diff --git a/bench/fgcs/barite_fgcs_2.R b/bench/fgcs/barite_fgcs_2.R index 500b372fd..bd157fabe 100644 --- a/bench/fgcs/barite_fgcs_2.R +++ b/bench/fgcs/barite_fgcs_2.R @@ -1,28 +1,28 @@ ## Time-stamp: "Last modified 2024-12-11 16:08:11 delucia" -cols <- 200 -rows <- 200 +cols <- 1000 +rows <- 1000 -dim_cols <- 10 -dim_rows <- 10 +dim_cols <- 50 +dim_rows <- 50 ncirc <- 20 ## number of crystals -rmax <- cols/10 ## max radius (in nodes) +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) +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)) +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) +inds <- do.call(rbind, tmpl) grid <- matrix(1, nrow = rows, ncol = cols) grid[inds] <- 2 -alpha <- matrix( 1e-5, ncol = cols, nrow = rows) +alpha <- matrix(1e-5, ncol = cols, nrow = rows) alpha[inds] <- 1e-7 ## image(grid, asp=1) @@ -30,13 +30,13 @@ alpha[inds] <- 1e-7 ## Define grid configuration for POET model grid_setup <- list( pqc_in_file = "./barite_fgcs_2.pqi", - pqc_db_file = "./db_barite.dat", ## database file - grid_def = grid, ## grid definition, IDs according to the Phreeqc input + 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 + constant_cells = c() ## IDs of cells with constant concentration ) -bound_length <- cols/10 +bound_length <- cols / 10 bound_N <- list( "type" = rep("constant", bound_length), @@ -52,13 +52,13 @@ bound_W <- list( bound_E <- list( "type" = rep("constant", bound_length), "sol_id" = rep(4, bound_length), - "cell" = seq(rows-bound_length+1, rows) + "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) + "cell" = seq(cols - bound_length + 1, cols) ) diffusion_setup <- list( @@ -77,7 +77,7 @@ dht_species <- c( "O" = 7, "Ba" = 7, "Cl" = 7, - "S(6)" = 7, + "S" = 7, "Sr" = 7, "Barite" = 4, "Celestite" = 4 @@ -86,10 +86,10 @@ dht_species <- c( pht_species <- c( "Ba" = 4, "Cl" = 3, - "S(6)" = 3, + "S" = 3, "Sr" = 3, - "Barite" = 2, - "Celestite" = 2 + "Barite" = 0, + "Celestite" = 0 ) chemistry_setup <- list(