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153 lines
3.6 KiB
R
153 lines
3.6 KiB
R
## Time-stamp: "Last modified 2023-04-24 15:43:26 mluebke"
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database <- normalizePath("../share/poet/examples/phreeqc_kin.dat")
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input_script <- normalizePath("../share/poet/bench/dolo/dolo_inner.pqi")
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#################################################################
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## Section 1 ##
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## Grid initialization ##
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#################################################################
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n <- 2000
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m <- 1000
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types <- c("scratch", "phreeqc", "rds")
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init_cell <- list(
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"H" = 110.683,
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"O" = 55.3413,
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"Charge" = -5.0822e-19,
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"C" = 1.2279E-4,
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"Ca" = 1.2279E-4,
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"Cl" = 0,
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"Mg" = 0,
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"O2g" = 0.499957,
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"Calcite" = 2.07e-4,
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"Dolomite" = 0
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)
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(2, 1),
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type = types[1],
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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)
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##################################################################
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## Section 2 ##
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## Diffusion parameters and boundary conditions ##
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##################################################################
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## initial conditions
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init_diffu <- list(
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"H" = 0.000211313883539788,
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"O" = 0.00398302904424952,
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"Charge" = -5.0822e-19,
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"C(4)" = 1.2279E-4,
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"Ca" = 1.2279E-4,
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"Cl" = 0,
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"Mg" = 0
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)
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## diffusion coefficients
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alpha_diffu <- c(
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"H" = 1E-6,
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"O" = 1E-6,
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"Charge" = 1E-6,
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"C(4)" = 1E-6,
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"Ca" = 1E-6,
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"Cl" = 1E-6,
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"Mg" = 1E-6
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)
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## list of boundary conditions/inner nodes
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vecinj_diffu <- list(
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list(
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"H" = 0.0001540445,
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"O" = 0.002148006,
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"Charge" = 1.90431e-16,
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"C(4)" = 0,
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"Ca" = 0,
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"Cl" = 0.002,
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"Mg" = 0.001
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),
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list(
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"H" = 0.0001610193,
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"O" = 0.002386934,
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"Charge" = 1.90431e-16,
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"C(4)" = 0,
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"Ca" = 0.0,
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"Cl" = 0.004,
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"Mg" = 0.002
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)
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)
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vecinj_inner <- list(
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l1 = c(1,400,200),
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l2 = c(2,1400,800),
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l3 = c(2,1600,800)
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)
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boundary <- list(
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# "N" = c(1, rep(0, n-1)),
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"N" = rep(0, n),
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"E" = rep(0, m),
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"S" = rep(0, n),
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"W" = rep(0, m)
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)
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diffu_list <- names(alpha_diffu)
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vecinj <- do.call(rbind.data.frame, vecinj_diffu)
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names(vecinj) <- names(init_diffu)
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diffusion <- list(
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init = as.data.frame(init_diffu, check.names = FALSE),
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vecinj = vecinj,
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vecinj_inner = vecinj_inner,
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vecinj_index = boundary,
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alpha = alpha_diffu
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)
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#################################################################
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## Section 3 ##
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## Chemistry module (Phreeqc) ##
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#################################################################
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## # Needed when using DHT
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dht_species <- c("H", "O", "Charge", "C(4)", "Ca", "Cl", "Mg", "Calcite",
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"Dolomite")
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#dht_signif <- rep(15, length(dht_species))
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dht_signif <- c(10, 10, 3, 5, 5, 5, 5, 5, 5)
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chemistry <- list(
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database = database,
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input_script = input_script,
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dht_species = dht_species,
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dht_signif = dht_signif
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)
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#################################################################
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## Section 4 ##
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## Putting all those things together ##
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#################################################################
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iterations <- 500
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dt <- 50
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setup <- list(
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grid = grid,
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diffusion = diffusion,
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chemistry = chemistry,
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iterations = iterations,
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timesteps = rep(dt, iterations),
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store_result = TRUE,
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out_save = seq(5, iterations, by=5)
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)
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