bin/dol.pqi

@@ -1,43 +0,0 @@
-SOLUTION 1
-    units	mol/kgw
-    water	1
-    temperature	25
-    pH	7
-    pe	4
-PURE 1
-    Calcite 0.0 1
-END
-
-RUN_CELLS 
-    -cells 1
-
-COPY solution 1 2
-
-PURE 2
-    O2g -0.1675 10
-KINETICS 2
-    Calcite
-    -m      0.000207
-    -parms  0.05
-    -tol    1e-10
-    Dolomite
-    -m      0.0
-    -parms  0.005
-    -tol    1e-10
-END
-
-SOLUTION 3
-    units	mol/kgw
-    water 1
-    temp 25 
-    Mg 0.001
-    Cl 0.002
-END
-
-SOLUTION 4
-    units mol/kgw 
-    water 1
-    temp 25
-    Mg 0.002
-    Cl 0.004
-END

bin/dolo_fgcs_3.R

@@ -1,135 +0,0 @@
-rows <- 400
-cols <- 400
-
-grid_def <- matrix(2, nrow = rows, ncol = cols)
-
-# Define grid configuration for POET model
-grid_setup <- list(
-    pqc_in_file = "./dolo_fgcs.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(5, 5), # Size of the grid in meters
-    constant_cells = c() # IDs of cells with constant concentration
-)
-
-bound_def_we <- list(
-    "type" = rep("constant", rows),
-    "sol_id" = rep(1, rows),
-    "cell" = seq(1, rows)
-)
-
-bound_def_ns <- list(
-    "type" = rep("constant", cols),
-    "sol_id" = rep(1, cols),
-    "cell" = seq(1, cols)
-)
-
-diffusion_setup <- list(
-    boundaries = list(
-        "W" = bound_def_we,
-        "E" = bound_def_we,
-        "N" = bound_def_ns,
-        "S" = bound_def_ns
-    ),
-    inner_boundaries = list(
-        "row" = floor(rows / 2),
-        "col" = floor(cols / 2),
-        "sol_id" = c(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)
-}
-
-check_sign_cal_dol_interp <- function(to_interp, data_set) {
-    dht_species <- c(
-        "H" = 3,
-        "O" = 3,
-        "C" = 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"  = 3,
-    "Ca" = 3,
-    "Mg" = 3,
-    "Cl" = 3,
-    "Calcite" = 3,
-    "Dolomite" = 3
-)
-
-
-dht_species <- c(
-        "H" = 3,
-        "O" = 3,
-        "C" = 6,
-        "Ca" = 6,
-        "Cl" = 3,
-        "Mg" = 5,
-        "Calcite" = 4,
-        "Dolomite" = 4)
-
-chemistry_setup <- list(
-    dht_species = dht_species,
-    pht_species = pht_species,
-    hooks = list(
-        dht_fill = check_sign_cal_dol_dht,
-        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
-)
-
-iterations <- 15000
-dt <- 200
-checkpoint_interval <- 100
-control_interval <- 100
-mape_threshold <- rep(0.1, 13)
-mape_threshold[5] <- 1 #Charge
-out_save <- seq(1000, iterations, by = 1000)
-#out_save = c(seq(1, 10), seq(10, 100, by= 10), seq(200, iterations, by=100))
-
-
-list(
-    timesteps = rep(dt, iterations),
-    store_result = TRUE,
-    out_save = out_save,
-    checkpoint_interval = checkpoint_interval,
-    control_interval = control_interval,
-    mape_threshold = mape_threshold
-)

bin/run_poet.sh

@@ -1,19 +0,0 @@
-#!/bin/bash
-#SBATCH --job-name=dolo_proto1_eps01
-#SBATCH --output=dolo_proto1_eps01_%j.out
-#SBATCH --error=dolo_proto1_eps01_%j.err
-#SBATCH --partition=long
-#SBATCH --nodes=6                                                    
-#SBATCH --ntasks-per-node=24 
-#SBATCH --ntasks=144                                  
-#SBATCH --exclusive
-#SBATCH --time=3-00:00:00                             
-
-
-source /etc/profile.d/modules.sh
-module purge
-module load cmake gcc openmpi
-
-#mpirun -n 144 ./poet dolo_fgcs_3.R dolo_fgcs_3.qs2 dolo_only_pqc
-mpirun -n 144 ./poet --interp dolo_fgcs_3.R dolo_fgcs_3.qs2 dolo_proto1_eps01
-#mpirun -n 144 ./poet --interp  barite_fgcs_4_new/barite_fgcs_4_new_rt.R barite_fgcs_4_new/barite_fgcs_4_new.qs2 barite