Add test cases for cookbooks

cookbooks/tian_parameterization_kinematic_slab/coupled-two-phase-tian-parameterization-kinematic-slab.prm

@@ -34,7 +34,7 @@ set End time                                   = 2e6
 set Surface pressure                           = 1e9
 set Maximum time step                          = 1000
 set Use operator splitting                     = true
-set Output directory                           = output-coupled-two-phase-tian-parameterization-kinematic-slab
+set Output directory                           = output_coupled_two_phase_tian_parameterization_kinematic_slab
 
 # Checkpoint the model so that a restart can be done if needed.
 subsection Checkpointing

cookbooks/tian_parameterization_kinematic_slab/uncoupled-two-phase-tian-parameterization-kinematic-slab.prm

@@ -7,7 +7,7 @@
 
 include $ASPECT_SOURCE_DIR/cookbooks/tian_parameterization_kinematic_slab/coupled-two-phase-tian-parameterization-kinematic-slab.prm
 
-set Output directory = output-uncoupled-two-phase-tian-parameterization-kinematic-slab
+set Output directory = output_uncoupled_two_phase_tian_parameterization_kinematic_slab
 
   subsection Stokes solver parameters
     # Lower solver tolerance to improve efficiency. Since the problem is simpler (i.e

tests/coupled_two_phase_tian_parameterization_kinematic_slab.prm

@@ -0,0 +1,47 @@
+# This test is for the fully coupled Simplified Subduction Model with Parameterized
+# Solid-Fluid Reactions cookbook. It also doubles as a test for the min/max
+# compaction viscosity.
+
+include $ASPECT_SOURCE_DIR/cookbooks/tian_parameterization_kinematic_slab/coupled-two-phase-tian-parameterization-kinematic-slab.prm
+set Adiabatic surface temperature              = 1600
+set Nonlinear solver scheme                    = single Advection, single Stokes
+set End time                                   = 2000
+
+subsection Mesh refinement
+  set Initial global refinement = 1
+  subsection Minimum refinement function
+    set Function expression = 1
+  end
+end
+
+# Slightly change composition model to ensure that there is bound_fluid
+# and porosity at the end of the test.
+subsection Boundary composition model
+  set Fixed composition boundary indicators         = left
+  set List of model names                           = function
+  subsection Function
+    set Function constants  = initial_porosity=0, initial_bound_sed=0.03, initial_bound_MORB=0.02, initial_bound_gabbro=0.01, \
+                              sediment_min=0, sediment_max=5e3, MORB_min=5e3, MORB_max=12e3, gabbro_min=12e3, gabbro_max=20e3, \
+                              onset_time=0, slab_thickness=20e3
+    set Function expression = initial_porosity; \
+                              if( t<=onset_time, 0, \
+                              if( (y<=slab_thickness - sediment_min) & (y>slab_thickness - sediment_max), initial_bound_sed, \
+                              if( (y<=slab_thickness - MORB_min) & (y>slab_thickness - MORB_max), initial_bound_MORB, \
+                              if( (y<=slab_thickness - gabbro_min) & (y>slab_thickness - gabbro_max), initial_bound_gabbro, 0.0)))); \
+                              if(y>slab_thickness, 1, 0); \
+                              if(y<=8e3, 1, 0); \
+                              if(y>8e3 & y<=15e3, 1, 0); \
+                              if(y>15e3 & y<=slab_thickness, 1, 0)
+  end
+end
+
+subsection Material model
+  subsection Reactive Fluid Transport Model
+    set Minimum compaction viscosity = 1e18
+    set Maximum compaction viscosity = 1e21
+  end
+end
+
+subsection Postprocess
+  set List of postprocessors = composition statistics
+end

tests/coupled_two_phase_tian_parameterization_kinematic_slab/screen-output

@@ -0,0 +1,73 @@
+
+Number of active cells: 16 (on 2 levels)
+Number of degrees of freedom: 989 (162+73+162+25+81+81+81+81+81+81+81)
+
+*** Timestep 0:  t=0 years, dt=0 years
+   Solving temperature system... 0 iterations.
+   Skipping porosity composition solve because RHS is zero.
+   Skipping bound_fluid composition solve because RHS is zero.
+   Solving peridotite system ... 0 iterations.
+   Skipping gabbro composition solve because RHS is zero.
+   Skipping MORB composition solve because RHS is zero.
+   Skipping sediment composition solve because RHS is zero.
+   Rebuilding Stokes preconditioner...
+   Solving Stokes system... 20+0 iterations.
+   Solving fluid velocity system... 1 iterations.
+
+Skipping mesh refinement, because the mesh did not change.
+
+*** Timestep 0:  t=0 years, dt=0 years
+   Solving temperature system... 0 iterations.
+   Skipping porosity composition solve because RHS is zero.
+   Skipping bound_fluid composition solve because RHS is zero.
+   Solving peridotite system ... 0 iterations.
+   Skipping gabbro composition solve because RHS is zero.
+   Skipping MORB composition solve because RHS is zero.
+   Skipping sediment composition solve because RHS is zero.
+   Rebuilding Stokes preconditioner...
+   Solving Stokes system... 20+0 iterations.
+   Solving fluid velocity system... 1 iterations.
+
+   Postprocessing:
+     Compositions min/max/mass: 0/0/0 // 0/0/0 // 0/1/9.913e+09 // 0/0/0 // 0/0/0 // 0/0/0
+
+*** Timestep 1:  t=1000 years, dt=1000 years
+   Solving composition reactions... in 10 substep(s).
+   Solving temperature system... 8 iterations.
+   Skipping porosity composition solve because RHS is zero.
+   Solving bound_fluid system ... 11 iterations.
+   Solving peridotite system ... 8 iterations.
+   Solving gabbro system ... 10 iterations.
+   Solving MORB system ... 11 iterations.
+   Skipping sediment composition solve because RHS is zero.
+   Rebuilding Stokes preconditioner...
+   Solving Stokes system... 15+0 iterations.
+   Solving fluid velocity system... 1 iterations.
+
+   Postprocessing:
+     Compositions min/max/mass: 0/0/0 // -0.002633/0.02/1.037e+06 // 0/1.008/9.91e+09 // -0.1319/1/1.296e+07 // -0.1316/1/5.185e+07 // 0/0/0
+
+*** Timestep 2:  t=2000 years, dt=1000 years
+   Solving composition reactions... in 10 substep(s).
+   Solving temperature system... 7 iterations.
+   Solving porosity system ... 10 iterations.
+   Solving bound_fluid system ... 11 iterations.
+   Solving peridotite system ... 7 iterations.
+   Solving gabbro system ... 10 iterations.
+   Solving MORB system ... 11 iterations.
+   Skipping sediment composition solve because RHS is zero.
+   Rebuilding Stokes preconditioner...
+   Solving Stokes system... 14+0 iterations.
+   Solving fluid velocity system... 1 iterations.
+
+   Postprocessing:
+     Compositions min/max/mass: -1.366e-07/4.974e-05/8415 // -0.002346/0.02/1.083e+06 // 0/1.016/9.907e+09 // -0.1179/1/1.364e+07 // -0.1173/1/5.457e+07 // 0/0/0
+
+Number of active cells: 25 (on 3 levels)
+Number of degrees of freedom: 1,570 (258+113+258+38+129+129+129+129+129+129+129)
+
+Termination requested by criterion: end time
+
+
+
+

tests/coupled_two_phase_tian_parameterization_kinematic_slab/statistics

@@ -0,0 +1,38 @@
+# 1: Time step number
+# 2: Time (years)
+# 3: Time step size (years)
+# 4: Number of mesh cells
+# 5: Number of Stokes degrees of freedom
+# 6: Number of temperature degrees of freedom
+# 7: Number of degrees of freedom for all compositions
+# 8: Iterations for temperature solver
+# 9: Iterations for composition solver 1
+# 10: Iterations for composition solver 2
+# 11: Iterations for composition solver 3
+# 12: Iterations for composition solver 4
+# 13: Iterations for composition solver 5
+# 14: Iterations for composition solver 6
+# 15: Iterations for Stokes solver
+# 16: Velocity iterations in Stokes preconditioner
+# 17: Schur complement iterations in Stokes preconditioner
+# 18: Minimal value for composition porosity
+# 19: Maximal value for composition porosity
+# 20: Global mass for composition porosity
+# 21: Minimal value for composition bound_fluid
+# 22: Maximal value for composition bound_fluid
+# 23: Global mass for composition bound_fluid
+# 24: Minimal value for composition peridotite
+# 25: Maximal value for composition peridotite
+# 26: Global mass for composition peridotite
+# 27: Minimal value for composition gabbro
+# 28: Maximal value for composition gabbro
+# 29: Global mass for composition gabbro
+# 30: Minimal value for composition MORB
+# 31: Maximal value for composition MORB
+# 32: Global mass for composition MORB
+# 33: Minimal value for composition sediment
+# 34: Maximal value for composition sediment
+# 35: Global mass for composition sediment
+0 0.000000000000e+00 0.000000000000e+00 16 187 81 486 0  0  0 0  0  0 0 19 21 147  0.00000000e+00 0.00000000e+00 0.00000000e+00  0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00 9.91319444e+09  0.00000000e+00 0.00000000e+00 0.00000000e+00  0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 
+1 1.000000000000e+03 1.000000000000e+03 16 187 81 486 8  0 11 8 10 11 0 14 16 112  0.00000000e+00 0.00000000e+00 0.00000000e+00 -2.63283793e-03 2.00000000e-02 1.03697004e+06 0.00000000e+00 1.00805359e+00 9.91030530e+09 -1.31885601e-01 1.00000000e+00 1.29620901e+07 -1.31641896e-01 1.00000000e+00 5.18485022e+07 0.00000000e+00 0.00000000e+00 0.00000000e+00 
+2 2.000000000000e+03 1.000000000000e+03 16 187 81 486 7 10 11 7 10 11 0 13 15 105 -1.36607082e-07 4.97421161e-05 8.41496117e+03 -2.34636340e-03 2.00000000e-02 1.08300325e+06 0.00000000e+00 1.01562005e+00 9.90743059e+09 -1.17891953e-01 1.00000000e+00 1.36420430e+07 -1.17303171e-01 1.00000000e+00 5.45709132e+07 0.00000000e+00 0.00000000e+00 0.00000000e+00 

tests/uncoupled_two_phase_tian_parameterization_kinematic_slab.prm

@@ -0,0 +1,55 @@
+# This test is for the fully coupled Simplified Subduction Model with Parameterized
+# Solid-Fluid Reactions cookbook. It also doubles as a test for the min/max
+# compaction viscosity.
+
+include $ASPECT_SOURCE_DIR/cookbooks/tian_parameterization_kinematic_slab/coupled-two-phase-tian-parameterization-kinematic-slab.prm
+set Adiabatic surface temperature              = 1600
+set Nonlinear solver scheme                    = single Advection, single Stokes
+set End time                                   = 2000
+
+subsection Mesh refinement
+  set Initial global refinement = 1
+  subsection Minimum refinement function
+    set Function expression = 1
+  end
+end
+
+subsection Compositional fields
+  set Compositional field methods = darcy field, field, field, field, field, field
+end
+
+# Slightly change composition model to ensure that there is bound_fluid
+# and porosity at the end of the test.
+subsection Boundary composition model
+  set Fixed composition boundary indicators         = left
+  set List of model names                           = function
+  subsection Function
+    set Function constants  = initial_porosity=0, initial_bound_sed=0.03, initial_bound_MORB=0.02, initial_bound_gabbro=0.01, \
+                              sediment_min=0, sediment_max=5e3, MORB_min=5e3, MORB_max=12e3, gabbro_min=12e3, gabbro_max=20e3, \
+                              onset_time=0, slab_thickness=20e3
+    set Function expression = initial_porosity; \
+                              if( t<=onset_time, 0, \
+                              if( (y<=slab_thickness - sediment_min) & (y>slab_thickness - sediment_max), initial_bound_sed, \
+                              if( (y<=slab_thickness - MORB_min) & (y>slab_thickness - MORB_max), initial_bound_MORB, \
+                              if( (y<=slab_thickness - gabbro_min) & (y>slab_thickness - gabbro_max), initial_bound_gabbro, 0.0)))); \
+                              if(y>slab_thickness, 1, 0); \
+                              if(y<=8e3, 1, 0); \
+                              if(y>8e3 & y<=15e3, 1, 0); \
+                              if(y>15e3 & y<=slab_thickness, 1, 0)
+  end
+end
+
+subsection Material model
+  subsection Reactive Fluid Transport Model
+    set Minimum compaction viscosity = 1e18
+    set Maximum compaction viscosity = 1e21
+  end
+end
+
+subsection Melt settings
+  set Include melt transport = false
+end
+
+subsection Postprocess
+  set List of postprocessors = composition statistics
+end

tests/uncoupled_two_phase_tian_parameterization_kinematic_slab/screen-output

@@ -0,0 +1,69 @@
+
+Number of active cells: 16 (on 2 levels)
+Number of degrees of freedom: 754 (162+25+81+81+81+81+81+81+81)
+
+*** Timestep 0:  t=0 years, dt=0 years
+   Solving temperature system... 0 iterations.
+   Skipping porosity composition solve because RHS is zero.
+   Skipping bound_fluid composition solve because RHS is zero.
+   Solving peridotite system ... 0 iterations.
+   Skipping gabbro composition solve because RHS is zero.
+   Skipping MORB composition solve because RHS is zero.
+   Skipping sediment composition solve because RHS is zero.
+   Rebuilding Stokes preconditioner...
+   Solving Stokes system... 33+0 iterations.
+
+Skipping mesh refinement, because the mesh did not change.
+
+*** Timestep 0:  t=0 years, dt=0 years
+   Solving temperature system... 0 iterations.
+   Skipping porosity composition solve because RHS is zero.
+   Skipping bound_fluid composition solve because RHS is zero.
+   Solving peridotite system ... 0 iterations.
+   Skipping gabbro composition solve because RHS is zero.
+   Skipping MORB composition solve because RHS is zero.
+   Skipping sediment composition solve because RHS is zero.
+   Rebuilding Stokes preconditioner...
+   Solving Stokes system... 33+0 iterations.
+
+   Postprocessing:
+     Compositions min/max/mass: 0/0/0 // 0/0/0 // 0/1/9.913e+09 // 0/0/0 // 0/0/0 // 0/0/0
+
+*** Timestep 1:  t=1000 years, dt=1000 years
+   Solving composition reactions... in 10 substep(s).
+   Solving temperature system... 8 iterations.
+   Skipping porosity composition solve because RHS is zero.
+   Solving bound_fluid system ... 11 iterations.
+   Solving peridotite system ... 8 iterations.
+   Solving gabbro system ... 10 iterations.
+   Solving MORB system ... 11 iterations.
+   Skipping sediment composition solve because RHS is zero.
+   Rebuilding Stokes preconditioner...
+   Solving Stokes system... 23+0 iterations.
+
+   Postprocessing:
+     Compositions min/max/mass: 0/0/0 // -0.002639/0.02/1.036e+06 // 0/1.008/9.91e+09 // -0.1322/1/1.295e+07 // -0.1319/1/5.179e+07 // 0/0/0
+
+*** Timestep 2:  t=2000 years, dt=1000 years
+   Solving composition reactions... in 10 substep(s).
+   Solving temperature system... 7 iterations.
+   Solving porosity system ... 10 iterations.
+   Solving bound_fluid system ... 11 iterations.
+   Solving peridotite system ... 7 iterations.
+   Solving gabbro system ... 10 iterations.
+   Solving MORB system ... 11 iterations.
+   Skipping sediment composition solve because RHS is zero.
+   Rebuilding Stokes preconditioner...
+   Solving Stokes system... 22+0 iterations.
+
+   Postprocessing:
+     Compositions min/max/mass: -1.355e-07/4.983e-05/8426 // -0.002357/0.02/1.081e+06 // 0/1.015/9.908e+09 // -0.1184/1/1.362e+07 // -0.1178/1/5.446e+07 // 0/0/0
+
+Number of active cells: 25 (on 3 levels)
+Number of degrees of freedom: 1,199 (258+38+129+129+129+129+129+129+129)
+
+Termination requested by criterion: end time
+
+
+
+

tests/uncoupled_two_phase_tian_parameterization_kinematic_slab/statistics

@@ -0,0 +1,38 @@
+# 1: Time step number
+# 2: Time (years)
+# 3: Time step size (years)
+# 4: Number of mesh cells
+# 5: Number of Stokes degrees of freedom
+# 6: Number of temperature degrees of freedom
+# 7: Number of degrees of freedom for all compositions
+# 8: Iterations for temperature solver
+# 9: Iterations for composition solver 1
+# 10: Iterations for composition solver 2
+# 11: Iterations for composition solver 3
+# 12: Iterations for composition solver 4
+# 13: Iterations for composition solver 5
+# 14: Iterations for composition solver 6
+# 15: Iterations for Stokes solver
+# 16: Velocity iterations in Stokes preconditioner
+# 17: Schur complement iterations in Stokes preconditioner
+# 18: Minimal value for composition porosity
+# 19: Maximal value for composition porosity
+# 20: Global mass for composition porosity
+# 21: Minimal value for composition bound_fluid
+# 22: Maximal value for composition bound_fluid
+# 23: Global mass for composition bound_fluid
+# 24: Minimal value for composition peridotite
+# 25: Maximal value for composition peridotite
+# 26: Global mass for composition peridotite
+# 27: Minimal value for composition gabbro
+# 28: Maximal value for composition gabbro
+# 29: Global mass for composition gabbro
+# 30: Minimal value for composition MORB
+# 31: Maximal value for composition MORB
+# 32: Global mass for composition MORB
+# 33: Minimal value for composition sediment
+# 34: Maximal value for composition sediment
+# 35: Global mass for composition sediment
+0 0.000000000000e+00 0.000000000000e+00 16 187 81 486 0  0  0 0  0  0 0 32 34 68  0.00000000e+00 0.00000000e+00 0.00000000e+00  0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00 9.91319444e+09  0.00000000e+00 0.00000000e+00 0.00000000e+00  0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00 
+1 1.000000000000e+03 1.000000000000e+03 16 187 81 486 8  0 11 8 10 11 0 22 24 49  0.00000000e+00 0.00000000e+00 0.00000000e+00 -2.63897272e-03 2.00000000e-02 1.03573618e+06 0.00000000e+00 1.00792232e+00 9.91036714e+09 -1.32154382e-01 1.00000000e+00 1.29474543e+07 -1.31948636e-01 1.00000000e+00 5.17868088e+07 0.00000000e+00 0.00000000e+00 0.00000000e+00 
+2 2.000000000000e+03 1.000000000000e+03 16 187 81 486 7 10 11 7 10 11 0 21 23 49 -1.35538213e-07 4.98262779e-05 8.42600735e+03 -2.35715286e-03 2.00000000e-02 1.08075722e+06 0.00000000e+00 1.01539290e+00 9.90754232e+09 -1.18366167e-01 1.00000000e+00 1.36157275e+07 -1.17842891e-01 1.00000000e+00 5.44591625e+07 0.00000000e+00 0.00000000e+00 0.00000000e+00