Add EGU debug model

bench/surfex/CMakeLists.txt

@@ -1,11 +1,13 @@
 set(bench_files
-    surfex.R
+    # surfex.R
-    ex.R
+    # ex.R
+    PoetEGU_surfex_500.R
 )
 
 set(runtime_files
-    surfex_rt.R 
+    # surfex_rt.R 
-    ex_rt.R
+    # ex_rt.R
+    PoetEGU_surfex_500_rt.R
 )
 
 ADD_BENCH_TARGET(

bench/surfex/PoetEGU_surfex_500.R

@@ -0,0 +1,40 @@
+rows <- 500
+cols <- 200
+
+grid_left <- matrix(1, nrow = rows, ncol = cols/2)
+grid_rght <- matrix(2, nrow = rows, ncol = cols/2)
+grid_def <- cbind(grid_left, grid_rght)
+
+
+# Define grid configuration for POET model
+grid_setup <- list(
+  pqc_in_file = "./SurfexEGU.pqi",
+  pqc_db_file = "./SMILE_2021_11_01_TH.dat", # Path to the database file for Phreeqc
+  grid_def = grid_def,    # Definition of the grid, containing IDs according to the Phreeqc input script
+  grid_size = c(10, 4),   # Size of the grid in meters
+  constant_cells = c()    # IDs of cells with constant concentration
+)
+
+bound_def <- list(
+  "type" = rep("constant", cols),
+  "sol_id" = rep(3, cols),
+  "cell" = seq(1, cols)
+)
+
+diffusion_setup <- list(
+  boundaries = list(
+    "N" = bound_def
+  ),
+  alpha_x = matrix(runif(rows*cols))*1e-8, 
+  alpha_y = matrix(runif(rows*cols))*1e-9## ,1e-10
+)
+
+
+chemistry_setup <- list()
+
+# Define a setup list for simulation configuration
+setup <- list(
+  Grid = grid_setup, # Parameters related to the grid structure
+  Diffusion = diffusion_setup, # Parameters related to the diffusion process
+  Chemistry = chemistry_setup # Parameters related to the chemistry process
+)

bench/surfex/PoetEGU_surfex_500_rt.R

@@ -0,0 +1,11 @@
+iterations <- 200
+dt <- 1000
+
+out_save <- c(1, 2, seq(5, iterations, by=5))
+## out_save <- seq(1, iterations)
+
+list(
+    timesteps = rep(dt, iterations),
+    store_result = TRUE,
+    out_save = out_save
+)

bench/surfex/SurfexEGU.pqi

@@ -0,0 +1,108 @@
+##  Time-stamp: "Last modified 2024-04-12 10:59:59 delucia"
+## KNOBS
+##  -logfile            false
+##  -iterations         10000
+##  -convergence_tolerance  1E-12
+##  -step_size          2
+##  -pe_step_size       2
+
+SOLUTION 1                     ## Porewater composition Opalinus Clay, WITHOUT radionuclides, AFTER EQUI_PHASES
+  pe           -2.627          ## Eh = -227 mV, Value from Bossart & Thury (2008)-> PC borehole measurement 2003, Eh still decreasing  
+  density      1.01583         ## kg/dm³ = g/cm³
+  temp         13              ## mean temperature Mont Terri, Bossart & Thury (2008), calculations performed for 25°C
+  units        mol/kgw
+  ## Mean composition   
+  pH           7.064                    
+  Na           2.763e-01
+  Cl           3.228e-01  charge 
+  S(6)         1.653e-02  as SO4
+  Ca           2.173e-02 
+  Mg           1.740e-02
+  K            1.902e-03 
+  Sr           4.520e-04 
+  Fe           1.435e-04                 
+  U            2.247e-09                
+
+SURFACE 1 Opalinus Clay, clay minerals 
+  ## calculated with rho_b=2.2903 kg/dm³, poro=0.1662
+  ## 1 dm³ = 13.565641 kg_sed/kg_pw
+  -equil 1                ## equilibrate with solution 1 
+  -sites_units density    ## set unit for binding site density to sites/nm2
+  -donnan 4.9e-10         ## calculated after Wigger & Van Loon (2018) for ionic strength after equilibration with minerales for pCO2=2.2 log10 bar    
+
+  # surface  density SSA (m2/g)  mass (g/kgw) 
+  Kln_aOH  1.155   11.         3798.4     ## Kaolinite 28 wt% (aluminol and silanol sites) 
+  Kln_siOH 1.155               
+  Ill_sOH  0.05    100.        4205.35    ## Illite 31 wt% (weak und strong binding sites) 
+  Ill_wOH  2.26                           ## 2 % strong binding sites  
+  Mll_sOH  0.05    100.        813.94     ## Montmorillonite = smektite = 6 wt% (weak und strong binding sites)            
+  Mll_wOH  2.26                           ## 2 % strong binding sites
+
+EXCHANGE 1 Exchanger, only illite+montmorillonite 
+  ## Illite = 0.225 eq/kg_rock, Montmorillonit = 0.87 eq/kg_rock 
+ -equil 1         ## equilibrate with solution 1
+  Z     0.9462    ## = Illite
+  Y     0.70813   ## = Montmorillonite
+END
+
+SOLUTION 2                     ##  Porewater composition Opalinus Clay, WITHOUT radionuclides, AFTER EQUI_PHASES
+  pe           -2.627          ## Eh = -227 mV, Value from Bossart & Thury (2008)-> PC borehole measurement 2003, Eh still decreasing  
+  density      1.01583         ## kg/dm³ = g/cm³
+  temp         13              ## mean temperature Mont Terri, Bossart & Thury (2008), calculations performed for 25°C
+  units        mol/kgw
+  ## Mean composition   
+  pH           7.064                    
+  Na           2.763e-01
+  Cl           3.228e-01  charge 
+  S(6)         1.653e-02  as SO4
+  Ca           2.173e-02 
+  Mg           1.740e-02
+  K            1.902e-03 
+  Sr           4.520e-04 
+  Fe           1.435e-04                 
+  U            2.247e-09                
+
+SURFACE 2 Opalinus Clay, clay minerals 
+  -equil 2                ## equilibrate with solution 2 
+  -sites_units density    ## set unit for binding site density to
+			  ## sites/nm2
+  -donnan 4.9e-10         ## calculated after Wigger & Van Loon (2018)
+			  ## for ionic strength after equilibration
+			  ## with minerales for pCO2=2.2 log10 bar
+
+  ## surface  density SSA (m2/g)  mass (g/kgw) 
+  Kln_aOH  1.155   11.         2798.4     ## Kaolinite 28 wt% (aluminol and silanol sites) 
+  Kln_siOH 1.155               
+  Ill_sOH  0.05    100.        1205.35    ## Illite 31 wt% (weak und strong binding sites) 
+  Ill_wOH  2.26                           ## 2 % strong binding sites  
+  Mll_sOH  0.05    100.        113.94     ## Montmorillonite = smektite = 6 wt% (weak und strong binding sites)            
+  Mll_wOH  2.26                           ## 2 % strong binding sites
+
+EXCHANGE 2 Exchanger, only illite+montmorillonite 
+  ## Illite = 0.225 eq/kg_rock, Montmorillonit = 0.87 eq/kg_rock 
+ -equil 2         ## equilibrate with solution 1
+  Z     0.5       ## = Illite
+  Y     0.2       ## = Montmorillonite
+END
+
+SOLUTION 3
+  pe           -2.627          ## Eh = -227 mV, Value from Bossart & Thury (2008)-> PC borehole measurement 2003, Eh still decreasing  
+  density      1.01583         ## kg/dm³ = g/cm³
+  temp         13              ## mean temperature Mont Terri, Bossart & Thury (2008), calculations performed for 25°C
+  units        mol/kgw
+  ## Mean composition   
+  pH           7.064                    
+  Na           3.763e-01
+  Cl           4.228e-01  charge 
+  S(6)         1.653e-02  as SO4
+  Ca           2.173e-02 
+  Mg           1.740e-02
+  K            1.902e-03 
+  Sr           4.520e-04 
+  Fe           1.435e-04                 
+  U            1e-6            
+  C            1.991e-03 
+END
+
+RUN_CELLS
+END