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b9fe09d937
| Author | SHA1 | Date | |
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b9fe09d937 | ||
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698621097f |
@ -40,4 +40,3 @@ add_custom_target(${BENCHTARGET} ALL)
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add_subdirectory(barite)
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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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set(bench_files
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barite_200.R
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barite_het.R
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)
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set(runtime_files
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barite_200_rt.R
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barite_het_rt.R
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)
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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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chemistry_setup <- list(
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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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dht_species = dht_species
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)
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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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dolo_inner_large.R
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dolo_interp.R
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)
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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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)
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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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|
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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
|
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constant_cells = c() # IDs of cells with constant concentration
|
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)
|
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bound_size <- 2
|
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|
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diffusion_setup <- list(
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inner_boundaries = list(
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"row" = c(400, 1400, 1600),
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"col" = c(200, 800, 800),
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"sol_id" = c(3, 4, 4)
|
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),
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alpha_x = 1e-6,
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alpha_y = 1e-6
|
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)
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|
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check_sign_cal_dol_dht <- function(old, new) {
|
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if ((old["Calcite"] == 0) != (new["Calcite"] == 0)) {
|
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return(TRUE)
|
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}
|
||||
if ((old["Dolomite"] == 0) != (new["Dolomite"] == 0)) {
|
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return(TRUE)
|
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}
|
||||
return(FALSE)
|
||||
}
|
||||
|
||||
fuzz_input_dht_keys <- function(input) {
|
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dht_species <- c(
|
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"H" = 3,
|
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"O" = 3,
|
||||
"Charge" = 3,
|
||||
"C(4)" = 6,
|
||||
"Ca" = 6,
|
||||
"Cl" = 3,
|
||||
"Mg" = 5,
|
||||
"Calcite" = 4,
|
||||
"Dolomite" = 4
|
||||
)
|
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return(input[names(dht_species)])
|
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}
|
||||
|
||||
check_sign_cal_dol_interp <- function(to_interp, data_set) {
|
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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,
|
||||
"C(4)" = 6,
|
||||
"Ca" = 6,
|
||||
"Cl" = 3,
|
||||
"Mg" = 5,
|
||||
"Calcite" = 4,
|
||||
"Dolomite" = 4
|
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)
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data_set <- as.data.frame(do.call(rbind, data_set), check.names = FALSE, optional = TRUE)
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names(data_set) <- names(dht_species)
|
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cal <- (data_set$Calcite == 0) == (to_interp["Calcite"] == 0)
|
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dol <- (data_set$Dolomite == 0) == (to_interp["Dolomite"] == 0)
|
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|
||||
cal_dol_same_sig <- cal == dol
|
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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
|
||||
)
|
||||
148
poet.yml
Normal file
148
poet.yml
Normal file
@ -0,0 +1,148 @@
|
||||
name: poet
|
||||
channels:
|
||||
- defaults
|
||||
- conda-forge
|
||||
- https://repo.anaconda.com/pkgs/main
|
||||
- https://repo.anaconda.com/pkgs/r
|
||||
dependencies:
|
||||
- _libgcc_mutex=0.1=conda_forge
|
||||
- _openmp_mutex=4.5=2_gnu
|
||||
- attr=2.5.2=h39aace5_0
|
||||
- binutils_impl_linux-64=2.43=h4bf12b8_5
|
||||
- binutils_linux-64=2.43=h4852527_5
|
||||
- bzip2=1.0.8=h5eee18b_6
|
||||
- c-ares=1.34.5=hb9d3cd8_0
|
||||
- ca-certificates=2025.11.12=hbd8a1cb_0
|
||||
- cached-property=1.5.2=py_0
|
||||
- cmake=4.1.2=hc946e07_0
|
||||
- eigen=3.4.0=h171cf75_1
|
||||
- expat=2.7.1=h6a678d5_0
|
||||
- gcc_impl_linux-64=13.3.0=h1e990d8_2
|
||||
- gcc_linux-64=13.3.0=h6f18a23_11
|
||||
- gettext=0.21.0=hedfda30_2
|
||||
- gxx_impl_linux-64=13.3.0=hae580e1_2
|
||||
- gxx_linux-64=13.3.0=hb14504d_11
|
||||
- h5py=3.14.0=nompi_py313hfaf8fd4_100
|
||||
- hdf5=1.14.6=nompi_h6e4c0c1_103
|
||||
- highfive=2.10.1=he6560a2_2
|
||||
- icu=73.1=h6a678d5_0
|
||||
- kernel-headers_linux-64=3.10.0=he073ed8_18
|
||||
- krb5=1.21.3=h143b758_0
|
||||
- ld_impl_linux-64=2.43=h712a8e2_5
|
||||
- libaec=1.1.4=h3f801dc_0
|
||||
- libblas=3.9.0=32_h59b9bed_openblas
|
||||
- libcap=2.77=h3ff7636_0
|
||||
- libcblas=3.9.0=32_he106b2a_openblas
|
||||
- libcurl=8.16.0=heebcbe5_0
|
||||
- libedit=3.1.20230828=h5eee18b_0
|
||||
- libev=4.33=h7f8727e_1
|
||||
- libevent=2.1.12=hf998b51_1
|
||||
- libexpat=2.7.1=hecca717_0
|
||||
- libfabric=2.3.1=ha770c72_1
|
||||
- libfabric1=2.3.1=h6c8fc0a_1
|
||||
- libffi=3.4.4=h6a678d5_1
|
||||
- libgcc=15.1.0=h767d61c_2
|
||||
- libgcc-devel_linux-64=13.3.0=hc03c837_102
|
||||
- libgcc-ng=15.1.0=h69a702a_2
|
||||
- libgfortran=15.1.0=h69a702a_2
|
||||
- libgfortran-ng=15.1.0=h69a702a_2
|
||||
- libgfortran5=15.1.0=hcea5267_2
|
||||
- libgomp=15.1.0=h767d61c_2
|
||||
- libhwloc=2.12.1=default_h3d81e11_1000
|
||||
- libiconv=1.16=h5eee18b_3
|
||||
- libidn2=2.3.8=hf80d704_0
|
||||
- liblapack=3.9.0=32_h7ac8fdf_openblas
|
||||
- liblzma=5.8.1=hb9d3cd8_2
|
||||
- liblzma-devel=5.8.1=hb9d3cd8_2
|
||||
- libmpdec=4.0.0=h5eee18b_0
|
||||
- libnghttp2=1.64.0=h161d5f1_0
|
||||
- libnl=3.11.0=hb9d3cd8_0
|
||||
- libopenblas=0.3.30=pthreads_h94d23a6_0
|
||||
- libpmix=5.0.8=h4bd6b51_2
|
||||
- libsanitizer=13.3.0=he8ea267_2
|
||||
- libsqlite=3.50.2=h6cd9bfd_0
|
||||
- libssh2=1.11.1=hcf80075_0
|
||||
- libstdcxx=15.1.0=h8f9b012_2
|
||||
- libstdcxx-devel_linux-64=13.3.0=hc03c837_102
|
||||
- libstdcxx-ng=15.1.0=h4852527_2
|
||||
- libsystemd0=257.10=hd0affe5_2
|
||||
- libudev1=257.10=hd0affe5_2
|
||||
- libunistring=1.3=hb25bd0a_0
|
||||
- libuuid=2.38.1=h0b41bf4_0
|
||||
- libuv=1.48.0=h5eee18b_0
|
||||
- libxcb=1.17.0=h9b100fa_0
|
||||
- libxml2=2.13.9=h2c43086_0
|
||||
- libzlib=1.3.1=hb9d3cd8_2
|
||||
- mpi=1.0.1=openmpi
|
||||
- ncurses=6.5=h2d0b736_3
|
||||
- numpy=2.3.0=py313h17eae1a_0
|
||||
- openmpi=5.0.8=h2fe1745_108
|
||||
- openssl=3.6.0=h26f9b46_0
|
||||
- pip=25.1=pyhc872135_2
|
||||
- pthread-stubs=0.3=h0ce48e5_1
|
||||
- pybind11=2.13.6=py313hdb19cb5_1
|
||||
- pybind11-global=2.13.6=py313hdb19cb5_1
|
||||
- python=3.13.2=hf636f53_101_cp313
|
||||
- python_abi=3.13=0_cp313
|
||||
- rdma-core=60.0=hecca717_0
|
||||
- readline=8.2=h5eee18b_0
|
||||
- rhash=1.4.6=ha914fed_0
|
||||
- setuptools=78.1.1=py313h06a4308_0
|
||||
- sqlite=3.31.1=h7b6447c_0
|
||||
- sysroot_linux-64=2.17=h0157908_18
|
||||
- tk=8.6.13=noxft_hd72426e_102
|
||||
- ucc=1.6.0=hb729f83_0
|
||||
- ucx=1.19.0=h63b5c0b_5
|
||||
- wheel=0.45.1=py313h06a4308_0
|
||||
- xorg-libx11=1.8.12=h9b100fa_1
|
||||
- xorg-libxau=1.0.12=h9b100fa_0
|
||||
- xorg-libxdmcp=1.1.5=h9b100fa_0
|
||||
- xorg-xorgproto=2024.1=h5eee18b_1
|
||||
- xz=5.8.1=hbcc6ac9_2
|
||||
- xz-gpl-tools=5.8.1=hbcc6ac9_2
|
||||
- xz-tools=5.8.1=hb9d3cd8_2
|
||||
- zlib=1.3.1=hb9d3cd8_2
|
||||
- zstd=1.5.7=hb8e6e7a_2
|
||||
- pip:
|
||||
- absl-py==2.3.1
|
||||
- ai-benchmarks-utils==0.1.0
|
||||
- astunparse==1.6.3
|
||||
- certifi==2025.11.12
|
||||
- charset-normalizer==3.4.4
|
||||
- flatbuffers==25.9.23
|
||||
- gast==0.6.0
|
||||
- google-pasta==0.2.0
|
||||
- grpcio==1.76.0
|
||||
- idna==3.11
|
||||
- joblib==1.5.2
|
||||
- keras==3.12.0
|
||||
- libclang==18.1.1
|
||||
- markdown==3.10
|
||||
- markdown-it-py==4.0.0
|
||||
- markupsafe==3.0.3
|
||||
- mdurl==0.1.2
|
||||
- ml-dtypes==0.5.4
|
||||
- namex==0.1.0
|
||||
- opt-einsum==3.4.0
|
||||
- optree==0.18.0
|
||||
- packaging==25.0
|
||||
- pandas==2.3.3
|
||||
- pillow==12.0.0
|
||||
- protobuf==6.33.1
|
||||
- pygments==2.19.2
|
||||
- python-dateutil==2.9.0.post0
|
||||
- pytz==2025.2
|
||||
- requests==2.32.5
|
||||
- rich==14.2.0
|
||||
- scikit-learn==1.7.2
|
||||
- scipy==1.16.3
|
||||
- six==1.17.0
|
||||
- tensorflow==2.20.0
|
||||
- termcolor==3.2.0
|
||||
- threadpoolctl==3.6.0
|
||||
- typing-extensions==4.15.0
|
||||
- tzdata==2025.2
|
||||
- urllib3==2.5.0
|
||||
- werkzeug==3.1.3
|
||||
- wrapt==2.0.1
|
||||
prefix: /mnt/scratch/miniconda3/envs/poet-dummy
|
||||
Loading…
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Reference in New Issue
Block a user