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0c2597d97f
feat: implement data clustering using PHT feat: implement interpolation refactor: use named vector for DHT species definition and significant digits data: remove unusable input scripts data: move Phreeqc database to benchmark dir refactor: rename dolomite benchmark directory refactor: remove DHT prop type from input script
152 lines
3.4 KiB
R
152 lines
3.4 KiB
R
## Time-stamp: "Last modified 2023-04-24 16:51:23 mluebke"
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database <- normalizePath("../share/poet/bench/barite/db_barite.dat")
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input_script <- normalizePath("../share/poet/bench/barite/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, 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" = 110.0124,
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"H" = 0.00000028904,
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#"O" = 55.5087,
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"O" = 0.000000165205,
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#"Charge" = -1.217E-09,
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"Charge" = -3.337E-08,
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"Ba" = 1.E-10,
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"Cl" = 1.E-10,
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"S(6)" = 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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"H" = 0.0000002890408,
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#"O" = 55.50622,
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"O" = 0.00002014464,
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#"Charge" = -3.337E-08,
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"Charge" = -3.337000004885E-08,
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"Ba" = 0.1,
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"Cl" = 0.2,
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"S(6)" = 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(6)" = 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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vecinj <- do.call(rbind.data.frame, injection_diff)
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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(
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"H" = 10,
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"O" = 10,
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"Charge" = 3,
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"Ba" = 5,
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"Cl" = 5,
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"S(6)" = 5,
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"Sr" = 5
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)
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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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)
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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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