mirror of
https://git.gfz-potsdam.de/naaice/poet.git
synced 2025-12-15 12:28:22 +01:00
fix: updated bench/barite/{barite.R, barite_interp_eval.R}, added bench/barite/barite_200.R
This commit is contained in:
Marco De Lucia
parent
2204f0f793
commit
3f89321e71
@ -1,5 +1,4 @@
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## Time-stamp: "Last modified 2023-08-02 13:59:22 mluebke"
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## Time-stamp: "Last modified 2024-01-12 12:39:14 delucia"
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database <- normalizePath("../share/poet/bench/barite/db_barite.dat")
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input_script <- normalizePath("../share/poet/bench/barite/barite.pqi")
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@ -16,11 +15,11 @@ types <- c("scratch", "phreeqc", "rds")
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init_cell <- list(
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"H" = 110.0124,
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"O" = 55.5087,
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"Charge" = -1.217E-09,
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"Ba" = 1.E-10,
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"Cl" = 2.E-10,
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"S" = 6.205E-4,
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"Sr" = 6.205E-4,
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"Charge" = -1.216307845207e-09,
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"Ba" = 1.E-12,
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"Cl" = 2.E-12,
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"S(6)" = 6.204727095976e-04,
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"Sr" = 6.204727095976e-04,
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"Barite" = 0.001,
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"Celestite" = 1
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)
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@ -28,7 +27,11 @@ init_cell <- list(
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(1, 1),
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type = types[1]
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type = types[1],
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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)
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@ -40,26 +43,20 @@ grid <- list(
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## initial conditions
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init_diffu <- list(
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#"H" = 110.0124,
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"H" = 0.00000028904,
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#"O" = 55.5087,
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"O" = 0.000000165205,
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#"Charge" = -1.217E-09,
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"Charge" = -3.337E-08,
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"Ba" = 1.E-10,
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"Cl" = 1.E-10,
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"S(6)" = 6.205E-4,
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"Sr" = 6.205E-4
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"H" = 110.0124,
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"O" = 55.5087,
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"Charge" = -1.216307845207e-09,
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"Ba" = 1.E-12,
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"Cl" = 2.E-12,
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"S(6)" = 6.204727095976e-04,
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"Sr" = 6.204727095976e-04
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)
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injection_diff <- list(
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list(
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#"H" = 111.0124,
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"H" = 0.0000002890408,
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#"O" = 55.50622,
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"O" = 0.00002014464,
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#"Charge" = -3.337E-08,
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"Charge" = -3.337000004885E-08,
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"H" = 111.0124,
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"O" = 55.50622,
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"Charge" = -3.336970273297e-08,
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"Ba" = 0.1,
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"Cl" = 0.2,
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"S(6)" = 0,
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@ -84,11 +81,12 @@ alpha_diffu <- c(
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## )
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boundary <- list(
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"N" = rep(1, n),
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"N" = c(1,1, rep(0, n-2)),
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## "N" = rep(0, 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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# "W" = rep(0, n)
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"W" = c(1,1, rep(0, n-2))
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)
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diffu_list <- names(alpha_diffu)
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@ -112,15 +110,19 @@ diffusion <- list(
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## # Needed when using DHT
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dht_species <- c(
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"H" = 10,
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"O" = 10,
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"Charge" = 3,
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"Ba" = 5,
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"Cl" = 5,
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"S(6)" = 5,
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"Sr" = 5
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"H" = 7,
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"O" = 7,
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"Charge" = 4,
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"Ba" = 7,
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"Cl" = 7,
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"S(6)" = 7,
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"Sr" = 7,
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"Barite" = 4,
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"Celestite" = 4
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)
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chemistry <- list(
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database = database,
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input_script = input_script,
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138
bench/barite/barite_200.R
Normal file
138
bench/barite/barite_200.R
Normal file
@ -0,0 +1,138 @@
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## Time-stamp: "Last modified 2024-01-12 12:49:03 delucia"
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database <- normalizePath("../share/poet/bench/barite/db_barite.dat")
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input_script <- normalizePath("../share/poet/bench/barite/barite.pqi")
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## database <- normalizePath("/home/work/simR/Rphree/poetsims/Sims/Hans/db_barite.dat")
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## input_script <- normalizePath("/home/work/simR/Rphree/poetsims/Sims/Hans/barite.pqi")
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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 <- 200
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m <- 200
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init_cell <- list(
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"H" = 110.0124,
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"O" = 55.5087,
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"Charge" = -1.216307845207e-09,
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"Ba" = 1.E-12,
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"Cl" = 2.E-12,
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"S(6)" = 6.204727095976e-04,
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"Sr" = 6.204727095976e-04,
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"Barite" = 0.001,
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"Celestite" = 1
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)
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(1, 1),
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type = "scratch",
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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database = database,
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input_script = input_script
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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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## initial conditions
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init_diffu <- list(
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"H" = 110.0124,
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"O" = 55.5087,
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"Charge" = -1.216307845207e-09,
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"Ba" = 1.E-12,
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"Cl" = 2.E-12,
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"S(6)" = 6.204727095976e-04,
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"Sr" = 6.204727095976e-04
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)
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injection_diff <- list(
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list(
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"H" = 111.0124,
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"O" = 55.50622,
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"Charge" = -3.336970273297e-08,
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"Ba" = 0.1,
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"Cl" = 0.2,
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"S(6)" = 0,
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"Sr" = 0)
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)
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## diffusion coefficients
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alpha_diffu <- c(
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"H" = 1E-06,
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"O" = 1E-06,
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"Charge" = 1E-06,
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"Ba" = 1E-06,
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"Cl" = 1E-06,
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"S(6)" = 1E-06,
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"Sr" = 1E-06
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)
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boundary <- list(
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"N" = c(1,1, rep(0, n-2)),
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"E" = rep(0, n),
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"S" = rep(0, n),
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"W" = c(1,1, rep(0, n-2))
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)
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diffu_list <- names(alpha_diffu)
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vecinj <- do.call(rbind.data.frame, injection_diff)
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names(vecinj) <- names(init_diffu)
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diffusion <- list(
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init = as.data.frame(init_diffu, check.names = FALSE),
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vecinj = vecinj,
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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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## Chemistry module (Phreeqc) ##
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#################################################################
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## DHT significant digits
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dht_species <- c(
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"H" = 7,
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"O" = 7,
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"Charge" = 4,
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"Ba" = 7,
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"Cl" = 7,
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"S(6)" = 7,
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"Sr" = 7,
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"Barite" = 4,
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"Celestite" = 4
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)
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chemistry <- list(
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database = database,
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input_script = input_script,
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dht_species = dht_species
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)
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#################################################################
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## Section 4 ##
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## Putting all those things together ##
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#################################################################
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iterations <- 50
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dt <- 100
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setup <- list(
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grid = grid,
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diffusion = diffusion,
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chemistry = chemistry,
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iterations = iterations,
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timesteps = rep(dt, iterations),
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store_result = TRUE,
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out_save = seq(1, iterations)
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## out_save = c(1, 5, 10, seq(50, iterations, by=50))
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)
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@ -1,4 +1,4 @@
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## Time-stamp: "Last modified 2023-07-21 15:04:49 mluebke"
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## Time-stamp: "Last modified 2024-01-12 11:35:11 delucia"
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database <- normalizePath("../share/poet/bench/barite/db_barite.dat")
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input_script <- normalizePath("../share/poet/bench/barite/barite.pqi")
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@ -16,18 +16,18 @@ types <- c("scratch", "phreeqc", "rds")
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init_cell <- list(
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"H" = 110.0124,
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"O" = 55.5087,
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"Charge" = -1.217E-09,
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"Ba" = 1.E-10,
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"Cl" = 2.E-10,
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"S" = 6.205E-4,
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"Sr" = 6.205E-4,
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"Charge" = -1.216307845207e-09,
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"Ba" = 1.E-12,
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"Cl" = 2.E-12,
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"S(6)" = 6.204727095976e-04,
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"Sr" = 6.204727095976e-04,
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"Barite" = 0.001,
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"Celestite" = 1
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)
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grid <- list(
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n_cells = c(n, m),
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s_cells = c(n / 10, m / 10),
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s_cells = c(1, 1),
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type = types[1],
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init_cell = as.data.frame(init_cell, check.names = FALSE),
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props = names(init_cell),
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@ -44,56 +44,42 @@ grid <- list(
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## initial conditions
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init_diffu <- list(
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# "H" = 110.0124,
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"H" = 0.00000028904,
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# "O" = 55.5087,
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"O" = 0.000000165205,
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# "Charge" = -1.217E-09,
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"Charge" = -3.337E-08,
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"Ba" = 1.E-10,
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"Cl" = 1.E-10,
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"S(6)" = 6.205E-4,
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"Sr" = 6.205E-4
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"H" = 110.0124,
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"O" = 55.5087,
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"Charge" = -1.216307845207e-09,
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"Ba" = 1.E-12,
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"Cl" = 2.E-12,
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"S(6)" = 6.204727095976e-04,
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"Sr" = 6.204727095976e-04
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)
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injection_diff <- list(
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list(
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# "H" = 111.0124,
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"H" = 0.0000002890408,
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# "O" = 55.50622,
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"O" = 0.00002014464,
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# "Charge" = -3.337E-08,
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"Charge" = -3.337000004885E-08,
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"Ba" = 0.1,
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"Cl" = 0.2,
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"S(6)" = 0,
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"Sr" = 0
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)
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list(
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"H" = 111.0124,
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"O" = 55.50622,
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"Charge" = -3.336970273297e-08,
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"Ba" = 0.1,
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"Cl" = 0.2,
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"S(6)" = 0,
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"Sr" = 0)
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)
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## diffusion coefficients
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alpha_diffu <- c(
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"H" = 1E-06,
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"O" = 1E-06,
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"H" = 1E-06,
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"O" = 1E-06,
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"Charge" = 1E-06,
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"Ba" = 1E-06,
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"Cl" = 1E-06,
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"S(6)" = 1E-06,
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"S(6)" = 1E-06,
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"Sr" = 1E-06
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)
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vecinj_inner <- list(
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l1 = c(1, floor(n / 2), floor(m / 2))
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## l2 = c(2,80,80),
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## l3 = c(2,60,80)
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)
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boundary <- list(
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# "N" = rep(1, n),
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"N" = rep(0, n),
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"N" = c(1,1, rep(0, n-2)),
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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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"W" = c(1,1, rep(0, n-2))
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)
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diffu_list <- names(alpha_diffu)
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@ -104,7 +90,6 @@ names(vecinj) <- names(init_diffu)
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diffusion <- list(
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init = as.data.frame(init_diffu, check.names = FALSE),
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vecinj = vecinj,
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vecinj_inner = vecinj_inner,
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vecinj_index = boundary,
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alpha = alpha_diffu
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)
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@ -116,13 +101,15 @@ diffusion <- list(
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## # Needed when using DHT
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dht_species <- c(
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"H" = 10,
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"O" = 10,
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"Charge" = 3,
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"Ba" = 5,
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"Cl" = 5,
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"S(6)" = 5,
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"Sr" = 5
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"H" = 7,
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"O" = 7,
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"Charge" = 4,
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"Ba" = 7,
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"Cl" = 7,
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"S(6)" = 7,
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"Sr" = 7,
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"Barite" = 4,
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"Celestite" = 4
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)
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chemistry <- list(
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@ -135,8 +122,6 @@ chemistry <- list(
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## Section 4 ##
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## Putting all those things together ##
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#################################################################
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iterations <- 200
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dt <- 250
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