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145 lines
3.2 KiB
R
145 lines
3.2 KiB
R
## Time-stamp: "Last modified 2023-01-10 13:51:40 delucia"
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database <- normalizePath("../share/poet/examples/phreeqc_kin.dat")
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input_script <- normalizePath("../share/poet/bench/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(1, 1),
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type = types[1],
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init_cell = as.data.frame(init_cell),
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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 <- c(
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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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)
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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" = 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" = 110.683,
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"O" = 55.3413,
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"Charge" = 1.90431e-16,
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"C" = 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" = 110.683,
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"O" = 55.3413,
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"Charge" = 1.90431e-16,
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"C" = 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(2,1600,800),
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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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diffusion <- list(
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init = init_diffu,
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vecinj = do.call(rbind.data.frame, vecinj_diffu),
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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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signif_vector <- c(10, 10, 2, 5, 5, 5, 5, 0, 5, 5)
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prop_type <- c("", "", "", "act", "act", "act", "act", "ignore", "", "")
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prop <- names(init_cell)
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chemistry <- list(
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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 4 ##
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## Putting all those things together ##
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#################################################################
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iterations <- 10
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dt <- 200
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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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)
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