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Commit 1d8f61f2 authored by Christoph Lehmann's avatar Christoph Lehmann
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[T/TRM] Added 1d column saturation test

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Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/1d_column_resaturation/bentonite_column.prj 0 → 100644
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<?xml version="1.0" encoding="ISO-8859-1"?>
<OpenGeoSysProject>
<meshes>
<mesh axially_symmetric="false">meshes/column.vtu</mesh>
<mesh axially_symmetric="false">meshes/column_zmin.vtu</mesh>
<mesh axially_symmetric="false">meshes/column_xmin.vtu</mesh>
<mesh axially_symmetric="false">meshes/column_xmax.vtu</mesh>
<mesh axially_symmetric="false">meshes/column_ymin.vtu</mesh>
<mesh axially_symmetric="false">meshes/column_ymax.vtu</mesh>
<mesh axially_symmetric="false">meshes/column_zmax.vtu</mesh>
</meshes>
<processes>
<process>
<name>TRM</name>
<type>THERMO_RICHARDS_MECHANICS</type>
<subtype>StressSaturation_StrainPressureTemperature</subtype>
<integration_order>4</integration_order>
<constitutive_relation>
<type>MFront</type>
<behaviour>BentoniteBehaviour</behaviour>
<library path_is_relative_to_prj_file="false">libOgsMFrontBehaviourBentoniteGeneralModForCTestsOnly</library>
<initial_values>
<state_variable name="e" parameter="e0"/>
<state_variable name="em" parameter="em0"/>
<state_variable name="eM" parameter="eM0"/>
<state_variable name="SrM" parameter="SrM0"/>
<state_variable name="a_scan" parameter="a_scan0"/>
<state_variable name="re" parameter="re0"/>
</initial_values>
</constitutive_relation>
<process_variables>
<temperature>temperature</temperature>
<pressure>pressure</pressure>
<displacement>displacement</displacement>
</process_variables>
<secondary_variables>
<secondary_variable internal_name="sigma_total" output_name="sigma_total"/>
<secondary_variable internal_name="epsilon" output_name="epsilon"/>
<secondary_variable internal_name="saturation" output_name="saturation"/>
<secondary_variable internal_name="porosity" output_name="porosity"/>
<secondary_variable internal_name="e" output_name="e"/>
<secondary_variable internal_name="em" output_name="em"/>
<secondary_variable internal_name="eM" output_name="eM"/>
<secondary_variable internal_name="SrM" output_name="SrM"/>
<secondary_variable internal_name="a_scan" output_name="a_scan"/>
<secondary_variable internal_name="re" output_name="re"/>
</secondary_variables>
<specific_body_force>0 0 0</specific_body_force>
<initial_stress type="total">initial_stress</initial_stress>
</process>
</processes>
<media>
<medium>
<phases>
<phase>
<type>AqueousLiquid</type>
<properties>
<property>
<name>specific_heat_capacity</name>
<type>Constant</type>
<value>4181.3</value> <!-- Pitz et al. -->
</property>
<property>
<name>thermal_conductivity</name>
<type>Constant</type>
<value>0.58</value> <!-- standard -->
</property>
<property>
<name>density</name>
<type>Constant</type>
<value>1000</value> <!-- standard -->
</property>
<property>
<name>thermal_expansivity</name>
<type>Constant</type>
<value>4e-4</value> <!-- Pitz et al., NB: this is beta_T=3*alpha_T -->
</property>
<property>
<name>viscosity</name>
<type>Constant</type>
<value>1.8e-3</value> <!-- standard -->
</property>
</properties>
</phase>
<phase>
<type>Solid</type> <!-- bentonite BVC -->
<properties>
<property>
<name>density</name>
<type>Constant</type>
<value>2758.0</value> <!-- for BCV, it must be 2758 kg/m³ (Nagra report); DM's bent powder 1700 kg/m^3 -->
</property>
<property>
<name>thermal_conductivity</name>
<type>Constant</type>
<value>1.06</value> <!-- 0.455 dry, 1.06 saturated (Nagra) -->
</property>
<property>
<name>specific_heat_capacity</name>
<type>Constant</type>
<value>880.0</value> <!-- Nagra -->
</property>
<property>
<name>thermal_expansivity</name>
<type>Constant</type>
<value>3e-4</value> <!-- Nagra -->
</property>
</properties>
</phase>
</phases>
<properties>
<property>
<name>saturation</name>
<type>Constant</type>
<value>0.345</value> <!-- ANY value here, to be overriden by the MFront -->
</property>
<property>
<name>relative_permeability</name>
<type>Constant</type>
<value>1</value> <!-- DM's email, it is a function of b,phi,phi0,S_L,lambda -->
</property>
<property>
<name>permeability</name>
<type>Constant</type>
<value>3e-20</value> <!-- DM's email , it is k0 -->
</property>
<!--property>
<name>porosity</name>
<type>Constant</type>
<value>0.403145</value>
</property-->
<property>
<name>porosity</name>
<type>PorosityFromMassBalance</type>
<initial_porosity>phi0</initial_porosity> <!-- the value 0.403145=:phi0 is recovered from DM's e=0.67545 -->
<minimal_porosity>0</minimal_porosity>
<maximal_porosity>1</maximal_porosity>
</property>
<property>
<name>bishops_effective_stress</name>
<type>BishopsPowerLaw</type>
<exponent>1.0</exponent> <!-- Pits et al., it is 1, if S_L<S_entry, 0 otherwise -->
</property>
<property>
<name>biot_coefficient</name>
<type>Constant</type>
<value>1.0</value> <!-- OK -->
</property>
<property>
<name>thermal_conductivity</name>
<type>EffectiveThermalConductivityPorosityMixing</type>
</property>
</properties>
</medium>
</media>
<parameters>
<parameter>
<mesh>column</mesh>
<name>initial_stress</name> <!-- suggetsed to be -2000 kPa -->
<type>Function</type>
<expression>-2000000</expression> <!-- originally, I tried out with -0.001 kPa-->
<expression>-2000000</expression>
<expression>-2000000</expression>
<expression>0</expression>
<expression>0</expression>
<expression>0</expression>
</parameter>
<parameter>
<name>e0</name>
<type>Constant</type>
<value>0.67545</value> <!-- DM's email -->
</parameter>
<parameter>
<name>em0</name>
<type>Constant</type>
<value>0.0</value> <!-- DM's email -->
</parameter>
<parameter>
<name>eM0</name>
<type>Constant</type>
<value>0.0</value> <!-- DM's email -->
</parameter>
<parameter>
<name>SrM0</name>
<type>Constant</type>
<value>0.0</value> <!-- DM's email -->
</parameter>
<parameter>
<name>a_scan0</name>
<type>Constant</type>
<value>0.0</value> <!-- DM's email -->
</parameter>
<parameter>
<name>re0</name>
<type>Constant</type>
<value>0.0</value> <!-- DM's email -->
</parameter>
<parameter>
<name>phi0</name>
<type>Constant</type>
<value>0.403145</value> <!-- this magnitude follows from e0=0.67545 -->
</parameter>
<parameter>
<name>temperature_IC</name>
<type>Constant</type>
<value>298.15</value> <!-- NB: in DM's email, T_ref=294 K -->
</parameter>
<parameter>
<name>pressure_IC</name>
<type>Constant</type>
<values>-100.e6</values> <!-- in kPa !!! DM's email, p_cap⁰=100000 kPa => p_LR⁰=-100 MPa -->
</parameter>
<parameter>
<name>displacement_IC</name>
<type>Constant</type>
<values>0 0 0</values> <!-- -->
</parameter>
<parameter>
<name>temperature_BC</name>
<type>Constant</type>
<value>298.15</value> <!-- same as the IC -->
</parameter>
<parameter>
<name>pressure_BC_bot</name>
<type>Constant</type>
<value>-100.e6</value> <!-- in kPa, DM's email -->
</parameter>
<parameter>
<name>pressure_BC_top</name>
<type>Function</type>
<expression>if (t &lt;=3600, -100.e6*(1-t/3600), 0)</expression> <!-- in kPa, DM's email -->
</parameter>
<parameter>
<name>displacement_BC_diriH</name>
<type>Constant</type>
<value>0</value>
</parameter>
</parameters>
<process_variables>
<process_variable>
<name>temperature</name>
<components>1</components>
<order>1</order>
<initial_condition>temperature_IC</initial_condition>
<boundary_conditions>
<boundary_condition>
<mesh>column</mesh>
<type>Dirichlet</type>
<parameter>temperature_BC</parameter>
</boundary_condition>
</boundary_conditions>
</process_variable>
<process_variable>
<name>pressure</name>
<components>1</components>
<order>1</order>
<initial_condition>pressure_IC</initial_condition>
<boundary_conditions>
<!--boundary_condition>
<mesh>column_zmin</mesh>
<type>Dirichlet</type>
<parameter>pressure_BC_bot</parameter>
</boundary_condition-->
<boundary_condition>
<mesh>column_zmax</mesh>
<type>Dirichlet</type>
<parameter>pressure_BC_top</parameter>
</boundary_condition>
</boundary_conditions>
</process_variable>
<process_variable>
<name>displacement</name>
<components>3</components>
<order>2</order> <!-- 1 when mO1, 2 when mO2 -->
<initial_condition>displacement_IC</initial_condition>
<boundary_conditions>
<boundary_condition>
<mesh>column_xmin</mesh>
<type>Dirichlet</type>
<component>0</component>
<parameter>displacement_BC_diriH</parameter>
</boundary_condition>
<boundary_condition>
<mesh>column_xmax</mesh>
<type>Dirichlet</type>
<component>0</component>
<parameter>displacement_BC_diriH</parameter>
</boundary_condition>
<boundary_condition>
<mesh>column_ymin</mesh>
<type>Dirichlet</type>
<component>1</component>
<parameter>displacement_BC_diriH</parameter>
</boundary_condition>
<boundary_condition>
<mesh>column_ymax</mesh>
<type>Dirichlet</type>
<component>1</component>
<parameter>displacement_BC_diriH</parameter>
</boundary_condition>
<boundary_condition>
<mesh>column_zmin</mesh>
<type>Dirichlet</type>
<component>2</component>
<parameter>displacement_BC_diriH</parameter>
</boundary_condition>
<boundary_condition>
<mesh>column_zmax</mesh>
<type>Dirichlet</type>
<component>2</component>
<parameter>displacement_BC_diriH</parameter>
</boundary_condition>
</boundary_conditions>
</process_variable>
</process_variables>
<time_loop>
<processes>
<process ref="TRM">
<nonlinear_solver>basic_newton</nonlinear_solver>
<convergence_criterion>
<type>PerComponentDeltaX</type>
<norm_type>NORM2</norm_type>
<!--abstols>1e0 1e-1 1e-5 1e-5 1e-5</abstols-->
<reltols>1e0 1e-2 1e-2 1e-2 1e-2</reltols> <!-- ref., 1e-2 -->
</convergence_criterion>
<time_discretization>
<type>BackwardEuler</type>
</time_discretization>
<time_stepping>
<type>IterationNumberBasedTimeStepping</type>
<t_initial>0</t_initial>
<t_end>360000</t_end> <!--this is 100 hours-->
<initial_dt>1e-2</initial_dt>
<minimum_dt>1e-4</minimum_dt>
<maximum_dt>3600</maximum_dt> <!-- first try dt_max=10 min => 60 min -->
<number_iterations>4 9 11</number_iterations>
<multiplier>2.0 1.0 0.5</multiplier> <!-- #iter\in[4,9), next dt is x2, #iter\in[9,11) next dt is x1, etc. -->
</time_stepping>
<!--time_stepping>
<type>FixedTimeStepping</type>
<t_initial>0</t_initial>
<t_end>3600</t_end>
<timesteps>
<pair>
<repeat>3600</repeat>
<delta_t>1</delta_t>
</pair>
</timesteps>
</time_stepping-->
</process>
</processes>
<output>
<type>VTK</type>
<prefix>bentonite_column</prefix>
<timesteps>
<pair>
<repeat>1</repeat>
<each_steps>1</each_steps>
</pair>
</timesteps>
<variables>
<!--variable>displacement</variable>
<variable>pressure</variable>
<variable>temperature</variable>
<variable>pressure_interpolated</variable>
<variable>temperature_interpolated</variable>
<variable>saturation</variable>
<variable>sigma_total</variable>
<variable>epsilon</variable>
<variable>e</variable>
<variable>em</variable>
<variable>eM</variable>
<variable>SrM</variable>
<variable>a_scan</variable>
<variable>re</variable>
<variable>porosity</variable>
<variable>permeability</variable-->
</variables>
<suffix>_ts_{:timestep}_t_{:gtime}_sec</suffix>
</output>
</time_loop>
<nonlinear_solvers>
<nonlinear_solver>
<name>basic_newton</name>
<type>Newton</type>
<max_iter>50</max_iter>
<linear_solver>general_linear_solver</linear_solver>
</nonlinear_solver>
</nonlinear_solvers>
<linear_solvers>
<linear_solver>
<name>general_linear_solver</name>
<eigen>
<!--solver_type>SparseLU</solver_type-->
<!--solver_type>PardisoLU</solver_type-->
<solver_type>BiCGSTAB</solver_type>
<precon_type>DIAGONAL</precon_type> <!--ILUT is also possible -->
<max_iteration_step>10000</max_iteration_step> <!-- 10000 is a default value -->
<error_tolerance>1e-16</error_tolerance> <!-- 1e-16 is a default value -->
<scaling>1</scaling>
</eigen>
<petsc>
<parameters>-ksp_type bcgs
-pc_type jacobi
-ksp_rtol 1.e-14 -ksp_atol 1.e-14
-ksp_max_it 4000
</parameters>
</petsc>
</linear_solver>
</linear_solvers>
<test_definition>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>HeatFlowRate</field>
<absolute_tolerance>2.2e-16</absolute_tolerance>
<relative_tolerance>0.0 <!-- inf --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>MassFlowRate</field>
<absolute_tolerance>2.8e-23</absolute_tolerance>
<relative_tolerance>0.0 <!-- 2.9e-09 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>NodalForces</field>
<absolute_tolerance>1.2e-13</absolute_tolerance>
<relative_tolerance>0.0 <!-- inf --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>SrM</field>
<absolute_tolerance>4.9e-14</absolute_tolerance>
<relative_tolerance>0.0 <!-- 1.8e-13 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>a_scan</field>
<absolute_tolerance>3.8e-13</absolute_tolerance>
<relative_tolerance>0.0 <!-- 0.0023 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>displacement</field>
<absolute_tolerance>1e-15</absolute_tolerance>
<relative_tolerance>0.0 <!-- 1400.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>dry_density_solid_ip</field>
<absolute_tolerance>5.7e-12</absolute_tolerance>
<relative_tolerance>0.0 <!-- 3.5e-15 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>e</field>
<absolute_tolerance>6.7e-15</absolute_tolerance>
<relative_tolerance>0.0 <!-- 9.9e-15 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>eM</field>
<absolute_tolerance>1.4e-14</absolute_tolerance>
<relative_tolerance>0.0 <!-- 6.3e-14 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>em</field>
<absolute_tolerance>1.3e-14</absolute_tolerance>
<relative_tolerance>0.0 <!-- 3.1e-14 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>epsilon</field>
<absolute_tolerance>2.9e-15</absolute_tolerance>
<relative_tolerance>0.0 <!-- inf --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>epsilon_ip</field>
<absolute_tolerance>2.8e-15</absolute_tolerance>
<relative_tolerance>0.0 <!-- inf --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>intrinsic_permeability_ip</field>
<absolute_tolerance>0.0</absolute_tolerance>
<relative_tolerance>0.0 <!-- 0.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>liquid_density_avg</field>
<absolute_tolerance>0.0</absolute_tolerance>
<relative_tolerance>0.0 <!-- 0.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>liquid_density_ip</field>
<absolute_tolerance>0.0</absolute_tolerance>
<relative_tolerance>0.0 <!-- 0.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>material_state_variable_RungeKutta_InternalStateVariables[0]_ip</field>
<absolute_tolerance>0.0</absolute_tolerance>
<relative_tolerance>0.0 <!-- 0.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>material_state_variable_RungeKutta_InternalStateVariables[1]_ip</field>
<absolute_tolerance>0.0</absolute_tolerance>
<relative_tolerance>0.0 <!-- 0.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>material_state_variable_RungeKutta_InternalStateVariables[2]_ip</field>
<absolute_tolerance>6.2e-12</absolute_tolerance>
<relative_tolerance>0.0 <!-- 1.5e-10 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>material_state_variable_RungeKutta_InternalStateVariables[3]_ip</field>
<absolute_tolerance>1.4e-10</absolute_tolerance>
<relative_tolerance>0.0 <!-- 2.1e-10 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>material_state_variable_SrM_ip</field>
<absolute_tolerance>5.4e-14</absolute_tolerance>
<relative_tolerance>0.0 <!-- 1.8e-13 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>material_state_variable_a_scan_ip</field>
<absolute_tolerance>4.3e-13</absolute_tolerance>
<relative_tolerance>0.0 <!-- 5.1e-05 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>material_state_variable_eM_ip</field>
<absolute_tolerance>1.4e-14</absolute_tolerance>
<relative_tolerance>0.0 <!-- 6.4e-14 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>material_state_variable_e_ip</field>
<absolute_tolerance>6.8e-15</absolute_tolerance>
<relative_tolerance>0.0 <!-- 9.9e-15 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>material_state_variable_em_ip</field>
<absolute_tolerance>1.2e-14</absolute_tolerance>
<relative_tolerance>0.0 <!-- 3.1e-14 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>material_state_variable_re_ip</field>
<absolute_tolerance>1.7e-13</absolute_tolerance>
<relative_tolerance>0.0 <!-- 1.7e-13 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>porosity</field>
<absolute_tolerance>2.8e-15</absolute_tolerance>
<relative_tolerance>0.0 <!-- 7e-15 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>porosity_avg</field>
<absolute_tolerance>2.2e-15</absolute_tolerance>
<relative_tolerance>0.0 <!-- 1.4e-15 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>porosity_ip</field>
<absolute_tolerance>2.2e-15</absolute_tolerance>
<relative_tolerance>0.0 <!-- 4.9e-15 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>pressure</field>
<absolute_tolerance>7e-06</absolute_tolerance>
<relative_tolerance>0.0 <!-- inf --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>pressure_interpolated</field>
<absolute_tolerance>7e-06</absolute_tolerance>
<relative_tolerance>0.0 <!-- inf --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>re</field>
<absolute_tolerance>1.9e-13</absolute_tolerance>
<relative_tolerance>0.0 <!-- 1.9e-13 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>relative_permeability_ip</field>
<absolute_tolerance>0.0</absolute_tolerance>
<relative_tolerance>0.0 <!-- 0.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>saturation</field>
<absolute_tolerance>2.5e-14</absolute_tolerance>
<relative_tolerance>0.0 <!-- 3.3e-14 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>saturation_avg</field>
<absolute_tolerance>8e-15</absolute_tolerance>
<relative_tolerance>0.0 <!-- 2.4e-14 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>saturation_ip</field>
<absolute_tolerance>2.8e-14</absolute_tolerance>
<relative_tolerance>0.0 <!-- 3.7e-14 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>sigma_total</field>
<absolute_tolerance>4.4e-07</absolute_tolerance>
<relative_tolerance>0.0 <!-- 28000.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>sigma_total_avg</field>
<absolute_tolerance>1.5e-07</absolute_tolerance>
<relative_tolerance>0.0 <!-- 600.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>sigma_total_ip</field>
<absolute_tolerance>4.5e-07</absolute_tolerance>
<relative_tolerance>0.0 <!-- 140000.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>temperature</field>
<absolute_tolerance>0.0</absolute_tolerance>
<relative_tolerance>0.0 <!-- 0.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>temperature_interpolated</field>
<absolute_tolerance>0.0</absolute_tolerance>
<relative_tolerance>0.0 <!-- 0.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>transport_porosity_ip</field>
<absolute_tolerance>2.2e-15</absolute_tolerance>
<relative_tolerance>0.0 <!-- 4.9e-15 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>velocity_ip</field>
<absolute_tolerance>8.8e-20</absolute_tolerance>
<relative_tolerance>0.0 <!-- inf --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>viscosity_avg</field>
<absolute_tolerance>0.0</absolute_tolerance>
<relative_tolerance>0.0 <!-- 0.0 --></relative_tolerance>
</vtkdiff>
<vtkdiff>
<regex>bentonite_column_ts_.*_t_.*_sec[.]vtu</regex>
<field>viscosity_ip</field>
<absolute_tolerance>0.0</absolute_tolerance>
<relative_tolerance>0.0 <!-- 0.0 --></relative_tolerance>
</vtkdiff>
</test_definition>
</OpenGeoSysProject>
Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/1d_column_resaturation/meshes 0 → 120000
+ 1
− 0
View file @ 1d8f61f2
../meshes_column/
\ No newline at end of file
Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/1d_column_resaturation/post.py 0 → 100755
+ 83
− 0
View file @ 1d8f61f2
#!/usr/bin/env python
from pathlib import Path
import numpy as np
from postprocessing_utils import (
IterPvd,
check_zero_and_constant_quantities,
extract_data,
is_checked_via_another_quantity,
plot_profiles,
plot_time_series,
select_profiles,
)
outdir = Path("out")
if not outdir.exists():
outdir.mkdir()
with (outdir / ".gitignore").open("w") as fh:
fh.write("*\n")
def run():
ts, line_mesh, dfs_aggregation, profiles = extract_data(
IterPvd("out/ogs/bentonite_column.pvd")
)
success, successfully_checked_quantities = check_zero_and_constant_quantities(
dfs_aggregation
)
ignored_quantities = {
"MaterialIDs",
"bulk_node_ids",
"bulk_element_ids",
"cell_ids",
"IntegrationPointMetaData",
"OGS_VERSION",
}
all_quantities = set(dfs_aggregation["min"].columns) - ignored_quantities
print("all quantities in the result meshes: ", sorted(all_quantities))
quantities_not_checked_via_another_quantity = {
q
for q in sorted(all_quantities)
if not is_checked_via_another_quantity(all_quantities, q)
}
assert quantities_not_checked_via_another_quantity
interesting_quantities = quantities_not_checked_via_another_quantity - set(
successfully_checked_quantities
)
plot_time_series(dfs_aggregation, interesting_quantities)
ts_filtered, profiles_filtered = select_profiles(
ts, profiles, ts[-1] * np.array([0, 0.01, 0.1, 0.25, 0.5, 0.75, 1.0])
)
profile_quantities = [
"sigma_total_avg[2]",
"epsilon_avg[2]",
"porosity_avg",
"saturation_avg",
"pressure_interpolated",
"displacement[2]",
]
plot_profiles(
ts_filtered,
line_mesh,
profiles_filtered,
profile_quantities,
"out/plot_profiles",
)
assert success
if __name__ == "__main__":
run()
Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/1d_column_resaturation/postprocessing_utils.py 0 → 100644
+ 280
− 0
View file @ 1d8f61f2
from pathlib import Path
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pyvista as pv
class IterPvd:
def __init__(self, pvd):
self._reader = pv.get_reader(pvd)
self._time_step = 0
def __iter__(self):
return self
def __next__(self):
if self._time_step == len(self.time_values):
raise StopIteration
self._reader.set_active_time_point(self._time_step)
mesh = self._reader.read()[0]
self._time_step += 1
return mesh
@property
def time_values(self):
return self._reader.time_values
class IterVtus:
def __init__(self, vtus, time_values):
assert len(vtus) == len(time_values)
self._vtus = vtus
self.time_values = time_values
self._time_step = 0
def __iter__(self):
return self
def __next__(self):
if self._time_step == len(self.time_values):
raise StopIteration
mesh = pv.read(self._vtus[self._time_step])
self._time_step += 1
return mesh
def extract_data(mesh_iterator, line_mesh=None):
ts = np.asarray(mesh_iterator.time_values)
profiles = []
agg_names = ["min", "max", "mean", "std"]
agg_fcts = [np.min, np.max, np.mean, np.std]
aggregations = {agg_n: [] for agg_n in agg_names}
for mesh in mesh_iterator:
# line profiles
if line_mesh is None:
bounds = np.array(mesh.bounds).reshape((3, -1))
center = np.mean(bounds, axis=1)
line_z = [
[center[0], center[1], bounds[2, 0]],
[center[0], center[1], bounds[2, 1]],
]
line_mesh = pv.Line(*line_z, resolution=1000)
profile = line_mesh.sample(mesh)
profiles.append(profile.point_data)
# aggregations
for agg_n, agg_f in zip(agg_names, agg_fcts):
agg_rec = {}
for n in mesh.array_names:
d = mesh.get_array(n)
d_agg = agg_f(d, axis=0)
if np.size(d_agg) == 1:
agg_rec[n] = d_agg
else:
for comp, v in enumerate(d_agg):
agg_rec[f"{n}[{comp}]"] = v
aggregations[agg_n].append(agg_rec)
dfs_aggregation = {}
for agg_n, agg_recs in aggregations.items():
dfs_aggregation[agg_n] = pd.DataFrame.from_records(
agg_recs, index=pd.Index(ts, name="time")
)
dfs_aggregation[agg_n]["time"] = ts
return ts, line_mesh, dfs_aggregation, profiles
def plot_time_series(dfs_aggregation, quantities=None):
plot_path = Path("out/plot_agg")
plot_path.mkdir(exist_ok=True)
if quantities is None:
quantities = dfs_aggregation["min"].columns
for qty_name in quantities:
qty_series = dfs_aggregation["min"][qty_name]
if qty_name == "time":
continue
n_comp = np.size(qty_series.iloc[0])
assert n_comp == 1 # components separated during reading
fig, ax = plt.subplots()
for agg_n in ["min", "max", "mean"]:
df_agg = dfs_aggregation[agg_n]
df_agg.plot("time", qty_name, ax=ax, label=agg_n)
ax.set_title(qty_name)
fig.savefig(plot_path / f"time_series_{qty_name}.png")
plt.close(fig)
def check_quantity(quantity, dfs_aggregation, checked_quantities, value, abstol):
success = True
for agg_n in ("min", "max"):
df_agg = dfs_aggregation[agg_n]
s = np.allclose(value, df_agg[quantity], atol=abstol, rtol=0)
if not s:
success = False
print(f"Error: check failed: {quantity} != {value} +/i {abstol} ({agg_n})")
if success:
print(f"all({quantity} = {value} ± {abstol})")
if success:
checked_quantities.append(quantity)
return success
def check_zero_and_constant_quantities(dfs_aggregation):
cqs = [] # checked quantities
dfs = dfs_aggregation
s = True # success
s &= check_quantity("displacement[0]", dfs, cqs, 0, 1e-15)
s &= check_quantity("displacement[1]", dfs, cqs, 0, 1e-15)
s &= check_quantity("epsilon_ip[0]", dfs, cqs, 0, 1e-15)
s &= check_quantity("epsilon_ip[1]", dfs, cqs, 0, 1e-15)
s &= check_quantity("epsilon_ip[3]", dfs, cqs, 0, 1e-15)
s &= check_quantity("epsilon_ip[4]", dfs, cqs, 0, 1e-15)
s &= check_quantity("epsilon_ip[5]", dfs, cqs, 0, 1e-15)
s &= check_quantity("intrinsic_permeability_ip[0]", dfs, cqs, 3e-20, 1e-30)
s &= check_quantity("intrinsic_permeability_ip[1]", dfs, cqs, 0, 1e-30)
s &= check_quantity("intrinsic_permeability_ip[2]", dfs, cqs, 0, 1e-30)
s &= check_quantity("intrinsic_permeability_ip[3]", dfs, cqs, 0, 1e-30)
s &= check_quantity("intrinsic_permeability_ip[4]", dfs, cqs, 3e-20, 1e-30)
s &= check_quantity("intrinsic_permeability_ip[5]", dfs, cqs, 0, 1e-30)
s &= check_quantity("intrinsic_permeability_ip[6]", dfs, cqs, 0, 1e-30)
s &= check_quantity("intrinsic_permeability_ip[7]", dfs, cqs, 0, 1e-30)
s &= check_quantity("intrinsic_permeability_ip[8]", dfs, cqs, 3e-20, 1e-30)
s &= check_quantity("relative_permeability_ip", dfs, cqs, 1, 1e-15)
s &= check_quantity("sigma_total_ip[3]", dfs, cqs, 0, 1e-7)
s &= check_quantity("sigma_total_ip[4]", dfs, cqs, 0, 1e-7)
s &= check_quantity("sigma_total_ip[5]", dfs, cqs, 0, 1e-7)
s &= check_quantity("velocity_ip[0]", dfs, cqs, 0, 1e-19)
s &= check_quantity("velocity_ip[1]", dfs, cqs, 0, 1e-19)
s &= check_quantity("viscosity_ip", dfs, cqs, 0.0018, 1e-15)
s &= check_quantity("temperature_interpolated", dfs, cqs, 298.15, 1e-13)
s &= check_quantity("liquid_density_ip", dfs, cqs, 1000, 1e-10)
s &= check_quantity("HeatFlowRate", dfs, cqs, 0, 1e-15)
return s, cqs
# Cf. https://stackoverflow.com/a/26026189
def find_nearest_sorted(array, value):
idx = np.searchsorted(array, value, side="left")
if idx > 0 and (
idx == len(array) or np.abs(value - array[idx - 1]) < np.abs(value - array[idx])
):
return idx - 1
return idx
def select_profiles(ts, profiles, ts_selected):
idcs = np.array([find_nearest_sorted(ts, t) for t in ts_selected])
return ts[idcs], [profiles[i] for i in idcs]
def plot_profiles(ts, line_mesh, profiles, quantities, out_dir, profiles_ref=None):
out_dir = Path(out_dir)
out_dir.mkdir(exist_ok=True)
coords = line_mesh.points[:, 2]
for qty in quantities:
if qty.endswith("]"):
assert qty[-3] == "["
qty_name = qty[:-3]
comp = int(qty[-2])
else:
qty_name = qty
comp = None
if profiles_ref is None:
fig, ax = plt.subplots()
axs = [ax]
else:
fig, axs = plt.subplots(2, sharex=True)
ax = axs[0]
for a in axs:
a.set_prop_cycle(color=mpl.colormaps["rainbow"](np.linspace(0, 1, len(ts))))
for ti, (t, prof) in enumerate(zip(ts, profiles)):
qty_values = prof[qty_name] if comp is None else prof[qty_name][:, comp]
(h,) = ax.plot(
coords,
qty_values,
label=f"$t$ = {t:.3g} s",
)
if profiles_ref is not None:
prof_ref = profiles_ref[ti]
qty_ref_values = (
prof_ref[qty_name] if comp is None else prof_ref[qty_name][:, comp]
)
ax.plot(
coords,
qty_ref_values,
color=h.get_color(),
label="ref" if ti == len(ts) - 1 else None,
ls="--",
linewidth=3,
)
axs[-1].plot(
coords, qty_values - qty_ref_values, label=f"$t$ = {t:.3g} s"
)
for a in axs:
a.legend(loc="upper left", bbox_to_anchor=(1, 1))
axs[-1].set_xlabel("$z$ / m")
ax.set_title(qty)
if profiles_ref is not None:
axs[-1].set_ylabel("actual - reference")
fig.set_size_inches(8, 5)
fig.subplots_adjust(right=0.75)
fig.savefig(out_dir / f"profile_{qty}.png", dpi=200)
plt.close(fig)
def is_checked_via_another_quantity(all_quantities, q):
for q2 in [
q.replace("_avg", "_ip"),
q + "_ip",
q + "_interpolated",
q.replace("[", "_ip["),
]:
if q2 != q and q2 in all_quantities:
break
else:
return False
print(f"{q} is already checked via {q2}")
return True
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