Merge branch 'develop' into feature/algiane/pangea3-action

GEOS-DEV · Aug 14, 2024 · f422517 · f422517
2 parents df5622c + f3eb4dc
commit f422517
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diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.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.
diff --git a/.integrated_tests.yaml b/.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: ''

diff --git a/BASELINE_NOTES.md b/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)
 ======================

diff --git a/inputFiles/compositionalMultiphaseWell/benchmarks/Class09Pb3/class09_pb3_benchmark.xml b/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"

diff --git a/inputFiles/compositionalMultiphaseWell/benchmarks/Class09Pb3/class09_pb3_benchmark_mc.xml b/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"

diff --git a/inputFiles/compositionalMultiphaseWell/benchmarks/Class09Pb3/class09_pb3_benchmark_mct.xml b/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"

diff --git a/inputFiles/compositionalMultiphaseWell/benchmarks/Egg/deadOilEggVTK_benchmark.xml b/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"

diff --git a/inputFiles/compositionalMultiphaseWell/benchmarks/Egg/deadOilEgg_benchmark.xml b/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"

diff --git a/inputFiles/compositionalMultiphaseWell/staircase_co2_wells_hybrid_3d.xml b/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">
 

diff --git a/inputFiles/poromechanics/PoroElastic_hybridHexPrism_co2_base.xml b/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>

diff --git a/inputFiles/poromechanics/nonlinearAcceleration/smallEggModel/smallEggModel.xml b/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>

diff --git a/inputFiles/poromechanicsFractures/PoroElastic_efem-edfm_eggModel_large.xml b/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>

diff --git a/inputFiles/poromechanicsFractures/PoroElastic_efem-edfm_eggModel_small.xml b/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>

diff --git a/inputFiles/poromechanicsFractures/verticalFault_ExternalMesh.vtm b/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" 

diff --git a/inputFiles/singlePhaseFlow/incompressible_pebi3d.xml b/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>

diff --git a/inputFiles/thermoPoromechanicsFractures/ThermoPoroElastic_efem-edfm_eggModel_small.xml b/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>

diff --git a/src/conf.py b/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'),
 ]
 

diff --git a/src/coreComponents/LvArray b/src/coreComponents/LvArray
diff --git a/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/BrineEnthalpy.hpp b/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/BrineEnthalpy.hpp
@@ -144,7 +144,7 @@ void BrineEnthalpyUpdate::compute( real64 const & pressure,
                                    arraySlice1d< real64, USD3 > const & dValue,
                                    bool useMass ) const
 {
-  using Deriv = multifluid::DerivativeOffset;
+  using Deriv = constitutive::multifluid::DerivativeOffset;
 
   real64 const input[2] = { pressure, temperature };
   real64 brineEnthalpy_dTemperature = 0.0;

diff --git a/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/CO2Enthalpy.hpp b/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/CO2Enthalpy.hpp
@@ -131,7 +131,7 @@ void CO2EnthalpyUpdate::compute( real64 const & pressure,
 {
   GEOS_UNUSED_VAR( phaseComposition, dPhaseComposition );
 
-  using Deriv = multifluid::DerivativeOffset;
+  using Deriv = constitutive::multifluid::DerivativeOffset;
 
   real64 const input[2] = { pressure, temperature };
   real64 CO2EnthalpyDeriv[2]{};

diff --git a/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/CO2Solubility.hpp b/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/CO2Solubility.hpp
@@ -42,8 +42,8 @@ class CO2SolubilityUpdate final : public FlashModelBaseUpdate
 {
 public:
 
-  using PhaseProp = MultiFluidVar< real64, 3, multifluid::LAYOUT_PHASE, multifluid::LAYOUT_PHASE_DC >;
-  using PhaseComp = MultiFluidVar< real64, 4, multifluid::LAYOUT_PHASE_COMP, multifluid::LAYOUT_PHASE_COMP_DC >;
+  using PhaseProp = MultiFluidVar< real64, 3, constitutive::multifluid::LAYOUT_PHASE, constitutive::multifluid::LAYOUT_PHASE_DC >;
+  using PhaseComp = MultiFluidVar< real64, 4, constitutive::multifluid::LAYOUT_PHASE_COMP, constitutive::multifluid::LAYOUT_PHASE_COMP_DC >;
 
   CO2SolubilityUpdate( arrayView1d< real64 const > const & componentMolarWeight,
                        TableFunction const & CO2SolubilityTable,
@@ -167,7 +167,7 @@ CO2SolubilityUpdate::compute( real64 const & pressure,
                               PhaseProp::SliceType const phaseFraction,
                               PhaseComp::SliceType const phaseCompFraction ) const
 {
-  using Deriv = multifluid::DerivativeOffset;
+  using Deriv = constitutive::multifluid::DerivativeOffset;
 
   // Solubility of CO2 is read from the tables in the form of moles of CO2 per kg of water
   // Solubility of water is read from the tables in the form of moles of water per kg of CO2

diff --git a/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/EzrokhiBrineDensity.hpp b/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/EzrokhiBrineDensity.hpp
@@ -173,7 +173,7 @@ void EzrokhiBrineDensityUpdate::compute( real64 const & pressure,
                                          bool useMass ) const
 {
   constexpr integer numDof = 4;
-  using Deriv = multifluid::DerivativeOffset;
+  using Deriv = constitutive::multifluid::DerivativeOffset;
 
   real64 waterSatDensity_dTemperature = 0.0;
   real64 waterSatPressure_dTemperature = 0.0;

diff --git a/...coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/EzrokhiBrineViscosity.hpp b/...coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/EzrokhiBrineViscosity.hpp
@@ -158,7 +158,7 @@ void EzrokhiBrineViscosityUpdate::compute( real64 const & pressure,
 {
   GEOS_UNUSED_VAR( pressure, useMass );
 
-  using Deriv = multifluid::DerivativeOffset;
+  using Deriv = constitutive::multifluid::DerivativeOffset;
 
   real64 waterVisc_dTemperature = 0.0;
   real64 const waterVisc = m_waterViscosityTable.compute( &temperature, &waterVisc_dTemperature );

diff --git a/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/FenghourCO2Viscosity.hpp b/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/FenghourCO2Viscosity.hpp
@@ -125,7 +125,7 @@ void FenghourCO2ViscosityUpdate::compute( real64 const & pressure,
                    dPhaseComposition,
                    useMass );
 
-  using Deriv = multifluid::DerivativeOffset;
+  using Deriv = constitutive::multifluid::DerivativeOffset;
 
   real64 const input[2] = { pressure, temperature };
   real64 densityDeriv[2]{};

diff --git a/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/PhillipsBrineDensity.hpp b/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/PhillipsBrineDensity.hpp
@@ -136,7 +136,7 @@ void PhillipsBrineDensityUpdate::compute( real64 const & pressure,
                                           arraySlice1d< real64, USD3 > const & dValue,
                                           bool useMass ) const
 {
-  using Deriv = multifluid::DerivativeOffset;
+  using Deriv = constitutive::multifluid::DerivativeOffset;
 
   // this method implements the method proposed by E. Garcia (2001)
 

diff --git a/...oreComponents/constitutive/fluid/multifluid/CO2Brine/functions/PhillipsBrineViscosity.hpp b/...oreComponents/constitutive/fluid/multifluid/CO2Brine/functions/PhillipsBrineViscosity.hpp
@@ -140,7 +140,7 @@ void PhillipsBrineViscosityUpdate::compute( real64 const & pressure,
                    dPhaseComposition,
                    useMass );
 
-  using Deriv = multifluid::DerivativeOffset;
+  using Deriv = constitutive::multifluid::DerivativeOffset;
 
   // compute the viscosity of pure water as a function of temperature
   real64 dPureWaterVisc_dTemperature;

diff --git a/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/SpanWagnerCO2Density.hpp b/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/SpanWagnerCO2Density.hpp
@@ -135,7 +135,7 @@ void SpanWagnerCO2DensityUpdate::compute( real64 const & pressure,
 {
   GEOS_UNUSED_VAR( phaseComposition, dPhaseComposition );
 
-  using Deriv = multifluid::DerivativeOffset;
+  using Deriv = constitutive::multifluid::DerivativeOffset;
 
   real64 const input[2] = { pressure, temperature };
   real64 densityDeriv[2]{};

diff --git a/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/WaterDensity.hpp b/src/coreComponents/constitutive/fluid/multifluid/CO2Brine/functions/WaterDensity.hpp
@@ -118,7 +118,7 @@ void WaterDensityUpdate::compute( real64 const & pressure,
 {
   GEOS_UNUSED_VAR( phaseComposition, dPhaseComposition, useMass );
 
-  using Deriv = multifluid::DerivativeOffset;
+  using Deriv = constitutive::multifluid::DerivativeOffset;
 
   real64 const input[2] = { pressure, temperature };
   real64 densityDeriv[2]{};