feat: Plug in HPCReact Activity Model

inputFiles/singlePhaseReactiveTransport/MoMaSEasy_1DDiffusive_base.xml

@@ -19,7 +19,7 @@
         lineSearchAction="None"
         timeStepIncreaseFactor="1.2"
         logLevel="2"
-        maxAllowedResidualNorm="1e100"/>
+        maxAllowedResidualNorm="1e8"/>
       <LinearSolverParameters
         directParallel="0"/>
     </SinglePhaseReactiveTransport>

inputFiles/singlePhaseReactiveTransport/mixedReactionCarbonateSystemBdot_1D_base.xml

@@ -0,0 +1,155 @@
+<?xml version="1.0" ?>
+
+<Problem>
+  <Solvers
+    gravityVector="{ 0.0, 0.0, 0.0 }">
+    <SinglePhaseReactiveTransport
+      name="SinglePhaseReactiveFlow"
+      discretization="singlePhaseTPFA"
+      targetRegions="{ Region1 }"
+      writeLinearSystem="0"
+      logLevel="2">
+      <NonlinearSolverParameters
+        newtonTol="1.0e-6"
+        maxTimeStepCuts="5"
+        newtonMaxIter="40"
+        logLevel="2"
+        lineSearchAction="None"
+        maxAllowedResidualNorm="1e100"/>
+      <LinearSolverParameters
+        directParallel="0"/>
+    </SinglePhaseReactiveTransport>
+  </Solvers>
+
+  <NumericalMethods>
+    <FiniteVolume>
+      <TwoPointFluxApproximation
+        name="singlePhaseTPFA"/>
+    </FiniteVolume>
+  </NumericalMethods>
+
+  <ElementRegions>
+    <CellElementRegion
+      name="Region1"
+      cellBlocks="{ * }"
+      materialList="{ water, rock, diffusion }"/>
+  </ElementRegions>
+
+  <Constitutive>
+    <ReactiveCompressibleSinglePhaseFluid
+      name="water"
+      defaultDensity="1000"
+      defaultViscosity="0.001"
+      referencePressure="0.0"
+      compressibility="0.0"
+      viscosibility="0.0"
+      chemicalSystemType="carbonate"
+      activityModelType="bdot"/>
+
+    <CompressibleSolidConstantPermeability
+      name="rock"
+      solidModelName="nullSolid"
+      porosityModelName="rockPorosity"
+      permeabilityModelName="rockPerm"/>
+
+    <NullModel
+      name="nullSolid"/>
+
+    <PressurePorosity
+      name="rockPorosity"
+      defaultReferencePorosity="0.1"
+      referencePressure="0.0"
+      compressibility="0.0"/>
+
+    <ConstantPermeability
+      name="rockPerm"
+      permeabilityComponents="{ 3.0e-16, 3.0e-16, 3.0e-16 }"/>
+
+    <ConstantDiffusion
+      name="diffusion"
+      phaseNames="{ water }"
+      defaultPhaseDiffusivityMultipliers="{ 1 }"
+      diffusivityComponents="{ 1e-2, 1e-2, 1e-2 }"/>
+  </Constitutive>
+
+  <FieldSpecifications>
+    <FieldSpecification
+      name="Porosity"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="rockPorosity_referencePorosity"
+      scale="0.1"/>
+
+    <FieldSpecification
+      name="initialPressure"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="pressure"
+      scale="1e6"/>
+
+    <FieldSpecification
+      name="sourcePressure"
+      setNames="{ source }"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="pressure"
+      scale="4e6"/>
+
+    <FieldSpecification
+      name="sinkPressure"
+      setNames="{ xpos }"
+      objectPath="faceManager"
+      fieldName="pressure"
+      scale="1.0e6"/>
+
+    <FieldSpecification
+      name="surfaceArea"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="initialSurfaceArea"
+      component="0"
+      scale="2.4573e+06"/>
+  </FieldSpecifications>
+
+  <Tasks>
+    <PackCollection
+      name="logPrimarySpeciesCollection"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="logPrimarySpeciesConcentration"/>
+
+    <PackCollection
+      name="pressureCollection"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="pressure"/>
+
+    <PackCollection
+      name="kineticRateCollection"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="water_kineticReactionRates"/>
+  </Tasks>
+
+  <Outputs>
+    <TimeHistory
+      name="logPrimarySpeciesHistoryOutput"
+      sources="{ /Tasks/logPrimarySpeciesCollection }"
+      filename="logPrimarySpeciesHistory"/>
+
+    <TimeHistory
+      name="pressureHistoryOutput"
+      sources="{ /Tasks/pressureCollection }"
+      filename="pressureHistory"/>
+
+    <TimeHistory
+      name="kineticReactionHistoryOutput"
+      sources="{ /Tasks/kineticRateCollection }"
+      filename="kineticReactionHistory"/>
+
+    <VTK
+      name="vtkOutput"/>
+
+    <Restart
+      name="restartOutput"/>
+  </Outputs>
+</Problem>

inputFiles/singlePhaseReactiveTransport/mixedReactionCarbonateSystemBdot_1D_smoke.xml

@@ -0,0 +1,76 @@
+<?xml version="1.0" ?>
+
+<Problem>
+  <Included>
+    <File name="./mixedReactionCarbonateSystemBdot_1D_base.xml" />
+    <File name="./mixedReactionCarbonateSystem_initialAggregate.xml" />
+    <File name="./mixedReactionCarbonateSystem_initialPrimaryConc.xml" />
+    <File name="./mixedReactionCarbonateSystem_logConc.xml" />
+  </Included>
+
+  <Mesh>
+    <InternalMesh
+      name="mesh1"
+      elementTypes="{ C3D8 }"
+      xCoords="{ 0, 10 }"
+      yCoords="{ 0, 1 }"
+      zCoords="{ 0, 1 }"
+      nx="{ 100 }"
+      ny="{ 1 }"
+      nz="{ 1 }"
+      cellBlockNames="{ block1 }"/>
+  </Mesh>
+
+  <Geometry>
+    <Box
+      name="source"
+      xMin="{ -0.01, -0.01, -0.01 }"
+      xMax="{ 0.11, 1.01, 1.01 }"/>
+  </Geometry>
+
+  <Events
+    maxTime="20">
+    <PeriodicEvent
+      name="outputs"
+      cycleFrequency="1"
+      target="/Outputs/vtkOutput"/>
+
+    <PeriodicEvent
+      name="logPrimarySpeciesHistoryCollection"
+      cycleFrequency="1"
+      target="/Tasks/logPrimarySpeciesCollection"/>
+    <PeriodicEvent
+      name="logPrimarySpeciesTimeHistoryOutput"
+      cycleFrequency="1"
+      target="/Outputs/logPrimarySpeciesHistoryOutput"/>
+
+    <PeriodicEvent
+      name="pressureHistoryCollection"
+      cycleFrequency="1"
+      target="/Tasks/pressureCollection"/>
+    <PeriodicEvent
+      name="pressureTimeHistoryOutput"
+      cycleFrequency="1"
+      target="/Outputs/pressureHistoryOutput"/>
+
+    <PeriodicEvent
+      name="kineticRateHistoryCollection"
+      cycleFrequency="1"
+      target="/Tasks/kineticRateCollection"/>
+    <PeriodicEvent
+      name="kineticRateTimeHistoryOutput"
+      cycleFrequency="1"
+      target="/Outputs/kineticReactionHistoryOutput"/>
+
+    <PeriodicEvent
+      name="solverApplications"
+      forceDt="1"
+      target="/Solvers/SinglePhaseReactiveFlow"/>
+
+    <PeriodicEvent
+      name="restarts"
+      cycleFrequency="10"
+      target="/Outputs/restartOutput"/>
+  </Events>
+
+</Problem>

inputFiles/singlePhaseReactiveTransport/mixedReactionCarbonateSystemBdot_2D_base.xml

@@ -0,0 +1,133 @@
+<?xml version="1.0" ?>
+
+<Problem>
+  <Solvers
+    gravityVector="{ 0.0, 0.0, 0.0 }">
+    <SinglePhaseReactiveTransport
+      name="SinglePhaseReactiveFlow"
+      discretization="singlePhaseTPFA"
+      targetRegions="{ Region1 }"
+      writeLinearSystem="0"
+      logLevel="2">
+      <NonlinearSolverParameters
+        newtonTol="1.0e-5"
+        maxTimeStepCuts="5"
+        maxSubSteps="200"
+        newtonMaxIter="40"
+        logLevel="2"
+        lineSearchAction="None"
+        maxAllowedResidualNorm="1e100"/>
+      <LinearSolverParameters
+        directParallel="0"/>
+    </SinglePhaseReactiveTransport>
+  </Solvers>
+
+  <NumericalMethods>
+    <FiniteVolume>
+      <TwoPointFluxApproximation
+        name="singlePhaseTPFA"/>
+    </FiniteVolume>
+  </NumericalMethods>
+
+  <ElementRegions>
+    <CellElementRegion
+      name="Region1"
+      cellBlocks="{ * }"
+      materialList="{ water, rock, diffusion }"/>
+  </ElementRegions>
+
+  <Constitutive>
+    <ReactiveCompressibleSinglePhaseFluid
+      name="water"
+      defaultDensity="1000"
+      defaultViscosity="0.001"
+      referencePressure="0.0"
+      compressibility="5e-10"
+      viscosibility="0.0"
+      chemicalSystemType="carbonate"
+      activityModelType="bdot"/>
+
+    <CompressibleSolidConstantPermeability
+      name="rock"
+      solidModelName="nullSolid"
+      porosityModelName="rockPorosity"
+      permeabilityModelName="rockPerm"/>
+
+    <NullModel
+      name="nullSolid"/>
+
+    <PressurePorosity
+      name="rockPorosity"
+      defaultReferencePorosity="0.1"
+      referencePressure="0.0"
+      compressibility="0.0"/>
+
+    <ConstantPermeability
+      name="rockPerm"
+      permeabilityComponents="{ 3.0e-14, 3.0e-14, 3.0e-14 }"/>
+
+    <ConstantDiffusion
+      name="diffusion"
+      phaseNames="{ water }"
+      defaultPhaseDiffusivityMultipliers="{ 1 }"
+      diffusivityComponents="{ 10, 10, 10 }"/>
+  </Constitutive>
+
+  <FieldSpecifications>
+    <FieldSpecification
+      name="Porosity"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="rockPorosity_referencePorosity"
+      scale="0.1"/>
+
+    <FieldSpecification
+      name="initialPressure"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="pressure"
+      scale="1e6"/>
+
+    <FieldSpecification
+      name="sourcePressure"
+      setNames="{ source }"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="pressure"
+      scale="3e6"/>
+
+    <FieldSpecification
+      name="sinkPressure"
+      setNames="{ ypos }"
+      objectPath="faceManager"
+      fieldName="pressure"
+      scale="1e6"/>
+
+    <FieldSpecification
+      name="surfaceArea"
+      initialCondition="1"
+      setNames="{ all }"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="initialSurfaceArea"
+      component="0"
+      scale="2.4573e+02"/>
+
+    <FieldSpecification
+      name="surfaceAreaSource"
+      initialCondition="1"
+      setNames="{ source }"
+      objectPath="ElementRegions/Region1/block1"
+      fieldName="initialSurfaceArea"
+      component="0"
+      scale="0.0"/>
+  </FieldSpecifications>
+
+  <Outputs>
+    <VTK
+      name="vtkOutput"/>
+
+    <Restart
+      name="restartOutput"/>
+  </Outputs>
+</Problem>