgconcs = bgconcs, # Optional. If not set: std values
# addparams = addparams, # Optional. If not set: std values
run_name = run_name,
output_dir = output_dir,
params_allgrids = calmet_result$params,
gis_dir = gis_dir,
calpuff_exe = calpuff_exe,
calpuff_template = calpuff_template,
)
}
# Execute each CALPUFF bat file
for(run in queue) {
emissions_data_run <- emissions_data %>% filter(emission_names == run) %>% head(1)
run_name <- emissions_data_run$emission_names
bat_file <- file.path(output_dir, paste0(run_name, '_1', '.bat'))
shell.exec(normalizePath(bat_file))
Sys.sleep(10)
}
# All-in-one solution: only one CALPUFF simulation for all sources
# calpuff_result <- creapuff::runCalpuff(
# emissions_data = emissions_data, # For constant emission data
# source_names = emissions_data$emission_names, # Optional. If not set: read from emissions_data (if not present, set automatically)
# FGD = emissions_data$FGD, # Optional. If not set: read from emissions_data (if not present an error occurs)
# receptors = receptors, # Optional. If not set: full domain grid
# o3dat = o3dat, # Optional. If not set: no surface data
# species_configuration = "so2_nox_pm_hg", # Two possible values: "so2_nox_pm" or "so2_nox_pm_hg"
# bgconcs = bgconcs, # Optional. If not set: std values
# # addparams = addparams, # Optional. If not set: std values
# run_name = calmet_result$run_name,
# output_dir = output_dir,
# params_allgrids = calmet_result$params,
# gis_dir = gis_dir,
# calpuff_exe = calpuff_exe,
# calpuff_template = calpuff_template)
}
if (emission_type == "varying") {
queue = unique(emissions_data$emission_names)
for(run in queue) {
emissions_data_run <- emissions_data %>% filter(emission_names == run) %>% head(1)
# run_name <- paste(calmet_result$run_name, emissions_data_run$emission_names,sep='_') # TO DO : delete calmet_result$run_name in run name !
run_name <- emissions_data_run$emission_names
NPT2 <- emissions_data_run$N_sources # Number of emission sources per file
print(paste0("CALPUFF run name: ", run_name, ", n_sources: ", NPT2))
calpuff_result <- creapuff::runCalpuff(
# emissions_data = emissions_data, # For constant emissions
# source_names = source_names, # Optional. If not set: read from emissions_data (if not present, set automatically)
# FGD = "T", # Optional. If not set: read from emissions_data (if not present, an error occurs)
receptors=receptors, # Optional. If not set: full domain grid
o3dat=o3dat, # Optional. If not set: no surface data
bgconcs=bgconcs, # Optional. If not set: std values
species_configuration = "so2_nox_pm_hg", # Two possible values: "so2_nox_pm", "so2_nox_pm_hg"
addparams = list(NPTDAT = 1, # For arbitrary-varying emissions
PTDAT = emissions_data_run$Path,
NPT2 = NPT2),
run_name=run_name,
output_dir = output_dir,
params_allgrids = calmet_result$params,
gis_dir = gis_dir,
calpuff_exe = calpuff_exe,
calpuff_template = calpuff_template
)
}
# Execute each CALPUFF bat file
for(run in queue) {
emissions_data_run <- emissions_data %>% filter(emission_names == run) %>% head(1)
run_name <- emissions_data_run$emission_names
bat_file <- file.path(output_dir, paste0(run_name, '_1', '.bat'))
# shell.exec(normalizePath(bat_file))
# Sys.sleep(10)
}
}
browser()
for (i_Sc in seq(1,2)) {
# POST-PROCESSING ##############################################################
# ============================ All clusters together ============================
# 1. Sum up all output CALPUFF concentrations (.CON), using POSTUTIL
# Load all CAPUFF results, from calpuff_result_*.RDS
calpuff_results_all <- file.path(output_dir, list.files(output_dir, pattern = 'calpuff_result.*\\.RDS')) %>% lapply(readRDS)
calpuff_results_all %>% lapply('[[', 'inpfiles_created') %>% unlist -> inpfiles_created
names(calpuff_results_all) <- gsub(paste0('.*/','|_CALPUFF.*\\.inp'), '', inpfiles_created) # TO DO : delete calmet_result$run_name in run name !
names(inpfiles_created) <- names(calpuff_results_all)
# ========================== Scenario definition ===============================
# # --- Scenario ScA : old limits (2008), from coal consumption
# scenario_prefix <- "ScA" # Max 8 char # included_stations = names(inpfiles_created)
# included_stations <- names(inpfiles_created)[grep("oCC", names(inpfiles_created) )]
# --- Two main scenarios :
if (i_Sc==1) {scenario_prefix <- "ScA"; included_stations <- emissions_data$emission_names[emissions_data$Scenario=='2008 standards, FGD']}
if (i_Sc==2) {scenario_prefix <- "ScB"; included_stations <- emissions_data$emission_names[emissions_data$Scenario=='2019 standards, FGD']}
# if (i_Sc==3) {scenario_prefix <- "ScS" ; included_stations <- emissions_data$emission_names[emissions_data$Scenario=='2008 standards, FGD, 130 degrees']}
# if (i_Sc==4) {scenario_prefix <- "ScW"; included_stations <- emissions_data$emission_names[emissions_data$Scenario=='2008 standards, no FGD']}
# ---
calpuff_results_all[names(calpuff_results_all) %in% included_stations == TRUE] -> calpuff_results_all
inpfiles_created[names(inpfiles_created) %in% included_stations == TRUE] -> inpfiles_created
emissions_data %>% filter(emissions_data$emission_names %in% names(inpfiles_created) == TRUE) -> emissions_data_scenario
write_xlsx(list("CALPUFF input"=emissions_data_scenario), file.path(emissions_dir, paste0("coordinates_",scenario_prefix,".xlsx")))
# ==============================================================================
# 1. Create "SUMRUNS" INP files for summing up all CALPUFF outputs for each station, for :
# - concentrations (.CON), no need for nitrate reparation (MNITRATE = 0), a further run will do the repartition
# - deposition (.DRY, .WET) (together with acid, mercury, dust species)
files_met <- out_files # or calpuff_results_all[[1]]$out_files # All clusters have the same meteo
first_cluster_inp <- inpfiles_created[1]
first_cluster_name <- names(inpfiles_created)[1]
calpuff_results_all %>% lapply('[[', 'pm10fraction') %>% unlist %>% mean() -> pm10fraction
# Generate "generic" PU and CP INP files (only for the first cluster, run_pu=F, run_calpost=F)
creapuff::runPostprocessing(
calpuff_inp=first_cluster_inp,
output_dir=output_dir,
files_met = files_met,
pm10fraction=pm10fraction,
METRUN = 0,
nper = NULL,
pu_start_hour = NULL,
cp_species = c('PM25', 'TPM10', 'SO2', 'NO2'), # c('PM25', 'TPM10', 'TSP', 'SO2', 'NO2'),
cp_period_function = get_cp_period,
run_discrete_receptors=T,
run_gridded_receptors=F,
run_concentrations=T,
run_deposition=T,
run_timeseries = T,
run_hourly = c('PM25', 'NO2', 'SO2'),
run_pu=F,
run_calpost=F,
pu_templates = pu_templates,
calpost_templates=calpost_templates
)
# Read generic inp files
pu_template_desinence <- pu_templates %>% lapply(function(x) gsub("^[^_]*", "", x))
pu_sumruns_template_generic=paste0(first_cluster_name, pu_template_desinence$repartition)
pu_sumruns_depo_template_generic=paste0(first_cluster_name, pu_template_desinence$depo)
readLines(file.path(output_dir,pu_sumruns_template_generic)) -> inp
readLines(file.path(output_dir,pu_sumruns_depo_template_generic)) -> inp_depo
# Define current input-data list
sumfiles = paste0(toupper(names(inpfiles_created)), '.CON')
sumfiles_depo = append (paste0(toupper(names(inpfiles_created)), '.DRY'), paste0(toupper(names(inpfiles_created)), '.WET'))
# Fill generic inp files with current parameters and output-data names
inp %<>% set_puff(list(NFILES = length(sumfiles), # Function to set parameters in a CALPUFF input file
MNITRATE = 0, # Recompute the HNO3/NO3 partition for concentrations, for all sources combined
UTLLST = file.path(output_dir,paste0(scenario_prefix,"_POSTUTIL_SUMRUNS.LST")), # Output LST file
UTLDAT = file.path(output_dir,paste0(scenario_prefix,".CON")))) # Output data file, for concentrations (.CON)
inp_depo %<>% set_puff(list(NFILES = length(sumfiles_depo), # Function to set parameters in a CALPUFF input file
UTLLST = file.path(output_dir,paste0(scenario_prefix,"_POSTUTIL_Depo.LST")), # Output LST file. Filename-format as ScAll_POSTUTIL_Depo.LST
UTLDAT = file.path(output_dir,paste0(scenario_prefix,"_Depo.FLX")))) # Output data file, for fluxes (.FLX). Filename-format as ScAll_Depo.FLX
# Fill the corresponding lines for with current input-data list (CALPUFF outputs)
con_line <- grep("!MODDAT=", gsub(" ", "", inp)) # Looking for input-data position index
inp <- c(inp[1:(con_line-1)],
paste(" ",1:length(sumfiles)," CALPUFF.DAT ! MODDAT =",file.path(output_dir, sumfiles),"! !END!"), # For concentrations (.CON)
inp[-1:-con_line])
con_line_depo <- grep("!MODDAT=", gsub(" ", "", inp_depo)) # Looking for input-data position index
inp_depo <- c(inp_depo[1:(con_line_depo-1)],
paste(" ",1:length(sumfiles_depo)," CALPUFF.DAT ! MODDAT =",file.path(output_dir, sumfiles_depo),"! !END!"), # For deposition (.DRY, .WET)
inp_depo[-1:-con_line_depo[2]])
# Write the _POSTUTIL_SUMRUNS.INP and _postutil_depo.inp files
pu_sumruns_template_all <- file.path(output_dir, paste0(scenario_prefix,"_POSTUTIL_SUMRUNS.INP"))
writeLines(inp, pu_sumruns_template_all)
pu_sumruns_depo_template_all <- file.path(output_dir, paste0(scenario_prefix,"_postutil_depo.inp")) # Filename-format for PU bat files (ex: pu_ScAll.bat)
writeLines(inp_depo, pu_sumruns_depo_template_all)
# Create the _SUMRUNS.bat bat file
pu_sumruns_bat <- file.path(output_dir, paste0("pu_",scenario_prefix,"_SUMRUNS.bat"))
writeLines(c(paste("cd", output_dir),
paste0(pu_exe, " ", normalizePath(pu_sumruns_template_all)),
"pause"),
pu_sumruns_bat) # shell.exec(normalizePath(pu_sumruns_bat))
# 2. Define PU and CP INP and bat files, for summed-up concentrations
name_generic=first_cluster_name
# PU INP: change names of input and output parameters, from generic "first_cluster_name" to selected scenario (ScAll, or ScB, ...)
file.path(output_dir, list.files(output_dir, pattern=paste0('^',first_cluster_name,'_postutil'))) -> pu_files_generic
pu_files_generic <- pu_files_generic[c(grep("Repartition", pu_files_generic),grep("PM10", pu_files_generic))] # No need for _postutil_depo.inp, already created
for(f in pu_files_generic) {
f %>% readLines %>% gsub(name_generic, scenario_prefix, .) %>%
writeLines(file.path (output_dir, gsub(paste0('^',first_cluster_name), scenario_prefix, basename(f))))
}
# CP INP: change names of input and output parameters, from generic "first_cluster_name" to selected scenario (ScAll, or ScB, ...)
file.path(output_dir, list.files(output_dir, pattern=paste0('^',first_cluster_name,'_.*calpost'))) -> cp_files_generic
for(f in cp_files_generic) {
f %>% readLines %>% gsub(name_generic, scenario_prefix, .) %>%
gsub(first_cluster_name, scenario_prefix, .) %>%
writeLines(file.path (output_dir, gsub(paste0('^',first_cluster_name), scenario_prefix, basename(f))))
}
# Bat files
file.path(output_dir,list.files(output_dir, pattern=paste0(first_cluster_name,'\\.bat'))) -> bat_files_generic
for(f in bat_files_generic) {
f %>% readLines %>% gsub(name_generic, scenario_prefix, .) %>%
gsub(first_cluster_name, scenario_prefix, .) %>%
writeLines(file.path (output_dir, gsub(paste0(first_cluster_name), scenario_prefix, basename(f))))
}
pu_bat <- file.path(output_dir, paste0("pu_", scenario_prefix, ".bat")) # shell.exec(normalizePath(pu_bat))
cp_bat <- file.path(output_dir, paste0("calpost_", scenario_prefix, ".bat")) # shell.exec(normalizePath(cp_bat))
# Remove generic INP and bat files
file.remove(pu_files_generic)
file.remove(cp_files_generic)
file.remove(bat_files_generic)
# 3. Run all bat files, in sequence
system2(pu_sumruns_bat) -> exit_code
if(exit_code != 0) stop("errors in POSTUTIL SUMRUNS execution")
system2(pu_bat) -> exit_code
if(exit_code != 0) stop("errors in POSTUTIL execution")
system2(cp_bat) -> exit_code
if(exit_code != 0) stop("errors in CALPOST execution")
}
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