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Add EGU debug model
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Max Lübke
parent
480dd146f4
commit
20a0c453b0
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set(bench_files
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surfex.R
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ex.R
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# surfex.R
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# ex.R
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PoetEGU_surfex_500.R
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)
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set(runtime_files
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surfex_rt.R
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ex_rt.R
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# surfex_rt.R
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# ex_rt.R
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PoetEGU_surfex_500_rt.R
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)
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ADD_BENCH_TARGET(
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40
bench/surfex/PoetEGU_surfex_500.R
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40
bench/surfex/PoetEGU_surfex_500.R
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rows <- 500
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cols <- 200
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grid_left <- matrix(1, nrow = rows, ncol = cols/2)
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grid_rght <- matrix(2, nrow = rows, ncol = cols/2)
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grid_def <- cbind(grid_left, grid_rght)
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# Define grid configuration for POET model
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grid_setup <- list(
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pqc_in_file = "./SurfexEGU.pqi",
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pqc_db_file = "./SMILE_2021_11_01_TH.dat", # Path to the database file for Phreeqc
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grid_def = grid_def, # Definition of the grid, containing IDs according to the Phreeqc input script
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grid_size = c(10, 4), # Size of the grid in meters
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constant_cells = c() # IDs of cells with constant concentration
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)
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bound_def <- list(
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"type" = rep("constant", cols),
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"sol_id" = rep(3, cols),
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"cell" = seq(1, cols)
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)
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diffusion_setup <- list(
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boundaries = list(
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"N" = bound_def
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),
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alpha_x = matrix(runif(rows*cols))*1e-8,
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alpha_y = matrix(runif(rows*cols))*1e-9## ,1e-10
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)
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chemistry_setup <- list()
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# Define a setup list for simulation configuration
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setup <- list(
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Grid = grid_setup, # Parameters related to the grid structure
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Diffusion = diffusion_setup, # Parameters related to the diffusion process
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Chemistry = chemistry_setup # Parameters related to the chemistry process
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)
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11
bench/surfex/PoetEGU_surfex_500_rt.R
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bench/surfex/PoetEGU_surfex_500_rt.R
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iterations <- 200
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dt <- 1000
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out_save <- c(1, 2, seq(5, iterations, by=5))
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## out_save <- seq(1, iterations)
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list(
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timesteps = rep(dt, iterations),
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store_result = TRUE,
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out_save = out_save
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)
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108
bench/surfex/SurfexEGU.pqi
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bench/surfex/SurfexEGU.pqi
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## Time-stamp: "Last modified 2024-04-12 10:59:59 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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SOLUTION 1 ## Porewater composition Opalinus Clay, WITHOUT radionuclides, AFTER EQUI_PHASES
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pe -2.627 ## Eh = -227 mV, Value from Bossart & Thury (2008)-> PC borehole measurement 2003, Eh still decreasing
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density 1.01583 ## kg/dm³ = g/cm³
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temp 13 ## mean temperature Mont Terri, Bossart & Thury (2008), calculations performed for 25°C
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units mol/kgw
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## Mean composition
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pH 7.064
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Na 2.763e-01
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Cl 3.228e-01 charge
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S(6) 1.653e-02 as SO4
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Ca 2.173e-02
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Mg 1.740e-02
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K 1.902e-03
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Sr 4.520e-04
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Fe 1.435e-04
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U 2.247e-09
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SURFACE 1 Opalinus Clay, clay minerals
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## calculated with rho_b=2.2903 kg/dm³, poro=0.1662
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## 1 dm³ = 13.565641 kg_sed/kg_pw
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-equil 1 ## equilibrate with solution 1
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-sites_units density ## set unit for binding site density to sites/nm2
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-donnan 4.9e-10 ## calculated after Wigger & Van Loon (2018) for ionic strength after equilibration with minerales for pCO2=2.2 log10 bar
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# surface density SSA (m2/g) mass (g/kgw)
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Kln_aOH 1.155 11. 3798.4 ## Kaolinite 28 wt% (aluminol and silanol sites)
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Kln_siOH 1.155
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Ill_sOH 0.05 100. 4205.35 ## Illite 31 wt% (weak und strong binding sites)
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Ill_wOH 2.26 ## 2 % strong binding sites
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Mll_sOH 0.05 100. 813.94 ## Montmorillonite = smektite = 6 wt% (weak und strong binding sites)
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Mll_wOH 2.26 ## 2 % strong binding sites
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EXCHANGE 1 Exchanger, only illite+montmorillonite
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## Illite = 0.225 eq/kg_rock, Montmorillonit = 0.87 eq/kg_rock
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-equil 1 ## equilibrate with solution 1
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Z 0.9462 ## = Illite
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Y 0.70813 ## = Montmorillonite
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END
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SOLUTION 2 ## Porewater composition Opalinus Clay, WITHOUT radionuclides, AFTER EQUI_PHASES
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pe -2.627 ## Eh = -227 mV, Value from Bossart & Thury (2008)-> PC borehole measurement 2003, Eh still decreasing
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density 1.01583 ## kg/dm³ = g/cm³
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temp 13 ## mean temperature Mont Terri, Bossart & Thury (2008), calculations performed for 25°C
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units mol/kgw
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## Mean composition
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pH 7.064
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Na 2.763e-01
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Cl 3.228e-01 charge
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S(6) 1.653e-02 as SO4
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Ca 2.173e-02
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Mg 1.740e-02
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K 1.902e-03
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Sr 4.520e-04
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Fe 1.435e-04
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U 2.247e-09
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SURFACE 2 Opalinus Clay, clay minerals
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-equil 2 ## equilibrate with solution 2
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-sites_units density ## set unit for binding site density to
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## sites/nm2
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-donnan 4.9e-10 ## calculated after Wigger & Van Loon (2018)
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## for ionic strength after equilibration
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## with minerales for pCO2=2.2 log10 bar
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## surface density SSA (m2/g) mass (g/kgw)
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Kln_aOH 1.155 11. 2798.4 ## Kaolinite 28 wt% (aluminol and silanol sites)
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Kln_siOH 1.155
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Ill_sOH 0.05 100. 1205.35 ## Illite 31 wt% (weak und strong binding sites)
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Ill_wOH 2.26 ## 2 % strong binding sites
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Mll_sOH 0.05 100. 113.94 ## Montmorillonite = smektite = 6 wt% (weak und strong binding sites)
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Mll_wOH 2.26 ## 2 % strong binding sites
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EXCHANGE 2 Exchanger, only illite+montmorillonite
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## Illite = 0.225 eq/kg_rock, Montmorillonit = 0.87 eq/kg_rock
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-equil 2 ## equilibrate with solution 1
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Z 0.5 ## = Illite
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Y 0.2 ## = Montmorillonite
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END
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SOLUTION 3
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pe -2.627 ## Eh = -227 mV, Value from Bossart & Thury (2008)-> PC borehole measurement 2003, Eh still decreasing
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density 1.01583 ## kg/dm³ = g/cm³
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temp 13 ## mean temperature Mont Terri, Bossart & Thury (2008), calculations performed for 25°C
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units mol/kgw
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## Mean composition
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pH 7.064
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Na 3.763e-01
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Cl 4.228e-01 charge
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S(6) 1.653e-02 as SO4
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Ca 2.173e-02
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Mg 1.740e-02
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K 1.902e-03
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Sr 4.520e-04
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Fe 1.435e-04
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U 1e-6
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C 1.991e-03
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END
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RUN_CELLS
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END
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