<OpenGeoSysProject>
  <meshes>
    <mesh>bulk.vtu</mesh>
    <mesh>Left.vtu</mesh>
    <mesh>Right.vtu</mesh>
  </meshes>
  <overwrite_mesh_data>
    <remove>
      <field_name>cell_centres</field_name>
      <mesh_item_type>cell</mesh_item_type>
    </remove>
    <set>
      <field_name>sigma_ip</field_name>
      <mesh_item_type>integration_point</mesh_item_type>
      <material_ids>1 2</material_ids>
      <parameter_name>sigma_bent</parameter_name>
    </set>
    <set>
      <field_name>temperature</field_name>
      <mesh_item_type>node</mesh_item_type>
      <material_ids>1</material_ids>
      <parameter_name>temp_inner1</parameter_name>
    </set>
    <take_original>
      <field_name>temperature</field_name>
      <mesh_item_type>node</mesh_item_type>
      <material_ids>0</material_ids>
    </take_original>
    <set>
      <field_name>temperature</field_name>
      <mesh_item_type>node</mesh_item_type>
      <material_ids>2</material_ids>
      <parameter_name>temp_inner2</parameter_name>
    </set>
    <set>
      <field_name>porosity_avg</field_name>
      <mesh_item_type>cell</mesh_item_type>
      <material_ids>0:2</material_ids>
      <parameter_name>porosity_clay</parameter_name>
    </set>
    <set>
      <field_name>p_left</field_name>
      <mesh>Left</mesh>
      <mesh_item_type>node</mesh_item_type>
      <parameter_name>u_bc</parameter_name>
    </set>
  </overwrite_mesh_data>
  <processes>
    <process>
      <name>SD</name>
      <type>SMALL_DEFORMATION</type>
      <integration_order>2</integration_order>
      <constitutive_relation>
        <type>LinearElasticIsotropic</type>
        <youngs_modulus>E</youngs_modulus>
        <poissons_ratio>nu</poissons_ratio>
      </constitutive_relation>
      <specific_body_force>0 0</specific_body_force>
      <process_variables>
        <process_variable>displacement</process_variable>
      </process_variables>
      <secondary_variables>
        <secondary_variable name="sigma" />
      </secondary_variables>
    </process>
  </processes>
  <time_loop>
    <processes>
      <process ref="SD">
        <nonlinear_solver>basic_newton</nonlinear_solver>
        <convergence_criterion>
          <type>DeltaX</type>
          <norm_type>NORM2</norm_type>
          <reltol>1e-12</reltol>
        </convergence_criterion>
        <time_discretization>
          <type>BackwardEuler</type>
        </time_discretization>
        <time_stepping>
          <type>FixedTimeStepping</type>
          <t_initial>0</t_initial>
          <t_end>1</t_end>
          <timesteps>
            <pair>
              <repeat>1</repeat>
              <delta_t>1</delta_t>
            </pair>
          </timesteps>
        </time_stepping>
      </process>
    </processes>
    <output>
      <type>VTK</type>
      <prefix>overwrite_mesh_data</prefix>
      <timesteps>
        <pair>
          <repeat>1</repeat>
          <each_steps>10000000</each_steps>
        </pair>
      </timesteps>
      <variables>
        <variable>sigma</variable>
        <variable>displacement</variable>
        <variable>porosity_avg</variable>
        <variable>temperature</variable>
      </variables>
      <suffix>ts{:timestep}_t_{:time}</suffix>
    </output>
  </time_loop>
  <media>
    <medium id="0:2">
      <phases>
        <phase>
          <type>Solid</type>
          <properties>
            <property>
              <name>density</name>
              <type>Constant</type>
              <value>3000</value>
            </property>
          </properties>
        </phase>
      </phases>
    </medium>
  </media>
  <parameters>
    <parameter>
      <name>E</name>
      <type>Constant</type>
      <value>1e11</value>
    </parameter>
    <parameter>
      <name>nu</name>
      <type>Constant</type>
      <value>.3</value>
    </parameter>
    <parameter>
      <name>displacement0</name>
      <type>Constant</type>
      <values>0 0</values>
    </parameter>
    <parameter>
      <name>dirichlet0</name>
      <type>Constant</type>
      <value>0</value>
    </parameter>
    <parameter>
      <name>neumann_force</name>
      <type>Constant</type>
      <values>0.01</values>
    </parameter>
    <parameter>
      <name>temp_inner1</name>
      <type>Constant</type>
      <value>310</value>
    </parameter>
    <parameter>
      <name>temp_inner2</name>
      <type>Constant</type>
      <value>320</value>
    </parameter>
    <parameter>
      <name>sigma_bent</name>
      <type>Constant</type>
      <values>1e5 1e5 1e5 0.0</values>
    </parameter>
    <parameter>
      <name>porosity_clay</name>
      <type>Function</type>
      <expression>0.1*sin(x)+0.1*sin(y)+0.3</expression>
    </parameter>
    <parameter>
      <name>u_bc</name>
      <type>Function</type>
      <expression>sin(y/50*6*3.14)*1e-3</expression>
    </parameter>
    <parameter>
      <name>u_left</name>
      <mesh>Left</mesh>
      <type>MeshNode</type>
      <field_name>p_left</field_name>
    </parameter>
  </parameters>
  <process_variables>
    <process_variable>
      <name>displacement</name>
      <components>2</components>
      <order>1</order>
      <initial_condition>displacement0</initial_condition>
      <boundary_conditions>
        <boundary_condition>
          <mesh>Left</mesh>
          <type>Dirichlet</type>
          <component>0</component>
          <parameter>u_left</parameter>
        </boundary_condition>
        <boundary_condition>
          <mesh>Right</mesh>
          <type>Dirichlet</type>
          <component>0</component>
          <parameter>dirichlet0</parameter>
        </boundary_condition>
        <boundary_condition>
          <mesh>Right</mesh>
          <type>Dirichlet</type>
          <component>1</component>
          <parameter>dirichlet0</parameter>
        </boundary_condition>
      </boundary_conditions>
    </process_variable>
  </process_variables>
  <nonlinear_solvers>
    <nonlinear_solver>
      <name>basic_newton</name>
      <type>Newton</type>
      <max_iter>5</max_iter>
      <linear_solver>general_linear_solver</linear_solver>
    </nonlinear_solver>
  </nonlinear_solvers>
  <linear_solvers>
    <linear_solver>
      <name>general_linear_solver</name>
      <lis>-i cg -p jacobi -tol 1e-16 -maxiter 10000</lis>
      <eigen>
        <solver_type>CG</solver_type>
        <precon_type>DIAGONAL</precon_type>
        <max_iteration_step>10000</max_iteration_step>
        <error_tolerance>1e-16</error_tolerance>
      </eigen>
      <petsc>
        <prefix>sd</prefix>
        <parameters>-sd_ksp_type cg -sd_pc_type bjacobi -sd_ksp_rtol 1e-16 -sd_ksp_max_it 10000</parameters>
      </petsc>
    </linear_solver>
  </linear_solvers>
  <test_definition>
    <vtkdiff>
      <file>overwrite_mesh_data_ts_0_t_0.000000.vtu</file>
      <field>sigma</field>
      <absolute_tolerance>2e-7</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
    <vtkdiff>
      <file>overwrite_mesh_data_ts_0_t_0.000000.vtu</file>
      <field>temperature</field>
      <absolute_tolerance>1e-15</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
    <vtkdiff>
      <file>overwrite_mesh_data_ts_0_t_0.000000.vtu</file>
      <field>porosity_avg</field>
      <absolute_tolerance>1e-15</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
    <vtkdiff>
      <file>overwrite_mesh_data_ts_0_t_0.000000.vtu</file>
      <field>displacement</field>
      <absolute_tolerance>1e-15</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
    <vtkdiff>
      <file>overwrite_mesh_data_ts_1_t_1.000000.vtu</file>
      <field>displacement</field>
      <absolute_tolerance>1e-12</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
    <vtkdiff>
      <file>overwrite_mesh_data_ts_1_t_1.000000.vtu</file>
      <field>sigma</field>
      <absolute_tolerance>2e-7</absolute_tolerance>
      <relative_tolerance>0</relative_tolerance>
    </vtkdiff>
  </test_definition>
</OpenGeoSysProject>