Merge remote-tracking branch 'origin/develop' into feature/dudes/sect…

…ion-log
GEOS-DEV · Dec 9, 2024 · aea7a98 · aea7a98
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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": "284-535"
+            "GEOS_TPL_TAG": "286-547"
         }
     },
     "runArgs": [

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -10,37 +10,80 @@
 /.github/ @rrsettgast
 
 /BASELINE_NOTES.md
-/.integrated_tests.yaml                               @CusiniM @cssherman @rrsettgast @wrtobin @castelletto1 @jhuang2601 @paveltomin
-/inputFiles/                                          @CusiniM @cssherman @jhuang2601 @rrsettgast
-/src/coreComponents/LvArray                           @rrsettgast @wrtobin @corbett5 @CusiniM 
-/src/coreComponents/codingUtilities                   @rrsettgast @untereiner @corbett5 @wrtobin
+/.integrated_tests.yaml                               @rrsettgast @CusiniM @cssherman @wrtobin @castelletto1 @jhuang2601 @paveltomin
+/inputFiles                                           @rrsettgast @CusiniM  @cssherman @paveltomin @jhuang2601
+/inputFiles/compositionalMultiphaseFlow               @paveltomin @dkachuma
+/inputFiles/compositionalMultiphaseWell               @CusiniM @paveltomin @tjb-ltk @dkachuma
+/inputFiles/efemFractureMechanics                     @CusiniM @matteofrigo5 @Guotong-Ren
+/inputFiles/hydraulicFracturing                       @CusiniM @rrsettgast @frankfeifan @Guotong-Ren @cssherman @jhuang2601
+/inputFiles/inducedSeismicity                         @CusiniM @matteofrigo5 @VidarStiernstrom 
+/inputFiles/initialization                            @rrsettgast @jhuang2601 
+/inputFiles/lagrangianContactMechanics                @CusiniM @jhuang2601 @matteofrigo5 
+/inputFiles/materialPointMethod                       @homel1 @cmcrook5 
+/inputFiles/meshGeneration                            @rrsettgast @cssherman
+/inputFiles/multiphaseFlowFractures                   @CusiniM @paveltomin @jhuang2601
+/inputFiles/multipleMeshBodies                        @rrsettgast @wrtobin
+/inputFiles/phaseField                                @CusiniM @frankfeifan 
+/inputFiles/poromechanics                             @CusiniM @castelletto1 @paveltomin @jhuang2601 @ryar9534 
+/inputFiles/poromechanicsFractures                    @CusiniM @castelletto1 @paveltomin @jhuang2601
+/inputFiles/proppant                                  @rrsettgast @jhuang2601 
+/inputFiles/relpermDriver                             @dkachuma @paveltomin @jafranc
+/inputFiles/simplePDE                                 @rrsettgast @castelletto1 
+/inputFiles/singlePhaseFlow                           @CusiniM @castelletto1 @paveltomin
+/inputFiles/singlePhaseFlowFractures                  @CusiniM @castelletto1 @paveltomin @jhuang2601 
+/inputFiles/singlePhaseWell                           @CusiniM @paveltomin @tjb-ltk
+/inputFiles/solidMechanics                            @CusiniM @castelletto1 @jhuang2601 
+/inputFiles/surfaceGeneration                         @CusiniM @castelletto1 @rrsettgast 
+/inputFiles/thermalMultiphaseFlow                     @paveltomin @dkachuma
+/inputFiles/thermalSinglePhaseFlowFractures           @CusiniM @castelletto1 @paveltomin @jhuang2601 @frankfeifan
+/inputFiles/thermoPoromechanics                       @paveltomin @jhuang2601 @castelletto1 @frankfeifan
+/inputFiles/thermoPoromechanicsFractures              @CusiniM @castelletto1 @paveltomin @jhuang2601 
+/inputFiles/triaxialDriver                            @rrsettgast @jhuang2601
+/inputFiles/wavePropagation                           @acitrain @sframba
+/inputFiles/wellbore                                  @rrsettgast @jhuang2601
+/inputFiles/wellboreECP                               @rrsettgast 
+/src/coreComponents/LvArray                           @rrsettgast @CusiniM @wrtobin @corbett5 
+/src/coreComponents/codingUtilities                   @rrsettgast @untereiner @corbett5 @wrtobin @MelReyCG
 /src/coreComponents/common                            @rrsettgast @MelReyCG @corbett5 @wrtobin
-/src/coreComponents/constitutive                      @rrsettgast @CusiniM @dkachuma @paveltomin @joshua-white
-/src/coreComponents/dataRepository                    @rrsettgast @wrtobin @corbett5
+/src/coreComponents/constitutive                      @rrsettgast @CusiniM @dkachuma @paveltomin @castelletto1
+/src/coreComponents/constitutive/capillaryPressure    @CusiniM @dkachuma @paveltomin
+/src/coreComponents/constitutive/contact              @rrsettgast @CusiniM @matteofrigo5 @Guotong-Ren @jhuang2601 
+/src/coreComponents/constitutive/diffusion            @CusiniM @dkachuma @paveltomin 
+/src/coreComponents/constitutive/dispersion           @CusiniM @dkachuma @paveltomin 
+/src/coreComponents/constitutive/docs                  
+/src/coreComponents/constitutive/fluid                @CusiniM @dkachuma @paveltomin 
+/src/coreComponents/constitutive/permeability         @CusiniM @dkachuma @paveltomin @jhuang2601 
+/src/coreComponents/constitutive/pvtPackage           @CusiniM @dkachuma @paveltomin
+/src/coreComponents/constitutive/relativePermeability @dkachuma @paveltomin 
+/src/coreComponents/constitutive/solid                @rrsettgast @CusiniM @paveltomin @castelletto1 @jhuang2601 
+/src/coreComponents/constitutive/thermalConductivity  @CusiniM @dkachuma @paveltomin @jhuang2601 
+/src/coreComponents/constitutive/unitTests            @rrsettgast @CusiniM @dkachuma @paveltomin
+/src/coreComponents/constitutiveDrivers               @rrsettgast @CusiniM @dkachuma @jhuang2601
+/src/coreComponents/dataRepository                    @rrsettgast @wrtobin @corbett5 @MelReyCG 
 /src/coreComponents/denseLinearAlgebra                @rrsettgast @CusiniM @castelletto1 
 /src/coreComponents/discretizationMethods             @rrsettgast @CusiniM @castelletto1 
 /src/coreComponents/events                            @rrsettgast @corbett5 @cssherman 
 /src/coreComponents/fieldSpecification                @rrsettgast @CusiniM @corbett5 @cssherman 
 /src/coreComponents/fileIO                            @rrsettgast @wrtobin @MelReyCG @untereiner
 /src/coreComponents/finiteElement                     @rrsettgast @castelletto1 @andrea-borio @CusiniM
-/src/coreComponents/finiteVolume                      @rrsettgast @castelletto1 @CusiniM @paveltomin
-/src/coreComponents/functions                         @cssherman  @wrtobin @rrsettgast
-/src/coreComponents/linearAlgebra                     @rrsettgast @castelletto1 @victorapm 
+/src/coreComponents/finiteVolume                      @rrsettgast @castelletto1 @CusiniM @paveltomin @ryar9534
+/src/coreComponents/functions                         @rrsettgast @cssherman @wrtobin 
+/src/coreComponents/linearAlgebra                     @rrsettgast @CusiniM @castelletto1 @victorapm   
 /src/coreComponents/mainInterface                     @rrsettgast @corbett5 @wrtobin 
 /src/coreComponents/math                              @rrsettgast @corbett5 @wrtobin 
-/src/coreComponents/mesh                              @rrsettgast @wrtobin @untereiner @CusiniM 
+/src/coreComponents/mesh                              @rrsettgast @CusiniM  @wrtobin @untereiner 
 /src/coreComponents/physicsSolvers                    @rrsettgast @CusiniM
-/src/coreComponents/physicsSolvers/contact            @CusiniM @rrsettgast @matteofrigo5
-/src/coreComponents/physicsSolvers/fluidFlow          @CusiniM @paveltomin @klevzoff @francoishamon
-/src/coreComponents/physicsSolvers/inducedSeismicity  @CusiniM @rrsettgast
-/src/coreComponents/physicsSolvers/multiphysics       @CusiniM @paveltomin @castelletto1 @rrsettgast
-/src/coreComponents/physicsSolvers/python             @cssherman @corbett5
-/src/coreComponents/physicsSolvers/simplePDE          @castelletto1 @rrsettgast @CusiniM 
-/src/coreComponents/physicsSolvers/solidMechanics     @rrsettgast @castelletto1 @CusiniM 
+/src/coreComponents/physicsSolvers/contact            @rrsettgast @CusiniM @matteofrigo5 @Guotong-Ren
+/src/coreComponents/physicsSolvers/fluidFlow          @CusiniM @paveltomin @ryar9534
+/src/coreComponents/physicsSolvers/inducedSeismicity  @rrsettgast @CusiniM @matteofrigo5 @VidarStiernstrom
+/src/coreComponents/physicsSolvers/multiphysics       @rrsettgast @CusiniM @paveltomin @castelletto1 @frankfeifan @ryar9534 @jhuang2601
+/src/coreComponents/physicsSolvers/python             @cssherman @corbett5 @alexbenedicto 
+/src/coreComponents/physicsSolvers/simplePDE          @CusiniM @castelletto1 @rrsettgast  @frankfeifan
+/src/coreComponents/physicsSolvers/solidMechanics     @rrsettgast @CusiniM @castelletto1 @jhuang2601
 /src/coreComponents/physicsSolvers/surfaceGeneration  @rrsettgast @CusiniM @jhuang2601
 /src/coreComponents/physicsSolvers/wavePropagation    @sframba @acitrain
 /src/coreComponents/schema
-/src/coreComponents/unitTests                         @rrsettgast @corbett5 @wrtobin
+/src/coreComponents/unitTests                         @rrsettgast @CusiniM @corbett5 @wrtobin 
 
 # Here is a list of GEOS-DEV members as of 2024-07-02
 # username           name

diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml
@@ -103,22 +103,22 @@ jobs:
         ls -la ./
 
     - name: Checkout Repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.2
       with:
         submodules: true
         lfs: ${{ inputs.BUILD_TYPE == 'integrated_tests' }}
         fetch-depth: 1
 
     - id: 'auth'
       if: ${{ inputs.GCP_BUCKET || inputs.USE_SCCACHE }}
-      uses: 'google-github-actions/[email protected].5'
+      uses: 'google-github-actions/[email protected].7'
       with:
         credentials_json: '${{ secrets.GOOGLE_CLOUD_GCP }}'
         create_credentials_file: true
 
     - name: 'Set up Cloud SDK'
       if: inputs.GCP_BUCKET
-      uses: 'google-github-actions/[email protected].1'
+      uses: 'google-github-actions/[email protected].2'
       with:
         version: '>= 363.0.0'
 
@@ -334,7 +334,7 @@ jobs:
 
     - name: Upload coverage to Codecov
       if: inputs.CODE_COVERAGE
-      uses: codecov/codecov-action@v4.5.0
+      uses: codecov/codecov-action@v4.6.0
       with:
         files: ${GITHUB_WORKSPACE}/geos_coverage.info.cleaned
         fail_ci_if_error: true

diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -69,7 +69,7 @@ jobs:
         
     # The TPL tag is contained in the codespaces configuration to avoid duplications.
     - name: Checkout .devcontainer/devcontainer.json
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.2
       with:
         sparse-checkout: |
           .devcontainer/devcontainer.json
@@ -105,7 +105,7 @@ jobs:
     # The integrated test submodule repository contains large data (using git lfs).
     # To save time (and money) we do not let Github Actions automatically clone all our (lfs) subrepositories and do it by hand.
     - name: Checkout Repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.2
       with:
         # Let script update submodules; Github Actions submodule history causes error
         submodules: false
@@ -225,7 +225,7 @@ jobs:
     runs-on: ubuntu-22.04
     steps:
     - name: Checkout Repository
-      uses: actions/checkout@v4.1.7
+      uses: actions/checkout@v4.2.2
       with:
         submodules: false
         lfs: false

diff --git a/.integrated_tests.yaml b/.integrated_tests.yaml
@@ -1,7 +1,6 @@
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr2878-8188-ed2ded2
-
+  baseline: integratedTests/baseline_integratedTests-pr3480-9217-caaecb8
 allow_fail:
   all: ''
   streak: ''
diff --git a/BASELINE_NOTES.md b/BASELINE_NOTES.md
@@ -6,6 +6,90 @@ 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 #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.
+
+PR #3439 (2024-11-20)
+=====================
+EDFM bugfixes: derivatives sign, frac/cell element volume, fix apertures inconsistency in test cases.
+
+PR ##3440 (2024-11-18)
+=====================
+Added Lagrange multiplier with bubble functions stabilization (sli only) and possibility to specify a slip.
+
+PR #3339 (2024-11-14)
+=====================
+Hypre improvements, rebaseline is due to field value change (amgNumFunctions).
+
+PR #3434 (2024-11-09)
+=====================
+Bugfix: Fixed output of ArrayOfArray objects to restart files.
+
+PR #3374 (2024-11-09)
+====================
+Bugfix for gravity treatment in flux for thermal.
+
+PR #3372 (2024-11-09)
+====================
+Fix a bug related to mass and energy updates for poromechanics.
+
+PR #3426 (2024-11-08)
+====================
+Bugfix: reset accumulation in fracture when time step cut occurs in hydrofrac solver.
+
+PR #3413 (2024-11-07)
+====================
+Add tests for poro-thermo-plastic model.
+
+PR #3337 (2024-11-06)
+====================
+Change density treatment for gravity in multiphase flow solver.
+
+PR #3408 (2024-11-06)
+====================
+EFEM bugfixes: effective traction + oldStress.
+
+PR #3280 (2024-11-05)
+====================
+Added Sprig-slider test.
+
+PR #2909 (2024-10-30)
+=====================
+Add routine for automatic time steps in waveSolvers with new attributes
+
+PR #3156 (2024-10-29)
+====================
+Restart check errors due to 1) schema node added to enable thermal option in well model and 2) arrays removed/added for option.  Max difference errors due treatment of shutin wells.  Previously non-zero rate value reported for shutin well, new code will set rate arrays to zero. 
+
 PR #2878 (2024-10-17)
 =====================
 Sorted region cellBlocks names alphabetically. Therefore affected ordering of: faceManager/elemSubRegionList, nodeManager/elemList, nodeManager/elemSubRegionList, SurfaceElementSubRegion::fractureElementsToCellSubRegions, field::perforation::reservoirElementSubregion.
@@ -48,7 +132,7 @@ Added restartcheks to hydrofrac cases and reduced time of cases that were too lo
 
 PR #3135 (2024-09-04)
 ======================
-Temperature dependent single phase thermal conductivity. Rebaseline all thermal cases. 
+Temperature dependent single phase thermal conductivity. Rebaseline all thermal cases.
 
 PR #3294 (2024-09-01)
 ======================
@@ -64,13 +148,13 @@ Reuse computeSinglePhaseFlux. Rebaseline due to minor numerical diffs.
 
 PR #3249 (2024-08-14)
 ======================
-Two initialization options for poromechanical models. Rebaseline the corresponding cases. 
+Two initialization options for poromechanical models. Rebaseline the corresponding cases.
 
 PR #3278 (2024-08-12)
 ======================
-Renamed GEOSX to GEOS in enternal mesh import, so rebaseline to change these names is the baselines. 
+Renamed GEOSX to GEOS in enternal mesh import, so rebaseline to change these names is the baselines.
 
-202 (2024-08-03)
+PR #3202 (2024-08-03)
 ======================
 Acoustic VTI tests needed rebaselining after update in source and receiver location algorithm.
 

diff --git a/host-configs/apple/darwin-clang.cmake b/host-configs/apple/darwin-clang.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/hydraulicFracturing/kgdEdgeBased_C3D6_base.xml b/inputFiles/hydraulicFracturing/kgdEdgeBased_C3D6_base.xml
@@ -17,7 +17,7 @@
       <NonlinearSolverParameters
         newtonTol="1.0e-5"
         newtonMaxIter="50"
-        lineSearchMaxCuts="10"/>
+	lineSearchAction="None"/>
       <LinearSolverParameters
         directParallel="0"/>
     </Hydrofracture>

diff --git a/inputFiles/hydraulicFracturing/kgdNodeBased_C3D6_base.xml b/inputFiles/hydraulicFracturing/kgdNodeBased_C3D6_base.xml
@@ -18,7 +18,7 @@
       <NonlinearSolverParameters
         newtonTol="1.0e-5"
         newtonMaxIter="50"
-        lineSearchMaxCuts="10"/>
+	lineSearchAction="None"/>
       <LinearSolverParameters
         directParallel="0"/>
     </Hydrofracture>