feat: Sequential ChemoMechanics Coupling

.gitmodules

@@ -10,3 +10,6 @@
 [submodule "src/coreComponents/fileIO/coupling/hdf5_interface"]
 	path = src/coreComponents/fileIO/coupling/hdf5_interface
 	url = ../../GEOS-DEV/hdf5_interface.git
+[submodule "src/coreComponents/constitutive/HPCReact"]
+	path = src/coreComponents/constitutive/HPCReact
+	url = [email protected]:GEOS-DEV/HPCReact.git

inputFiles/chemoMechanics/ChemoMechanics_CarbonateSystem_base.xml

@@ -0,0 +1,139 @@
+<?xml version="1.0" ?>
+
+<Problem>
+
+  <NumericalMethods>
+    <FiniteElements>
+      <FiniteElementSpace
+        name="FE1"
+        order="1"/>
+    </FiniteElements>
+
+    <FiniteVolume>
+      <TwoPointFluxApproximation
+        name="singlePhaseTPFA"/>
+    </FiniteVolume>
+  </NumericalMethods>
+
+  <ElementRegions>
+    <CellElementRegion
+      name="Barrier"
+      cellBlocks="{ cb-0_0_0, cb-0_2_0 }"
+      materialList="{ reactiveRock, water }"/>
+
+    <CellElementRegion
+      name="Reaction"
+      cellBlocks="{ cb-0_1_0 }"
+      materialList="{ reactiveRock, water }"/>
+  </ElementRegions>
+
+  <Constitutive>
+    <PorousReactiveElasticIsotropic
+      name="reactiveRock"
+      solidModelName="rockSolid"
+      porosityModelName="rockPorosity"
+      permeabilityModelName="rockPerm"/>
+
+    <ElasticIsotropic
+      name="rockSolid"
+      defaultDensity="0"
+      defaultBulkModulus="6.6667e7"
+      defaultShearModulus="4.0e7"/>
+
+    <ReactivePorosity
+      name="rockPorosity"
+      defaultReferencePorosity="0.1"
+      defaultInitialVolumeFractions="{ 0.1 }"
+      molarWeights="{ 0.100087 }"
+      mineralDensities="{ 2710 }"/>
+
+    <ConstantPermeability
+      name="rockPerm"
+      permeabilityComponents="{ 1e-20, 1e-20, 1e-20 }"/>
+
+    <ReactiveCompressibleSinglePhaseFluid
+      name="water"
+      defaultDensity="1000"
+      defaultViscosity="0.001"
+      referencePressure="0.0"
+      compressibility="5e-10"
+      viscosibility="0.0"
+      chemicalSystemType="carbonate"/>
+  </Constitutive>
+
+  <FieldSpecifications>
+    <FieldSpecification
+      name="initialPressureBarrier"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Barrier"
+      fieldName="pressure"
+      scale="0.0"/>
+
+    <FieldSpecification
+      name="initialPressureReaction"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Reaction"
+      fieldName="pressure"
+      scale="0.0"/>
+
+    <FieldSpecification
+      name="fixPressureBarrier"
+      setNames="{ all }"
+      objectPath="ElementRegions/Barrier"
+      fieldName="pressure"
+      scale="0.0"/>
+
+    <FieldSpecification
+      name="fixPressureReaction"
+      setNames="{ all }"
+      objectPath="ElementRegions/Reaction"
+      fieldName="pressure"
+      scale="0.0"/>
+
+    <FieldSpecification
+      name="xconstraint"
+      fieldName="totalDisplacement"
+      component="0"
+      objectPath="nodeManager"
+      setNames="{ yneg, ypos  }"/>
+
+    <FieldSpecification
+      name="yconstraint"
+      fieldName="totalDisplacement"
+      component="1"
+      objectPath="nodeManager"
+      setNames="{ yneg, ypos }"/>
+
+    <FieldSpecification
+      name="zconstraint"
+      fieldName="totalDisplacement"
+      component="2"
+      objectPath="nodeManager"
+      setNames="{ yneg, ypos  }"/>
+
+    <FieldSpecification
+      name="surfaceAreaReaction"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Reaction"
+      fieldName="initialSurfaceArea"
+      component="0"
+      scale="2.4573e+06"/>
+
+    <FieldSpecification
+      name="surfaceAreaBarrier"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Barrier"
+      fieldName="initialSurfaceArea"
+      component="0"
+      scale="0.0"/>
+  </FieldSpecifications>
+
+  <Outputs>
+    <VTK
+      name="vtkOutput"/>
+  </Outputs>
+</Problem>

inputFiles/chemoMechanics/ChemoMechanics_CarbonateSystem_explicitUpdate_1DBar.xml

@@ -0,0 +1,85 @@
+<?xml version="1.0" ?>
+
+<Problem>
+  <Included>
+    <File name="./ChemoMechanics_CarbonateSystem_base.xml"/>
+    <File name="./ChemoMechanics_CarbonateSystem_initialAggregate.xml" />
+    <File name="./ChemoMechanics_CarbonateSystem_initialPrimaryConc.xml" />
+  </Included>  
+
+  <Solvers
+    gravityVector="{ 0.0, 0.0, 0.0 }">
+    <SinglePhaseReactiveTransportPoromechanics
+      name="chemomechSolve"
+      solidSolverName="lagsolve"
+      flowSolverName="SinglePhaseReactiveFlow"
+      logLevel="1"
+      targetRegions="{ Reaction, Barrier  }">
+      <NonlinearSolverParameters
+        newtonMaxIter="2"
+        newtonTol="1.0e-4"
+        couplingType="Sequential"  
+        lineSearchAction="None"
+        subcycling="1"
+        maxTimeStepCuts="1"
+        lineSearchMaxCuts="0"/>
+      <LinearSolverParameters
+        directParallel="0"/>
+    </SinglePhaseReactiveTransportPoromechanics>
+
+    <SolidMechanicsLagrangianFEM
+      name="lagsolve"
+      logLevel="1"
+      discretization="FE1"
+      targetRegions="{ Reaction, Barrier  }">
+      <NonlinearSolverParameters
+        newtonTol="1.0e-4"
+        newtonMaxIter="40"/>
+      <LinearSolverParameters
+        directParallel="0"/>
+    </SolidMechanicsLagrangianFEM>      
+
+    <SinglePhaseReactiveTransport
+      name="SinglePhaseReactiveFlow"
+      logLevel="1"
+      discretization="singlePhaseTPFA"
+      targetRegions="{ Reaction, Barrier }">
+      <NonlinearSolverParameters
+        newtonTol="1.0e-4"
+        maxTimeStepCuts="5"
+        newtonMaxIter="40"
+        logLevel="2"
+        maxAllowedResidualNorm="1e100"/>
+      <LinearSolverParameters
+        directParallel="0"/>
+    </SinglePhaseReactiveTransport>
+  </Solvers>
+
+  <Mesh>
+    <InternalMesh
+      name="mesh1"
+      elementTypes="{ C3D8 }"
+      xCoords="{ 0.0, 1.0 }"
+      yCoords="{ 0.0, 4.0, 6.0, 10.0 }"
+      zCoords="{ 0.0, 1.0 }"
+      nx="{ 1 }"
+      ny="{ 4, 2, 4 }"
+      nz="{ 1 }"
+      cellBlockNames="{ cb-0_0_0, cb-0_1_0, cb-0_2_0 }"/>
+  </Mesh>
+
+  <Events
+    maxTime="10.0">
+
+    <PeriodicEvent
+      name="outputs"
+      cycleFrequency="1"
+      target="/Outputs/vtkOutput"/>
+
+    <PeriodicEvent
+      name="solverApplication0"
+      maxEventDt="0.1"
+      target="/Solvers/chemomechSolve"/> 
+  </Events>
+
+</Problem>

inputFiles/chemoMechanics/ChemoMechanics_CarbonateSystem_initialAggregate.xml

@@ -0,0 +1,133 @@
+<?xml version="1.0" ?>
+
+<Problem>
+  <FieldSpecifications>
+  <!-- AGGREGATE CONCENTRATIONS AT REACTION -->
+    <FieldSpecification
+      name="initialAggregate_H_reaction"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Reaction"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="0"
+      scale="1.585e-7"/>
+
+    <FieldSpecification
+      name="initialAggregate_HCO3_reaction"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Reaction"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="1"
+      scale="8.293e-3"/>
+
+    <FieldSpecification
+      name="initialAggregate_Ca_reaction"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Reaction"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="2"
+      scale="2.171e-3"/>
+
+    <FieldSpecification
+      name="initialAggregate_SO4_reaction"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Reaction"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="3"
+      scale="1.666e-6"/>
+
+    <FieldSpecification
+      name="initialAggregate_Cl_reaction"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Reaction"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="4"
+      scale="2.821e-5"/>
+
+    <FieldSpecification
+      name="initialAggregate_Mg_reaction"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Reaction"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="5"
+      scale="1.605e-3"/>
+
+    <FieldSpecification
+      name="initialAggregate_Na_reaction"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Reaction"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="6"
+      scale="7.817e-4"/>
+
+  <!-- AGGREGATE CONCENTRATIONS AT BARRIER -->
+    <FieldSpecification
+      name="initialAggregate_H_barrier"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Barrier"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="0"
+      scale="1.585e-7"/>
+
+    <FieldSpecification
+      name="initialAggregate_HCO3_barrier"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Barrier"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="1"
+      scale="8.293e-3"/>
+
+    <FieldSpecification
+      name="initialAggregate_Ca_barrier"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Barrier"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="2"
+      scale="2.171e-3"/>
+
+    <FieldSpecification
+      name="initialAggregate_SO4_barrier"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Barrier"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="3"
+      scale="1.666e-6"/>
+
+    <FieldSpecification
+      name="initialAggregate_Cl_barrier"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Barrier"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="4"
+      scale="2.821e-5"/>
+
+    <FieldSpecification
+      name="initialAggregate_Mg_barrier"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Barrier"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="5"
+      scale="1.605e-3"/>
+
+    <FieldSpecification
+      name="initialAggregate_Na_barrier"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Barrier"
+      fieldName="water_primarySpeciesAggregateConcentration"
+      component="6"
+      scale="7.817e-4"/>
+  </FieldSpecifications>
+</Problem>