Merge branch 'develop' into pt/deltaVolume-fix

GEOS-DEV · Dec 23, 2024 · 10fadd4 · 10fadd4
2 parents 805e889 + b3592de
commit 10fadd4
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,7 +2,7 @@
     "build": {
         "dockerfile": "Dockerfile",
         "args": {
-            "GEOS_TPL_TAG": "286-547"
+            "GEOS_TPL_TAG": "288-584"
         }
     },
     "runArgs": [

diff --git a/.github/workflows/ci_tests.yml b/.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"

diff --git a/.integrated_tests.yaml b/.integrated_tests.yaml
@@ -1,6 +1,6 @@
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr2637-8940-3c0fc5c
+  baseline: integratedTests/baseline_integratedTests-pr3479-9362-cffefcc
 allow_fail:
   all: ''
   streak: ''
diff --git a/BASELINE_NOTES.md b/BASELINE_NOTES.md
@@ -6,6 +6,46 @@ 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 #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.

diff --git a/COPYRIGHT b/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

diff --git a/RELEASE b/RELEASE
diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
diff --git a/examples/ObjectCatalog/Base.hpp b/examples/ObjectCatalog/Base.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

diff --git a/examples/ObjectCatalog/Derived1.cpp b/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

diff --git a/examples/ObjectCatalog/Derived1.hpp b/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

diff --git a/examples/ObjectCatalog/Derived2.cpp b/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.

diff --git a/examples/ObjectCatalog/Derived2.hpp b/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

diff --git a/examples/ObjectCatalog/main.cpp b/examples/ObjectCatalog/main.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

diff --git a/host-configs/LLNL/lassen-clang-10-cuda-11.cmake b/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 "")
diff --git a/host-configs/LLNL/lassen-clang-13-cuda-11.cmake b/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)
 

diff --git a/host-configs/LLNL/lassen-gcc-8-cuda-11.cmake b/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)
diff --git a/host-configs/apple/macOS_base.cmake b/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)
 
 
 

diff --git a/inputFiles/compositionalMultiphaseFlow/2ph_cap_1d_ihu.xml b/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

diff --git a/inputFiles/compositionalMultiphaseFlow/4comp_2ph_1d.xml b/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

diff --git a/inputFiles/compositionalMultiphaseFlow/4comp_2ph_cap_1d.xml b/inputFiles/compositionalMultiphaseFlow/4comp_2ph_cap_1d.xml
@@ -45,7 +45,7 @@
     maxTime="2e7">
     <PeriodicEvent
       name="outputs"
-      timeFrequency="1e6"
+      timeFrequency="1e7"
       target="/Outputs/siloOutput"/>
 
     <PeriodicEvent
@@ -77,8 +77,7 @@
   <NumericalMethods>
     <FiniteVolume>
       <TwoPointFluxApproximation
-        name="fluidTPFA"
-        />
+        name="fluidTPFA"/>
     </FiniteVolume>
   </NumericalMethods>
 
@@ -117,7 +116,7 @@
     <PressurePorosity
       name="rockPorosity"
       defaultReferencePorosity="0.2"
-      referencePressure="0.0"
+      referencePressure="5e6"
       compressibility="1.0e-9"/>
 
     <BrooksCoreyRelativePermeability

diff --git a/inputFiles/compositionalMultiphaseFlow/co2_flux_3d.xml b/inputFiles/compositionalMultiphaseFlow/co2_flux_3d.xml
@@ -9,12 +9,10 @@
       temperature="368.15"
       useMass="1"
       useTotalMassEquation="0"
-      useSimpleAccumulation="1"
       targetRegions="{ region }">
       <NonlinearSolverParameters
         newtonTol="1.0e-5"
-        newtonMaxIter="100"
-        maxTimeStepCuts="5"
+        newtonMaxIter="10"
         lineSearchAction="None"/>
       <LinearSolverParameters
         directParallel="0"/>
@@ -92,7 +90,7 @@
 
     <PeriodicEvent
       name="outputs"
-      timeFrequency="1e5"
+      timeFrequency="5e5"
       target="/Outputs/vtkOutput"/>
 
     <PeriodicEvent
@@ -136,7 +134,7 @@
     <PressurePorosity
       name="rockPorosity"
       defaultReferencePorosity="0.2"
-      referencePressure="0.0"
+      referencePressure="1.1e7"
       compressibility="1.0e-9"/>
     <ConstantPermeability
       name="rockPerm"

diff --git a/inputFiles/compositionalMultiphaseFlow/co2_flux_dirichlet.xml b/inputFiles/compositionalMultiphaseFlow/co2_flux_dirichlet.xml
@@ -11,8 +11,7 @@
       targetRegions="{ region }">
       <NonlinearSolverParameters
         newtonTol="1.0e-4"
-        newtonMaxIter="100"
-        maxTimeStepCuts="5"
+        newtonMaxIter="20"
         lineSearchAction="None"/>
       <LinearSolverParameters
         solverType="fgmres"
@@ -61,7 +60,7 @@
 
     <PeriodicEvent
       name="outputs"
-      timeFrequency="1e5"
+      timeFrequency="5e5"
       targetExactTimestep="1"
       target="/Outputs/vtkOutput" />