mirror of
https://git.gfz-potsdam.de/naaice/poet.git
synced 2025-12-16 12:54:50 +01:00
refactor: edit input scripts to be expected input
This commit is contained in:
Max Lübke
parent
b5813d0530
commit
3f532562c7
@ -1,28 +1,117 @@
|
|||||||
## chemical database
|
#################################################################
|
||||||
# NOTE: not needed now
|
## Section 1 ##
|
||||||
|
## Grid initialization ##
|
||||||
|
#################################################################
|
||||||
|
|
||||||
|
n <- 5
|
||||||
|
m <- 5
|
||||||
|
|
||||||
|
types <- c("scratch", "phreeqc", "rds")
|
||||||
|
|
||||||
|
# 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")
|
||||||
|
|
||||||
|
# needed if init type is set to "scratch"
|
||||||
|
# prop <- c("C", "Ca", "Cl", "Mg", "pH", "pe", "O2g", "Calcite", "Dolomite")
|
||||||
|
|
||||||
|
init_cell <- list(
|
||||||
|
"C" = 1.2279E-4,
|
||||||
|
"Ca" = 1.2279E-4,
|
||||||
|
"Cl" = 0,
|
||||||
|
"Mg" = 0,
|
||||||
|
"pH" = 9.91,
|
||||||
|
"pe" = 4,
|
||||||
|
"O2g" = 10,
|
||||||
|
"Calcite" = 2.07e-4,
|
||||||
|
"Dolomite" = 0
|
||||||
|
)
|
||||||
|
|
||||||
|
grid <- list(
|
||||||
|
n_cells = n,
|
||||||
|
s_cells = n,
|
||||||
|
type = types[1],
|
||||||
|
init_cell = as.data.frame(init_cell),
|
||||||
|
props = names(init_cell),
|
||||||
|
init_script = NULL
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
##################################################################
|
||||||
|
## Section 2 ##
|
||||||
|
## Diffusion parameters and boundary conditions ##
|
||||||
|
##################################################################
|
||||||
|
|
||||||
|
init_diffu <- c(
|
||||||
|
"C" = 1.2279E-4,
|
||||||
|
"Ca" = 1.2279E-4,
|
||||||
|
"Cl" = 0,
|
||||||
|
"Mg" = 0,
|
||||||
|
"pe" = 4,
|
||||||
|
"pH" = 7
|
||||||
|
)
|
||||||
|
|
||||||
|
alpha_diffu <- c(
|
||||||
|
"C" = 1E-4,
|
||||||
|
"Ca" = 1E-4,
|
||||||
|
"Cl" = 1E-4,
|
||||||
|
"Mg" = 1E-4,
|
||||||
|
"pe" = 1E-4,
|
||||||
|
"pH" = 1E-4
|
||||||
|
)
|
||||||
|
|
||||||
|
vecinj_diffu <- list(
|
||||||
|
list(
|
||||||
|
"C" = 0,
|
||||||
|
"Ca" = 0,
|
||||||
|
"Cl" = 0.002,
|
||||||
|
"Mg" = 0.001,
|
||||||
|
"pe" = 4,
|
||||||
|
"pH" = 9.91
|
||||||
|
)
|
||||||
|
)
|
||||||
|
|
||||||
|
boundary <- list(
|
||||||
|
"E" = 0,
|
||||||
|
"W" = 1
|
||||||
|
)
|
||||||
|
|
||||||
|
diffu_list <- names(alpha_diffu)
|
||||||
|
|
||||||
|
diffusion <- list(
|
||||||
|
init = init_diffu,
|
||||||
|
vecinj = do.call(rbind.data.frame, vecinj_diffu),
|
||||||
|
vecinj_index = boundary,
|
||||||
|
alpha = alpha_diffu
|
||||||
|
)
|
||||||
|
|
||||||
|
##################################################################
|
||||||
|
## Section 3 ##
|
||||||
|
## Phreeqc simulation ##
|
||||||
|
##################################################################
|
||||||
|
|
||||||
db <- RPhreeFile(system.file("extdata", "phreeqc_kin.dat",
|
db <- RPhreeFile(system.file("extdata", "phreeqc_kin.dat",
|
||||||
package = "RedModRphree"
|
package = "RedModRphree"
|
||||||
), is.db = TRUE)
|
), is.db = TRUE)
|
||||||
|
|
||||||
phreeqc::phrLoadDatabaseString(db)
|
phreeqc::phrLoadDatabaseString(db)
|
||||||
|
|
||||||
## only the directory
|
|
||||||
# demodir <- system.file("extdata", "demo_rtwithmufits", package="Rmufits")
|
|
||||||
|
|
||||||
n <- 10
|
|
||||||
m <- 10
|
|
||||||
|
|
||||||
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")
|
|
||||||
|
|
||||||
grid <- list(
|
|
||||||
n_cells = c(n),
|
|
||||||
s_cells = c(n)
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
# NOTE: This won't be needed in the future either. Could also be done in a. pqi
|
# NOTE: This won't be needed in the future either. Could also be done in a. pqi
|
||||||
# file
|
# file
|
||||||
base <- c(
|
base <- c(
|
||||||
@ -56,116 +145,11 @@ selout <- c(
|
|||||||
"-pH", "-pe", "-totals C Ca Cl Mg",
|
"-pH", "-pe", "-totals C Ca Cl Mg",
|
||||||
"-kinetic_reactants Calcite Dolomite", "-equilibrium O2g"
|
"-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")
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
init_diffu <- c(
|
|
||||||
"C" = 1.2279E-4,
|
|
||||||
"Ca" = 1.2279E-4,
|
|
||||||
"Cl" = 0,
|
|
||||||
"Mg" = 0,
|
|
||||||
"pe" = 4,
|
|
||||||
"pH" = 7
|
|
||||||
)
|
|
||||||
|
|
||||||
alpha_diffu <- c(
|
|
||||||
"C" = 1E-6,
|
|
||||||
"Ca" = 1E-6,
|
|
||||||
"Cl" = 1E-6,
|
|
||||||
"Mg" = 1E-6,
|
|
||||||
"pe" = 1E-8,
|
|
||||||
"pH" = 1E-8
|
|
||||||
)
|
|
||||||
|
|
||||||
vecinj_diffu <- list(
|
|
||||||
list(
|
|
||||||
"C" = 0,
|
|
||||||
"Ca" = 0,
|
|
||||||
"Cl" = 0.002,
|
|
||||||
"Mg" = 0.001,
|
|
||||||
"pe" = 4,
|
|
||||||
"pH" = 7
|
|
||||||
)
|
|
||||||
)
|
|
||||||
|
|
||||||
inner_index <- c(5)
|
|
||||||
inner_vecinj_index <- rep(1, 3)
|
|
||||||
|
|
||||||
vecinj_inner <- cbind(inner_index, inner_vecinj_index)
|
|
||||||
|
|
||||||
# constant_boundary <- list(
|
|
||||||
# n_cell = seq(1, n),
|
|
||||||
# i_vecinj = rep(1, n)
|
|
||||||
# )
|
|
||||||
#
|
|
||||||
# closed_boundary <- list(
|
|
||||||
# n_cell = seq(1, n),
|
|
||||||
# i_vecinj = rep(0, n)
|
|
||||||
# )
|
|
||||||
|
|
||||||
boundary <- list(
|
|
||||||
"N" = rep(1, n),
|
|
||||||
"E" = rep(0, n),
|
|
||||||
"S" = rep(0, n),
|
|
||||||
"W" = rep(0, n)
|
|
||||||
)
|
|
||||||
|
|
||||||
diffusion <- list(
|
|
||||||
init = init_diffu,
|
|
||||||
vecinj = do.call(rbind.data.frame, vecinj_diffu),
|
|
||||||
vecinj_inner = vecinj_inner,
|
|
||||||
boundary = boundary,
|
|
||||||
alpha = alpha_diffu
|
|
||||||
)
|
|
||||||
|
|
||||||
# cbound <- seq(from = 0, to = n - 1)
|
|
||||||
|
|
||||||
## 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
|
# TODO: dt and iterations
|
||||||
|
|
||||||
|
iterations <- 500
|
||||||
|
|
||||||
setup <- list(
|
setup <- list(
|
||||||
# bound = myboundmat,
|
# bound = myboundmat,
|
||||||
base = base,
|
base = base,
|
||||||
@ -174,7 +158,7 @@ setup <- list(
|
|||||||
# Cf = 1,
|
# Cf = 1,
|
||||||
grid = grid,
|
grid = grid,
|
||||||
diffusion = diffusion,
|
diffusion = diffusion,
|
||||||
prop = prop,
|
prop = names(init_cell),
|
||||||
immobile = c(7, 8, 9),
|
immobile = c(7, 8, 9),
|
||||||
kin = c(8, 9),
|
kin = c(8, 9),
|
||||||
ann = list(O2g = -0.1675),
|
ann = list(O2g = -0.1675),
|
||||||
@ -188,9 +172,10 @@ setup <- list(
|
|||||||
# cinj = c(0,1),
|
# cinj = c(0,1),
|
||||||
# boundary = boundary,
|
# boundary = boundary,
|
||||||
# injections = FALSE,
|
# injections = FALSE,
|
||||||
s_grid = c(n),
|
iterations = iterations,
|
||||||
n_grid = c(n),
|
timesteps = rep(10, iterations)
|
||||||
dt = 1,
|
|
||||||
iterations = 1,
|
|
||||||
timesteps = rep(1, 10)
|
|
||||||
)
|
)
|
||||||
|
|
||||||
|
# not needed yet
|
||||||
|
# signif_vector <- c(7, 7, 7, 7, 7, 7, 7, 5, 5)
|
||||||
|
# prop_type <- c("act", "act", "act", "act", "logact", "logact", "ignore", "act", "act")
|
||||||
|
|||||||
@ -156,7 +156,7 @@ selout <- c(
|
|||||||
|
|
||||||
# TODO: dt and iterations
|
# TODO: dt and iterations
|
||||||
|
|
||||||
iterations <- 10
|
iterations <- 500
|
||||||
|
|
||||||
setup <- list(
|
setup <- list(
|
||||||
# bound = myboundmat,
|
# bound = myboundmat,
|
||||||
@ -180,11 +180,8 @@ setup <- list(
|
|||||||
# cinj = c(0,1),
|
# cinj = c(0,1),
|
||||||
# boundary = boundary,
|
# boundary = boundary,
|
||||||
# injections = FALSE,
|
# injections = FALSE,
|
||||||
s_grid = c(n, m),
|
|
||||||
n_grid = c(n, m),
|
|
||||||
dt = 1,
|
|
||||||
iterations = iterations,
|
iterations = iterations,
|
||||||
timesteps = rep(1, iterations)
|
timesteps = rep(10, iterations)
|
||||||
)
|
)
|
||||||
|
|
||||||
# not needed yet
|
# not needed yet
|
||||||
|
|||||||
Loading…
x
Reference in New Issue
Block a user