Merge branch 'develop' into aronson/testStressAveraging

.github/ISSUE_TEMPLATE/bug-report.md

@@ -27,7 +27,7 @@ If applicable, add screenshots to help explain your problem.
 **Platform (please complete the following information):**
 - Machine [e.g. LLNL/Quartz] 
 - Compiler: [e.g. gcc 8.1.0]
-- GEOSX Version [e.g. 0.2]
+- GEOS Version [e.g. 0.2]
 
 **Additional context**
 Add any other context about the problem here.

.integrated_tests.yaml

@@ -1,6 +1,6 @@
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr3197-6679-a003f43
+  baseline: integratedTests/baseline_integratedTests-pr3278-6753-f7f9add
 
 allow_fail:
   all: ''

BASELINE_NOTES.md

@@ -6,9 +6,11 @@ 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 3197 (2024-08-07)
+
+
+PR 3278 (2024-08-12)
 ====================
-Separation of contact and friction laws.
+Renamed GEOSX to GEOS in enternal mesh import, so rebaseline to change these names is the baselines. 
 
 PR #3202 (2024-08-03)
 ======================

inputFiles/compositionalMultiphaseWell/benchmarks/Class09Pb3/class09_pb3_benchmark.xml

@@ -16,7 +16,7 @@
       logLevel="5"  
       file="../../../../../GEOSDATA/DataSets/Class09_p3/Johansen_faces.vtu"
       fieldsToImport="{ perm, poro }"
-      fieldNamesInGEOSX="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
+      fieldNamesInGEOS="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
       <InternalWell
         name="wellInjector1"
         wellRegionName="wellRegion"

inputFiles/compositionalMultiphaseWell/benchmarks/Class09Pb3/class09_pb3_benchmark_mc.xml

@@ -16,7 +16,7 @@
       logLevel="5"  
       file="../../../../../GEOSXDATA/DataSets/Class09_p3/Johansen_faces.vtu"
       fieldsToImport="{ perm, poro }"
-      fieldNamesInGEOSX="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
+      fieldNamesInGEOS="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
       <InternalWell
         name="wellInjector1"
         wellRegionName="wellRegion"

inputFiles/compositionalMultiphaseWell/benchmarks/Class09Pb3/class09_pb3_benchmark_mct.xml

@@ -16,7 +16,7 @@
       logLevel="5"  
       file="../../../../../GEOSXDATA/DataSets/Class09_p3/Johansen_faces.vtu"
       fieldsToImport="{ perm, poro }"
-      fieldNamesInGEOSX="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
+      fieldNamesInGEOS="{ rockPerm_permeability, rockPorosity_referencePorosity }" >
       <InternalWell
         name="wellInjector1"
         wellRegionName="wellRegion"

inputFiles/compositionalMultiphaseWell/benchmarks/Egg/deadOilEggVTK_benchmark.xml

@@ -13,7 +13,7 @@
       name="mesh"
       file="../../../../../GEOSDATA/DataSets/Egg/egg.vtu"
       fieldsToImport="{ PERM }"
-      fieldNamesInGEOSX="{ rockPerm_permeability }">
+      fieldNamesInGEOS="{ rockPerm_permeability }">
 
       <VTKWell
         name="wellProducer1"

inputFiles/compositionalMultiphaseWell/benchmarks/Egg/deadOilEgg_benchmark.xml

@@ -13,7 +13,7 @@
       name="mesh"
       file="../../../../../GEOSDATA/DataSets/Egg/egg.vtu"
       fieldsToImport="{ PERM }"
-      fieldNamesInGEOSX="{ rockPerm_permeability }">
+      fieldNamesInGEOS="{ rockPerm_permeability }">
 
       <InternalWell
         name="wellProducer1"

inputFiles/compositionalMultiphaseWell/staircase_co2_wells_hybrid_3d.xml

@@ -61,7 +61,7 @@
       name="mesh1"
       file="staircase3d_tet_with_properties.vtu"
       fieldsToImport="{ FluidComposition, PERM, PORO }"
-      fieldNamesInGEOSX="{ globalCompFraction, rockPerm_permeability, rockPorosity_referencePorosity }"
+      fieldNamesInGEOS="{ globalCompFraction, rockPerm_permeability, rockPorosity_referencePorosity }"
       partitionRefinement="1"
       logLevel="2">
 

inputFiles/poromechanics/PoroElastic_hybridHexPrism_co2_base.xml

@@ -10,7 +10,7 @@
       partitionMethod="ptscotch"
       scale="{ 50, 50, 50 }"
       fieldsToImport="{ PORO, NTG, DENSITY, BULKMOD }"
-      fieldNamesInGEOSX="{ rockPorosity_referencePorosity, netToGross, skeleton_density, skeleton_bulkModulus }"
+      fieldNamesInGEOS="{ rockPorosity_referencePorosity, netToGross, skeleton_density, skeleton_bulkModulus }"
       file="../singlePhaseFlow/pebi3d_with_properties.vtu"/>
 
   </Mesh>

inputFiles/poromechanics/nonlinearAcceleration/smallEggModel/smallEggModel.xml

@@ -69,7 +69,7 @@
       file="../../../GEOSDATA/DataSets/Egg/egg_withBurdens_small.vts"
       regionAttribute="elementRegionMarker"
       fieldsToImport="{ PERM }"
-      fieldNamesInGEOSX="{ rockPermeability_permeability }"/>
+      fieldNamesInGEOS="{ rockPermeability_permeability }"/>
   </Mesh>
 
   <Geometry>

inputFiles/poromechanicsFractures/PoroElastic_efem-edfm_eggModel_large.xml

@@ -63,7 +63,7 @@
       file="../../../GEOSDATA/DataSets/Egg/egg_withBurdens_large.vts"
       regionAttribute="regionAttribute"
       fieldsToImport="{ PERM }"
-      fieldNamesInGEOSX="{ rockPermeability_permeability }"/>
+      fieldNamesInGEOS="{ rockPermeability_permeability }"/>
   </Mesh>
 
   <Geometry>

inputFiles/poromechanicsFractures/PoroElastic_efem-edfm_eggModel_small.xml

@@ -63,7 +63,7 @@
       file="../../../GEOSDATA/DataSets/Egg/egg_withBurdens_small.vts"
       regionAttribute="elementRegionMarker"
       fieldsToImport="{ PERM }"
-      fieldNamesInGEOSX="{ rockPermeability_permeability }"/>
+      fieldNamesInGEOS="{ rockPermeability_permeability }"/>
   </Mesh>
 
   <Geometry>

inputFiles/poromechanicsFractures/verticalFault_ExternalMesh.vtm

@@ -5,7 +5,7 @@
           name="main" 
           file="Domain_Mesh_FaultModel.vtu"
           fieldsToImport="{ YoungModulus, PoissonRatio  }"
-          fieldNamesInGEOSX="{ rock_youngModulus, rock_poissonRatio }"
+          fieldNamesInGEOS="{ rock_youngModulus, rock_poissonRatio }"
         />
         <DataSet 
           name="fracture" 

inputFiles/singlePhaseFlow/incompressible_pebi3d.xml

@@ -23,7 +23,7 @@
       partitionRefinement="3"
       useGlobalIds="1"
       fieldsToImport="{ PERM, PORO, NTG }"
-      fieldNamesInGEOSX="{ rockPerm_permeability, rockPorosity_referencePorosity, netToGross }"
+      fieldNamesInGEOS="{ rockPerm_permeability, rockPorosity_referencePorosity, netToGross }"
 
       file="pebi3d_with_properties.vtu"/>
   </Mesh>

inputFiles/thermoPoromechanicsFractures/ThermoPoroElastic_efem-edfm_eggModel_small.xml

@@ -66,7 +66,7 @@
       file="../../../GEOSDATA/DataSets/Egg/egg_withBurdens_small.vts"
       regionAttribute="elementRegionMarker"
       fieldsToImport="{ PERM }"
-      fieldNamesInGEOSX="{ rockPermeability_permeability }"/>
+      fieldNamesInGEOS="{ rockPermeability_permeability }"/>
   </Mesh>
 
   <Geometry>

src/conf.py

@@ -79,9 +79,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = u'GEOSX'
-copyright = u'2018-2021 Lawrence Livermore National Security, The Board of Trustees of the Leland Stanford Junior University, TotalEnergies, and GEOSX Contributors.'
-author = u'GEOSX Contributors'
+project = u'GEOS'
+copyright = u'2016-2024 Lawrence Livermore National Security LLC, 2018-2024 Total, S.A, The Board of Trustees of the Leland Stanford Junior University, 2023-2024 Chevron, 2019- GEOS/GEOSX Contributors'
+author = u'GEOS/GEOSX Contributors'
 
 # The short X.Y version
 version = u''
@@ -220,8 +220,8 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'GEOSX.tex', u'GEOSX Documentation',
-     u'Randolph Settgast', 'manual'),
+    (master_doc, 'GEOS.tex', u'GEOS Documentation',
+     u'GEOS/GEOSX Developers', 'manual'),
 ]
 
 
@@ -230,7 +230,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'geosx', u'GEOSX Documentation',
+    (master_doc, 'geos', u'GEOS Documentation',
      [author], 1)
 ]
 
@@ -241,8 +241,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'GEOSX', u'GEOSX Documentation',
-     author, 'GEOSX', 'One line description of project.',
+    (master_doc, 'GEOS', u'GEOS Documentation',
+     author, 'GEOS', 'GEOS simulation framework.',
      'Miscellaneous'),
 ]
 

src/coreComponents/mesh/generators/ExternalMeshGeneratorBase.cpp

@@ -46,20 +46,20 @@ ExternalMeshGeneratorBase::ExternalMeshGeneratorBase( string const & name,
     setInputFlag( InputFlags::OPTIONAL ).
     setDescription( "Volumic fields to be imported from the external mesh file" );
 
-  registerWrapper( viewKeyStruct::volumicFieldsInGEOSXString(), &m_volumicFieldsInGEOSX ).
+  registerWrapper( viewKeyStruct::volumicFieldsInGEOSString(), &m_volumicFieldsInGEOS ).
     setRTTypeName( rtTypes::CustomTypes::groupNameRefArray ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Names of the volumic fields in GEOSX to import into" );
+    setDescription( "Names of the volumic fields in GEOS to import into" );
 
   registerWrapper( viewKeyStruct::surfacicFieldsToImportString(), &m_surfacicFieldsToImport ).
     setRTTypeName( rtTypes::CustomTypes::groupNameRefArray ).
     setInputFlag( InputFlags::OPTIONAL ).
     setDescription( "Surfacic fields to be imported from the external mesh file" );
 
-  registerWrapper( viewKeyStruct::surfacicFieldsInGEOSXString(), &m_surfacicFieldsInGEOSX ).
+  registerWrapper( viewKeyStruct::surfacicFieldsInGEOSString(), &m_surfacicFieldsInGEOS ).
     setRTTypeName( rtTypes::CustomTypes::groupNameRefArray ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Names of the surfacic fields in GEOSX to import into" );
+    setDescription( "Names of the surfacic fields in GEOS to import into" );
 }
 
 void ExternalMeshGeneratorBase::postInputInitialization()
@@ -73,8 +73,8 @@ void ExternalMeshGeneratorBase::postInputInitialization()
                           " must contain the same number of values.",
                           InputError );
   };
-  checkSizes( m_volumicFieldsToImport, m_volumicFieldsInGEOSX, viewKeyStruct::volumicFieldsToImportString(), viewKeyStruct::volumicFieldsInGEOSXString() );
-  checkSizes( m_surfacicFieldsToImport, m_surfacicFieldsInGEOSX, viewKeyStruct::surfacicFieldsToImportString(), viewKeyStruct::surfacicFieldsInGEOSXString() );
+  checkSizes( m_volumicFieldsToImport, m_volumicFieldsInGEOS, viewKeyStruct::volumicFieldsToImportString(), viewKeyStruct::volumicFieldsInGEOSString() );
+  checkSizes( m_surfacicFieldsToImport, m_surfacicFieldsInGEOS, viewKeyStruct::surfacicFieldsToImportString(), viewKeyStruct::surfacicFieldsInGEOSString() );
 
   auto const checkDuplicates = [this]( arrayView1d< string const > v, string const & key )
   {
@@ -86,8 +86,8 @@ void ExternalMeshGeneratorBase::postInputInitialization()
                    "' already present in list of fields to import.",
                    InputError );
   };
-  checkDuplicates( m_volumicFieldsInGEOSX, viewKeyStruct::volumicFieldsInGEOSXString() );
-  checkDuplicates( m_surfacicFieldsInGEOSX, viewKeyStruct::surfacicFieldsInGEOSXString() );
+  checkDuplicates( m_volumicFieldsInGEOS, viewKeyStruct::volumicFieldsInGEOSString() );
+  checkDuplicates( m_surfacicFieldsInGEOS, viewKeyStruct::surfacicFieldsInGEOSString() );
 
   // Building the fields mapping from the two separated input/output vectors.
   auto const buildMapping = [&]( arrayView1d< string const > from,
@@ -101,8 +101,8 @@ void ExternalMeshGeneratorBase::postInputInitialization()
     return mapping;
   };
 
-  MeshGeneratorBase::m_volumicFields = buildMapping( m_volumicFieldsToImport.toViewConst(), m_volumicFieldsInGEOSX.toViewConst() );
-  MeshGeneratorBase::m_surfacicFields = buildMapping( m_surfacicFieldsToImport.toViewConst(), m_surfacicFieldsInGEOSX.toViewConst() );
+  MeshGeneratorBase::m_volumicFields = buildMapping( m_volumicFieldsToImport.toViewConst(), m_volumicFieldsInGEOS.toViewConst() );
+  MeshGeneratorBase::m_surfacicFields = buildMapping( m_surfacicFieldsToImport.toViewConst(), m_surfacicFieldsInGEOS.toViewConst() );
 }
 
 } // namespace geos

src/coreComponents/mesh/generators/ExternalMeshGeneratorBase.hpp

@@ -49,9 +49,9 @@ class ExternalMeshGeneratorBase : public MeshGeneratorBase
     constexpr static char const * scaleString() { return "scale"; }
     constexpr static char const * translateString() { return "translate"; }
     constexpr static char const * volumicFieldsToImportString() { return "fieldsToImport"; }
-    constexpr static char const * volumicFieldsInGEOSXString() { return "fieldNamesInGEOSX"; }
+    constexpr static char const * volumicFieldsInGEOSString() { return "fieldNamesInGEOS"; }
     constexpr static char const * surfacicFieldsToImportString() { return "surfacicFieldsToImport"; }
-    constexpr static char const * surfacicFieldsInGEOSXString() { return "surfacicFieldsInGEOSX"; }
+    constexpr static char const * surfacicFieldsInGEOSString() { return "surfacicFieldsInGEOS"; }
   };
   /// @endcond
 
@@ -66,17 +66,17 @@ class ExternalMeshGeneratorBase : public MeshGeneratorBase
   /// Scale factor that will be applied to the point coordinates (after translation)
   R1Tensor m_scale;
 
-  /// Names of the fields to be copied from an external reader into GEOSX data structure
+  /// Names of the fields to be copied from an external reader into GEOS data structure
   array1d< string > m_volumicFieldsToImport;
 
-  /// String array of the GEOSX user declared volumic fields
-  array1d< string > m_volumicFieldsInGEOSX;
+  /// String array of the GEOS user declared volumic fields
+  array1d< string > m_volumicFieldsInGEOS;
 
-  /// Names of the surfacic fields to be copied from an external reader into GEOSX data structure
+  /// Names of the surfacic fields to be copied from an external reader into GEOS data structure
   array1d< string > m_surfacicFieldsToImport;
 
-  /// String array of the GEOSX user declared surfacic fields
-  array1d< string > m_surfacicFieldsInGEOSX;
+  /// String array of the GEOS user declared surfacic fields
+  array1d< string > m_surfacicFieldsInGEOS;
 };
 
 } // namespace geos

src/coreComponents/mesh/generators/MeshGeneratorBase.hpp

@@ -114,22 +114,22 @@ class MeshGeneratorBase : public dataRepository::Group
   virtual void freeResources() {}
 
   /**
-   * @brief Get the name mapping between mesh volumic field names and internal GEOSX volumic field names.
+   * @brief Get the name mapping between mesh volumic field names and internal GEOS volumic field names.
    * @return The string to string mapping of field names.
    */
   std::map< string, string > const & getVolumicFieldsMapping() const { return m_volumicFields; }
 
   /**
-   * @brief Get the name mapping between mesh surfacic field names and internal GEOSX surfacic field names.
+   * @brief Get the name mapping between mesh surfacic field names and internal GEOS surfacic field names.
    * @return The string to string mapping of field names.
    */
   std::map< string, string > const & getSurfacicFieldsMapping() const { return m_surfacicFields; }
 
 protected:
-  /// Mapping from volumic field source to GEOSX field.
+  /// Mapping from volumic field source to GEOS field.
   std::map< string, string > m_volumicFields;
 
-  /// Mapping from surfacic field source to GEOSX field.
+  /// Mapping from surfacic field source to GEOS field.
   std::map< string, string > m_surfacicFields;
 
 private: