Merge branch 'develop' into refactor/dkachuma/use-lapack-matrix-matri…

…x-interface
GEOS-DEV · Aug 16, 2024 · 5fee5af · 5fee5af
2 parents 006e81e + c29c4ec
commit 5fee5af
Show file tree

Hide file tree

Showing 32 changed files with 3,349 additions and 3 deletions.
diff --git a/.integrated_tests.yaml b/.integrated_tests.yaml
@@ -1,6 +1,6 @@
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr3278-6753-f7f9add
+  baseline: integratedTests/baseline_integratedTests-pr3249-6781-4998bc8
 
 allow_fail:
   all: ''

diff --git a/BASELINE_NOTES.md b/BASELINE_NOTES.md
@@ -8,14 +8,21 @@ These notes should be in reverse-chronological order, and use the following time
 
 
 
-PR 3278 (2024-08-12)
-====================
+PR #3249 (2024-08-14)
+======================
+Two initialization options for poromechanical models. Rebaseline the corresponding cases. 
+
+
+PR #3278 (2024-08-12)
+======================
 Renamed GEOSX to GEOS in enternal mesh import, so rebaseline to change these names is the baselines. 
 
+
 PR #3202 (2024-08-03)
 ======================
 Acoustic VTI tests needed rebaselining after update in source and receiver location algorithm.
 
+
 PR #3215 (2024-07-23)
 ======================
 Changed the default value for massCreation and name of the wrapper.

diff --git a/inputFiles/initialization/gravityInducedStress_initialization_base.xml b/inputFiles/initialization/gravityInducedStress_initialization_base.xml
@@ -0,0 +1,155 @@
+<?xml version="1.0"?>
+
+<Problem>
+  <Solvers
+    gravityVector="{ 0.0, 0.0, -9.81 }">
+    <!-- SPHINX_POROMECHANICSSOLVER -->
+    <SinglePhasePoromechanics
+      name="poroSolve"
+      solidSolverName="lagsolve"
+      flowSolverName="SinglePhaseFlow"
+      logLevel="1"
+      targetRegions="{ Domain }">
+      <NonlinearSolverParameters
+        newtonMaxIter="2"
+        newtonTol="1.0e-2"
+        maxTimeStepCuts="1"
+        lineSearchMaxCuts="0" />
+      <LinearSolverParameters
+        directParallel="0" />
+    </SinglePhasePoromechanics>
+    <!-- SPHINX_POROMECHANICSSOLVER_END -->
+
+    <!-- SPHINX_MECHANICALSOLVER -->
+    <SolidMechanicsLagrangianSSLE
+      name="lagsolve"
+      timeIntegrationOption="QuasiStatic"
+      logLevel="1"
+      discretization="FE1"
+      targetRegions="{ Domain }" />
+    <!-- SPHINX_MECHANICALSOLVER_END -->
+
+    <!-- SPHINX_SINGLEPHASEFVM -->
+    <SinglePhaseFVM
+      name="SinglePhaseFlow"
+      logLevel="1"
+      discretization="fluidTPFA"
+      targetRegions="{ Domain }" />
+    <!-- SPHINX_SINGLEPHASEFVM_END -->
+  </Solvers>
+
+  <!-- SPHINX_NUMERICAL -->
+  <NumericalMethods>
+    <FiniteElements>
+      <FiniteElementSpace
+        name="FE1"
+        order="1" />
+    </FiniteElements>
+
+    <FiniteVolume>
+      <TwoPointFluxApproximation
+        name="fluidTPFA" />
+    </FiniteVolume>
+  </NumericalMethods>
+  <!-- SPHINX_NUMERICAL_END -->
+
+  <!-- SPHINX_ELEMENTREGIONS -->
+  <ElementRegions>
+    <CellElementRegion
+      name="Domain"
+      cellBlocks="{ cb1 }"
+      materialList="{ water, rock }" />
+  </ElementRegions>
+  <!-- SPHINX_ELEMENTREGIONS_END -->
+
+  <!-- SPHINX_MATERIAL -->
+  <Constitutive>
+    <PorousElasticIsotropic
+      name="rock"
+      solidModelName="rockSolid"
+      porosityModelName="rockPorosity"
+      permeabilityModelName="rockPerm" />
+
+    <ElasticIsotropic
+      name="rockSolid"
+      defaultDensity="2500"
+      defaultPoissonRatio="0.25"
+      defaultYoungModulus="100.0e6" />
+
+    <BiotPorosity
+      name="rockPorosity"
+      defaultGrainBulkModulus="1.0e27"
+      defaultReferencePorosity="0.375" />
+
+    <ConstantPermeability
+      name="rockPerm"
+      permeabilityComponents="{ 1.0e-12, 1.0e-12, 1.0e-12 }" />
+
+    <CompressibleSinglePhaseFluid
+      name="water"
+      defaultDensity="1000"
+      defaultViscosity="0.001"
+      referencePressure="0.000"
+      referenceDensity="1000"
+      compressibility="4.4e-10"
+      referenceViscosity="0.001"
+      viscosibility="0.0" />
+  </Constitutive>
+  <!-- SPHINX_MATERIAL_END -->
+
+
+  <!-- SPHINX_BC -->
+  <FieldSpecifications>
+    <HydrostaticEquilibrium
+      datumElevation="0.0"
+      datumPressure="0.0"
+      name="equil"
+      objectPath="ElementRegions/Domain" />
+
+    <FieldSpecification
+      name="xconstraint"
+      objectPath="nodeManager"
+      fieldName="totalDisplacement"
+      component="0"
+      scale="0.0"
+      setNames="{ xneg, xpos }" />
+
+    <FieldSpecification
+      name="yconstraint"
+      objectPath="nodeManager"
+      fieldName="totalDisplacement"
+      component="1"
+      scale="0.0"
+      setNames="{ yneg, ypos }" />
+
+    <FieldSpecification
+      name="zconstraint"
+      objectPath="nodeManager"
+      fieldName="totalDisplacement"
+      component="2"
+      scale="0.0"
+      setNames="{ zneg }" />
+
+  </FieldSpecifications>
+  <!-- SPHINX_BC_END -->
+
+
+  <!-- SPHINX_TASKS -->
+  <Tasks>
+    <SinglePhasePoromechanicsInitialization 
+      logLevel="1"
+      name="singlephasePoromechanicsPreEquilibrationStep"
+      poromechanicsSolverName="poroSolve" />
+  </Tasks>
+  <!-- SPHINX_TASKS_END -->
+
+  <!-- SPHINX_OUTPUT -->
+  <Outputs>
+    <VTK
+      name="vtkOutput" />
+
+    <Restart
+      name="restartOutput"/>
+  </Outputs>
+  <!-- SPHINX_OUTPUT_END -->
+</Problem>
diff --git a/inputFiles/initialization/gravityInducedStress_initialization_benchmark.xml b/inputFiles/initialization/gravityInducedStress_initialization_benchmark.xml
@@ -0,0 +1,47 @@
+<?xml version="1.0"?>
+
+<Problem>
+  <Included>
+    <File name="./gravityInducedStress_initialization_base.xml" />
+  </Included>
+
+  <!-- SPHINX_MESH -->
+  <Mesh>
+    <InternalMesh
+      name="mesh1"
+      elementTypes="{ C3D8 }"
+      xCoords="{ 0.0, 1000 }"
+      yCoords="{ 0.0, 1000 }"
+      zCoords="{ -1000, 0 }"
+      nx="{ 20 }"
+      ny="{ 20 }"
+      nz="{ 40 }"
+      cellBlockNames="{ cb1 }" />
+  </Mesh>
+  <!-- SPHINX_MESH_END -->
+
+  <!-- SPHINX_EVENTS -->
+  <Events
+    maxTime="10.0"
+    minTime="-1e10">
+
+    <PeriodicEvent
+      name="outputs"
+      timeFrequency="10.0"
+      target="/Outputs/vtkOutput" />
+
+    <PeriodicEvent
+      name="solverApplication0"
+      beginTime="0.0"
+      endTime="10.0"
+      target="/Solvers/poroSolve" />
+
+    <SoloEvent 
+      beginTime="-1e10" 
+      name="singlephasePoromechanicsPreEquilibrationStep"
+      target="/Tasks/singlephasePoromechanicsPreEquilibrationStep"
+      targetTime="-1e10" />
+
+  </Events>
+   <!-- SPHINX_EVENTS_END -->
+</Problem>
diff --git a/inputFiles/initialization/gravityInducedStress_initialization_smoke.xml b/inputFiles/initialization/gravityInducedStress_initialization_smoke.xml
@@ -0,0 +1,53 @@
+<?xml version="1.0"?>
+
+<Problem>
+  <Included>
+    <File name="./gravityInducedStress_initialization_base.xml" />
+  </Included>
+
+  <!-- SPHINX_MESH -->
+  <Mesh>
+    <InternalMesh
+      name="mesh1"
+      elementTypes="{ C3D8 }"
+      xCoords="{ 0.0, 1000 }"
+      yCoords="{ 0.0, 1000 }"
+      zCoords="{ -1000, 0 }"
+      nx="{ 2 }"
+      ny="{ 2 }"
+      nz="{ 4 }"
+      cellBlockNames="{ cb1 }" />
+  </Mesh>
+  <!-- SPHINX_MESH_END -->
+
+  <!-- SPHINX_EVENTS -->
+  <Events
+    maxTime="10.0"
+    minTime="-1e10">
+
+    <PeriodicEvent
+      name="outputs"
+      timeFrequency="10.0"
+      target="/Outputs/vtkOutput" />
+
+    <PeriodicEvent
+      name="solverApplication0"
+      beginTime="0.0"
+      endTime="10.0"
+      target="/Solvers/poroSolve" />
+
+    <SoloEvent 
+      beginTime="-1e10" 
+      name="singlephasePoromechanicsPreEquilibrationStep"
+      target="/Tasks/singlephasePoromechanicsPreEquilibrationStep"
+      targetTime="-1e10" />
+
+    <PeriodicEvent
+      name="restarts"
+      timeFrequency="10.0"
+      targetExactTimestep="0"
+      target="/Outputs/restartOutput"/>
+
+  </Events>
+   <!-- SPHINX_EVENTS_END -->
+</Problem>
diff --git a/inputFiles/initialization/initialization.ats b/inputFiles/initialization/initialization.ats
@@ -0,0 +1,27 @@
+import os
+from geos.ats.test_builder import TestDeck, RestartcheckParameters, generate_geos_tests
+
+restartcheck_params = {}
+restartcheck_params["atol"] = 2.0E-4
+restartcheck_params["rtol"] = 1.0E-7
+
+decks = [
+    TestDeck(
+        name="gravityInducedStress_initialization_smoke",
+        description=
+        "model intialization with gravity induced stress",
+        partitions=((1, 1, 1), (2, 2, 1)),
+        restart_step=1,
+        check_step=2,
+        restartcheck_params=RestartcheckParameters(**restartcheck_params)),
+    TestDeck(
+        name="userdefinedStress_initialization_smoke",
+        description=
+        "model intialization with user defined tables",
+        partitions=((1, 1, 1), (2, 2, 1)),
+        restart_step=1,
+        check_step=2,
+        restartcheck_params=RestartcheckParameters(**restartcheck_params))
+]
+
+generate_geos_tests(decks)
diff --git a/inputFiles/initialization/userTables/effectiveSigma_xx.csv b/inputFiles/initialization/userTables/effectiveSigma_xx.csv
@@ -0,0 +1,2 @@
+-7000000.00
+0.00
diff --git a/inputFiles/initialization/userTables/effectiveSigma_yy.csv b/inputFiles/initialization/userTables/effectiveSigma_yy.csv
@@ -0,0 +1,2 @@
+-17000000.00
+0.00
diff --git a/inputFiles/initialization/userTables/effectiveSigma_zz.csv b/inputFiles/initialization/userTables/effectiveSigma_zz.csv
@@ -0,0 +1,2 @@
+-14000000.00
+0.00
diff --git a/inputFiles/initialization/userTables/porePressure.csv b/inputFiles/initialization/userTables/porePressure.csv
@@ -0,0 +1,2 @@
+10000000.00
+0.00
diff --git a/inputFiles/initialization/userTables/x.csv b/inputFiles/initialization/userTables/x.csv
@@ -0,0 +1 @@
+0.00
diff --git a/inputFiles/initialization/userTables/y.csv b/inputFiles/initialization/userTables/y.csv
@@ -0,0 +1 @@
+0.00
diff --git a/inputFiles/initialization/userTables/z.csv b/inputFiles/initialization/userTables/z.csv
@@ -0,0 +1,2 @@
+-1000.00
+0.00