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136 lines
3.0 KiB
R
136 lines
3.0 KiB
R
## Time-stamp: "Last modified 2023-04-11 14:29:51 delucia"
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database <- normalizePath("./db_barite.dat")
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input_script <- normalizePath("./barite.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 <- 20
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m <- 20
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types <- c("scratch", "phreeqc", "rds")
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init_cell <- list(
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"H" = 110.0124,
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"O" = 55.5087,
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"Charge" = -1.217E-09,
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"Ba" = 1.E-10,
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"Cl" = 2.E-10,
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"S" = 6.205E-4,
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"Sr" = 6.205E-4,
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"Barite" = 0.001,
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"Celestite" = 1
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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" = 110.0124,
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"O" = 55.5087,
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"Charge" = -1.217E-09,
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"Ba" = 1.E-10,
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"Cl" = 1.E-10,
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"S" = 6.205E-4,
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"Sr" = 6.205E-4
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)
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injection_diff <- list(
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list(
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"H" = 111.0124,
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"O" = 55.50622,
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"Charge" = -3.337E-08,
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"Ba" = 0.1,
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"Cl" = 0.2,
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"S" = 0,
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"Sr" = 0)
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)
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## diffusion coefficients
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alpha_diffu <- c(
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"H" = 1E-06,
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"O" = 1E-06,
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"Charge" = 1E-06,
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"Ba" = 1E-06,
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"Cl" = 1E-06,
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"S" = 1E-06,
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"Sr" = 1E-06
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)
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## vecinj_inner <- list(
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## l1 = c(1,20,20),
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## l2 = c(2,80,80),
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## l3 = c(2,60,80)
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## )
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boundary <- list(
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"N" = rep(1, n),
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## "N" = rep(0, n),
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"E" = rep(0, n),
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"S" = rep(0, n),
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"W" = rep(0, n)
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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, injection_diff),
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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(9, 9, 10, 5, 5, 5, 5, 5, 5)
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prop_type <- c("", "", "", "act", "act", "act", "act", "", "")
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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 <- 4
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dt <- 100
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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(1, iterations)
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)
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