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add bench/barite
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Marco De Lucia
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135
bench/barite/barite.R
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135
bench/barite/barite.R
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## Time-stamp: "Last modified 2023-04-11 14:29:51 delucia"
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database <- normalizePath("./db_barite.dat")
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input_script <- normalizePath("./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 <- 20
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m <- 20
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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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"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 = types[1],
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init_cell = as.data.frame(init_cell),
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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 <- c(
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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" = 1.E-10,
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"S" = 6.205E-4,
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"Sr" = 6.205E-4
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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" = -3.337E-08,
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"Ba" = 0.1,
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"Cl" = 0.2,
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"S" = 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" = 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(1,20,20),
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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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"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_diffu,
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vecinj = do.call(rbind.data.frame, injection_diff),
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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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## # Needed when using DHT
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signif_vector <- c(9, 9, 10, 5, 5, 5, 5, 5, 5)
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prop_type <- c("", "", "", "act", "act", "act", "act", "", "")
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prop <- names(init_cell)
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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 <- 4
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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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)
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25
bench/barite/barite.pqi
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25
bench/barite/barite.pqi
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SELECTED_OUTPUT
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-high_precision true
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-reset false
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-kinetic_reactants Barite Celestite
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-saturation_indices Barite Celestite
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SOLUTION 1
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units mol/kgw
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water 1
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temperature 25
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pH 7
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pe 10.799
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Ba 0.1
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Cl 0.2
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S 1e-9
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Sr 1e-9
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KINETICS 1
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Barite
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-m 0.001
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-parms 50. # reactive surface area
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-tol 1e-9
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Celestite
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-m 1
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-parms 10.0 # reactive surface area
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-tol 1e-9
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END
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195
bench/barite/db_barite.dat
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195
bench/barite/db_barite.dat
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DATABASE
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###########################
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SOLUTION_MASTER_SPECIES
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H H+ -1 H 1.008 # phreeqc/
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H(0) H2 0 H # phreeqc/
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H(1) H+ -1 0.0 # phreeqc/
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E e- 0 0.0 0.0 # phreeqc/
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O H2O 0 O 16.0 # phreeqc/
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O(0) O2 0 O # phreeqc/
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O(-2) H2O 0 0.0 # phreeqc/
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Na Na+ 0 Na 22.9898 # phreeqc/
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Ba Ba+2 0 Ba 137.34 # phreeqc/
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Sr Sr+2 0 Sr 87.62 # phreeqc/
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Cl Cl- 0 Cl 35.453 # phreeqc/
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S SO4-2 0 SO4 32.064 # phreeqc/
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S(6) SO4-2 0 SO4 # phreeqc/
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S(-2) HS- 1 S # phreeqc/
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SOLUTION_SPECIES
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H+ = H+
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-gamma 9 0
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-dw 9.31e-09
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# source: phreeqc
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e- = e-
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# source: phreeqc
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H2O = H2O
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# source: phreeqc
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Na+ = Na+
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-gamma 4.08 0.082
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-dw 1.33e-09
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-Vm 2.28 -4.38 -4.1 -0.586 0.09 4 0.3 52 -0.00333 0.566
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# source: phreeqc
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Ba+2 = Ba+2
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-gamma 4 0.153
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-dw 8.48e-10
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-Vm 2.063 -10.06 1.9534 -2.36 0.4218 5 1.58 -12.03 -0.00835 1
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# source: phreeqc
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Sr+2 = Sr+2
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-gamma 5.26 0.121
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-dw 7.94e-10
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-Vm -0.0157 -10.15 10.18 -2.36 0.86 5.26 0.859 -27 -0.0041 1.97
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# source: phreeqc
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Cl- = Cl-
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-gamma 3.63 0.017
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-dw 2.03e-09
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-Vm 4.465 4.801 4.325 -2.847 1.748 0 -0.331 20.16 0 1
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# source: phreeqc
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SO4-2 = SO4-2
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-gamma 5 -0.04
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-dw 1.07e-09
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-Vm 8 2.3 -46.04 6.245 3.82 0 0 0 0 1
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# source: phreeqc
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H2O = OH- + H+
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-analytical_expression 293.29227 0.1360833 -10576.913 -123.73158 0 -6.996455e-05
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-gamma 3.5 0
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-dw 5.27e-09
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-Vm -9.66 28.5 80 -22.9 1.89 0 1.09 0 0 1
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# source: phreeqc
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2 H2O = O2 + 4 H+ + 4 e-
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-log_k -86.08
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-delta_h 134.79 kcal
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-dw 2.35e-09
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-Vm 5.7889 6.3536 3.2528 -3.0417 -0.3943
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# source: phreeqc
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2 H+ + 2 e- = H2
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-log_k -3.15
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-delta_h -1.759 kcal
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-dw 5.13e-09
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-Vm 6.52 0.78 0.12
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# source: phreeqc
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SO4-2 + H+ = HSO4-
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-log_k 1.988
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-delta_h 3.85 kcal
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-analytical_expression -56.889 0.006473 2307.9 19.8858
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-dw 1.33e-09
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-Vm 8.2 9.259 2.1108 -3.1618 1.1748 0 -0.3 15 0 1
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# source: phreeqc
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HS- = S-2 + H+
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-log_k -12.918
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-delta_h 12.1 kcal
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-gamma 5 0
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-dw 7.31e-10
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# source: phreeqc
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SO4-2 + 9 H+ + 8 e- = HS- + 4 H2O
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-log_k 33.65
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-delta_h -60.140 kcal
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-gamma 3.5 0
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-dw 1.73e-09
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-Vm 5.0119 4.9799 3.4765 -2.9849 1.441
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# source: phreeqc
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HS- + H+ = H2S
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-log_k 6.994
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-delta_h -5.30 kcal
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-analytical_expression -11.17 0.02386 3279
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-dw 2.1e-09
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-Vm 7.81 2.96 -0.46
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# source: phreeqc
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Na+ + OH- = NaOH
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-log_k -10
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# source: phreeqc
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Na+ + SO4-2 = NaSO4-
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-log_k 0.7
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-delta_h 1.120 kcal
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-gamma 5.4 0
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-dw 1.33e-09
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-Vm 1e-05 16.4 -0.0678 -1.05 4.14 0 6.86 0 0.0242 0.53
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# source: phreeqc
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Ba+2 + H2O = BaOH+ + H+
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-log_k -13.47
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-gamma 5 0
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# source: phreeqc
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Ba+2 + SO4-2 = BaSO4
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-log_k 2.7
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# source: phreeqc
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Sr+2 + H2O = SrOH+ + H+
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-log_k -13.29
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-gamma 5 0
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# source: phreeqc
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Sr+2 + SO4-2 = SrSO4
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-log_k 2.29
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-delta_h 2.08 kcal
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-Vm 6.791 -0.9666 6.13 -2.739 -0.001
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# source: phreeqc
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PHASES
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Barite
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BaSO4 = Ba+2 + SO4-2
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-log_k -9.97
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-delta_h 6.35 kcal
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-analytical_expression -282.43 -0.08972 5822 113.08
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-Vm 52.9
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# source: phreeqc
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# comment:
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Celestite
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SrSO4 = Sr+2 + SO4-2
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-log_k -6.63
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-delta_h -4.037 kcal
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-analytical_expression -7.14 0.00611 75 0 0 -1.79e-05
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-Vm 46.4
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# source: phreeqc
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# comment:
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RATES
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Celestite # Palandri & Kharaka 2004<--------------------------------change me
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# PARM(1): reactive surface area
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# am: acid mechanism, nm: neutral mechanism, bm: base mechanism
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-start
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10 sr_i = SR("Celestite") # saturation ratio, (-)<----------change me
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20 moles = 0 # init target variable, (mol)
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30 IF ((M <= 0) AND (sr_i < 1)) OR (sr_i = 1.0) THEN GOTO 310
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40 sa = PARM(1) # reactive surface area, (m2)
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100 r = 8.314462 # gas constant, (J K-1 mol-1)
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110 dTi = (1 / TK) - (1 / 298.15) # (K-1)
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120 ea_am = 23800 # activation energy am, (J mol-1)<-----------change me
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130 ea_nm = 0 # activation energy nm, (J mol-1)<-----------change me
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140 ea_bm = 0 # activation energy bm, (J mol-1)<-----------change me
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150 log_k_am = -5.66 # reaction constant am<-------------------change me
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rem log_k_nm = -99 # reaction constant nm<-------------------change me
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rem log_k_bm = -99 # reaction constant bm<-------------------change me
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180 n_am = 0.109 # H+ reaction order am<-----------------------change me
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rem n_bm = 0 # H+ reaction order bm<-----------------------change me
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200 am = (10 ^ log_k_am) * EXP(-ea_am * dTi / r) * ACT("H+") ^ n_am
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rem nm = (10 ^ log_k_nm) * EXP(-ea_nm * dTi / r)
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rem bm = (10 ^ log_k_bm) * EXP(-ea_bm * dTi / r) * ACT("H+") ^ n_bm
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300 moles = sa * (am) * (1 - sr_i)
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310 save moles * time
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-end
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Barite # Palandri & Kharaka 2004<-----------------------------------change me
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# PARM(1): reactive surface area
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# am: acid mechanism, nm: neutral mechanism, bm: base mechanism
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-start
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10 sr_i = SR("Barite") # saturation ratio, (-)<----------change me
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20 moles = 0 # init target variable, (mol)
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30 IF ((M <= 0) AND (sr_i < 1)) OR (sr_i = 1.0) THEN GOTO 310
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40 sa = PARM(1) # reactive surface area, (m2)
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100 r = 8.314462 # gas constant, (J K-1 mol-1)
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110 dTi = (1 / TK) - (1 / 298.15) # (K-1)
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120 ea_am = 30800 # activation energy am, (J mol-1)<---------change me
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130 ea_nm = 30800 # activation energy nm, (J mol-1)<---------change me
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rem ea_bm = 0 # activation energy bm, (J mol-1)<---------change me
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150 log_k_am = -6.90 # reaction constant am<-----------------change me
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160 log_k_nm = -7.90 # reaction constant nm<-----------------change me
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rem log_k_bm = -99 # reaction constant bm<-------------------change me
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180 n_am = 0.22 # H+ reaction order am<----------------------change me
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rem n_bm = 0 # H+ reaction order bm<-----------------------change me
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200 am = (10 ^ log_k_am) * EXP(-ea_am * dTi / r) * ACT("H+") ^ n_am
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210 nm = (10 ^ log_k_nm) * EXP(-ea_nm * dTi / r)
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rem bm = (10 ^ log_k_bm) * EXP(-ea_bm * dTi / r) * ACT("H+") ^ n_bm
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300 moles = sa * (am + nm) * (1 - sr_i)
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310 save moles * time
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-end
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END
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