Add dolo_inner benchmark

bench/dolo/dolo_inner.R

@@ -0,0 +1,112 @@
+grid_def <- matrix(2, nrow = 10, ncol = 10)
+
+# Define grid configuration for POET model
+grid_setup <- list(
+    pqc_in_file = "./dol.pqi",
+    pqc_db_file = "./phreeqc_kin.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(ncol(grid_def) / 10, nrow(grid_def) / 10), # 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(1, 10),
+        "col" = c(1, 10),
+        "sol_id" = c(3, 3)
+    ),
+    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
+)

bench/dolo/dolo_inner_rt.R

@@ -0,0 +1,7 @@
+iterations <- 200
+dt <- 3600
+
+list(
+    timesteps = rep(dt, iterations),
+    store_result = TRUE
+)