Merge branch 'naa-naaice' of git.gfz-potsdam.de:naaice/poet into naa-naaice

bench/dolo/dol.pqi

@@ -1,9 +1,11 @@
 SOLUTION 1
-    units	mol/kgw
-    water	1
-    temperature	25
-    pH	7
-    pe	4
+  units	mol/kgw
+  water 1
+  temperature  25
+  pH    7
+  pe    4
+  Mg    1E-12
+  Cl    2E-12
 PURE 1
     Calcite 0.0 1
 END
@@ -41,3 +43,7 @@ SOLUTION 4
     Mg 0.002
     Cl 0.004
 END
+
+RUN_CELLS 
+    -cells 2 3 4
+END    

bench/dolo/dolo_interp.R

@@ -1,15 +1,15 @@
-rows <- 400
-cols <- 200
+rows <- 200
+cols <- 400
 
 grid_def <- matrix(2, nrow = rows, ncol = cols)
 
-# Define grid configuration for POET model
+## 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(2.5, 5), # Size of the grid in meters
-    constant_cells = c() # IDs of cells with constant concentration
+    pqc_db_file = "./phreeqc_kin.dat",
+    grid_def = grid_def,
+    grid_size = c(5, 2.5),
+    constant_cells = c()
 )
 
 bound_def_we <- list(
@@ -41,29 +41,29 @@ diffusion_setup <- list(
 )
 
 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)
-    # }
+    ## 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" = 6,
-#         "Ca" = 6,
-#         "Cl" = 3,
-#         "Mg" = 5,
-#         "Calcite" = 4,
-#         "Dolomite" = 4
-#     )
-#     return(input[names(dht_species)])
-# }
+## fuzz_input_dht_keys <- function(input) {
+##     dht_species <- c(
+##         "H" = 3,
+##         "O" = 3,
+##         "Charge" = 3,
+##         "C" = 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(
@@ -74,32 +74,32 @@ check_sign_cal_dol_interp <- function(to_interp, data_set) {
         "Ca" = 6,
         "Cl" = 3,
         "Mg" = 5,
-        "Calcite" = 4,
-        "Dolomite" = 4
+        "Calcite_kin" = 4,
+        "Dolomite_kin" = 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 <- (data_set$Calcite_kin == 0) == (to_interp["Calcite_kin"] == 0)
+    dol <- (data_set$Dolomite_kin == 0) == (to_interp["Dolomite_kin"] == 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)
+    neg_sign <- (result["Calcite_kin"] < 0) || (result["Dolomite_kin"] < 0)
     return(neg_sign)
 }
 
-# Optional when using Interpolation (example with less key species and custom
-# significant digits)
+## Optional when using Interpolation (example with less key species
+## and custom significant digits)
 
 pht_species <- c(
     "C" = 3,
     "Ca" = 3,
     "Mg" = 2,
-    "Calcite" = 2,
-    "Dolomite" = 2
+    "Calcite_kin" = 2,
+    "Dolomite_kin" = 2
 )
 
 chemistry_setup <- list(
@@ -111,21 +111,21 @@ chemistry_setup <- list(
         "Ca" = 6,
         "Cl" = 3,
         "Mg" = 5,
-        "Calcite" = 4,
-        "Dolomite" = 4
+        "Calcite_kin" = 4,
+        "Dolomite_kin" = 4
     ),
     pht_species = pht_species,
     hooks = list(
         dht_fill = check_sign_cal_dol_dht,
-        # dht_fuzz = fuzz_input_dht_keys,
+        ## 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
+## 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
+    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_interp_rt.R

@@ -1,7 +1,7 @@
-iterations <- 20000
+iterations <- 2000
 dt <- 200
 
-out_save <- seq(50, iterations, by = 50)
+out_save <- c(1, 10, 20, seq(40, iterations, by = 40))
 
 list(
     timesteps = rep(dt, iterations),

bench/dolo/dolo_interp_rt_dt2000.R

@@ -0,0 +1,10 @@
+iterations <- 2000
+dt <- 2000
+
+out_save <- c(1, 10, 20, seq(40, iterations, by = 40))
+
+list(
+    timesteps = rep(dt, iterations),
+    store_result = TRUE,
+    out_save = out_save
+)