1d_vertical_test.prj

<OpenGeoSysProject>
  <meshes>
    <mesh>1d_vertical_test_mid_fine_ReactionDomain.vtu</mesh>
    <mesh>1d_vertical_test_bc_top.vtu</mesh>
    <mesh>1d_vertical_test_bc_bot.vtu</mesh>
  </meshes>
  <processes>
    <process>
      <name>hc</name>
      <type>ComponentTransport</type>
      <integration_order>2</integration_order>
      <coupling_scheme>staggered</coupling_scheme>
      <process_variables>
        <pressure>pressure</pressure>
        <concentration>I</concentration>
        <concentration>H</concentration>
      </process_variables>
      <secondary_variables />
      <specific_body_force>0 0 0</specific_body_force>
    </process>
  </processes>
  <media>
    <medium id="0">
      <phases>
        <phase>
          <type>AqueousLiquid</type>
          <components>
            <component>
              <name>I</name>
              <properties>
                <property>
                  <name>pore_diffusion</name>
                  <type>Parameter</type>
                  <parameter_name>Diff</parameter_name>
                </property>
                <property>
                  <name>retardation_factor</name>
                  <type>Constant</type>
                  <value>1</value>
                </property>
                <property>
                  <name>decay_rate</name>
                  <type>Constant</type>
                  <value>0</value>
                </property>
              </properties>
            </component>
            <component>
              <name>H</name>
              <properties>
                <property>
                  <name>pore_diffusion</name>
                  <type>Constant</type>
                  <value>1e-9</value>
                </property>
                <property>
                  <name>retardation_factor</name>
                  <type>Constant</type>
                  <value>1</value>
                </property>
                <property>
                  <name>decay_rate</name>
                  <type>Parameter</type>
                  <parameter_name>decay</parameter_name>
                </property>
              </properties>
            </component>
          </components>
          <properties>
            <property>
              <name>density</name>
              <type>Constant</type>
              <value>1e3</value>
            </property>
            <property>
              <name>viscosity</name>
              <type>Constant</type>
              <value>1e-3</value>
            </property>
          </properties>
        </phase>
        <phase>
          <type>Solid</type>
          <components>
            <component>
              <name>Calcite</name>
              <properties>
                <property>
                  <name>molality</name>
                  <type>Constant</type>
                  <value>10</value>
                </property>
              </properties>
            </component>
            <component>
              <name>Decay_UO2</name>
              <properties>
                <property>
                  <name>molality</name>
                  <type>Parameter</type>
                  <parameter_name>cU238_mol_per_L_ic</parameter_name>
                </property>
              </properties>
            </component>
            <component>
              <name>Decay_I</name>
              <properties>
                <property>
                  <name>molality</name>
                  <type>Constant</type>
                  <value>1</value>
                </property>
              </properties>
            </component>
          </components>
        </phase>
      </phases>
      <properties>
        <property>
          <name>permeability</name>
          <type>Parameter</type>
          <parameter_name>kappa</parameter_name>
        </property>
        <property>
          <name>porosity</name>
          <type>Parameter</type>
          <parameter_name>porosity</parameter_name>
        </property>
        <property>
          <name>longitudinal_dispersivity</name>
          <type>Constant</type>
          <value>0</value>
        </property>
        <property>
          <name>transversal_dispersivity</name>
          <type>Constant</type>
          <value>0</value>
        </property>
      </properties>
    </medium>
  </media>
  <time_loop>
    <global_process_coupling>
      <max_iter>6</max_iter>
      <convergence_criteria>
        <convergence_criterion>
          <type>DeltaX</type>
          <norm_type>NORM2</norm_type>
          <reltol>1e-13</reltol>
        </convergence_criterion>
        <convergence_criterion>
          <type>DeltaX</type>
          <norm_type>NORM2</norm_type>
          <reltol>1e-13</reltol>
        </convergence_criterion>
        <convergence_criterion>
          <type>DeltaX</type>
          <norm_type>NORM2</norm_type>
          <reltol>1e-13</reltol>
        </convergence_criterion>
      </convergence_criteria>
    </global_process_coupling>
    <processes>
      <process ref="hc">
        <nonlinear_solver>basic_picard</nonlinear_solver>
        <convergence_criterion>
          <type>DeltaX</type>
          <norm_type>NORM2</norm_type>
          <reltol>1e-13</reltol>
        </convergence_criterion>
        <time_discretization>
          <type>BackwardEuler</type>
        </time_discretization>
        <time_stepping>
          <type>FixedTimeStepping</type>
          <t_initial>0.0</t_initial>
          <t_end>5e11</t_end>
          <timesteps>
            <pair>
              <repeat>100000</repeat>
              <delta_t>5e11</delta_t>
            </pair>
          </timesteps>
        </time_stepping>
      </process>
      <process ref="hc">
        <nonlinear_solver>basic_picard</nonlinear_solver>
        <convergence_criterion>
          <type>DeltaX</type>
          <norm_type>NORM2</norm_type>
          <reltol>1e-13</reltol>
        </convergence_criterion>
        <time_discretization>
          <type>BackwardEuler</type>
        </time_discretization>
        <time_stepping>
          <type>FixedTimeStepping</type>
          <t_initial>0.0</t_initial>
          <t_end>5e11</t_end>
          <timesteps>
            <pair>
              <repeat>100000</repeat>
              <delta_t>5e11</delta_t>
            </pair>
          </timesteps>
        </time_stepping>
      </process>
      <process ref="hc">
        <nonlinear_solver>basic_picard</nonlinear_solver>
        <convergence_criterion>
          <type>DeltaX</type>
          <norm_type>NORM2</norm_type>
          <reltol>1e-13</reltol>
        </convergence_criterion>
        <time_discretization>
          <type>BackwardEuler</type>
        </time_discretization>
        <time_stepping>
          <type>FixedTimeStepping</type>
          <t_initial>0.0</t_initial>
          <t_end>5e11</t_end>
          <timesteps>
            <pair>
              <repeat>100000</repeat>
              <delta_t>5e11</delta_t>
            </pair>
          </timesteps>
        </time_stepping>
      </process>
    </processes>
    <output>
      <type>VTK</type>
      <prefix>1d_vertical_test</prefix>
      <suffix>ts{:timestep}_t_{:.3gtime}</suffix>
      <timesteps>
        <pair>
          <repeat>10000</repeat>
          <each_steps>1</each_steps>
        </pair>
      </timesteps>
      <variables />
      <output_extrapolation_residuals>true</output_extrapolation_residuals>
    </output>
  </time_loop>
  <chemical_system chemical_solver="Phreeqc">
    <mesh>1d_vertical_test_mid_fine_ReactionDomain</mesh>
    <linear_solver>general_linear_solver</linear_solver>
    <database>PSINA_12_07_110615_DAV_s_hzdr.dat</database>
    <solution>
      <temperature>14</temperature>
      <pressure>1</pressure>
      <pe>4</pe>
      <components>
        <component>I</component>
      </components>
    </solution>
    <kinetic_reactants>
      <kinetic_reactant>
        <name>Decay_UO2</name>
        <chemical_formula>I 2.398e-9</chemical_formula>
      </kinetic_reactant>
      <kinetic_reactant>
        <name>Decay_I</name>
        <chemical_formula>I -1</chemical_formula>
      </kinetic_reactant>
    </kinetic_reactants>
    <rates>
      <rate>
        <kinetic_reactant>Decay_UO2</kinetic_reactant>
        <expression>
          <statement>rate = 4.915937450779754e-18 * M</statement>
          <statement>moles = rate * TIME</statement>
          <statement>save moles</statement>
        </expression>
      </rate>
      <rate>
        <kinetic_reactant>Decay_I</kinetic_reactant>
        <expression>
          <statement>rate = 1.3995114095699806e-15 * TOT("I")</statement>
          <statement>moles = rate * TIME</statement>
          <statement>save moles</statement>
        </expression>
      </rate>
    </rates>
    <knobs>
      <max_iter>200</max_iter>
      <relative_convergence_tolerance>1e-6</relative_convergence_tolerance>
      <tolerance>1e-20</tolerance>
      <step_size>5</step_size>
      <scaling>1</scaling>
    </knobs>
  </chemical_system>
  <parameters>
    <parameter>
      <name>Diff</name>
      <type>Constant</type>
      <values>5e-13</values>
    </parameter>
    <parameter>
      <name>kappa</name>
      <type>Constant</type>
      <values>1e-20</values>
    </parameter>
    <parameter>
      <name>porosity</name>
      <type>Constant</type>
      <value>0.1</value>
    </parameter>
    <parameter>
      <name>decay</name>
      <type>Constant</type>
      <value>0</value>
    </parameter>
    <parameter>
      <name>p0</name>
      <type>Constant</type>
      <value>1e5</value>
    </parameter>
    <parameter>
      <name>c0_default</name>
      <type>Constant</type>
      <value>0</value>
    </parameter>
    <parameter>
      <name>cI(0)</name>
      <type>Constant</type>
      <value>1e-20</value>
    </parameter>
    <parameter>
      <name>c0_H</name>
      <type>Constant</type>
      <value>1e-7</value>
    </parameter>
    <parameter>
      <name>cU238_mol_per_L_ic</name>
      <type>Function</type>
      <expression>var cU238_mol_per_L_max := 180.1;
            var z0 := 3.759e-1;
            var sigma := 1.724;
            cU238_mol_per_L_max * exp(-(z-z0)^2/(2*sigma^2)) - x - y;</expression>
    </parameter>
  </parameters>
  <process_variables>
    <process_variable>
      <name>pressure</name>
      <components>1</components>
      <order>1</order>
      <initial_condition>p0</initial_condition>
      <boundary_conditions>
        <boundary_condition>
          <mesh>1d_vertical_test_bc_top</mesh>
          <type>Dirichlet</type>
          <parameter>p0</parameter>
        </boundary_condition>
        <boundary_condition>
          <mesh>1d_vertical_test_bc_bot</mesh>
          <type>Dirichlet</type>
          <parameter>p0</parameter>
        </boundary_condition>
      </boundary_conditions>
    </process_variable>
    <process_variable>
      <name>I</name>
      <components>1</components>
      <order>1</order>
      <initial_condition>cI(0)</initial_condition>
      <boundary_conditions>
        <boundary_condition>
          <mesh>1d_vertical_test_bc_top</mesh>
          <type>Dirichlet</type>
          <parameter>cI(0)</parameter>
        </boundary_condition>
        <boundary_condition>
          <mesh>1d_vertical_test_bc_bot</mesh>
          <type>Dirichlet</type>
          <parameter>cI(0)</parameter>
        </boundary_condition>
      </boundary_conditions>
    </process_variable>
    <process_variable>
      <name>H</name>
      <components>1</components>
      <order>1</order>
      <initial_condition>c0_H</initial_condition>
      <boundary_conditions>
        <boundary_condition>
          <mesh>1d_vertical_test_bc_top</mesh>
          <type>Dirichlet</type>
          <parameter>c0_H</parameter>
        </boundary_condition>
        <boundary_condition>
          <mesh>1d_vertical_test_bc_top</mesh>
          <type>Dirichlet</type>
          <parameter>c0_H</parameter>
        </boundary_condition>
      </boundary_conditions>
    </process_variable>
  </process_variables>
  <nonlinear_solvers>
    <nonlinear_solver>
      <name>basic_picard</name>
      <type>Picard</type>
      <max_iter>20</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>
        <scaling>true</scaling>
        <max_iteration_step>10000</max_iteration_step>
        <error_tolerance>1e-14</error_tolerance>
      </eigen>
      <petsc>
        <prefix>hc</prefix>
        <parameters>-hc_ksp_type bcgs -hc_pc_type bjacobi -hc_ksp_rtol 1e-8 -hc_ksp_max_it 20000</parameters>
      </petsc>
    </linear_solver>
  </linear_solvers>
  <test_definition>
    <vtkdiff>
      <file>1d_vertical_test_ts_0_t_0.vtu</file>
      <field>I</field>
      <absolute_tolerance>9e-25</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
    <vtkdiff>
      <file>1d_vertical_test_ts_0_t_0.vtu</file>
      <field>H</field>
      <absolute_tolerance>2e-22</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
    <vtkdiff>
      <file>1d_vertical_test_ts_0_t_0.vtu</file>
      <field>pressure</field>
      <absolute_tolerance>2e-9</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
    <vtkdiff>
      <file>1d_vertical_test_ts_1_t_5e+11.vtu</file>
      <field>Decay_UO2</field>
      <absolute_tolerance>2e-17</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
    <vtkdiff>
      <file>1d_vertical_test_ts_1_t_5e+11.vtu</file>
      <field>I</field>
      <absolute_tolerance>9e-25</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
    <vtkdiff>
      <file>1d_vertical_test_ts_1_t_5e+11.vtu</file>
      <field>H</field>
      <absolute_tolerance>2e-22</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
    <vtkdiff>
      <file>1d_vertical_test_ts_1_t_5e+11.vtu</file>
      <field>pressure</field>
      <absolute_tolerance>2e-9</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
  </test_definition>
</OpenGeoSysProject>