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data: added surfex benchmark
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Marco De Lucia
Max Lübke
parent
32d35190cb
commit
27b94065ea
3718
bench/surfex/SMILE_2021_11_01_TH.dat
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3718
bench/surfex/SMILE_2021_11_01_TH.dat
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56
bench/surfex/SurfExBase.pqi
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56
bench/surfex/SurfExBase.pqi
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## Time-stamp: "Last modified 2023-02-27 14:31:11 delucia"
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KNOBS
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-logfile false
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-iterations 10000
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-convergence_tolerance 1E-12
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-step_size 2
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-pe_step_size 2
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SELECTED_OUTPUT
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-reset false
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-high_precision true
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-solution true
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-state true
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-step true
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-pH true
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-pe true
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-ionic_strength true
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-water true
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USER_PUNCH
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-head total_o total_h cb C(-4) C(4) Ca Cl Fe(2) Fe(3) H(0) K Mg Na S(-2) S(2) S(4) S(6) Sr U(4) U(5) U(6) UO2(am,hyd) KdU
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-start
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5 w=TOT("water")
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10 PUNCH TOTMOLE("O"), TOTMOLE("H"), CHARGE_BALANCE, w*TOT("C(-4)"), w*TOT("C(4)"), w*TOT("Ca"), w*TOT("Cl"), w*TOT("Fe(2)"), w*TOT("Fe(3)"), w*TOT("H(0)"), w*TOT("K"), w*TOT("Mg"), w*TOT("Na"), w*TOT("S(-2)"), w*TOT("S(2)"), w*TOT("S(4)"), w*TOT("S(6)"), w*TOT("Sr"), w*TOT("U(4)"), w*TOT("U(5)"), w*TOT("U(6)"), EQUI("UO2(am,hyd)")
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20 PUNCH ((SURF("U, Ill")+SURF("U, Mll")+SURF("U, Kln")+EDL("U, Ill")+EDL("U, Mll")+EDL("U, Kln"))/((TOT("U")*1.01583)))/(0.002251896406*1000)
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-end
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SOLUTION 1
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temp 13
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units mol/kgw
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pH 7.06355
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pe -2.626517
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C(4) 0.001990694
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Ca 0.02172649
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Cl 0.3227673 charge
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Fe 0.0001434717
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K 0.001902357
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Mg 0.01739704
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Na 0.2762882
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S(6) 0.01652701
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Sr 0.0004520361
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U(4) 8.147792e-12
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U(6) 2.237946e-09
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-water 0.00133
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SURFACE 1
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-equil 1
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-sites_units density
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-donnan 4.9e-10
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Kln_aOH 1.155 11. 5.0518
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Kln_siOH 1.155
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Ill_sOH 0.05 100. 5.5931
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Ill_wOH 2.26
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Mll_sOH 0.05 100. 1.0825
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Mll_wOH 2.26
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EXCHANGE 1
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-equil 1
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Z 0.0012585
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Y 0.0009418
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END
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139
bench/surfex/surfex.R
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bench/surfex/surfex.R
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## Time-stamp: "Last modified 2023-02-27 18:33:30 delucia"
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database <- normalizePath("./SMILE_2021_11_01_TH.dat")
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input_script <- normalizePath("./SurfExBase.pqi")
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cat(paste(":: R This is a test 1\n"))
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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 <- 10
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m <- 10
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types <- c("scratch", "phreeqc", "rds")
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init_cell <- list(H = 1.476571028625e-01,
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O = 7.392297218936e-02,
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Charge = -1.765225732724e-18,
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`C(-4)` = 2.477908970828e-21,
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`C(4)` = 2.647623016916e-06,
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Ca = 2.889623169138e-05,
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Cl = 4.292806181039e-04,
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`Fe(2)` =1.908142472666e-07,
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`Fe(3)` =3.173306589931e-12,
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`H(0)` =2.675642675119e-15,
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K = 2.530134809667e-06,
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Mg =2.313806319294e-05,
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Na =3.674633059628e-04,
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`S(-2)` = 8.589766637180e-15,
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`S(2)` = 1.205284362720e-19,
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`S(4)` = 9.108958772790e-18,
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`S(6)` = 2.198092329098e-05,
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Sr = 6.012080128154e-07,
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`U(4)` = 1.039668623852e-14,
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`U(5)` = 1.208394829796e-15,
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`U(6)` = 2.976409147150e-12)
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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),
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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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vecinj_diffu <- list(
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list(H = 0.147659686316291,
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O = 0.0739242798146046,
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Charge = 7.46361643222701e-20,
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`C(-4)` = 2.92438561098248e-21,
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`C(4)` = 2.65160558871092e-06,
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Ca = 2.89001071336443e-05,
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Cl = 0.000429291158114428,
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`Fe(2)` = 1.90823391198114e-07,
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`Fe(3)` = 3.10832423034763e-12,
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`H(0)` = 2.7888235127385e-15,
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K = 2.5301787e-06,
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Mg = 2.31391999937907e-05,
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Na = 0.00036746969,
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`S(-2)` = 1.01376078438546e-14,
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`S(2)` = 1.42247026981542e-19,
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`S(4)` = 9.49422092568557e-18,
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`S(6)` = 2.19812504654191e-05,
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Sr = 6.01218519999999e-07,
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`U(4)` = 4.82255946569383e-12,
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`U(5)` = 5.49050615347901e-13,
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`U(6)` = 1.32462838991902e-09)
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)
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## diffusion coefficients
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alpha_diffu <- c(H = 1E-6, O = 1E-6, Charge = 1E-6, `C(-4)` = 1E-6,
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`C(4)` = 1E-6, Ca = 1E-6, Cl = 1E-6, `Fe(2)` = 1E-6,
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`Fe(3)` = 1E-6, `H(0)` = 1E-6, K = 1E-6, Mg = 1E-6,
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Na = 1E-6, `S(-2)` = 1E-6, `S(2)` = 1E-6,
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`S(4)` = 1E-6, `S(6)` = 1E-6, Sr = 1E-6,
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`U(4)` = 1E-6, `U(5)` = 1E-6, `U(6)` = 1E-6)
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## list of boundary conditions/inner nodes
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## vecinj_inner <- list(
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## list(1,1,1)
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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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diffu_list <- names(alpha_diffu)
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diffusion <- list(
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init = init_cell,
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vecinj = do.call(rbind.data.frame, vecinj_diffu),
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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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#################################################################
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## Section 3 ##
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## Chemistry module (Phreeqc) ##
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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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)
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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 <- 10
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dt <- 200
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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 = c(5, iterations)
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)
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