Merge branch 'develop' into feature/sframbat/viscoacoustic

.integrated_tests.yaml

@@ -1,6 +1,6 @@
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr3361-9139-2fc4131
+  baseline: integratedTests/baseline_integratedTests-pr3450-9221-37d940c
 allow_fail:
   all: ''
   streak: ''

BASELINE_NOTES.md

@@ -6,6 +6,18 @@ This file is designed to track changes to the integrated test baselines.
 Any developer who updates the baseline ID in the .integrated_tests.yaml file is expected to create an entry in this file with the pull request number, date, and their justification for rebaselining.
 These notes should be in reverse-chronological order, and use the following time format: (YYYY-MM-DD).
 
+PR #3450 (2024-12-08)
+=====================
+Added test for explicit runge kutta sprinslider.
+
+PR #3480 (2024-12-06)
+=====================
+Add "logLevel" parameter under /Problem/Outputs in baseline files
+
+PR #3361 (2024-12-03)
+=====================
+Revert default gravity treatment to old version. Make the way introduced in #3337 optional.
+
 PR #3361 (2024-12-03)
 =====================
 Baseline diffs after reimplementation of wave equation acoustic gradient for velocity and density parameters: new field "partialGradient2" and "pressureForward" field replacing "pressureDoubleDerivative".

inputFiles/inducedSeismicity/SpringSliderExplicit_base.xml

@@ -0,0 +1,167 @@
+<?xml version="1.0" ?>
+<Problem>
+  <Solvers>
+    <QuasiDynamicEQRK32
+      name="SpringSlider"
+      targetRegions="{ Fault }"
+      shearImpedance="4.41"
+      initialDt="1e-5"
+      logLevel="1"
+      discretization="FE1">
+    </QuasiDynamicEQRK32>
+
+    <SurfaceGenerator
+      name="SurfaceGen"
+      targetRegions="{ Domain }"
+      rockToughness="1.0"
+      mpiCommOrder="1"
+      fractureRegion="Fault"/>  
+  </Solvers>
+
+  <NumericalMethods>
+    <FiniteElements>
+      <FiniteElementSpace
+        name="FE1"
+        order="1"/>
+    </FiniteElements>
+  </NumericalMethods>
+
+  <Mesh>
+    <InternalMesh
+      name="mesh"
+      elementTypes="{ C3D8 }"
+      xCoords="{ 0, 1 }"
+      yCoords="{ 0, 2 }"
+      zCoords="{ 0, 1 }"
+      nx="{ 1 }"
+      ny="{ 2 }"
+      nz="{ 1 }"
+      cellBlockNames="{ cb1 }"/>
+  </Mesh>
+
+  <Geometry>    
+    <ThickPlane
+      name="faultPlane"
+      normal="{ 0, 1, 0 }"
+      origin="{ 0, 1, 0 }"
+      thickness="0.1"/>
+  </Geometry>
+
+  <ElementRegions>
+    <CellElementRegion
+      name="Domain"
+      cellBlocks="{ cb1 }"
+      materialList="{}"/>
+
+    <SurfaceElementRegion
+      name="Fault"
+      materialList="{frictionLaw}"
+      defaultAperture="1e-3"/>  
+    </ElementRegions>
+
+  <Constitutive>
+    <RateAndStateFriction
+      name="frictionLaw"
+      defaultA="0.01"
+      defaultB="0.015"
+      defaultDc="1.0e-5"  
+      defaultReferenceVelocity="1.0e-6"
+      defaultReferenceFrictionCoefficient="0.6"/>  
+  </Constitutive>
+
+  <FieldSpecifications>
+    <FieldSpecification
+      name="fault"
+      fieldName="ruptureState"
+      initialCondition="1"
+      objectPath="faceManager"
+      scale="1"
+      setNames="{ faultPlane }"/>
+
+    <FieldSpecification
+      name="normalTraction"
+      fieldName="traction"
+      initialCondition="1"
+      objectPath="ElementRegions/Fault/FractureSubRegion"
+      component="0"
+      scale="50"
+      setNames="{all}"/>
+
+    <FieldSpecification
+      name="shearTraction1"
+      fieldName="traction"
+      initialCondition="1"
+      objectPath="ElementRegions/Fault/FractureSubRegion"
+      component="1"
+      scale="21.2132034356"
+      setNames="{all}"/>
+    <FieldSpecification
+      name="shearTraction2"
+      fieldName="traction"
+      initialCondition="1"
+      objectPath="ElementRegions/Fault/FractureSubRegion"
+      component="2"
+      scale="21.2132034356"
+      setNames="{all}"/>  
+    <FieldSpecification
+      name="stateVariable"
+      fieldName="stateVariable"
+      initialCondition="1"
+      objectPath="ElementRegions/Fault/FractureSubRegion"
+      scale="0.6"
+      setNames="{all}"/>
+    <FieldSpecification
+      name="slipRate"
+      fieldName="slipRate"
+      initialCondition="1"
+      objectPath="ElementRegions/Fault/FractureSubRegion"
+      scale="1.0e-6"
+      setNames="{all}"/>
+    <FieldSpecification
+      name="slipVelocity1"
+      fieldName="slipVelocity"
+      initialCondition="1"
+      objectPath="ElementRegions/Fault/FractureSubRegion"
+      component="0"
+      scale="0.70710678118e-6"
+      setNames="{all}"/>               
+    <FieldSpecification
+      name="slipVelocity2"
+      fieldName="slipVelocity"
+      initialCondition="1"
+      objectPath="ElementRegions/Fault/FractureSubRegion"
+      component="1"
+      scale="0.70710678118e-6"
+      setNames="{all}"/>               
+  </FieldSpecifications>
+
+  <Outputs>
+    <VTK
+      name="vtkOutput"
+      plotFileRoot="springSliderExplicit"/>
+    <Restart
+      name="restart"/>  
+
+    <TimeHistory
+      name="timeHistoryOutput"
+      sources="{/Tasks/slipCollection,/Tasks/slipRateCollection,/Tasks/stateVariableCollection}"
+      filename="springSliderExplicit"/>
+  </Outputs>
+
+  <Tasks>
+    <PackCollection
+      name="slipCollection"
+      objectPath="ElementRegions/Fault/FractureSubRegion"
+      fieldName="displacementJump"/>
+
+    <PackCollection
+      name="slipRateCollection"
+      objectPath="ElementRegions/Fault/FractureSubRegion"
+      fieldName="slipRate"/>
+
+    <PackCollection
+      name="stateVariableCollection"
+      objectPath="ElementRegions/Fault/FractureSubRegion"
+      fieldName="stateVariable"/>  
+  </Tasks>
+</Problem>

inputFiles/inducedSeismicity/SpringSliderExplicit_smoke.xml

@@ -0,0 +1,32 @@
+<?xml version="1.0" ?>
+<Problem>
+  <Included>
+    <File
+      name="./SpringSliderExplicit_base.xml"/>
+  </Included>
+
+  <Events
+    maxTime="4.5e4">
+
+    <SoloEvent 
+      name="generateFault"
+      target="/Solvers/SurfaceGen"/>
+
+    <PeriodicEvent
+      name="vtkOutput"
+      cycleFrequency="1"
+      targetExactTimestep="0"
+      target="/Outputs/vtkOutput"/>  
+
+    <PeriodicEvent
+      name="solverApplications"
+      maxEventDt="1e4"
+      target="/Solvers/SpringSlider"/>
+
+    <PeriodicEvent
+      name="resarts"
+      timeFrequency="2e4"
+      targetExactTimestep="0"
+      target="/Outputs/restart"/>  
+  </Events>
+</Problem>

inputFiles/inducedSeismicity/SpringSlider_base.xml

@@ -123,15 +123,15 @@
       initialCondition="1"
       objectPath="ElementRegions/Fault/FractureSubRegion"
       component="0"
-      scale="0."
+      scale="0.70710678118e-6"
       setNames="{all}"/>               
     <FieldSpecification
       name="slipVelocity2"
       fieldName="slipVelocity"
       initialCondition="1"
       objectPath="ElementRegions/Fault/FractureSubRegion"
       component="1"
-      scale="0."
+      scale="0.70710678118e-6"
       setNames="{all}"/>               
   </FieldSpecifications>
 

inputFiles/inducedSeismicity/inducedSeismicity.ats

@@ -28,6 +28,13 @@ decks = [
         partitions=((1, 1, 1), ),
         restart_step=0,
         check_step=3262,
-        restartcheck_params=RestartcheckParameters(atol=1e-4, rtol=1e-3)) 
+        restartcheck_params=RestartcheckParameters(atol=1e-4, rtol=1e-3)),
+    TestDeck(
+        name="SpringSliderExplicit_smoke",
+        description="Spring slider 0D system",
+        partitions=((1, 1, 1), ),
+        restart_step=0,
+        check_step=532,
+        restartcheck_params=RestartcheckParameters(atol=1e-4, rtol=1e-3))     
     ]
 generate_geos_tests(decks)

src/coreComponents/fileIO/Outputs/BlueprintOutput.cpp

@@ -129,53 +129,57 @@ BlueprintOutput::BlueprintOutput( string const & name,
 }
 
 ///////////////////////////////////////////////////////////////////////////////////////////////////
-bool BlueprintOutput::execute( real64 const time,
-                               real64 const,
-                               integer const cycle,
-                               integer const,
-                               real64 const,
+bool BlueprintOutput::execute( real64 const time_n,
+                               real64 const GEOS_UNUSED_PARAM( dt ),
+                               integer const cycleNumber,
+                               integer const GEOS_UNUSED_PARAM( eventCounter ),
+                               real64 const GEOS_UNUSED_PARAM( eventProgress ),
                                DomainPartition & domain )
 {
   GEOS_MARK_FUNCTION;
 
-  MeshLevel const & meshLevel = domain.getMeshBody( 0 ).getBaseDiscretization();
+  {
+    Timer timer( m_outputTimer );
 
-  conduit::Node meshRoot;
-  conduit::Node & mesh = meshRoot[ "mesh" ];
-  conduit::Node & coordset = mesh[ "coordsets/nodes" ];
-  conduit::Node & topologies = mesh[ "topologies" ];
+    MeshLevel const & meshLevel = domain.getMeshBody( 0 ).getBaseDiscretization();
 
-  mesh[ "state/time" ] = time;
-  mesh[ "state/cycle" ] = cycle;
+    conduit::Node meshRoot;
+    conduit::Node & mesh = meshRoot[ "mesh" ];
+    conduit::Node & coordset = mesh[ "coordsets/nodes" ];
+    conduit::Node & topologies = mesh[ "topologies" ];
 
-  addNodalData( meshLevel.getNodeManager(), coordset, topologies, mesh[ "fields" ] );
+    mesh[ "state/time" ] = time_n;
+    mesh[ "state/cycle" ] = cycleNumber;
 
-  dataRepository::Group averagedElementData( "averagedElementData", this );
-  addElementData( meshLevel.getElemManager(), coordset, topologies, mesh[ "fields" ], averagedElementData );
+    addNodalData( meshLevel.getNodeManager(), coordset, topologies, mesh[ "fields" ] );
 
-  /// The Blueprint will complain if the fields node is present but empty.
-  if( mesh[ "fields" ].number_of_children() == 0 )
-  {
-    mesh.remove( "fields" );
-  }
+    dataRepository::Group averagedElementData( "averagedElementData", this );
+    addElementData( meshLevel.getElemManager(), coordset, topologies, mesh[ "fields" ], averagedElementData );
+
+    /// The Blueprint will complain if the fields node is present but empty.
+    if( mesh[ "fields" ].number_of_children() == 0 )
+    {
+      mesh.remove( "fields" );
+    }
 
-  /// Verify that the mesh conforms to the Blueprint.
-  conduit::Node info;
-  GEOS_ASSERT_MSG( conduit::blueprint::verify( "mesh", meshRoot, info ), info.to_json() );
+    /// Verify that the mesh conforms to the Blueprint.
+    conduit::Node info;
+    GEOS_ASSERT_MSG( conduit::blueprint::verify( "mesh", meshRoot, info ), info.to_json() );
 
-  /// Generate the Blueprint index.
-  conduit::Node fileRoot;
-  conduit::Node & index = fileRoot[ "blueprint_index/mesh" ];
-  conduit::blueprint::mesh::generate_index( mesh, "mesh", MpiWrapper::commSize(), index );
+    /// Generate the Blueprint index.
+    conduit::Node fileRoot;
+    conduit::Node & index = fileRoot[ "blueprint_index/mesh" ];
+    conduit::blueprint::mesh::generate_index( mesh, "mesh", MpiWrapper::commSize(), index );
 
-  /// Verify that the index conforms to the Blueprint.
-  info.reset();
-  GEOS_ASSERT_MSG( conduit::blueprint::mesh::index::verify( index, info ), info.to_json() );
+    /// Verify that the index conforms to the Blueprint.
+    info.reset();
+    GEOS_ASSERT_MSG( conduit::blueprint::mesh::index::verify( index, info ), info.to_json() );
 
-  /// Write out the root index file, then write out the mesh.
-  string const completePath = GEOS_FMT( "{}/blueprintFiles/cycle_{:07}", OutputBase::getOutputDirectory(), cycle );
-  string const filePathForRank = dataRepository::writeRootFile( fileRoot, completePath );
-  conduit::relay::io::save( meshRoot, filePathForRank, "hdf5" );
+    /// Write out the root index file, then write out the mesh.
+    string const completePath = GEOS_FMT( "{}/blueprintFiles/cycle_{:07}", OutputBase::getOutputDirectory(), cycleNumber );
+    string const filePathForRank = dataRepository::writeRootFile( fileRoot, completePath );
+    conduit::relay::io::save( meshRoot, filePathForRank, "hdf5" );
+  }
 
   return false;
 }
@@ -307,7 +311,19 @@ void BlueprintOutput::writeOutConstitutiveData( dataRepository::Group const & co
   } );
 }
 
+namespace logInfo
+{
+struct BlueprintOutputTimer : public OutputTimerBase
+{
+  std::string_view getDescription() const override { return "Blueprint output timing"; }
+};
+}
 
+logInfo::OutputTimerBase const & BlueprintOutput::getTimerCategory() const
+{
+  static logInfo::BlueprintOutputTimer timer;
+  return timer;
+}
 
 REGISTER_CATALOG_ENTRY( OutputBase, BlueprintOutput, string const &, dataRepository::Group * const )
 

src/coreComponents/fileIO/Outputs/BlueprintOutput.hpp

@@ -36,6 +36,12 @@ class ElementRegionManager;
  */
 class BlueprintOutput : public OutputBase
 {
+protected:
+  /**
+   * @copydoc OutputBase::getTimerCategory
+   */
+  logInfo::OutputTimerBase const & getTimerCategory() const override;
+
 public:
 
   /**