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110 lines
2.6 KiB
R
110 lines
2.6 KiB
R
## Time-stamp: "Last modified 2024-12-20 15:30:05 delucia"
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cols <- 400
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rows <- 400
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dim_cols <- 80
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dim_rows <- 80
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rad <- cols/40 ## circle radius (in nodes)
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boxs <- cols/16 ## box side (in nodes)
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cc <- seq(boxs/2, cols - boxs/2, by = boxs)
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length(cc)
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colcen <- rep(cc, length(cc))
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rowcen <- rep(cc, each = length(cc))
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centers <- cbind(rowcen, colcen)
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mr <- matrix(rep(seq_len(cols), each = rows), byrow = TRUE, nrow = rows)
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mc <- matrix(rep(seq_len(cols), rows), byrow = TRUE, nrow = rows)
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tmpl <- lapply(seq_len(nrow(centers)), function(x) which((mr-centers[x, 1])^2 + (mc-centers[x, 2])^2 < rad^2, arr.ind = TRUE))
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inds <- do.call(rbind, tmpl)
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grid <- matrix(1, nrow = rows, ncol = cols)
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grid[inds] <- 2
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alpha <- matrix( 1e-5, ncol = cols, nrow = rows)
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alpha[inds] <- 1e-8
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## PoetUtils::PlotField(grid, cols = cols, rows = rows, contour = FALSE, scale = FALSE, las=1)
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## Define grid configuration for POET model
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grid_setup <- list(
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pqc_in_file = "./barite_fgcs_3.pqi",
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pqc_db_file = "../barite/db_barite.dat", ## database file
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grid_def = grid, ## grid definition, IDs according to the Phreeqc input
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grid_size = c(dim_cols, dim_rows), ## grid size in meters
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constant_cells = c() ## IDs of cells with constant concentration
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)
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bound_length <- cols/10
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bound_N <- list(
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"type" = rep("constant", bound_length),
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"sol_id" = rep(3, bound_length),
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"cell" = seq(1, bound_length)
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)
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bound_W <- list(
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"type" = rep("constant", bound_length),
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"sol_id" = rep(3, bound_length),
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"cell" = seq(1, bound_length)
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)
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bound_E <- list(
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"type" = rep("constant", bound_length),
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"sol_id" = rep(4, bound_length),
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"cell" = seq(rows-bound_length+1, rows)
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)
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bound_S <- list(
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"type" = rep("constant", bound_length),
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"sol_id" = rep(4, bound_length),
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"cell" = seq(cols-bound_length+1, cols)
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)
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diffusion_setup <- list(
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boundaries = list(
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"W" = bound_W,
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"N" = bound_N,
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"E" = bound_E,
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"S" = bound_S
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),
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alpha_x = alpha,
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alpha_y = alpha
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)
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dht_species <- c(
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"H" = 7,
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"O" = 7,
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"Ba" = 7,
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"Cl" = 7,
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"S" = 7,
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"Sr" = 7,
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"Barite" = 4,
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"Celestite" = 4
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)
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pht_species <- c(
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"Ba" = 3,
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"Cl" = 3,
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"S" = 3,
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"Sr" = 3,
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"Barite" = 1,
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"Celestite" = 1
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)
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chemistry_setup <- list(
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dht_species = dht_species,
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pht_species = pht_species
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)
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## Define a setup list for simulation configuration
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setup <- list(
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Grid = grid_setup, ## Parameters related to the grid structure
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Diffusion = diffusion_setup, ## Parameters related to the diffusion process
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Chemistry = chemistry_setup
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)
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