calcite.prj 26.4 KB
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<?xml version="1.0" encoding="ISO-8859-1"?>
<OpenGeoSysProject>
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    <meshes>
        <mesh>calcite.vtu</mesh>
        <mesh>calcite_upstream.vtu</mesh>
        <mesh>calcite_downstream.vtu</mesh>
        <mesh>calcite_ReactiveDomain.vtu</mesh>
    </meshes>
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    <processes>
        <process>
            <name>hc</name>
            <type>ComponentTransport</type>
            <integration_order>2</integration_order>
            <coupling_scheme>staggered</coupling_scheme>
            <process_variables>
                <concentration>C(4)</concentration>
                <concentration>Ca</concentration>
                <concentration>Mg</concentration>
                <concentration>Cl</concentration>
                <concentration>H</concentration>
                <pressure>pressure</pressure>
            </process_variables>
            <specific_body_force>0 0</specific_body_force>
            <secondary_variables>
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                <secondary_variable internal_name="darcy_velocity" output_name="darcy_velocity"/>
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            </secondary_variables>
        </process>
    </processes>
    <media>
        <medium id="0">
            <phases>
                <phase>
                    <type>AqueousLiquid</type>
                    <components>
                        <component>
                            <name>C(4)</name>
                            <properties>
                                <property>
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                                    <name>pore_diffusion</name>
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                                    <type>Constant</type>
                                    <value>0</value>
                                </property>
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                                <property>
                                    <name>retardation_factor</name>
                                    <type>Constant</type>
                                    <value>1</value>
                                </property>
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                                <property>
                                    <name>decay_rate</name>
                                    <type>Parameter</type>
                                    <parameter_name>decay</parameter_name>
                                </property>
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                            </properties>
                        </component>
                        <component>
                            <name>Ca</name>
                            <properties>
                                <property>
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                                    <name>pore_diffusion</name>
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                                    <type>Constant</type>
                                    <value>0</value>
                                </property>
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                                <property>
                                    <name>retardation_factor</name>
                                    <type>Constant</type>
                                    <value>1</value>
                                </property>
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                                <property>
                                    <name>decay_rate</name>
                                    <type>Parameter</type>
                                    <parameter_name>decay</parameter_name>
                                </property>
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                            </properties>
                        </component>
                        <component>
                            <name>Mg</name>
                            <properties>
                                <property>
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                                    <name>pore_diffusion</name>
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                                    <type>Constant</type>
                                    <value>0</value>
                                </property>
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                                <property>
                                    <name>retardation_factor</name>
                                    <type>Constant</type>
                                    <value>1</value>
                                </property>
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                                <property>
                                    <name>decay_rate</name>
                                    <type>Parameter</type>
                                    <parameter_name>decay</parameter_name>
                                </property>
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                            </properties>
                        </component>
                        <component>
                            <name>Cl</name>
                            <properties>
                                <property>
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                                    <name>pore_diffusion</name>
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                                    <type>Constant</type>
                                    <value>0</value>
                                </property>
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                                <property>
                                    <name>retardation_factor</name>
                                    <type>Constant</type>
                                    <value>1</value>
                                </property>
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                                <property>
                                    <name>decay_rate</name>
                                    <type>Parameter</type>
                                    <parameter_name>decay</parameter_name>
                                </property>
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                            </properties>
                        </component>
                        <component>
                            <name>H</name>
                            <properties>
                                <property>
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                                    <name>pore_diffusion</name>
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                                    <type>Constant</type>
                                    <value>0</value>
                                </property>
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                                <property>
                                    <name>retardation_factor</name>
                                    <type>Constant</type>
                                    <value>1</value>
                                </property>
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                                <property>
                                    <name>decay_rate</name>
                                    <type>Parameter</type>
                                    <parameter_name>decay</parameter_name>
                                </property>
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                            </properties>
                        </component>
                    </components>
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                    <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>
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                </phase>
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                <phase>
                    <type>Solid</type>
                    <components>
                        <component>
                            <name>Calcite</name>
                            <properties>
                                <property>
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                                    <name>molality</name>
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                                    <type>Constant</type>
                                    <value>2.07e-4</value>
                                </property>
                            </properties>
                        </component>
                        <component>
                            <name>Dolomite(dis)</name>
                            <properties>
                                <property>
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                                    <name>molality</name>
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                                    <type>Constant</type>
                                    <value>1e-10</value>
                                </property>
                            </properties>
                        </component>
                    </components>
                </phase>
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            </phases>
            <properties>
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                <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>
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                <property>
                    <name>longitudinal_dispersivity</name>
                    <type>Constant</type>
                    <value>0.0067</value>
                </property>
                <property>
                    <name>transversal_dispersivity</name>
                    <type>Constant</type>
                    <value>0.1</value>
                </property>
            </properties>
        </medium>
    </media>
    <time_loop>
        <global_process_coupling>
            <max_iter>6</max_iter>
            <convergence_criteria>
                <!-- convergence criterion for the first process (p) -->
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
                <!-- convergence criterion for the second process (C(4)) -->
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
                <!-- convergence criterion for the second process (Ca) -->
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
                <!-- convergence criterion for the second process (Mg) -->
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
                <!-- convergence criterion for the second process (Cl) -->
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
                <!-- convergence criterion for the second process (H) -->
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
            </convergence_criteria>
        </global_process_coupling>
        <processes>
            <!-- convergence criterion for hydraulic equation -->
            <process ref="hc">
                <nonlinear_solver>basic_picard</nonlinear_solver>
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
                <time_discretization>
                    <type>BackwardEuler</type>
                </time_discretization>
                <time_stepping>
                    <type>FixedTimeStepping</type>
                    <t_initial>0.0</t_initial>
                    <t_end>21000</t_end>
                    <timesteps>
                        <pair>
                            <repeat>210</repeat>
                            <delta_t>100</delta_t>
                        </pair>
                    </timesteps>
                </time_stepping>
            </process>
            <!-- convergence criterion for component transport equation (C(4)) -->
            <process ref="hc">
                <nonlinear_solver>basic_picard</nonlinear_solver>
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
                <time_discretization>
                    <type>BackwardEuler</type>
                </time_discretization>
                <time_stepping>
                    <type>FixedTimeStepping</type>
                    <t_initial>0.0</t_initial>
                    <t_end>21000</t_end>
                    <timesteps>
                        <pair>
                            <repeat>210</repeat>
                            <delta_t>100</delta_t>
                        </pair>
                    </timesteps>
                </time_stepping>
            </process>
            <!-- convergence criterion for component transport equation (Ca) -->
            <process ref="hc">
                <nonlinear_solver>basic_picard</nonlinear_solver>
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
                <time_discretization>
                    <type>BackwardEuler</type>
                </time_discretization>
                <time_stepping>
                    <type>FixedTimeStepping</type>
                    <t_initial>0.0</t_initial>
                    <t_end>21000</t_end>
                    <timesteps>
                        <pair>
                            <repeat>210</repeat>
                            <delta_t>100</delta_t>
                        </pair>
                    </timesteps>
                </time_stepping>
            </process>
            <!-- convergence criterion for component transport equation (Mg) -->
            <process ref="hc">
                <nonlinear_solver>basic_picard</nonlinear_solver>
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
                <time_discretization>
                    <type>BackwardEuler</type>
                </time_discretization>
                <time_stepping>
                    <type>FixedTimeStepping</type>
                    <t_initial>0.0</t_initial>
                    <t_end>21000</t_end>
                    <timesteps>
                        <pair>
                            <repeat>210</repeat>
                            <delta_t>100</delta_t>
                        </pair>
                    </timesteps>
                </time_stepping>
            </process>
            <!-- convergence criterion for component transport equation (Cl) -->
            <process ref="hc">
                <nonlinear_solver>basic_picard</nonlinear_solver>
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
                <time_discretization>
                    <type>BackwardEuler</type>
                </time_discretization>
                <time_stepping>
                    <type>FixedTimeStepping</type>
                    <t_initial>0.0</t_initial>
                    <t_end>21000</t_end>
                    <timesteps>
                        <pair>
                            <repeat>210</repeat>
                            <delta_t>100</delta_t>
                        </pair>
                    </timesteps>
                </time_stepping>
            </process>
            <!-- convergence criterion for component transport equation (H) -->
            <process ref="hc">
                <nonlinear_solver>basic_picard</nonlinear_solver>
                <convergence_criterion>
                    <type>DeltaX</type>
                    <norm_type>NORM2</norm_type>
                    <reltol>1e-14</reltol>
                </convergence_criterion>
                <time_discretization>
                    <type>BackwardEuler</type>
                </time_discretization>
                <time_stepping>
                    <type>FixedTimeStepping</type>
                    <t_initial>0.0</t_initial>
                    <t_end>21000</t_end>
                    <timesteps>
                        <pair>
                            <repeat>210</repeat>
                            <delta_t>100</delta_t>
                        </pair>
                    </timesteps>
                </time_stepping>
            </process>
        </processes>
        <output>
            <type>VTK</type>
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            <prefix>calcite</prefix>
            <suffix>_ts_{:timestep}_t_{:time}</suffix>
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            <timesteps>
                <pair>
                    <repeat>5</repeat>
                    <each_steps>42</each_steps>
                </pair>
            </timesteps>
            <variables>
                <variable>C(4)</variable>
                <variable>Ca</variable>
                <variable>Mg</variable>
                <variable>Cl</variable>
                <variable>H</variable>
                <variable>pressure</variable>
                <variable>darcy_velocity</variable>
            </variables>
        </output>
    </time_loop>
    <chemical_system chemical_solver="Phreeqc">
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        <mesh>calcite_ReactiveDomain</mesh>
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        <linear_solver>general_linear_solver</linear_solver>
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        <database>PSINA_12_07_110615_DAV_s.dat</database>
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        <solution>
            <temperature>25</temperature>
            <pressure>1</pressure>
            <pe>4</pe>
            <components>
                <component>C(4)</component>
                <component>Ca</component>
                <component>Mg</component>
                <component>Cl</component>
            </components>
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            <charge_balance>pH</charge_balance>
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        </solution>
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        <equilibrium_reactants>
            <phase_component>
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                <name>Calcite</name>
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                <saturation_index>0.0</saturation_index>
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            </phase_component>
            <phase_component>
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                <name>Dolomite(dis)</name>
                <saturation_index>0.0</saturation_index>
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            </phase_component>
        </equilibrium_reactants>
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        <knobs>
            <max_iter>100</max_iter>
            <relative_convergence_tolerance>1e-12</relative_convergence_tolerance>
            <tolerance>1e-15</tolerance>
            <step_size>100</step_size>
            <scaling>0</scaling>
        </knobs>
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    </chemical_system>
    <parameters>
        <parameter>
            <name>kappa</name>
            <type>Constant</type>
            <values>1.157e-12</values>
        </parameter>
        <parameter>
            <name>porosity</name>
            <type>Constant</type>
            <value>0.32</value>
        </parameter>
        <parameter>
            <name>decay</name>
            <type>Constant</type>
            <value>0</value>
        </parameter>
        <parameter>
            <name>p0</name>
            <type>Constant</type>
            <value>1</value>
        </parameter>
        <parameter>
            <name>p_upstream</name>
            <type>Constant</type>
            <value>1e5</value>
        </parameter>
        <parameter>
            <name>p_downstream_Neumann</name>
            <type>Constant</type>
            <value>-2.9976852e-3</value>
        </parameter>
        <parameter>
            <name>c0_C(4)</name>
            <type>Constant</type>
            <value>1.23e-4</value>
        </parameter>
        <parameter>
            <name>c0_Ca</name>
            <type>Constant</type>
            <value>1.23e-4</value>
        </parameter>
        <parameter>
            <name>c0_Mg</name>
            <type>Constant</type>
            <value>1e-12</value>
        </parameter>
        <parameter>
            <name>c0_Cl</name>
            <type>Constant</type>
            <value>1e-12</value>
        </parameter>
        <parameter>
            <name>c0_H</name>
            <type>Constant</type>
            <!--pH=9.91-->
            <value>1.2302687708123812e-10</value>
        </parameter>
        <parameter>
            <name>c_C(4)</name>
            <type>Constant</type>
            <value>1e-10</value>
        </parameter>
        <parameter>
            <name>c_Ca</name>
            <type>Constant</type>
            <value>1e-10</value>
        </parameter>
        <parameter>
            <name>c_Mg</name>
            <type>Constant</type>
            <value>1e-3</value>
        </parameter>
        <parameter>
            <name>c_Cl</name>
            <type>Constant</type>
            <value>2e-3</value>
        </parameter>
        <parameter>
            <name>c_H</name>
            <type>Constant</type>
            <!--pH=7-->
            <value>1e-7</value>
        </parameter>
    </parameters>
    <process_variables>
        <process_variable>
            <name>pressure</name>
            <components>1</components>
            <order>1</order>
            <initial_condition>p0</initial_condition>
            <boundary_conditions>
                <boundary_condition>
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                    <mesh>calcite_upstream</mesh>
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                    <type>Dirichlet</type>
                    <parameter>p_upstream</parameter>
                </boundary_condition>
                <boundary_condition>
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                    <mesh>calcite_downstream</mesh>
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                    <type>Neumann</type>
                    <parameter>p_downstream_Neumann</parameter>
                </boundary_condition>
            </boundary_conditions>
        </process_variable>
        <process_variable>
            <name>C(4)</name>
            <components>1</components>
            <order>1</order>
            <initial_condition>c0_C(4)</initial_condition>
            <boundary_conditions>
                <boundary_condition>
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                    <mesh>calcite_upstream</mesh>
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                    <type>Dirichlet</type>
                    <parameter>c_C(4)</parameter>
                </boundary_condition>
            </boundary_conditions>
        </process_variable>
        <process_variable>
            <name>Ca</name>
            <components>1</components>
            <order>1</order>
            <initial_condition>c0_Ca</initial_condition>
            <boundary_conditions>
                <boundary_condition>
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                    <mesh>calcite_upstream</mesh>
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                    <type>Dirichlet</type>
                    <parameter>c_Ca</parameter>
                </boundary_condition>
            </boundary_conditions>
        </process_variable>
        <process_variable>
            <name>Mg</name>
            <components>1</components>
            <order>1</order>
            <initial_condition>c0_Mg</initial_condition>
            <boundary_conditions>
                <boundary_condition>
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                    <mesh>calcite_upstream</mesh>
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                    <type>Dirichlet</type>
                    <parameter>c_Mg</parameter>
                </boundary_condition>
            </boundary_conditions>
        </process_variable>
        <process_variable>
            <name>Cl</name>
            <components>1</components>
            <order>1</order>
            <initial_condition>c0_Cl</initial_condition>
            <boundary_conditions>
                <boundary_condition>
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                    <mesh>calcite_upstream</mesh>
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                    <type>Dirichlet</type>
                    <parameter>c_Cl</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>
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                    <mesh>calcite_upstream</mesh>
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                    <type>Dirichlet</type>
                    <parameter>c_H</parameter>
                </boundary_condition>
            </boundary_conditions>
        </process_variable>
    </process_variables>
    <nonlinear_solvers>
        <nonlinear_solver>
            <name>basic_picard</name>
            <type>Picard</type>
            <max_iter>10</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 20000</lis>
            <eigen>
                <solver_type>BiCGSTAB</solver_type>
                <precon_type>ILUT</precon_type>
                <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>
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    <test_definition>
        <vtkdiff>
            <regex>calcite_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
            <field>pressure</field>
            <absolute_tolerance>1e-6</absolute_tolerance>
            <relative_tolerance>1e-10</relative_tolerance>
        </vtkdiff>
        <vtkdiff>
            <regex>calcite_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
            <field>Ca</field>
            <absolute_tolerance>1e-10</absolute_tolerance>
            <relative_tolerance>1e-16</relative_tolerance>
        </vtkdiff>
        <vtkdiff>
            <regex>calcite_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
            <field>Cl</field>
            <absolute_tolerance>1e-10</absolute_tolerance>
            <relative_tolerance>1e-16</relative_tolerance>
        </vtkdiff>
        <vtkdiff>
            <regex>calcite_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
            <field>H</field>
            <absolute_tolerance>1e-10</absolute_tolerance>
            <relative_tolerance>1e-16</relative_tolerance>
        </vtkdiff>
        <vtkdiff>
            <regex>calcite_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
            <field>Mg</field>
            <absolute_tolerance>1e-10</absolute_tolerance>
            <relative_tolerance>1e-16</relative_tolerance>
        </vtkdiff>
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        <vtkdiff>
            <regex>calcite_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
            <field>Calcite_avg</field>
            <absolute_tolerance>1e-10</absolute_tolerance>
            <relative_tolerance>1e-16</relative_tolerance>
        </vtkdiff>
        <vtkdiff>
            <regex>calcite_ts_[0-9]*_t_[0-9]*.000000.vtu</regex>
            <field>Dolomite(dis)_avg</field>
            <absolute_tolerance>1e-10</absolute_tolerance>
            <relative_tolerance>1e-16</relative_tolerance>
        </vtkdiff>
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    </test_definition>
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</OpenGeoSysProject>