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refactor: edit input scripts to be expected input
This commit is contained in:
Max Lübke
parent
b5813d0530
commit
3f532562c7
@ -1,28 +1,117 @@
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## chemical database
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# NOTE: not needed now
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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 <- 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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## only the directory
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# demodir <- system.file("extdata", "demo_rtwithmufits", package="Rmufits")
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n <- 10
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m <- 10
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prop <- c("C", "Ca", "Cl", "Mg", "pH", "pe", "O2g", "Calcite", "Dolomite")
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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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grid <- list(
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n_cells = c(n),
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s_cells = c(n)
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)
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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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@ -56,116 +145,11 @@ selout <- c(
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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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#
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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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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-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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"pe" = 1E-8,
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"pH" = 1E-8
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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" = 7
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)
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)
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inner_index <- c(5)
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inner_vecinj_index <- rep(1, 3)
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vecinj_inner <- cbind(inner_index, inner_vecinj_index)
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# constant_boundary <- list(
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# n_cell = seq(1, n),
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# i_vecinj = rep(1, n)
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# )
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#
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# closed_boundary <- list(
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# n_cell = seq(1, n),
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# i_vecinj = rep(0, n)
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# )
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boundary <- list(
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"N" = rep(1, 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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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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boundary = boundary,
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alpha = alpha_diffu
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)
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# cbound <- seq(from = 0, to = n - 1)
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## setup boundary conditions for transport - we have already read the
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## GRID with the following code:
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## grid <- Rmufits::ReadGrid(paste0(demodir,"/d2ascii.run.GRID.SUM"))
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## cbound <- which(grid$cell$ACTNUM == 2)
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## dput(cbound)
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# cbound <- c(
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# 1L, 50L, 100L, 150L, 200L, 250L, 300L, 350L, 400L, 450L, 500L,
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# 550L, 600L, 650L, 700L, 750L, 800L, 850L, 900L, 950L, 1000L,
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# 1050L, 1100L, 1150L, 1200L, 1250L, 1300L, 1350L, 1400L, 1450L,
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# 1500L, 1550L, 1600L, 1650L, 1700L, 1750L, 1800L, 1850L, 1900L,
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# 1950L, 2000L, 2050L, 2100L, 2150L, 2200L, 2250L, 2300L, 2350L,
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# 2400L, 2450L, 2451L, 2452L, 2453L, 2454L, 2455L, 2456L, 2457L,
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# 2458L, 2459L, 2460L, 2461L, 2462L, 2463L, 2464L, 2465L, 2466L,
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# 2467L, 2468L, 2469L, 2470L, 2471L, 2472L, 2473L, 2474L, 2475L,
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# 2476L, 2477L, 2478L, 2479L, 2480L, 2481L, 2482L, 2483L, 2484L,
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# 2485L, 2486L, 2487L, 2488L, 2489L, 2490L, 2491L, 2492L, 2493L,
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# 2494L, 2495L, 2496L, 2497L, 2498L, 2499L, 2500L
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# )
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# boundinit <- matrix(rep(init[-c(7, 8)], length(cbound)), byrow = TRUE, nrow = length(cbound))
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# myboundmat <- cbind(cbound, boundinit)
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# myboundmat[cbound == 1, c(2:7)] <- vecinj
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# colnames(myboundmat) <- c("cbound", names(vecinj))
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# TODO: dt and iterations
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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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@ -174,7 +158,7 @@ setup <- list(
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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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prop = names(init_cell),
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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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@ -188,9 +172,10 @@ setup <- list(
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# cinj = c(0,1),
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# boundary = boundary,
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# injections = FALSE,
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s_grid = c(n),
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n_grid = c(n),
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dt = 1,
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iterations = 1,
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timesteps = rep(1, 10)
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iterations = iterations,
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timesteps = rep(10, iterations)
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)
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# not needed yet
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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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@ -156,7 +156,7 @@ selout <- c(
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# TODO: dt and iterations
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iterations <- 10
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iterations <- 500
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setup <- list(
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# bound = myboundmat,
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@ -180,11 +180,8 @@ setup <- list(
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# cinj = c(0,1),
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# boundary = boundary,
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# injections = FALSE,
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s_grid = c(n, m),
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n_grid = c(n, m),
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dt = 1,
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iterations = iterations,
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timesteps = rep(1, iterations)
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timesteps = rep(10, iterations)
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)
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# not needed yet
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