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28b59ff6c3
It is now possible to run a simulation for one iteration in sequential mode without the use of Rmufits. According scripts are provided. refactor: TransportSim renamed to DiffusionModule refactor: parsing of R input script is now done outside of simulation modules (except ChemSim)
121 lines
4.1 KiB
R
121 lines
4.1 KiB
R
## 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,
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"pe" =4,
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"pH" =7,
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"Calcite"= 2.07e-4,
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"Dolomite"= 0)
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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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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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setup <- list(n=2500,
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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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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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)
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