## Time-stamp: "Last modified 2024-12-11 16:08:11 delucia"

cols <- 1000
rows <- 1000

dim_cols <- 50
dim_rows <- 50

ncirc <- 20 ## number of crystals
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)
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))

inds <- do.call(rbind, tmpl)
grid <- matrix(1, nrow = rows, ncol = cols)
grid[inds] <- 2

alpha <- matrix(1e-5, ncol = cols, nrow = rows)
alpha[inds] <- 1e-7

## image(grid, asp=1)

## Define grid configuration for POET model
grid_setup <- list(
  pqc_in_file    = "./barite_fgcs_2.pqi",
  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
)

bound_length <- cols / 10

bound_N <- list(
  "type"   = rep("constant", bound_length),
  "sol_id" = rep(3, bound_length),
  "cell"   = seq(1, bound_length)
)

bound_W <- list(
  "type"   = rep("constant", bound_length),
  "sol_id" = rep(3, bound_length),
  "cell"   = seq(1, bound_length)
)
bound_E <- list(
  "type"   = rep("constant", bound_length),
  "sol_id" = rep(4, bound_length),
  "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)
)

diffusion_setup <- list(
  boundaries = list(
    "W" = bound_W,
    "N" = bound_N,
    "E" = bound_E,
    "S" = bound_S
  ),
  alpha_x = alpha,
  alpha_y = alpha
)

dht_species <- c(
  "H"         = 7,
  "O"         = 7,
  "Ba"        = 7,
  "Cl"        = 7,
  "S"         = 7,
  "Sr"        = 7,
  "Barite"    = 4,
  "Celestite" = 4
)

pht_species <- c(
  "Ba"        = 4,
  "Cl"        = 3,
  "S"         = 3,
  "Sr"        = 3,
  "Barite"    = 0,
  "Celestite" = 0
)

chemistry_setup <- list(
  dht_species = dht_species,
  pht_species = pht_species
)

## 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
)