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181 lines
4.2 KiB
R
181 lines
4.2 KiB
R
#################################################################
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## Section 1 ##
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## Grid initialization ##
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#################################################################
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n <- 5
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m <- 5
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types <- c("scratch", "phreeqc", "rds")
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# initsim <- c("SELECTED_OUTPUT", "-high_precision true",
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# "-reset false",
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# "USER_PUNCH",
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# "-head C Ca Cl Mg pH pe O2g Calcite Dolomite",
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# "10 PUNCH TOT(\"C\"), TOT(\"Ca\"), TOT(\"Cl\"), TOT(\"Mg\"), -LA(\"H+\"), -LA(\"e-\"), EQUI(\"O2g\"), EQUI(\"Calcite\"), EQUI(\"Dolomite\")",
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# "SOLUTION 1",
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# "units mol/kgw",
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# "temp 25.0", "water 1",
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# "pH 9.91 charge",
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# "pe 4.0",
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# "C 1.2279E-04",
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# "Ca 1.2279E-04",
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# "Cl 1E-12",
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# "Mg 1E-12",
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# "PURE 1",
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# "O2g -0.6788 10.0",
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# "Calcite 0.0 2.07E-3",
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# "Dolomite 0.0 0.0",
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# "END")
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# needed if init type is set to "scratch"
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# prop <- c("C", "Ca", "Cl", "Mg", "pH", "pe", "O2g", "Calcite", "Dolomite")
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init_cell <- list(
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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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"pH" = 9.91,
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"pe" = 4,
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"O2g" = 10,
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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 = n,
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s_cells = n,
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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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init_script = NULL
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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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init_diffu <- c(
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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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"pe" = 4,
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"pH" = 7
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)
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alpha_diffu <- c(
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"C" = 1E-4,
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"Ca" = 1E-4,
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"Cl" = 1E-4,
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"Mg" = 1E-4,
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"pe" = 1E-4,
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"pH" = 1E-4
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)
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vecinj_diffu <- list(
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list(
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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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"pe" = 4,
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"pH" = 9.91
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)
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)
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boundary <- list(
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"E" = 0,
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"W" = 1
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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_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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## Phreeqc simulation ##
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##################################################################
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db <- RPhreeFile(system.file("extdata", "phreeqc_kin.dat",
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package = "RedModRphree"
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), is.db = TRUE)
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phreeqc::phrLoadDatabaseString(db)
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# NOTE: This won't be needed in the future either. Could also be done in a. pqi
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# file
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base <- c(
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"SOLUTION 1",
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"units mol/kgw",
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"temp 25.0",
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"water 1",
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"pH 9.91 charge",
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"pe 4.0",
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"C 1.2279E-04",
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"Ca 1.2279E-04",
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"Mg 0.001",
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"Cl 0.002",
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"PURE 1",
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"O2g -0.1675 10",
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"KINETICS 1",
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"-steps 100",
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"-step_divide 100",
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"-bad_step_max 2000",
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"Calcite", "-m 0.000207",
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"-parms 0.0032",
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"Dolomite",
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"-m 0.0",
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"-parms 0.00032",
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"END"
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)
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selout <- c(
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"SELECTED_OUTPUT", "-high_precision true", "-reset false",
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"-time", "-soln", "-temperature true", "-water true",
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"-pH", "-pe", "-totals C Ca Cl Mg",
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"-kinetic_reactants Calcite Dolomite", "-equilibrium O2g"
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)
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# Needed when using DHT
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signif_vector <- c(7, 7, 7, 7, 7, 7, 7, 5, 5)
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prop_type <- c("act", "act", "act", "act", "logact", "logact", "ignore", "act", "act")
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prop <- names(init_cell)
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iterations <- 500
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setup <- list(
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# bound = myboundmat,
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base = base,
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first = selout,
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# initsim = initsim,
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# Cf = 1,
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grid = grid,
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diffusion = diffusion,
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prop = prop,
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immobile = c(7, 8, 9),
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kin = c(8, 9),
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ann = list(O2g = -0.1675),
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# phase = "FLUX1",
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# density = "DEN1",
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reduce = FALSE,
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# snapshots = demodir, ## directory where we will read MUFITS SUM files
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# gridfile = paste0(demodir, "/d2ascii.run.GRID.SUM")
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# init = init,
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# vecinj = vecinj,
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# cinj = c(0,1),
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# boundary = boundary,
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# injections = FALSE,
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iterations = iterations,
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timesteps = rep(10, iterations)
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)
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