data: added surfex benchmark

bench/surfex/SurfExBase.pqi

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+##  Time-stamp: "Last modified 2023-02-27 14:31:11 delucia"
+KNOBS
+ -logfile            false
+ -iterations         10000
+ -convergence_tolerance  1E-12
+ -step_size          2
+ -pe_step_size       2
+SELECTED_OUTPUT
+ -reset false
+ -high_precision true
+ -solution true
+ -state true
+ -step true 
+ -pH true 
+ -pe true
+ -ionic_strength true 
+ -water true
+USER_PUNCH
+-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
+-start
+5 w=TOT("water")
+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)")
+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)
+-end
+SOLUTION 1
+temp         13
+units        mol/kgw
+pH           7.06355
+pe          -2.626517
+C(4)         0.001990694
+Ca           0.02172649
+Cl           0.3227673 charge
+Fe           0.0001434717
+K            0.001902357
+Mg           0.01739704
+Na           0.2762882
+S(6)         0.01652701
+Sr           0.0004520361
+U(4)         8.147792e-12
+U(6)         2.237946e-09
+-water       0.00133
+SURFACE 1
+-equil 1
+-sites_units density
+-donnan 4.9e-10
+  Kln_aOH  1.155    11.  5.0518
+  Kln_siOH 1.155
+  Ill_sOH  0.05    100.  5.5931
+  Ill_wOH  2.26
+  Mll_sOH  0.05    100.  1.0825
+  Mll_wOH  2.26
+EXCHANGE 1
+ -equil 1
+  Z     0.0012585
+  Y     0.0009418
+END

bench/surfex/surfex.R

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+## Time-stamp: "Last modified 2023-02-27 18:33:30 delucia"
+
+database <- normalizePath("./SMILE_2021_11_01_TH.dat")
+input_script <- normalizePath("./SurfExBase.pqi")
+
+cat(paste(":: R This is a test 1\n"))
+
+#################################################################
+##                          Section 1                          ##
+##                     Grid initialization                     ##
+#################################################################
+
+n <- 10
+m <- 10
+
+types <- c("scratch", "phreeqc", "rds")
+
+init_cell <- list(H = 1.476571028625e-01,
+                  O = 7.392297218936e-02,
+                  Charge = -1.765225732724e-18,
+                  `C(-4)` = 2.477908970828e-21,
+                  `C(4)` = 2.647623016916e-06,
+                  Ca = 2.889623169138e-05,
+                  Cl = 4.292806181039e-04,
+                  `Fe(2)` =1.908142472666e-07,
+                  `Fe(3)` =3.173306589931e-12,
+                  `H(0)` =2.675642675119e-15,
+                  K = 2.530134809667e-06,
+                  Mg =2.313806319294e-05,
+                  Na =3.674633059628e-04,
+                  `S(-2)` = 8.589766637180e-15,
+                  `S(2)` = 1.205284362720e-19,
+                  `S(4)` = 9.108958772790e-18,
+                  `S(6)` = 2.198092329098e-05,
+                  Sr = 6.012080128154e-07,
+                  `U(4)` = 1.039668623852e-14,
+                  `U(5)` = 1.208394829796e-15,
+                  `U(6)` = 2.976409147150e-12)
+
+
+grid <- list(
+  n_cells = c(n, m),
+  s_cells = c(1, 1),
+  type = "scratch",
+  init_cell = as.data.frame(init_cell),
+  database = database,
+  input_script = input_script
+)
+
+
+##################################################################
+##                          Section 2                           ##
+##         Diffusion parameters and boundary conditions         ##
+##################################################################
+
+vecinj_diffu <- list(
+    list(H = 0.147659686316291,
+         O = 0.0739242798146046,
+         Charge = 7.46361643222701e-20,
+         `C(-4)` = 2.92438561098248e-21,
+         `C(4)` = 2.65160558871092e-06,
+         Ca = 2.89001071336443e-05,
+         Cl = 0.000429291158114428,
+         `Fe(2)` = 1.90823391198114e-07,
+         `Fe(3)` = 3.10832423034763e-12,
+         `H(0)` = 2.7888235127385e-15,
+         K = 2.5301787e-06,
+         Mg = 2.31391999937907e-05,
+         Na = 0.00036746969,
+         `S(-2)` = 1.01376078438546e-14,
+         `S(2)` = 1.42247026981542e-19,
+         `S(4)` = 9.49422092568557e-18,
+         `S(6)` = 2.19812504654191e-05,
+         Sr = 6.01218519999999e-07,
+         `U(4)` = 4.82255946569383e-12,
+         `U(5)` = 5.49050615347901e-13,
+         `U(6)` = 1.32462838991902e-09)
+)
+
+## diffusion coefficients
+alpha_diffu <- c(H = 1E-6, O = 1E-6, Charge = 1E-6, `C(-4)` = 1E-6,
+                 `C(4)` = 1E-6, Ca = 1E-6, Cl = 1E-6, `Fe(2)` = 1E-6,
+                 `Fe(3)` = 1E-6, `H(0)` = 1E-6, K = 1E-6, Mg = 1E-6,
+                 Na = 1E-6, `S(-2)` = 1E-6, `S(2)` = 1E-6,
+                 `S(4)` = 1E-6, `S(6)` = 1E-6, Sr = 1E-6,
+                 `U(4)` = 1E-6, `U(5)` = 1E-6, `U(6)` = 1E-6)
+
+## list of boundary conditions/inner nodes
+
+## vecinj_inner <- list(
+##    list(1,1,1)
+## )
+
+boundary <- list(
+  "N" = rep(1, n),
+  "E" = rep(0, n),
+  "S" = rep(0, n),
+  "W" = rep(0, n)
+)
+
+diffu_list <- names(alpha_diffu)
+
+diffusion <- list(
+  init = init_cell,
+  vecinj = do.call(rbind.data.frame, vecinj_diffu),
+#  vecinj_inner = vecinj_inner,
+  vecinj_index = boundary,
+  alpha = alpha_diffu
+)
+
+#################################################################
+##                          Section 3                          ##
+##                  Chemistry module (Phreeqc)                 ##
+#################################################################
+
+
+chemistry <- list(
+  database = database,
+  input_script = input_script
+)
+
+#################################################################
+##                          Section 4                          ##
+##              Putting all those things together              ##
+#################################################################
+
+
+iterations <- 10
+dt <- 200
+
+setup <- list(
+  grid = grid,
+  diffusion = diffusion,
+  chemistry = chemistry,
+  iterations = iterations,
+  timesteps = rep(dt, iterations),
+  store_result = TRUE,
+  out_save = c(5, iterations)
+)