mirror of
https://git.gfz-potsdam.de/naaice/poet.git
synced 2025-12-15 12:28:22 +01:00
remove non relevant benchmarks
This commit is contained in:
Hannes Signer
parent
698621097f
commit
b9fe09d937
@ -40,4 +40,3 @@ add_custom_target(${BENCHTARGET} ALL)
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add_subdirectory(barite)
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add_subdirectory(barite)
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add_subdirectory(dolo)
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add_subdirectory(dolo)
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add_subdirectory(surfex)
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@ -1,12 +1,10 @@
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# Create a list of files
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# Create a list of files
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set(bench_files
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set(bench_files
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barite_200.R
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barite_200.R
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barite_het.R
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)
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)
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set(runtime_files
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set(runtime_files
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barite_200_rt.R
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barite_200_rt.R
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barite_het_rt.R
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)
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)
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# add_custom_target(barite_bench DEPENDS ${bench_files} ${runtime_files})
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# add_custom_target(barite_bench DEPENDS ${bench_files} ${runtime_files})
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@ -47,8 +47,7 @@ dht_species <- c(
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)
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)
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chemistry_setup <- list(
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chemistry_setup <- list(
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dht_species = dht_species,
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dht_species = dht_species
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ai_surrogate_input_script = "./barite_200ai_surrogate_input_script.R"
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)
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)
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# Define a setup list for simulation configuration
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# Define a setup list for simulation configuration
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@ -1,48 +0,0 @@
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## load a pretrained model from tensorflow file
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## Use the global variable "ai_surrogate_base_path" when using file paths
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## relative to the input script
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initiate_model <- function() {
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init_model <- normalizePath(paste0(ai_surrogate_base_path,
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"model_min_max_float64.keras"))
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return(load_model_tf(init_model))
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}
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scale_min_max <- function(x, min, max, backtransform) {
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if (backtransform) {
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return((x * (max - min)) + min)
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} else {
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return((x - min) / (max - min))
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}
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}
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preprocess <- function(df, backtransform = FALSE, outputs = FALSE) {
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minmax_file <- normalizePath(paste0(ai_surrogate_base_path,
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"min_max_bounds.rds"))
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global_minmax <- readRDS(minmax_file)
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for (column in colnames(df)) {
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df[column] <- lapply(df[column],
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scale_min_max,
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global_minmax$min[column],
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global_minmax$max[column],
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backtransform)
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}
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return(df)
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}
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mass_balance <- function(predictors, prediction) {
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dBa <- abs(prediction$Ba + prediction$Barite -
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predictors$Ba - predictors$Barite)
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dSr <- abs(prediction$Sr + prediction$Celestite -
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predictors$Sr - predictors$Celestite)
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return(dBa + dSr)
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}
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validate_predictions <- function(predictors, prediction) {
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epsilon <- 3e-5
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mb <- mass_balance(predictors, prediction)
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msgm("Mass balance mean:", mean(mb))
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msgm("Mass balance variance:", var(mb))
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msgm("Rows where mass balance meets threshold", epsilon, ":",
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sum(mb < epsilon))
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return(mb < epsilon)
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}
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@ -1,60 +0,0 @@
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## Time-stamp: "Last modified 2024-05-30 13:34:14 delucia"
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cols <- 50
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rows <- 50
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s_cols <- 0.25
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s_rows <- 0.25
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grid_def <- matrix(2, nrow = rows, ncol = cols)
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# Define grid configuration for POET model
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grid_setup <- list(
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pqc_in_file = "./barite.pqi",
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pqc_db_file = "./db_barite.dat", ## Path to the database file for Phreeqc
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grid_def = grid_def, ## Definition of the grid, containing IDs according to the Phreeqc input script
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grid_size = c(s_rows, s_cols), ## Size of the grid in meters
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constant_cells = c() ## IDs of cells with constant concentration
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)
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bound_length <- 2
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bound_def <- list(
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"type" = rep("constant", bound_length),
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"sol_id" = rep(3, bound_length),
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"cell" = seq(1, bound_length)
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)
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homogenous_alpha <- 1e-8
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diffusion_setup <- list(
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boundaries = list(
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"W" = bound_def,
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"N" = bound_def
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),
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alpha_x = homogenous_alpha,
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alpha_y = homogenous_alpha
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)
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dht_species <- c(
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"H" = 3,
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"O" = 3,
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"Charge" = 3,
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"Ba" = 6,
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"Cl" = 6,
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"S" = 6,
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"Sr" = 6,
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"Barite" = 5,
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"Celestite" = 5
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)
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chemistry_setup <- list(
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dht_species = dht_species,
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ai_surrogate_input_script = "./barite_50ai_surr_mdl.R"
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)
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# Define a setup list for simulation configuration
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setup <- list(
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Grid = grid_setup, # Parameters related to the grid structure
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Diffusion = diffusion_setup, # Parameters related to the diffusion process
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Chemistry = chemistry_setup
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)
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Binary file not shown.
@ -1,9 +0,0 @@
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iterations <- 1000
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dt <- 200
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list(
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timesteps = rep(dt, iterations),
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store_result = TRUE,
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out_save = c(1, 5, seq(20, iterations, by=20))
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)
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@ -1,90 +0,0 @@
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## Time-stamp: "Last modified 2024-05-30 13:27:06 delucia"
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## load a pretrained model from tensorflow file
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## Use the global variable "ai_surrogate_base_path" when using file paths
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## relative to the input script
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initiate_model <- function() {
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require(keras3)
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require(tensorflow)
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init_model <- normalizePath(paste0(ai_surrogate_base_path,
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"barite_50ai_all.keras"))
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Model <- keras3::load_model(init_model)
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msgm("Loaded model:")
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print(str(Model))
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return(Model)
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}
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scale_min_max <- function(x, min, max, backtransform) {
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if (backtransform) {
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return((x * (max - min)) + min)
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} else {
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return((x - min) / (max - min))
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}
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}
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minmax <- list(min = c(H = 111.012433592824, O = 55.5062185549492, Charge = -3.1028354471876e-08,
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Ba = 1.87312878574393e-141, Cl = 0, `S(6)` = 4.24227510643685e-07,
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Sr = 0.00049382996130541, Barite = 0.000999542409828586, Celestite = 0.244801877115968),
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max = c(H = 111.012433679682, O = 55.5087003521685, Charge = 5.27666636082035e-07,
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Ba = 0.0908849779513762, Cl = 0.195697626449355, `S(6)` = 0.000620774752665846,
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Sr = 0.0558680070692722, Barite = 0.756779139057097, Celestite = 1.00075422160624
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))
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preprocess <- function(df) {
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if (!is.data.frame(df))
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df <- as.data.frame(df, check.names = FALSE)
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as.data.frame(lapply(colnames(df),
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function(x) scale_min_max(x=df[x],
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min=minmax$min[x],
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max=minmax$max[x],
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backtransform=FALSE)),
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check.names = FALSE)
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}
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postprocess <- function(df) {
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if (!is.data.frame(df))
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df <- as.data.frame(df, check.names = FALSE)
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as.data.frame(lapply(colnames(df),
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function(x) scale_min_max(x=df[x],
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min=minmax$min[x],
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max=minmax$max[x],
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backtransform=TRUE)),
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check.names = FALSE)
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}
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mass_balance <- function(predictors, prediction) {
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dBa <- abs(prediction$Ba + prediction$Barite -
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predictors$Ba - predictors$Barite)
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dSr <- abs(prediction$Sr + prediction$Celestite -
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predictors$Sr - predictors$Celestite)
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return(dBa + dSr)
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}
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validate_predictions <- function(predictors, prediction) {
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epsilon <- 1E-7
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mb <- mass_balance(predictors, prediction)
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msgm("Mass balance mean:", mean(mb))
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msgm("Mass balance variance:", var(mb))
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ret <- mb < epsilon
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msgm("Rows where mass balance meets threshold", epsilon, ":",
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sum(ret))
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return(ret)
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}
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training_step <- function(model, predictor, target, validity) {
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msgm("Starting incremental training:")
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## x <- as.matrix(predictor)
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## y <- as.matrix(target[colnames(x)])
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history <- model %>% keras3::fit(x = data.matrix(predictor),
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y = data.matrix(target),
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epochs = 10, verbose=1)
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keras3::save_model(model,
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filepath = paste0(out_dir, "/current_model.keras"),
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overwrite=TRUE)
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return(model)
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}
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@ -1,32 +0,0 @@
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grid_def <- matrix(c(2, 3), nrow = 2, ncol = 5)
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# Define grid configuration for POET model
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grid_setup <- list(
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pqc_in_file = "./barite_het.pqi",
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pqc_db_file = "./db_barite.dat", # Path to the database file for Phreeqc
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grid_def = grid_def, # Definition of the grid, containing IDs according to the Phreeqc input script
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grid_size = c(ncol(grid_def), nrow(grid_def)), # Size of the grid in meters
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constant_cells = c() # IDs of cells with constant concentration
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)
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diffusion_setup <- list(
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boundaries = list(
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"W" = list(
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"type" = rep("constant", nrow(grid_def)),
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"sol_id" = rep(4, nrow(grid_def)),
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"cell" = seq_len(nrow(grid_def))
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)
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),
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alpha_x = 1e-6,
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alpha_y = matrix(runif(10, 1e-8, 1e-7),
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nrow = nrow(grid_def),
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ncol = ncol(grid_def)
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)
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)
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# Define a setup list for simulation configuration
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setup <- list(
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Grid = grid_setup, # Parameters related to the grid structure
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Diffusion = diffusion_setup, # Parameters related to the diffusion process
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Chemistry = list()
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)
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@ -1,80 +0,0 @@
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## Initial: everywhere equilibrium with Celestite NB: The aqueous
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## solution *resulting* from this calculation is to be used as initial
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## state everywhere in the domain
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SOLUTION 1
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units mol/kgw
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water 1
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temperature 25
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pH 7
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pe 4
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S(6) 1e-12
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Sr 1e-12
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Ba 1e-12
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Cl 1e-12
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PURE 1
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Celestite 0.0 1
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SAVE SOLUTION 2 # <- phreeqc keyword to store and later reuse these results
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END
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RUN_CELLS
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-cells 1
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COPY solution 1 2-3
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## Here a 5x2 domain:
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|---+---+---+---+---|
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-> | 2 | 2 | 2 | 2 | 2 |
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4 |---+---+---+---+---|
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-> | 3 | 3 | 3 | 3 | 3 |
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|---+---+---+---+---|
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## East boundary: "injection" of solution 4. North, W, S boundaries: closed
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## Here the two distinct zones: nr 2 with kinetics Celestite (initial
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## amount is 0, is then allowed to precipitate) and nr 3 with kinetic
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## Celestite and Barite (both initially > 0) where the actual
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## replacement takes place
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#USE SOLUTION 2 <- PHREEQC keyword to reuse the results from previous calculation
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KINETICS 2
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Celestite
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-m 0 # Allowed to precipitate
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-parms 10.0
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-tol 1e-9
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END
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#USE SOLUTION 2 <- PHREEQC keyword to reuse the results from previous calculation
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KINETICS 3
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Barite
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-m 0.001
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-parms 50.
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-tol 1e-9
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Celestite
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-m 1
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-parms 10.0
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-tol 1e-9
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END
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## A BaCl2 solution (nr 4) is "injected" from the left boundary:
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SOLUTION 4
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units mol/kgw
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pH 7
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water 1
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temp 25
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Ba 0.1
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Cl 0.2
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END
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## NB: again, the *result* of the SOLUTION 4 script defines the
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## concentration of all elements (+charge, tot H, tot O)
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## Ideally, in the initial state SOLUTION 1 we should not have to
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## define the 4 elemental concentrations (S(6), Sr, Ba and Cl) but
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## obtain them having run once the scripts with the aqueous solution
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## resulting from SOLUTION 1 once with KINETICS 2 and once with
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## KINETICS 3.
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RUN_CELLS
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-cells 2-4
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@ -1,4 +0,0 @@
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list(
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timesteps = rep(50, 100),
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store_result = TRUE
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)
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Binary file not shown.
@ -1,10 +1,8 @@
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set(bench_files
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set(bench_files
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dolo_inner_large.R
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dolo_interp.R
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dolo_interp.R
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)
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)
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set(runtime_files
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set(runtime_files
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dolo_inner_large_rt.R
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dolo_interp_rt.R
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dolo_interp_rt.R
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)
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)
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Binary file not shown.
@ -1,115 +0,0 @@
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rows <- 2000
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cols <- 1000
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grid_def <- matrix(2, nrow = rows, ncol = cols)
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# Define grid configuration for POET model
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grid_setup <- list(
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pqc_in_file = "./dol.pqi",
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pqc_db_file = "./phreeqc_kin.dat", # Path to the database file for Phreeqc
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grid_def = grid_def, # Definition of the grid, containing IDs according to the Phreeqc input script
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|
||||||
grid_size = c(cols, rows) / 100, # Size of the grid in meters
|
|
||||||
constant_cells = c() # IDs of cells with constant concentration
|
|
||||||
)
|
|
||||||
|
|
||||||
bound_size <- 2
|
|
||||||
|
|
||||||
diffusion_setup <- list(
|
|
||||||
inner_boundaries = list(
|
|
||||||
"row" = c(400, 1400, 1600),
|
|
||||||
"col" = c(200, 800, 800),
|
|
||||||
"sol_id" = c(3, 4, 4)
|
|
||||||
),
|
|
||||||
alpha_x = 1e-6,
|
|
||||||
alpha_y = 1e-6
|
|
||||||
)
|
|
||||||
|
|
||||||
check_sign_cal_dol_dht <- function(old, new) {
|
|
||||||
if ((old["Calcite"] == 0) != (new["Calcite"] == 0)) {
|
|
||||||
return(TRUE)
|
|
||||||
}
|
|
||||||
if ((old["Dolomite"] == 0) != (new["Dolomite"] == 0)) {
|
|
||||||
return(TRUE)
|
|
||||||
}
|
|
||||||
return(FALSE)
|
|
||||||
}
|
|
||||||
|
|
||||||
fuzz_input_dht_keys <- function(input) {
|
|
||||||
dht_species <- c(
|
|
||||||
"H" = 3,
|
|
||||||
"O" = 3,
|
|
||||||
"Charge" = 3,
|
|
||||||
"C(4)" = 6,
|
|
||||||
"Ca" = 6,
|
|
||||||
"Cl" = 3,
|
|
||||||
"Mg" = 5,
|
|
||||||
"Calcite" = 4,
|
|
||||||
"Dolomite" = 4
|
|
||||||
)
|
|
||||||
return(input[names(dht_species)])
|
|
||||||
}
|
|
||||||
|
|
||||||
check_sign_cal_dol_interp <- function(to_interp, data_set) {
|
|
||||||
dht_species <- c(
|
|
||||||
"H" = 3,
|
|
||||||
"O" = 3,
|
|
||||||
"Charge" = 3,
|
|
||||||
"C(4)" = 6,
|
|
||||||
"Ca" = 6,
|
|
||||||
"Cl" = 3,
|
|
||||||
"Mg" = 5,
|
|
||||||
"Calcite" = 4,
|
|
||||||
"Dolomite" = 4
|
|
||||||
)
|
|
||||||
data_set <- as.data.frame(do.call(rbind, data_set), check.names = FALSE, optional = TRUE)
|
|
||||||
names(data_set) <- names(dht_species)
|
|
||||||
cal <- (data_set$Calcite == 0) == (to_interp["Calcite"] == 0)
|
|
||||||
dol <- (data_set$Dolomite == 0) == (to_interp["Dolomite"] == 0)
|
|
||||||
|
|
||||||
cal_dol_same_sig <- cal == dol
|
|
||||||
return(rev(which(!cal_dol_same_sig)))
|
|
||||||
}
|
|
||||||
|
|
||||||
check_neg_cal_dol <- function(result) {
|
|
||||||
neg_sign <- (result["Calcite"] < 0) || (result["Dolomite"] < 0)
|
|
||||||
return(neg_sign)
|
|
||||||
}
|
|
||||||
|
|
||||||
# Optional when using Interpolation (example with less key species and custom
|
|
||||||
# significant digits)
|
|
||||||
|
|
||||||
pht_species <- c(
|
|
||||||
"C(4)" = 3,
|
|
||||||
"Ca" = 3,
|
|
||||||
"Mg" = 2,
|
|
||||||
"Calcite" = 2,
|
|
||||||
"Dolomite" = 2
|
|
||||||
)
|
|
||||||
|
|
||||||
chemistry_setup <- list(
|
|
||||||
dht_species = c(
|
|
||||||
"H" = 3,
|
|
||||||
"O" = 3,
|
|
||||||
"Charge" = 3,
|
|
||||||
"C(4)" = 6,
|
|
||||||
"Ca" = 6,
|
|
||||||
"Cl" = 3,
|
|
||||||
"Mg" = 5,
|
|
||||||
"Calcite" = 4,
|
|
||||||
"Dolomite" = 4
|
|
||||||
),
|
|
||||||
pht_species = pht_species,
|
|
||||||
hooks = list(
|
|
||||||
dht_fill = check_sign_cal_dol_dht,
|
|
||||||
dht_fuzz = fuzz_input_dht_keys,
|
|
||||||
interp_pre = check_sign_cal_dol_interp,
|
|
||||||
interp_post = check_neg_cal_dol
|
|
||||||
)
|
|
||||||
)
|
|
||||||
|
|
||||||
# Define a setup list for simulation configuration
|
|
||||||
setup <- list(
|
|
||||||
Grid = grid_setup, # Parameters related to the grid structure
|
|
||||||
Diffusion = diffusion_setup, # Parameters related to the diffusion process
|
|
||||||
Chemistry = chemistry_setup # Parameters related to the chemistry process
|
|
||||||
)
|
|
||||||
@ -1,10 +0,0 @@
|
|||||||
iterations <- 500
|
|
||||||
dt <- 50
|
|
||||||
|
|
||||||
out_save <- seq(5, iterations, by = 5)
|
|
||||||
|
|
||||||
list(
|
|
||||||
timesteps = rep(dt, iterations),
|
|
||||||
store_result = TRUE,
|
|
||||||
out_save = out_save
|
|
||||||
)
|
|
||||||
@ -1,12 +0,0 @@
|
|||||||
iterations <- 2000
|
|
||||||
dt <- 200
|
|
||||||
|
|
||||||
out_save <- c(1, 10, 20, seq(40, iterations, by = 40))
|
|
||||||
|
|
||||||
list(
|
|
||||||
timesteps = rep(dt, iterations),
|
|
||||||
store_result = TRUE,
|
|
||||||
out_save = out_save
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,90 +0,0 @@
|
|||||||
## Time-stamp: "Last modified 2024-12-11 23:21:25 delucia"
|
|
||||||
|
|
||||||
library(PoetUtils)
|
|
||||||
library(viridis)
|
|
||||||
|
|
||||||
|
|
||||||
res <- ReadPOETSims("./res_fgcs2_96/")
|
|
||||||
|
|
||||||
pp <- PlotField(res$iter_200$C$Barite, rows = 200, cols = 200, contour = FALSE,
|
|
||||||
nlevels=12, palette=terrain.colors)
|
|
||||||
|
|
||||||
cairo_pdf("fgcs_Celestite_init.pdf", family="serif")
|
|
||||||
par(mar=c(0,0,0,0))
|
|
||||||
pp <- PlotField((res$iter_000$Celestite), rows = 200, cols = 200,
|
|
||||||
contour = FALSE, breaks=c(-0.5,0.5,1.5),
|
|
||||||
palette = grey.colors, plot.axes = FALSE, scale = FALSE,
|
|
||||||
main="Initial Celestite crystals")
|
|
||||||
dev.off()
|
|
||||||
|
|
||||||
|
|
||||||
cairo_pdf("fgcs_Ba_init.pdf", family="serif")
|
|
||||||
par(mar=c(0,0,0,0))
|
|
||||||
pp <- PlotField(log10(res$iter_001$C$Cl), rows = 200, cols = 200,
|
|
||||||
contour = FALSE,
|
|
||||||
palette = terrain.colors, plot.axes = FALSE, scale = FALSE,
|
|
||||||
main="log10(Ba)")
|
|
||||||
dev.off()
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
pp <- PlotField(log10(res$iter_002$C$Ba), rows = 200, cols = 200,
|
|
||||||
contour = FALSE, palette = viridis, rev.palette = FALSE,
|
|
||||||
main = "log10(Ba) after 5 iterations")
|
|
||||||
|
|
||||||
pp <- PlotField(log10(res$iter_200$C$`S(6)`), rows = 200, cols = 200, contour = FALSE)
|
|
||||||
|
|
||||||
|
|
||||||
str(res$iter_00)
|
|
||||||
|
|
||||||
res$iter_178$C$Barite
|
|
||||||
|
|
||||||
pp <- res$iter_043$C$Barite
|
|
||||||
|
|
||||||
breaks <- pretty(pp, n = 5)
|
|
||||||
|
|
||||||
br <- c(0, 0.0005, 0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1)
|
|
||||||
|
|
||||||
pp <- PlotField(res$iter_200$C$Barite, rows = 200, cols = 200, contour = FALSE,
|
|
||||||
breaks = br, palette=terrain.colors)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
cairo_pdf("fgcs_Barite_200.pdf", family="serif")
|
|
||||||
pp <- PlotField(log10(res$iter_200$C$Barite), rows = 200, cols = 200,
|
|
||||||
contour = FALSE, palette = terrain.colors, plot.axes = FALSE,
|
|
||||||
rev.palette = FALSE, main = "log10(Barite) after 200 iter")
|
|
||||||
dev.off()
|
|
||||||
|
|
||||||
ref <- ReadPOETSims("./res_fgcs_2_ref")
|
|
||||||
|
|
||||||
rei <- ReadPOETSims("./res_fgcs_2_interp1/")
|
|
||||||
|
|
||||||
|
|
||||||
timref <- ReadRObj("./res_fgcs_2_ref/timings.qs")
|
|
||||||
timint <- ReadRObj("./res_fgcs_2_interp1/timings.qs")
|
|
||||||
|
|
||||||
timref
|
|
||||||
|
|
||||||
timint
|
|
||||||
|
|
||||||
wch <- c("H","O", "Ba", "Sr","Cl", "S(6)")
|
|
||||||
|
|
||||||
rf <- data.matrix(ref$iter_001$C[, wch])
|
|
||||||
r1 <- data.matrix(rei$iter_001$C[, wch])
|
|
||||||
|
|
||||||
r1[is.nan(r1)] <- NA
|
|
||||||
rf[is.nan(rf)] <- NA
|
|
||||||
|
|
||||||
cairo_pdf("fgcs_interp_1.pdf", family="serif", width = 10, height = 7)
|
|
||||||
PlotScatter(rf, r1, which = wch, labs = c("ref", "interp"), cols = 3, log="", las = 1, pch=4)
|
|
||||||
dev.off()
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
head(r1)
|
|
||||||
|
|
||||||
head(rf)
|
|
||||||
|
|
||||||
rf$O
|
|
||||||
r1$O
|
|
||||||
@ -1,2 +0,0 @@
|
|||||||
* Refer to the LaTeX file (and pdf) for more information
|
|
||||||
|
|
||||||
@ -1,105 +0,0 @@
|
|||||||
## Time-stamp: "Last modified 2024-12-11 16:08:11 delucia"
|
|
||||||
|
|
||||||
cols <- 1000
|
|
||||||
rows <- 1000
|
|
||||||
|
|
||||||
dim_cols <- 50
|
|
||||||
dim_rows <- 50
|
|
||||||
|
|
||||||
ncirc <- 20 ## number of crystals
|
|
||||||
rmax <- cols / 10 ## max radius (in nodes)
|
|
||||||
|
|
||||||
set.seed(22933)
|
|
||||||
|
|
||||||
centers <- cbind(sample(seq_len(cols), ncirc), sample(seq_len(rows), ncirc))
|
|
||||||
radii <- sample(seq_len(rmax), ncirc, replace = TRUE)
|
|
||||||
mi <- matrix(rep(seq_len(cols), rows), byrow = TRUE, nrow = rows)
|
|
||||||
mj <- matrix(rep(seq_len(cols), each = rows), byrow = TRUE, nrow = rows)
|
|
||||||
|
|
||||||
tmpl <- lapply(seq_len(ncirc), function(x) which((mi - centers[x, 1])^2 + (mj - centers[x, 2])^2 < radii[x]^2, arr.ind = TRUE))
|
|
||||||
|
|
||||||
inds <- do.call(rbind, tmpl)
|
|
||||||
grid <- matrix(1, nrow = rows, ncol = cols)
|
|
||||||
grid[inds] <- 2
|
|
||||||
|
|
||||||
alpha <- matrix(1e-5, ncol = cols, nrow = rows)
|
|
||||||
alpha[inds] <- 1e-7
|
|
||||||
|
|
||||||
## image(grid, asp=1)
|
|
||||||
|
|
||||||
## Define grid configuration for POET model
|
|
||||||
grid_setup <- list(
|
|
||||||
pqc_in_file = "./barite_fgcs_2.pqi",
|
|
||||||
pqc_db_file = "../barite/db_barite.dat", ## database file
|
|
||||||
grid_def = grid, ## grid definition, IDs according to the Phreeqc input
|
|
||||||
grid_size = c(dim_cols, dim_rows), ## grid size in meters
|
|
||||||
constant_cells = c() ## IDs of cells with constant concentration
|
|
||||||
)
|
|
||||||
|
|
||||||
bound_length <- cols / 10
|
|
||||||
|
|
||||||
bound_N <- list(
|
|
||||||
"type" = rep("constant", bound_length),
|
|
||||||
"sol_id" = rep(3, bound_length),
|
|
||||||
"cell" = seq(1, bound_length)
|
|
||||||
)
|
|
||||||
|
|
||||||
bound_W <- list(
|
|
||||||
"type" = rep("constant", bound_length),
|
|
||||||
"sol_id" = rep(3, bound_length),
|
|
||||||
"cell" = seq(1, bound_length)
|
|
||||||
)
|
|
||||||
bound_E <- list(
|
|
||||||
"type" = rep("constant", bound_length),
|
|
||||||
"sol_id" = rep(4, bound_length),
|
|
||||||
"cell" = seq(rows - bound_length + 1, rows)
|
|
||||||
)
|
|
||||||
|
|
||||||
bound_S <- list(
|
|
||||||
"type" = rep("constant", bound_length),
|
|
||||||
"sol_id" = rep(4, bound_length),
|
|
||||||
"cell" = seq(cols - bound_length + 1, cols)
|
|
||||||
)
|
|
||||||
|
|
||||||
diffusion_setup <- list(
|
|
||||||
boundaries = list(
|
|
||||||
"W" = bound_W,
|
|
||||||
"N" = bound_N,
|
|
||||||
"E" = bound_E,
|
|
||||||
"S" = bound_S
|
|
||||||
),
|
|
||||||
alpha_x = alpha,
|
|
||||||
alpha_y = alpha
|
|
||||||
)
|
|
||||||
|
|
||||||
dht_species <- c(
|
|
||||||
"H" = 7,
|
|
||||||
"O" = 7,
|
|
||||||
"Ba" = 7,
|
|
||||||
"Cl" = 7,
|
|
||||||
"S" = 7,
|
|
||||||
"Sr" = 7,
|
|
||||||
"Barite" = 4,
|
|
||||||
"Celestite" = 4
|
|
||||||
)
|
|
||||||
|
|
||||||
pht_species <- c(
|
|
||||||
"Ba" = 4,
|
|
||||||
"Cl" = 3,
|
|
||||||
"S" = 3,
|
|
||||||
"Sr" = 3,
|
|
||||||
"Barite" = 0,
|
|
||||||
"Celestite" = 0
|
|
||||||
)
|
|
||||||
|
|
||||||
chemistry_setup <- list(
|
|
||||||
dht_species = dht_species,
|
|
||||||
pht_species = pht_species
|
|
||||||
)
|
|
||||||
|
|
||||||
## Define a setup list for simulation configuration
|
|
||||||
setup <- list(
|
|
||||||
Grid = grid_setup, ## Parameters related to the grid structure
|
|
||||||
Diffusion = diffusion_setup, ## Parameters related to the diffusion process
|
|
||||||
Chemistry = chemistry_setup
|
|
||||||
)
|
|
||||||
@ -1,49 +0,0 @@
|
|||||||
SOLUTION 1
|
|
||||||
units mol/kgw
|
|
||||||
water 1
|
|
||||||
temperature 25
|
|
||||||
pH 7.008
|
|
||||||
pe 10.798
|
|
||||||
S 6.205e-04
|
|
||||||
Sr 6.205e-04
|
|
||||||
END
|
|
||||||
|
|
||||||
SOLUTION 2
|
|
||||||
units mol/kgw
|
|
||||||
water 1
|
|
||||||
temperature 25
|
|
||||||
pH 7.008
|
|
||||||
pe 10.798
|
|
||||||
S 6.205e-04
|
|
||||||
Sr 6.205e-04
|
|
||||||
KINETICS 2
|
|
||||||
Barite
|
|
||||||
-m 0.00
|
|
||||||
-parms 50. # reactive surface area
|
|
||||||
-tol 1e-9
|
|
||||||
Celestite
|
|
||||||
-m 1
|
|
||||||
-parms 10.0 # reactive surface area
|
|
||||||
-tol 1e-9
|
|
||||||
END
|
|
||||||
|
|
||||||
SOLUTION 3
|
|
||||||
units mol/kgw
|
|
||||||
water 1
|
|
||||||
temperature 25
|
|
||||||
Ba 0.1
|
|
||||||
Cl 0.2
|
|
||||||
END
|
|
||||||
|
|
||||||
SOLUTION 4
|
|
||||||
units mol/kgw
|
|
||||||
water 1
|
|
||||||
temperature 25
|
|
||||||
Ba 0.2
|
|
||||||
Cl 0.4
|
|
||||||
END
|
|
||||||
|
|
||||||
|
|
||||||
RUN_CELLS
|
|
||||||
-cells 1 2 3 4
|
|
||||||
END
|
|
||||||
@ -1,7 +0,0 @@
|
|||||||
iterations <- 200
|
|
||||||
dt <- 1000
|
|
||||||
|
|
||||||
list(
|
|
||||||
timesteps = rep(dt, iterations),
|
|
||||||
store_result = TRUE
|
|
||||||
)
|
|
||||||
@ -1,20 +0,0 @@
|
|||||||
set(bench_files
|
|
||||||
# surfex.R
|
|
||||||
# ex.R
|
|
||||||
PoetEGU_surfex_500.R
|
|
||||||
)
|
|
||||||
|
|
||||||
set(runtime_files
|
|
||||||
# surfex_rt.R
|
|
||||||
# ex_rt.R
|
|
||||||
PoetEGU_surfex_500_rt.R
|
|
||||||
)
|
|
||||||
|
|
||||||
ADD_BENCH_TARGET(
|
|
||||||
surfex_bench
|
|
||||||
bench_files
|
|
||||||
runtime_files
|
|
||||||
"surfex"
|
|
||||||
)
|
|
||||||
|
|
||||||
add_dependencies(${BENCHTARGET} surfex_bench)
|
|
||||||
@ -1,63 +0,0 @@
|
|||||||
## Time-stamp: "Last modified 2023-03-21 11:49:43 mluebke"
|
|
||||||
KNOBS
|
|
||||||
-logfile false
|
|
||||||
-iterations 10000
|
|
||||||
-convergence_tolerance 1E-12
|
|
||||||
-step_size 2
|
|
||||||
-pe_step_size 2
|
|
||||||
SELECTED_OUTPUT
|
|
||||||
-reset false
|
|
||||||
-high_precision true
|
|
||||||
-solution true
|
|
||||||
-state true
|
|
||||||
-step true
|
|
||||||
-pH true
|
|
||||||
-pe true
|
|
||||||
-ionic_strength true
|
|
||||||
-water true
|
|
||||||
SOLUTION 1
|
|
||||||
temp 13
|
|
||||||
units mol/kgw
|
|
||||||
pH 7.06355
|
|
||||||
pe -2.626517
|
|
||||||
C(4) 0.001990694
|
|
||||||
Ca 0.02172649
|
|
||||||
Cl 0.3227673 charge
|
|
||||||
Fe 0.0001434717
|
|
||||||
K 0.001902357
|
|
||||||
Mg 0.01739704
|
|
||||||
Na 0.2762882
|
|
||||||
S(6) 0.01652701
|
|
||||||
Sr 0.0004520361
|
|
||||||
U(4) 8.147792e-12
|
|
||||||
U(6) 2.237946e-09
|
|
||||||
-water 0.00133
|
|
||||||
EXCHANGE 1
|
|
||||||
-equil 1
|
|
||||||
Z 0.0012585
|
|
||||||
Y 0.0009418
|
|
||||||
END
|
|
||||||
|
|
||||||
SOLUTION 2
|
|
||||||
temp 13
|
|
||||||
units mol/kgw
|
|
||||||
|
|
||||||
C(-4) 2.92438561098248e-21
|
|
||||||
C(4) 2.65160558871092e-06
|
|
||||||
Ca 2.89001071336443e-05
|
|
||||||
Cl 0.000429291158114428
|
|
||||||
Fe(2) 1.90823391198114e-07
|
|
||||||
Fe(3) 3.10832423034763e-12
|
|
||||||
H(0) 2.7888235127385e-15
|
|
||||||
K 2.5301787e-06
|
|
||||||
Mg 2.31391999937907e-05
|
|
||||||
Na 0.00036746969
|
|
||||||
S(-2) 1.01376078438546e-14
|
|
||||||
S(2) 1.42247026981542e-19
|
|
||||||
S(4) 9.49422092568557e-18
|
|
||||||
S(6) 2.19812504654191e-05
|
|
||||||
Sr 6.01218519999999e-07
|
|
||||||
U(4) 4.82255946569383e-12
|
|
||||||
U(5) 5.49050615347901e-13
|
|
||||||
U(6) 1.32462838991902e-09
|
|
||||||
END
|
|
||||||
@ -1,40 +0,0 @@
|
|||||||
rows <- 500
|
|
||||||
cols <- 200
|
|
||||||
|
|
||||||
grid_left <- matrix(1, nrow = rows, ncol = cols/2)
|
|
||||||
grid_rght <- matrix(2, nrow = rows, ncol = cols/2)
|
|
||||||
grid_def <- cbind(grid_left, grid_rght)
|
|
||||||
|
|
||||||
|
|
||||||
# Define grid configuration for POET model
|
|
||||||
grid_setup <- list(
|
|
||||||
pqc_in_file = "./SurfexEGU.pqi",
|
|
||||||
pqc_db_file = "./SMILE_2021_11_01_TH.dat", # Path to the database file for Phreeqc
|
|
||||||
grid_def = grid_def, # Definition of the grid, containing IDs according to the Phreeqc input script
|
|
||||||
grid_size = c(10, 4), # Size of the grid in meters
|
|
||||||
constant_cells = c() # IDs of cells with constant concentration
|
|
||||||
)
|
|
||||||
|
|
||||||
bound_def <- list(
|
|
||||||
"type" = rep("constant", cols),
|
|
||||||
"sol_id" = rep(3, cols),
|
|
||||||
"cell" = seq(1, cols)
|
|
||||||
)
|
|
||||||
|
|
||||||
diffusion_setup <- list(
|
|
||||||
boundaries = list(
|
|
||||||
"N" = bound_def
|
|
||||||
),
|
|
||||||
alpha_x = matrix(runif(rows*cols))*1e-8,
|
|
||||||
alpha_y = matrix(runif(rows*cols))*1e-9## ,1e-10
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
chemistry_setup <- list()
|
|
||||||
|
|
||||||
# Define a setup list for simulation configuration
|
|
||||||
setup <- list(
|
|
||||||
Grid = grid_setup, # Parameters related to the grid structure
|
|
||||||
Diffusion = diffusion_setup, # Parameters related to the diffusion process
|
|
||||||
Chemistry = chemistry_setup # Parameters related to the chemistry process
|
|
||||||
)
|
|
||||||
@ -1,11 +0,0 @@
|
|||||||
iterations <- 200
|
|
||||||
dt <- 1000
|
|
||||||
|
|
||||||
out_save <- c(1, 2, seq(5, iterations, by=5))
|
|
||||||
## out_save <- seq(1, iterations)
|
|
||||||
|
|
||||||
list(
|
|
||||||
timesteps = rep(dt, iterations),
|
|
||||||
store_result = TRUE,
|
|
||||||
out_save = out_save
|
|
||||||
)
|
|
||||||
@ -1,100 +0,0 @@
|
|||||||
#+TITLE: Description of =surfex= benchmark
|
|
||||||
#+AUTHOR: MDL <delucia@gfz-potsdam.de>
|
|
||||||
#+DATE: 2023-08-26
|
|
||||||
#+STARTUP: inlineimages
|
|
||||||
#+LATEX_CLASS_OPTIONS: [a4paper,9pt]
|
|
||||||
#+LATEX_HEADER: \usepackage{fullpage}
|
|
||||||
#+LATEX_HEADER: \usepackage{amsmath, systeme}
|
|
||||||
#+LATEX_HEADER: \usepackage{graphicx}
|
|
||||||
#+LATEX_HEADER: \usepackage{charter}
|
|
||||||
#+OPTIONS: toc:nil
|
|
||||||
|
|
||||||
* Quick start
|
|
||||||
|
|
||||||
#+begin_src sh :language sh :frame single
|
|
||||||
mpirun -np 4 ./poet ex.R ex_res
|
|
||||||
mpirun -np 4 ./poet surfex.R surfex_res
|
|
||||||
#+end_src
|
|
||||||
|
|
||||||
* List of Files
|
|
||||||
- =ex.R=: POET input script for a 100x100 simulation grid, only
|
|
||||||
exchange
|
|
||||||
- =ExBase.pqi=: PHREEQC input script for the =ex.R= model
|
|
||||||
- =surfex.R=: POET input script for a 1000x1000 simulation grid
|
|
||||||
considering both cation exchange and surface complexation
|
|
||||||
- =SurfExBase.pqi=: PHREEQC input script for the =surfex.R= model
|
|
||||||
- =SMILE_2021_11_01_TH.dat=: PHREEQC database containing the
|
|
||||||
parametrized data for Surface and Exchange, based on the SMILE
|
|
||||||
Thermodynamic Database (Version 01-November-2021)
|
|
||||||
|
|
||||||
* Chemical system
|
|
||||||
|
|
||||||
This model describes migration of Uranium radionuclide in Opalinus
|
|
||||||
clay subject to surface complexation and cation exchange on the
|
|
||||||
surface of clay minerals. These two processes account for the binding
|
|
||||||
of aqueous complexes to the surfaces of minerals, which may have a
|
|
||||||
significant impact on safety of underground nuclear waste repository.
|
|
||||||
Namely, they can act as retardation buffer for uranium complexes
|
|
||||||
entering into a natural system. The system is kindly provided by Dr.
|
|
||||||
T. Hennig and is inspired to the sandy facies BWS-A3 sample from the
|
|
||||||
Mont Terri underground lab (Hennig and Kühn, 2021).
|
|
||||||
|
|
||||||
This chemical system is highly redox-sensitive, and several elements
|
|
||||||
are defined in significant amounts in different valence states. In
|
|
||||||
total, 20 elemental concentrations and valences are transported:
|
|
||||||
C(-4), C(4), Ca, Cl, Fe(2), Fe(3), K, Mg, Na, S(-2), S(2), S(4), S(6),
|
|
||||||
Sr , U(4), U(5), U(6); plus the total H, total O and Charge implicitly
|
|
||||||
required by PHREEQC_RM.
|
|
||||||
|
|
||||||
** Exchange
|
|
||||||
|
|
||||||
The SMILE database defines thermodynamical data for exchange of all
|
|
||||||
major cations and uranyl-ions on Illite and Montmorillonite. In
|
|
||||||
PHREEQC terms:
|
|
||||||
- *Y* for Montmorillonite, with a total amount of 1.2585
|
|
||||||
milliequivalents and
|
|
||||||
- *Z* for Illite, with a total amount of 0.9418 meq
|
|
||||||
|
|
||||||
** Surface
|
|
||||||
|
|
||||||
Here we consider a Donnan diffuse double layer of 0.49 nm. Six
|
|
||||||
distinct sorption sites are defined:
|
|
||||||
- Kln_aOH (aluminol site) and Kln_siOH (silanol) for Kaolinite
|
|
||||||
- For Illite, strong and weak sites Ill_sOH and Ill_wOH respectively
|
|
||||||
- For Montmorillonite, strong and weak sites Mll_sOH and Mll_wOH
|
|
||||||
respectively
|
|
||||||
|
|
||||||
Refer to the =SurfExBase.pqi= script for the actual numerical values
|
|
||||||
of the parameters.
|
|
||||||
|
|
||||||
* POET simulations
|
|
||||||
|
|
||||||
** =ex.R=
|
|
||||||
|
|
||||||
This benchmark only considers EXCHANGE, no mineral or SURFACE
|
|
||||||
complexation is involved.
|
|
||||||
|
|
||||||
- Grid discretization: square domain of 1 \cdot 1 m^{2} discretized in
|
|
||||||
100x100 cells
|
|
||||||
- Boundary conditions: E, S and W sides of the domain are closed.
|
|
||||||
*Fixed concentrations* are fixed at the N boundary.
|
|
||||||
- Diffusion coefficients: isotropic homogeneous \alpha = 1E-06
|
|
||||||
- Time steps & iterations: 10 iterations with \Delta t of 200 s
|
|
||||||
- *DHT* is not implemented as of yet for models including SURFACE and
|
|
||||||
EXCHANGE geochemical processes *TODO*
|
|
||||||
- Hooks: no hooks defined *TODO*
|
|
||||||
|
|
||||||
** =surfex.R=
|
|
||||||
|
|
||||||
- Grid discretization: rectangular domain of 1 \cdot 1 m^{2}
|
|
||||||
discretized in 10 \times 10 cells
|
|
||||||
- Boundary conditions: E, S and W sides of the domain are closed.
|
|
||||||
*Fixed concentrations* are fixed at the N boundary.
|
|
||||||
- Diffusion coefficients: isotropic homogeneous \alpha = 1E-06
|
|
||||||
- Time steps & iterations: 10 iterations with \Delta t of 200 s
|
|
||||||
|
|
||||||
* References
|
|
||||||
|
|
||||||
- Hennig, T.; Kühn, M.Surrogate Model for Multi-Component Diffusion of
|
|
||||||
Uranium through Opalinus Clay on the Host Rock Scale. Appl. Sci.
|
|
||||||
2021, 11, 786. https://doi.org/10.3390/app11020786
|
|
||||||
File diff suppressed because it is too large
Load Diff
@ -1,80 +0,0 @@
|
|||||||
## Time-stamp: "Last modified 2023-02-27 14:31:11 delucia"
|
|
||||||
KNOBS
|
|
||||||
-logfile false
|
|
||||||
-iterations 10000
|
|
||||||
-convergence_tolerance 1E-12
|
|
||||||
-step_size 2
|
|
||||||
-pe_step_size 2
|
|
||||||
SELECTED_OUTPUT
|
|
||||||
-reset false
|
|
||||||
-high_precision true
|
|
||||||
-solution true
|
|
||||||
-state true
|
|
||||||
-step true
|
|
||||||
-pH true
|
|
||||||
-pe true
|
|
||||||
-ionic_strength true
|
|
||||||
-water true
|
|
||||||
USER_PUNCH
|
|
||||||
-head total_o total_h cb C(-4) C(4) Ca Cl Fe(2) Fe(3) H(0) K Mg Na S(-2) S(2) S(4) S(6) Sr U(4) U(5) U(6) UO2(am,hyd) KdU
|
|
||||||
-start
|
|
||||||
5 w=TOT("water")
|
|
||||||
10 PUNCH TOTMOLE("O"), TOTMOLE("H"), CHARGE_BALANCE, w*TOT("C(-4)"), w*TOT("C(4)"), w*TOT("Ca"), w*TOT("Cl"), w*TOT("Fe(2)"), w*TOT("Fe(3)"), w*TOT("H(0)"), w*TOT("K"), w*TOT("Mg"), w*TOT("Na"), w*TOT("S(-2)"), w*TOT("S(2)"), w*TOT("S(4)"), w*TOT("S(6)"), w*TOT("Sr"), w*TOT("U(4)"), w*TOT("U(5)"), w*TOT("U(6)"), EQUI("UO2(am,hyd)")
|
|
||||||
20 PUNCH ((SURF("U, Ill")+SURF("U, Mll")+SURF("U, Kln")+EDL("U, Ill")+EDL("U, Mll")+EDL("U, Kln"))/((TOT("U")*1.01583)))/(0.002251896406*1000)
|
|
||||||
-end
|
|
||||||
SOLUTION 1
|
|
||||||
temp 13
|
|
||||||
units mol/kgw
|
|
||||||
pH 7.06355
|
|
||||||
pe -2.626517
|
|
||||||
C(4) 0.001990694
|
|
||||||
Ca 0.02172649
|
|
||||||
Cl 0.3227673 charge
|
|
||||||
Fe 0.0001434717
|
|
||||||
K 0.001902357
|
|
||||||
Mg 0.01739704
|
|
||||||
Na 0.2762882
|
|
||||||
S(6) 0.01652701
|
|
||||||
Sr 0.0004520361
|
|
||||||
U(4) 8.147792e-12
|
|
||||||
U(6) 2.237946e-09
|
|
||||||
-water 0.00133
|
|
||||||
SURFACE 1
|
|
||||||
-equil 1
|
|
||||||
-sites_units density
|
|
||||||
-donnan 4.9e-10
|
|
||||||
Kln_aOH 1.155 11. 5.0518
|
|
||||||
Kln_siOH 1.155
|
|
||||||
Ill_sOH 0.05 100. 5.5931
|
|
||||||
Ill_wOH 2.26
|
|
||||||
Mll_sOH 0.05 100. 1.0825
|
|
||||||
Mll_wOH 2.26
|
|
||||||
EXCHANGE 1
|
|
||||||
-equil 1
|
|
||||||
Z 0.0012585
|
|
||||||
Y 0.0009418
|
|
||||||
END
|
|
||||||
|
|
||||||
SOLUTION 2
|
|
||||||
temp 13
|
|
||||||
units mol/kgw
|
|
||||||
|
|
||||||
C(-4) 2.92438561098248e-21
|
|
||||||
C(4) 2.65160558871092e-06
|
|
||||||
Ca 2.89001071336443e-05
|
|
||||||
Cl 0.000429291158114428
|
|
||||||
Fe(2) 1.90823391198114e-07
|
|
||||||
Fe(3) 3.10832423034763e-12
|
|
||||||
H(0) 2.7888235127385e-15
|
|
||||||
K 2.5301787e-06
|
|
||||||
Mg 2.31391999937907e-05
|
|
||||||
Na 0.00036746969
|
|
||||||
S(-2) 1.01376078438546e-14
|
|
||||||
S(2) 1.42247026981542e-19
|
|
||||||
S(4) 9.49422092568557e-18
|
|
||||||
S(6) 2.19812504654191e-05
|
|
||||||
Sr 6.01218519999999e-07
|
|
||||||
U(4) 4.82255946569383e-12
|
|
||||||
U(5) 5.49050615347901e-13
|
|
||||||
U(6) 1.32462838991902e-09
|
|
||||||
END
|
|
||||||
@ -1,108 +0,0 @@
|
|||||||
## Time-stamp: "Last modified 2024-04-12 10:59:59 delucia"
|
|
||||||
## KNOBS
|
|
||||||
## -logfile false
|
|
||||||
## -iterations 10000
|
|
||||||
## -convergence_tolerance 1E-12
|
|
||||||
## -step_size 2
|
|
||||||
## -pe_step_size 2
|
|
||||||
|
|
||||||
SOLUTION 1 ## Porewater composition Opalinus Clay, WITHOUT radionuclides, AFTER EQUI_PHASES
|
|
||||||
pe -2.627 ## Eh = -227 mV, Value from Bossart & Thury (2008)-> PC borehole measurement 2003, Eh still decreasing
|
|
||||||
density 1.01583 ## kg/dm³ = g/cm³
|
|
||||||
temp 13 ## mean temperature Mont Terri, Bossart & Thury (2008), calculations performed for 25°C
|
|
||||||
units mol/kgw
|
|
||||||
## Mean composition
|
|
||||||
pH 7.064
|
|
||||||
Na 2.763e-01
|
|
||||||
Cl 3.228e-01 charge
|
|
||||||
S(6) 1.653e-02 as SO4
|
|
||||||
Ca 2.173e-02
|
|
||||||
Mg 1.740e-02
|
|
||||||
K 1.902e-03
|
|
||||||
Sr 4.520e-04
|
|
||||||
Fe 1.435e-04
|
|
||||||
U 2.247e-09
|
|
||||||
|
|
||||||
SURFACE 1 Opalinus Clay, clay minerals
|
|
||||||
## calculated with rho_b=2.2903 kg/dm³, poro=0.1662
|
|
||||||
## 1 dm³ = 13.565641 kg_sed/kg_pw
|
|
||||||
-equil 1 ## equilibrate with solution 1
|
|
||||||
-sites_units density ## set unit for binding site density to sites/nm2
|
|
||||||
-donnan 4.9e-10 ## calculated after Wigger & Van Loon (2018) for ionic strength after equilibration with minerales for pCO2=2.2 log10 bar
|
|
||||||
|
|
||||||
# surface density SSA (m2/g) mass (g/kgw)
|
|
||||||
Kln_aOH 1.155 11. 3798.4 ## Kaolinite 28 wt% (aluminol and silanol sites)
|
|
||||||
Kln_siOH 1.155
|
|
||||||
Ill_sOH 0.05 100. 4205.35 ## Illite 31 wt% (weak und strong binding sites)
|
|
||||||
Ill_wOH 2.26 ## 2 % strong binding sites
|
|
||||||
Mll_sOH 0.05 100. 813.94 ## Montmorillonite = smektite = 6 wt% (weak und strong binding sites)
|
|
||||||
Mll_wOH 2.26 ## 2 % strong binding sites
|
|
||||||
|
|
||||||
EXCHANGE 1 Exchanger, only illite+montmorillonite
|
|
||||||
## Illite = 0.225 eq/kg_rock, Montmorillonit = 0.87 eq/kg_rock
|
|
||||||
-equil 1 ## equilibrate with solution 1
|
|
||||||
Z 0.9462 ## = Illite
|
|
||||||
Y 0.70813 ## = Montmorillonite
|
|
||||||
END
|
|
||||||
|
|
||||||
SOLUTION 2 ## Porewater composition Opalinus Clay, WITHOUT radionuclides, AFTER EQUI_PHASES
|
|
||||||
pe -2.627 ## Eh = -227 mV, Value from Bossart & Thury (2008)-> PC borehole measurement 2003, Eh still decreasing
|
|
||||||
density 1.01583 ## kg/dm³ = g/cm³
|
|
||||||
temp 13 ## mean temperature Mont Terri, Bossart & Thury (2008), calculations performed for 25°C
|
|
||||||
units mol/kgw
|
|
||||||
## Mean composition
|
|
||||||
pH 7.064
|
|
||||||
Na 2.763e-01
|
|
||||||
Cl 3.228e-01 charge
|
|
||||||
S(6) 1.653e-02 as SO4
|
|
||||||
Ca 2.173e-02
|
|
||||||
Mg 1.740e-02
|
|
||||||
K 1.902e-03
|
|
||||||
Sr 4.520e-04
|
|
||||||
Fe 1.435e-04
|
|
||||||
U 2.247e-09
|
|
||||||
|
|
||||||
SURFACE 2 Opalinus Clay, clay minerals
|
|
||||||
-equil 2 ## equilibrate with solution 2
|
|
||||||
-sites_units density ## set unit for binding site density to
|
|
||||||
## sites/nm2
|
|
||||||
-donnan 4.9e-10 ## calculated after Wigger & Van Loon (2018)
|
|
||||||
## for ionic strength after equilibration
|
|
||||||
## with minerales for pCO2=2.2 log10 bar
|
|
||||||
|
|
||||||
## surface density SSA (m2/g) mass (g/kgw)
|
|
||||||
Kln_aOH 1.155 11. 2798.4 ## Kaolinite 28 wt% (aluminol and silanol sites)
|
|
||||||
Kln_siOH 1.155
|
|
||||||
Ill_sOH 0.05 100. 1205.35 ## Illite 31 wt% (weak und strong binding sites)
|
|
||||||
Ill_wOH 2.26 ## 2 % strong binding sites
|
|
||||||
Mll_sOH 0.05 100. 113.94 ## Montmorillonite = smektite = 6 wt% (weak und strong binding sites)
|
|
||||||
Mll_wOH 2.26 ## 2 % strong binding sites
|
|
||||||
|
|
||||||
EXCHANGE 2 Exchanger, only illite+montmorillonite
|
|
||||||
## Illite = 0.225 eq/kg_rock, Montmorillonit = 0.87 eq/kg_rock
|
|
||||||
-equil 2 ## equilibrate with solution 1
|
|
||||||
Z 0.5 ## = Illite
|
|
||||||
Y 0.2 ## = Montmorillonite
|
|
||||||
END
|
|
||||||
|
|
||||||
SOLUTION 3
|
|
||||||
pe -2.627 ## Eh = -227 mV, Value from Bossart & Thury (2008)-> PC borehole measurement 2003, Eh still decreasing
|
|
||||||
density 1.01583 ## kg/dm³ = g/cm³
|
|
||||||
temp 13 ## mean temperature Mont Terri, Bossart & Thury (2008), calculations performed for 25°C
|
|
||||||
units mol/kgw
|
|
||||||
## Mean composition
|
|
||||||
pH 7.064
|
|
||||||
Na 3.763e-01
|
|
||||||
Cl 4.228e-01 charge
|
|
||||||
S(6) 1.653e-02 as SO4
|
|
||||||
Ca 2.173e-02
|
|
||||||
Mg 1.740e-02
|
|
||||||
K 1.902e-03
|
|
||||||
Sr 4.520e-04
|
|
||||||
Fe 1.435e-04
|
|
||||||
U 1e-6
|
|
||||||
C 1.991e-03
|
|
||||||
END
|
|
||||||
|
|
||||||
RUN_CELLS
|
|
||||||
END
|
|
||||||
@ -1,37 +0,0 @@
|
|||||||
rows <- 100
|
|
||||||
cols <- 100
|
|
||||||
|
|
||||||
grid_def <- matrix(1, nrow = rows, ncol = cols)
|
|
||||||
|
|
||||||
# Define grid configuration for POET model
|
|
||||||
grid_setup <- list(
|
|
||||||
pqc_in_file = "./SurfExBase.pqi",
|
|
||||||
pqc_db_file = "./SMILE_2021_11_01_TH.dat", # Path to the database file for Phreeqc
|
|
||||||
grid_def = grid_def, # Definition of the grid, containing IDs according to the Phreeqc input script
|
|
||||||
grid_size = c(1, 1), # Size of the grid in meters
|
|
||||||
constant_cells = c() # IDs of cells with constant concentration
|
|
||||||
)
|
|
||||||
|
|
||||||
bound_def <- list(
|
|
||||||
"type" = rep("constant", cols),
|
|
||||||
"sol_id" = rep(2, cols),
|
|
||||||
"cell" = seq(1, cols)
|
|
||||||
)
|
|
||||||
|
|
||||||
diffusion_setup <- list(
|
|
||||||
boundaries = list(
|
|
||||||
"N" = bound_def
|
|
||||||
),
|
|
||||||
alpha_x = 1e-6,
|
|
||||||
alpha_y = 1e-6
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
chemistry_setup <- list()
|
|
||||||
|
|
||||||
# Define a setup list for simulation configuration
|
|
||||||
setup <- list(
|
|
||||||
Grid = grid_setup, # Parameters related to the grid structure
|
|
||||||
Diffusion = diffusion_setup, # Parameters related to the diffusion process
|
|
||||||
Chemistry = chemistry_setup # Parameters related to the chemistry process
|
|
||||||
)
|
|
||||||
@ -1,7 +0,0 @@
|
|||||||
iterations <- 10
|
|
||||||
dt <- 200
|
|
||||||
|
|
||||||
list(
|
|
||||||
timesteps = rep(dt, iterations),
|
|
||||||
store_result = TRUE
|
|
||||||
)
|
|
||||||
@ -1,37 +0,0 @@
|
|||||||
rows <- 1000
|
|
||||||
cols <- 1000
|
|
||||||
|
|
||||||
grid_def <- matrix(1, nrow = rows, ncol = cols)
|
|
||||||
|
|
||||||
# Define grid configuration for POET model
|
|
||||||
grid_setup <- list(
|
|
||||||
pqc_in_file = "./SurfExBase.pqi",
|
|
||||||
pqc_db_file = "./SMILE_2021_11_01_TH.dat", # Path to the database file for Phreeqc
|
|
||||||
grid_def = grid_def, # Definition of the grid, containing IDs according to the Phreeqc input script
|
|
||||||
grid_size = c(rows, cols) / 10, # Size of the grid in meters
|
|
||||||
constant_cells = c() # IDs of cells with constant concentration
|
|
||||||
)
|
|
||||||
|
|
||||||
bound_def <- list(
|
|
||||||
"type" = rep("constant", cols),
|
|
||||||
"sol_id" = rep(2, cols),
|
|
||||||
"cell" = seq(1, cols)
|
|
||||||
)
|
|
||||||
|
|
||||||
diffusion_setup <- list(
|
|
||||||
boundaries = list(
|
|
||||||
"N" = bound_def
|
|
||||||
),
|
|
||||||
alpha_x = 1e-6,
|
|
||||||
alpha_y = 1e-6
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
chemistry_setup <- list()
|
|
||||||
|
|
||||||
# Define a setup list for simulation configuration
|
|
||||||
setup <- list(
|
|
||||||
Grid = grid_setup, # Parameters related to the grid structure
|
|
||||||
Diffusion = diffusion_setup, # Parameters related to the diffusion process
|
|
||||||
Chemistry = chemistry_setup # Parameters related to the chemistry process
|
|
||||||
)
|
|
||||||
@ -1,10 +0,0 @@
|
|||||||
iterations <- 100
|
|
||||||
dt <- 200
|
|
||||||
|
|
||||||
out_save <- seq(5, iterations, by = 5)
|
|
||||||
|
|
||||||
list(
|
|
||||||
timesteps = rep(dt, iterations),
|
|
||||||
store_result = TRUE,
|
|
||||||
out_save = out_save
|
|
||||||
)
|
|
||||||
Loading…
x
Reference in New Issue
Block a user