Merge branch 'develop' into feature/byer3/single_phase_prop_refactor

.devcontainer/devcontainer.json

@@ -2,7 +2,7 @@
     "build": {
         "dockerfile": "Dockerfile",
         "args": {
-            "GEOS_TPL_TAG": "286-547"
+            "GEOS_TPL_TAG": "288-584"
         }
     },
     "runArgs": [

.github/workflows/ci_tests.yml

@@ -330,7 +330,7 @@ jobs:
             DOCKER_CERTS_DIR: "/etc/pki/ca-trust/source/anchors"
             DOCKER_CERTS_UPDATE_COMMAND: "update-ca-trust"
 
-          - name: Pangea 3 (AlmaLinux 8.8, gcc 9.4.0, open-mpi 4.1.2, cuda 11.5.0, openblas 0.3.10)
+          - name: Pangea 3 CUDA (AlmaLinux 8.8, gcc 9.4.0, open-mpi 4.1.2, cuda 11.5.0, openblas 0.3.10)
             BUILD_AND_TEST_CLI_ARGS: "--build-exe-only --no-install-schema"
             CMAKE_BUILD_TYPE: Release
             BUILD_GENERATOR: "--makefile"

.integrated_tests.yaml

@@ -1,6 +1,6 @@
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr2637-8940-3c0fc5c
+  baseline: integratedTests/baseline_integratedTests-pr3495-9552-257c87e
 allow_fail:
   all: ''
   streak: ''

BASELINE_NOTES.md

@@ -6,6 +6,58 @@ 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 #3495 (2024-01-08)
+=====================
+Add missing logic to support switching from fixed mass rate injection rate constraint to max injection pressure.
+
+PR #3384 (2024-01-07)
+=====================
+Added plastic strain output.
+
+PR #3486 (2025-01-06)
+=====================
+useNewGravity became gravityDensityScheme.
+
+PR #3479 (2024-12-15)
+=====================
+Refine inputFiles/compositionalMultiphaseFlow: shift reference pressures to initial pressures, make nonlinear tuning more reasonable, minimize output.
+
+PR #3450 (2024-12-14)
+=====================
+Fix timestep selector flaw in SolidMechanicsLagrangeContact.
+
+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".
+
+PR #3393 (2024-12-02)
+=====================
+Fix netToGross bug.
+
+PR #3381 (2024-12-01)
+=====================
+A few baseline diffs for order FaceElementSubRegion::m_toFacesRelation map. Not sure why this was changed by this PR, but the previous order seems incorrect for a couple of cases.
+
+PR #2957 (2024-11-27)
+=====================
+Added ExternalDataRepository.
+
+PR #3448 (2024-11-21)
+=====================
+Switched the FaceElementSubRegion::m_toFacesRelation and FaceElementSubRegion::m_2dElemToElems back to array2d instead of ArrayOfArray. This results in a reordering m_toFacesRelation back to the "correct" assumed order of "original face first". This fixes a bug that failed to remove the CellStencil entry when a FaceElement splits two cells.
+
 PR #2637 (2024-11-21)
 =====================
 Added numberOfTargetProcesses.

COPYRIGHT

@@ -8,7 +8,7 @@ contributors. The following copyright applies to each file in the GEOS
 distribution, unless otherwise stated in the file:
 
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
  * Copyright (c) 2023-2024 Chevron 
  * Copyright (c) 2019-     GEOS/GEOSX Contributors

examples/ObjectCatalog/Base.hpp

@@ -3,9 +3,9 @@
  * SPDX-License-Identifier: LGPL-2.1-only
  *
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
- * Copyright (c) 2023-2024 Chevron 
+ * Copyright (c) 2023-2024 Chevron
  * Copyright (c) 2019-     GEOS/GEOSX Contributors
  * All rights reserved
  *
@@ -46,7 +46,7 @@ class Parameter
 class Base
 {
 public:
-  Base( int junk, double const & junk2, Parameter& pbv )
+  Base( int junk, double const & junk2, Parameter & pbv )
   {
     GEOS_LOG( "calling Base constructor with arguments (" << junk << " " << junk2 << ")" );
   }
@@ -56,14 +56,20 @@ class Base
     GEOS_LOG( "calling Base destructor" );
   }
 
-  using CatalogInterface = dataRepository::CatalogInterface< Base, int, double const &, Parameter& >;
-  static CatalogInterface::CatalogType& getCatalog()
+  using CatalogInterface = dataRepository::CatalogInterface< Base, int, double const &, Parameter & >;
+  static CatalogInterface::CatalogType & getCatalog()
   {
     static CatalogInterface::CatalogType catalog;
     return catalog;
   }
 
   virtual std::string const getName() const = 0;
+
+  static DataContext const & getDataContext()
+  {
+    static DataFileContext const context = DataFileContext( "Base Test Class", __FILE__, __LINE__ );
+    return context;
+  }
 };
 
 #endif

examples/ObjectCatalog/Derived1.cpp

@@ -3,7 +3,7 @@
  * SPDX-License-Identifier: LGPL-2.1-only
  *
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
  * Copyright (c) 2023-2024 Chevron 
  * Copyright (c) 2019-     GEOS/GEOSX Contributors

examples/ObjectCatalog/Derived1.hpp

@@ -3,7 +3,7 @@
  * SPDX-License-Identifier: LGPL-2.1-only
  *
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
  * Copyright (c) 2023-2024 Chevron 
  * Copyright (c) 2019-     GEOS/GEOSX Contributors

examples/ObjectCatalog/Derived2.cpp

@@ -2,10 +2,11 @@
  * ------------------------------------------------------------------------------------------------------------
  * SPDX-License-Identifier: LGPL-2.1-only
  *
- * Copyright (c) 2018-2020 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2020 The Board of Trustees of the Leland Stanford Junior University
- * Copyright (c) 2018-2020 Total, S.A
- * Copyright (c) 2019-     GEOSX Contributors
+ * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
+ * Copyright (c) 2018-2024 TotalEnergies
+ * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
+ * Copyright (c) 2023-2024 Chevron
+ * Copyright (c) 2019-     GEOS/GEOSX Contributors
  * All rights reserved
  *
  * See top level LICENSE, COPYRIGHT, CONTRIBUTORS, NOTICE, and ACKNOWLEDGEMENTS files for details.

examples/ObjectCatalog/Derived2.hpp

@@ -3,7 +3,7 @@
  * SPDX-License-Identifier: LGPL-2.1-only
  *
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
  * Copyright (c) 2023-2024 Chevron 
  * Copyright (c) 2019-     GEOS/GEOSX Contributors

examples/ObjectCatalog/main.cpp

@@ -3,9 +3,9 @@
  * SPDX-License-Identifier: LGPL-2.1-only
  *
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
- * Copyright (c) 2023-2024 Chevron 
+ * Copyright (c) 2023-2024 Chevron
  * Copyright (c) 2019-     GEOS/GEOSX Contributors
  * All rights reserved
  *
@@ -31,10 +31,14 @@ int main( int argc, char *argv[] )
 
 
   GEOS_LOG( "Attempting to create a Derived1 object" );
-  std::unique_ptr<Base> derived1 = Base::CatalogInterface::Factory( "derived1", junk, junk2, param );
+  std::unique_ptr< Base > derived1 = Base::CatalogInterface::factory( "derived1",
+                                                                      Base::getDataContext(),
+                                                                      junk, junk2, param );
   GEOS_LOG( "Attempting to create a Derived2 object" );
-  std::unique_ptr<Base> derived2 = Base::CatalogInterface::Factory( "derived2", junk, junk3, param );
+  std::unique_ptr< Base > derived2 = Base::CatalogInterface::factory( "derived2",
+                                                                      Base::getDataContext(),
+                                                                      junk, junk3, param );
 
-  Base::CatalogInterface::catalog_cast<Derived1>( *(derived2.get()));
+  Base::CatalogInterface::catalog_cast< Derived1 >( *(derived2.get()));
   GEOS_LOG( "EXITING MAIN" );
 }

host-configs/LLNL/lassen-clang-10-cuda-11.cmake

@@ -1,16 +1,16 @@
 include(${CMAKE_CURRENT_LIST_DIR}/../../src/coreComponents/LvArray/host-configs/LLNL/lassen-clang-10-cuda-11.cmake)
 
 # Fortran
-set(CMAKE_Fortran_COMPILER /usr/tce/packages/xl/xl-2022.08.19-cuda-11.8.0/bin/xlf_r  CACHE PATH "")
+set(CMAKE_Fortran_COMPILER /usr/tce/packages/xl/xl-2023.06.28/xlf/16.1.1/bin/xlf  CACHE PATH "")
 set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -qarch=pwr9 -qtune=pwr9" CACHE STRING "")
 set(FORTRAN_MANGLE_NO_UNDERSCORE ON CACHE BOOL "")
 set(OpenMP_Fortran_FLAGS "-qsmp=omp" CACHE STRING "")
 set(OpenMP_Fortran_LIB_NAMES "" CACHE STRING "")
 
 # MPI
 set(MPI_HOME /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-clang-10.0.1-gcc-8.3.1 CACHE PATH "")
-set(MPI_Fortran_COMPILER /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-xl-2022.08.19-cuda-11.8.0/bin/mpifort CACHE PATH "")
+set(MPI_Fortran_COMPILER /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-xl-2023.06.28-cuda-11.8.0/bin/mpifort CACHE PATH "")
 
 include(${CMAKE_CURRENT_LIST_DIR}/lassen-base.cmake)
 
-set(ENABLE_CUDA_NVTOOLSEXT OFF CACHE BOOL "")
+set(ENABLE_CUDA_NVTOOLSEXT ON CACHE BOOL "")

host-configs/LLNL/lassen-clang-13-cuda-11.cmake

@@ -1,15 +1,15 @@
 include(${CMAKE_CURRENT_LIST_DIR}/../../src/coreComponents/LvArray/host-configs/LLNL/lassen-clang-13-cuda-11.cmake)
 
 # Fortran
-set(CMAKE_Fortran_COMPILER /usr/tce/packages/xl/xl-2022.08.19-cuda-11.8.0/bin/xlf_r  CACHE PATH "")
+set(CMAKE_Fortran_COMPILER /usr/tce/packages/xl/xl-2023.06.28/xlf/16.1.1/bin/xlf  CACHE PATH "")
 set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -qarch=pwr9 -qtune=pwr9" CACHE STRING "")
 set(FORTRAN_MANGLE_NO_UNDERSCORE ON CACHE BOOL "")
 set(OpenMP_Fortran_FLAGS "-qsmp=omp" CACHE STRING "")
 set(OpenMP_Fortran_LIB_NAMES "" CACHE STRING "")
 
 # MPI
 set(MPI_HOME /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-clang-13.0.1-gcc-8.3.1 CACHE PATH "")
-set(MPI_Fortran_COMPILER /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-xl-2022.08.19-cuda-11.8.0/bin/mpifort CACHE PATH "")
+set(MPI_Fortran_COMPILER /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-xl-2023.06.28-cuda-11.8.0/bin/mpifort CACHE PATH "")
 
 include(${CMAKE_CURRENT_LIST_DIR}/lassen-base.cmake)
 

host-configs/LLNL/lassen-gcc-8-cuda-11.cmake

@@ -14,4 +14,6 @@ set(FORTRAN_MANGLE_NO_UNDERSCORE OFF CACHE BOOL "")
 set(MPI_HOME /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-8.3.1 CACHE PATH "")
 set(MPI_Fortran_COMPILER ${MPI_HOME}/bin/mpifort CACHE PATH "")
 
+set(ENABLE_CUDA_NVTOOLSEXT ON CACHE BOOL "")
+
 include(${CMAKE_CURRENT_LIST_DIR}/lassen-base.cmake)

host-configs/apple/macOS_base.cmake

@@ -29,7 +29,7 @@ set(ENABLE_DOXYGEN ON CACHE BOOL "" FORCE)
 set(ENABLE_SPHINX ON CACHE BOOL "" FORCE)
 set(ENABLE_MATHPRESSO ON CACHE BOOL "" FORCE )
 
-set(GEOS_BUILD_SHARED_LIBS ON CACHE BOOL "" FORCE)
+set(GEOS_BUILD_SHARED_LIBS OFF CACHE BOOL "" FORCE)
 
 
 

inputFiles/compositionalMultiphaseFlow/2ph_cap_1d_ihu.xml

@@ -94,7 +94,7 @@
     <PressurePorosity
         name="rockPorosity"
         defaultReferencePorosity="0.2"
-        referencePressure="0.0"
+        referencePressure="7.5e6"
         compressibility="1.0e-9"/>
 
     <BrooksCoreyRelativePermeability

inputFiles/compositionalMultiphaseFlow/4comp_2ph_1d.xml

@@ -104,7 +104,7 @@
     <PressurePorosity
       name="rockPorosity"
       defaultReferencePorosity="0.2"
-      referencePressure="0.0"
+      referencePressure="5e6"
       compressibility="1.0e-9"/>
 
     <BrooksCoreyRelativePermeability