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chore: delete unused files
This commit is contained in:
Max Lübke
parent
5ea2fe5d6f
commit
7b48daf756
128
data/SimComp2D.R
128
data/SimComp2D.R
@ -1,128 +0,0 @@
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## chemical database
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db <- RPhreeFile("mdl_quint_kin.dat", 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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prop <- c("Al", "C","Ca","Cl","Fe", "K", "Mg","Na", "Si", "pH", ## "pe",
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"Albite", "Calcite", "Chlorite", "Illite", "Kaolinite")
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signif_vector <- c(7,7,7,7,7,7,7,7,7,6, 5,5,5,5,5)
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prop_type <- rep("normal", length(signif_vector))
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base <- c("SOLUTION 1",
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"units mol/kgw",
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"pH 6.77",
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"temp 35",
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"-water 1",
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"Al 8.06386e-09",
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"C 0.0006108294",
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"Ca 0.09709463",
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"Cl 4.340042",
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"Fe 1.234357e-05",
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"K 0.01117434",
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"Mg 0.0406959",
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"Na 4.189209",
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"Si 0.0001935754",
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"INCREMENTAL_REACTIONS true",
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"KINETICS 1 ",
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"-steps 86400",
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"-bad_step_max 10000",
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"-cvode true",
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"Albite",
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"-m 8.432165", ## 1540.0",
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"-parms 01.54 100",
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"Calcite",
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"-m 0.0",
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"-parms 10 100",
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"Chlorite",
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"-m 1.106585", ## 202.100",
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"-parms 64.84 100",
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"Illite",
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"-m 0.9549153", ## 174.400",
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"-parms 43.38 100",
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"Kaolinite",
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"-m 0.0",
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"-parms 29.17 100",
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"END")
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selout <- c("KNOBS",
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"-convergence_tolerance 1E-6",
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"SELECTED_OUTPUT",
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"-reset false",
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"USER_PUNCH",
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"-head Al C Ca Cl Fe K Mg Na Si pH Albite Calcite Chlorite Illite Kaolinite", ## pe
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"10 PUNCH TOT(\"Al\"), TOT(\"C\"), TOT(\"Ca\"), TOT(\"Cl\"), TOT(\"Fe\"), TOT(\"K\"), TOT(\"Mg\"), TOT(\"Na\"), TOT(\"Si\"), -LA(\"H+\"), KIN(\"Albite\"), KIN(\"Calcite\"), KIN(\"Chlorite\"), KIN(\"Illite\"), KIN(\"Kaolinite\")" )
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## Define initial conditions as equilibrium with primary minerals
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ipr <- c(Al = 8.689e-10,
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C = 0.0006108,
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Ca = 0.09709,
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Cl = 4.34,
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Fe = 1.802e-06,
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K = 0.01131,
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Mg = 0.04074,
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Na = 4.189,
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Si = 7.653e-05,
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pH = 6.889,
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Albite = 5.0,
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Calcite = 0.0,
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Chlorite = 10.0,
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Illite = 2.0,
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Kaolinite = 0.0
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)
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initstate <- matrix(rep(ipr, 2500), byrow=TRUE, ncol=length(ipr))
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colnames(initstate) <- names(ipr)
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vecinj <- c(Al= 8.694e-10,
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C = 8.182e-01,
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Ca= 9.710e-02,
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Cl= 4.340e+00,
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Fe= 1.778e-06,
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K = 1.131e-02,
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Mg= 4.074e-02,
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Na= 4.189e+00,
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Si= 7.652e-05,
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pH= 2.556228)
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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(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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boundary_matrix <- matrix(rep(ipr[1:10], length(cbound)), byrow=TRUE, nrow=length(cbound))
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colnames(boundary_matrix) <- names(ipr[1:10])
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boundary_matrix[1, ] <- vecinj
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boundary_matrix <- cbind(cbound,boundary_matrix)
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setup <- list(n = 2500,
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bound = boundary_matrix,
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base = base,
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first = selout,
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initsim = initstate,
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Cf = 1,
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prop = prop,
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immobile = seq(11,15),
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kin = seq(11,15),
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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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)
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@ -1,131 +0,0 @@
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db <- RPhreeFile("mdl_quint_kin.dat", is.db=TRUE)
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phreeqc::phrLoadDatabaseString(db)
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## only the directory
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demodir <- "./snaps/"
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base <- c("SOLUTION 1",
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"units mol/kgw",
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"pH 6.77",
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"temp 35",
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"-water 1",
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"Al 8.06386e-09",
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"C 0.0006108294",
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"Ca 0.09709463",
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"Cl 4.340042",
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"Fe 1.234357e-05",
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"K 0.01117434",
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"Mg 0.0406959",
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"Na 4.189209",
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"Si 0.0001935754",
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"INCREMENTAL_REACTIONS true",
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"KINETICS 1 ",
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"-steps 86400",
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"-bad_step_max 10000",
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"-cvode true",
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"Albite",
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"-m 8.432165", ## 1540.0",
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"-parms 01.54 100",
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"Calcite",
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"-m 0.0",
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"-parms 10 100",
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"Chlorite",
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"-m 1.106585", ## 202.100",
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"-parms 64.84 100",
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"Illite",
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"-m 0.9549153", ## 174.400",
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"-parms 43.38 100",
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"Kaolinite",
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"-m 0.0",
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"-parms 29.17 100",
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"END")
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selout <- c("KNOBS",
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"-convergence_tolerance 1E-6",
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"SELECTED_OUTPUT",
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"-reset false",
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"USER_PUNCH",
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"-head Al C Ca Cl Fe K Mg Na Si pH Albite Calcite Chlorite Illite Kaolinite", ## pe
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"10 PUNCH TOT(\"Al\"), TOT(\"C\"), TOT(\"Ca\"), TOT(\"Cl\"), TOT(\"Fe\"), TOT(\"K\"), TOT(\"Mg\"), TOT(\"Na\"), TOT(\"Si\"), -LA(\"H+\"), KIN(\"Albite\"), KIN(\"Calcite\"), KIN(\"Chlorite\"), KIN(\"Illite\"), KIN(\"Kaolinite\")" )
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## Define initial conditions as equilibrium with primary minerals
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ipr <- c(Al = 8.689e-10,
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C = 0.0006108,
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Ca = 0.09709,
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Cl = 4.34,
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Fe = 1.802e-06,
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K = 0.01131,
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Mg = 0.04074,
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Na = 4.189,
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Si = 7.653e-05,
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pH = 6.889,
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Albite = 5.0,
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Calcite = 0.0,
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Chlorite = 10.0,
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Illite = 2.0,
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Kaolinite = 0.0
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)
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initstate <- matrix(rep(ipr, 648420), byrow=TRUE, ncol=length(ipr))
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colnames(initstate) <- names(ipr)
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vecinj <- c(Al= 8.694e-10,
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C = 8.182e-01,
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Ca= 9.710e-02,
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Cl= 4.340e+00,
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Fe= 1.778e-06,
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K = 1.131e-02,
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Mg= 4.074e-02,
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Na= 4.189e+00,
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Si= 7.652e-05,
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pH= 2.556228)
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prop <- c("Al", "C","Ca","Cl","Fe", "K", "Mg","Na", "Si", "pH", ## "pe",
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"Albite", "Calcite", "Chlorite", "Illite", "Kaolinite")
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bound_elm <- c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L,
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15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L,
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28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L,
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41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L,
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54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L,
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67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L,
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80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L,
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93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L,
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105L, 106L, 107L, 108L, 214L, 215L)
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inj_elm <- c(7426L, 18233L, 29040L, 39847L,
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50654L, 61461L, 72268L, 83075L, 93882L, 104689L, 115496L, 126303L,
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137110L, 147917L, 158724L, 169531L, 180338L, 191145L, 201952L,
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212759L, 223566L, 234373L, 245180L, 255987L, 266794L, 277601L,
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288408L, 299215L, 310022L, 320829L, 331636L, 342443L, 353250L,
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364057L, 374864L, 385671L, 396478L, 407285L, 418092L, 428899L,
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439706L, 450513L, 461320L, 472127L, 482934L, 493741L, 504548L,
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515355L)
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cbound <- inj_elm
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boundinit <- matrix(rep(vecinj, length(cbound)), ncol=length(vecinj), byrow=TRUE)
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myboundmat <- cbind(cbound,boundinit)
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## distinguish between injection and real boundaries
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colnames(myboundmat) <- c("cbound", names(vecinj))
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setup <- list(n=648420,
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base=base,
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bound=myboundmat,
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first=selout,
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initsim=initstate,
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Cf=1,
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prop=prop,
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immobile=seq(11,15),
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kin= seq(11,15),
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phase="FLUX1",
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density="DENS",
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reduce=TRUE,
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snapshots="snaps/AllSnaps_cmp_v3.rds",
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gridfile ="snaps/GridKtz_cmp_v3.rds")
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120
data/SimDol2D.R
120
data/SimDol2D.R
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## chemical database
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db <- RPhreeFile(system.file("extdata", "phreeqc_kin.dat",
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package="RedModRphree"), 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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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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base <- c("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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selout <- c("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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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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vecinj <- c("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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init <- c("C(4)"= 1.2279E-4,
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"Ca" =1.2279E-4,
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"Cl" =0,
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"Mg" =0,
|
|
||||||
"pe" =4,
|
|
||||||
"pH" =7,
|
|
||||||
"Calcite"= 2.07e-4,
|
|
||||||
"Dolomite"= 0)
|
|
||||||
|
|
||||||
|
|
||||||
## setup boundary conditions for transport - we have already read the
|
|
||||||
## GRID with the following code:
|
|
||||||
## grid <- Rmufits::ReadGrid(paste0(demodir,"/d2ascii.run.GRID.SUM"))
|
|
||||||
## cbound <- which(grid$cell$ACTNUM == 2)
|
|
||||||
## dput(cbound)
|
|
||||||
cbound <- c(1L, 50L, 100L, 150L, 200L, 250L, 300L, 350L, 400L, 450L, 500L,
|
|
||||||
550L, 600L, 650L, 700L, 750L, 800L, 850L, 900L, 950L, 1000L,
|
|
||||||
1050L, 1100L, 1150L, 1200L, 1250L, 1300L, 1350L, 1400L, 1450L,
|
|
||||||
1500L, 1550L, 1600L, 1650L, 1700L, 1750L, 1800L, 1850L, 1900L,
|
|
||||||
1950L, 2000L, 2050L, 2100L, 2150L, 2200L, 2250L, 2300L, 2350L,
|
|
||||||
2400L, 2450L, 2451L, 2452L, 2453L, 2454L, 2455L, 2456L, 2457L,
|
|
||||||
2458L, 2459L, 2460L, 2461L, 2462L, 2463L, 2464L, 2465L, 2466L,
|
|
||||||
2467L, 2468L, 2469L, 2470L, 2471L, 2472L, 2473L, 2474L, 2475L,
|
|
||||||
2476L, 2477L, 2478L, 2479L, 2480L, 2481L, 2482L, 2483L, 2484L,
|
|
||||||
2485L, 2486L, 2487L, 2488L, 2489L, 2490L, 2491L, 2492L, 2493L,
|
|
||||||
2494L, 2495L, 2496L, 2497L, 2498L, 2499L, 2500L)
|
|
||||||
|
|
||||||
boundinit <- matrix(rep(init[-c(7,8)], length(cbound)), byrow=TRUE, nrow=length(cbound))
|
|
||||||
myboundmat <- cbind(cbound,boundinit)
|
|
||||||
myboundmat[cbound==1, c(2:7)] <- vecinj
|
|
||||||
colnames(myboundmat) <- c("cbound", names(vecinj))
|
|
||||||
|
|
||||||
# TODO: dt and iterations
|
|
||||||
|
|
||||||
setup <- list(n=2500,
|
|
||||||
bound=myboundmat,
|
|
||||||
base=base,
|
|
||||||
first=selout,
|
|
||||||
initsim=initsim,
|
|
||||||
Cf=1,
|
|
||||||
prop=prop,
|
|
||||||
immobile=c(7,8,9),
|
|
||||||
kin= c(8,9),
|
|
||||||
ann=list(O2g=-0.1675),
|
|
||||||
phase="FLUX1",
|
|
||||||
density="DEN1",
|
|
||||||
reduce=FALSE,
|
|
||||||
snapshots=demodir, ## directory where we will read MUFITS SUM files
|
|
||||||
gridfile=paste0(demodir,"/d2ascii.run.GRID.SUM")
|
|
||||||
)
|
|
||||||
130
data/SimDolKtz.R
130
data/SimDolKtz.R
@ -1,130 +0,0 @@
|
|||||||
# library(RedModRphree)
|
|
||||||
# library(Rmufits)
|
|
||||||
# library(RcppVTK)
|
|
||||||
|
|
||||||
db <- RPhreeFile(system.file("extdata", "phreeqc_kin.dat",
|
|
||||||
package="RedModRphree"), is.db=TRUE)
|
|
||||||
|
|
||||||
phreeqc::phrLoadDatabaseString(db)
|
|
||||||
|
|
||||||
prop <- c("C","Ca","Cl","Mg","pH","pe","O2g", "Calcite","Dolomite")
|
|
||||||
signif_vector <- c(7,7,7,7,7,7,7,5,5)
|
|
||||||
prop_type <- c("act","act","act","act","logact","logact","ignore","act","act")
|
|
||||||
|
|
||||||
|
|
||||||
base <- c("SOLUTION 1",
|
|
||||||
"units mol/kgw",
|
|
||||||
"temp 25.0",
|
|
||||||
"water 1",
|
|
||||||
"pH 9.91 charge",
|
|
||||||
"pe 4.0",
|
|
||||||
"C 1.2279E-04",
|
|
||||||
"Ca 1.2279E-04",
|
|
||||||
"Mg 0.001",
|
|
||||||
"Cl 0.002",
|
|
||||||
"PURE 1",
|
|
||||||
"O2g -0.1675 10",
|
|
||||||
"KINETICS 1",
|
|
||||||
"-steps 100",
|
|
||||||
"-step_divide 100",
|
|
||||||
"-bad_step_max 2000",
|
|
||||||
"Calcite", "-m 0.000207",
|
|
||||||
"-parms 0.0032",
|
|
||||||
"Dolomite",
|
|
||||||
"-m 0.0",
|
|
||||||
"-parms 0.00032",
|
|
||||||
"END")
|
|
||||||
|
|
||||||
selout <- c("SELECTED_OUTPUT",
|
|
||||||
"-high_precision true",
|
|
||||||
"-reset false",
|
|
||||||
"-time",
|
|
||||||
"-soln",
|
|
||||||
"-temperature true",
|
|
||||||
"-water true",
|
|
||||||
"-pH",
|
|
||||||
"-pe",
|
|
||||||
"-totals C Ca Cl Mg",
|
|
||||||
"-kinetic_reactants Calcite Dolomite",
|
|
||||||
"-equilibrium O2g")
|
|
||||||
|
|
||||||
initsim <- c("SELECTED_OUTPUT",
|
|
||||||
"-high_precision true",
|
|
||||||
"-reset false",
|
|
||||||
"USER_PUNCH",
|
|
||||||
"-head C Ca Cl Mg pH pe O2g Calcite Dolomite",
|
|
||||||
"10 PUNCH TOT(\"C\"), TOT(\"Ca\"), TOT(\"Cl\"), TOT(\"Mg\"), -LA(\"H+\"), -LA(\"e-\"), EQUI(\"O2g\"), EQUI(\"Calcite\"), EQUI(\"Dolomite\")",
|
|
||||||
"SOLUTION 1",
|
|
||||||
"units mol/kgw",
|
|
||||||
"temp 25.0", "water 1",
|
|
||||||
"pH 9.91 charge",
|
|
||||||
"pe 4.0",
|
|
||||||
"C 1.2279E-04",
|
|
||||||
"Ca 1.2279E-04",
|
|
||||||
"Cl 1E-12",
|
|
||||||
"Mg 1E-12",
|
|
||||||
"PURE 1",
|
|
||||||
"O2g -0.6788 10.0",
|
|
||||||
"Calcite 0.0 2.07E-3",
|
|
||||||
"Dolomite 0.0 0.0",
|
|
||||||
"END")
|
|
||||||
|
|
||||||
vecinj <- c("C"= 0,
|
|
||||||
"Ca" = 0,
|
|
||||||
"Cl" = 0.002,
|
|
||||||
"Mg" = 0.001,
|
|
||||||
"pe" = 4,
|
|
||||||
"pH" = 7)
|
|
||||||
|
|
||||||
init <- c("C(4)"= 1.2279E-4,
|
|
||||||
"Ca" =1.2279E-4,
|
|
||||||
"Cl" =0,
|
|
||||||
"Mg" =0,
|
|
||||||
"pe" =4,
|
|
||||||
"pH" =7,
|
|
||||||
"Calcite"= 2.07e-4,
|
|
||||||
"Dolomite"= 0)
|
|
||||||
|
|
||||||
bound_elm <- c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L,
|
|
||||||
15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L,
|
|
||||||
28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L,
|
|
||||||
41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 53L,
|
|
||||||
54L, 55L, 56L, 57L, 58L, 59L, 60L, 61L, 62L, 63L, 64L, 65L, 66L,
|
|
||||||
67L, 68L, 69L, 70L, 71L, 72L, 73L, 74L, 75L, 76L, 77L, 78L, 79L,
|
|
||||||
80L, 81L, 82L, 83L, 84L, 85L, 86L, 87L, 88L, 89L, 90L, 91L, 92L,
|
|
||||||
93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L,
|
|
||||||
105L, 106L, 107L, 108L, 214L, 215L)
|
|
||||||
|
|
||||||
inj_elm <- c(7426L, 18233L, 29040L, 39847L,
|
|
||||||
50654L, 61461L, 72268L, 83075L, 93882L, 104689L, 115496L, 126303L,
|
|
||||||
137110L, 147917L, 158724L, 169531L, 180338L, 191145L, 201952L,
|
|
||||||
212759L, 223566L, 234373L, 245180L, 255987L, 266794L, 277601L,
|
|
||||||
288408L, 299215L, 310022L, 320829L, 331636L, 342443L, 353250L,
|
|
||||||
364057L, 374864L, 385671L, 396478L, 407285L, 418092L, 428899L,
|
|
||||||
439706L, 450513L, 461320L, 472127L, 482934L, 493741L, 504548L,
|
|
||||||
515355L)
|
|
||||||
|
|
||||||
cbound <- inj_elm
|
|
||||||
|
|
||||||
boundinit <- matrix(rep(vecinj, length(cbound)), ncol=length(vecinj), byrow=TRUE)
|
|
||||||
myboundmat <- cbind(cbound,boundinit)
|
|
||||||
|
|
||||||
## distinguish between injection and real boundaries
|
|
||||||
colnames(myboundmat) <- c("cbound", names(vecinj))
|
|
||||||
|
|
||||||
setup <- list(n=648420,
|
|
||||||
bound=myboundmat,
|
|
||||||
base=base,
|
|
||||||
first=selout,
|
|
||||||
initsim=initsim,
|
|
||||||
Cf=1,
|
|
||||||
prop=prop,
|
|
||||||
immobile=c(7,8,9),
|
|
||||||
kin= c(8,9),
|
|
||||||
ann=list(O2g=-0.1675),
|
|
||||||
phase="FLUX1",
|
|
||||||
density="DENS",
|
|
||||||
reduce=FALSE,
|
|
||||||
snapshots="snaps/AllSnaps_cmp_v3.rds",
|
|
||||||
gridfile ="snaps/GridKtz_cmp_v3.rds"
|
|
||||||
)
|
|
||||||
File diff suppressed because it is too large
Load Diff
2633
docs/Doxyfile.in
2633
docs/Doxyfile.in
File diff suppressed because it is too large
Load Diff
Loading…
x
Reference in New Issue
Block a user