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132 lines
3.1 KiB
R
132 lines
3.1 KiB
R
rows <- 200
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cols <- 400
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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",
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grid_def = grid_def,
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grid_size = c(5, 2.5),
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constant_cells = c()
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)
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bound_def_we <- list(
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"type" = rep("constant", rows),
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"sol_id" = rep(1, rows),
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"cell" = seq(1, rows)
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)
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bound_def_ns <- list(
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"type" = rep("constant", cols),
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"sol_id" = rep(1, cols),
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"cell" = seq(1, cols)
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)
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diffusion_setup <- list(
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boundaries = list(
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"W" = bound_def_we,
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"E" = bound_def_we,
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"N" = bound_def_ns,
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"S" = bound_def_ns
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),
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inner_boundaries = list(
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"row" = floor(rows / 2),
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"col" = floor(cols / 2),
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"sol_id" = c(3)
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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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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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## }
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## if ((old["Dolomite"] == 0) != (new["Dolomite"] == 0)) {
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## return(TRUE)
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## }
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return(FALSE)
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}
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## 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,
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## "Charge" = 3,
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## "C" = 6,
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## "Ca" = 6,
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## "Cl" = 3,
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## "Mg" = 5,
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## "Calcite" = 4,
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## "Dolomite" = 4
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## )
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## return(input[names(dht_species)])
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## }
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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,
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"C" = 6,
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"Ca" = 6,
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"Cl" = 3,
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"Mg" = 5,
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"Calcite_kin" = 4,
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"Dolomite_kin" = 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$Calcite_kin == 0) == (to_interp["Calcite_kin"] == 0)
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dol <- (data_set$Dolomite_kin == 0) == (to_interp["Dolomite_kin"] == 0)
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cal_dol_same_sig <- cal == dol
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return(rev(which(!cal_dol_same_sig)))
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}
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check_neg_cal_dol <- function(result) {
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neg_sign <- (result["Calcite_kin"] < 0) || (result["Dolomite_kin"] < 0)
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return(neg_sign)
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}
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## Optional when using Interpolation (example with less key species
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## and custom significant digits)
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pht_species <- c(
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"C" = 3,
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"Ca" = 3,
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"Mg" = 2,
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"Calcite_kin" = 2,
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"Dolomite_kin" = 2
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)
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chemistry_setup <- list(
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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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"C" = 6,
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"Ca" = 6,
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"Cl" = 3,
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"Mg" = 5,
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"Calcite_kin" = 4,
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"Dolomite_kin" = 4
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),
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pht_species = pht_species,
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hooks = list(
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dht_fill = check_sign_cal_dol_dht,
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## dht_fuzz = fuzz_input_dht_keys,
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interp_pre = check_sign_cal_dol_interp,
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interp_post = check_neg_cal_dol
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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 = chemistry_setup ## Parameters related to the chemistry process
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)
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