Merge branch 'docs/cusini/joss-review-docs-suggetions' into documenta…

…tion/updateBuildDocs
GEOS-DEV · Aug 21, 2024 · edf7a2a · edf7a2a
2 parents 5d6ea67 + a83d507
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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": "275-480"
+            "GEOS_TPL_TAG": "278-500"
         }
     },
     "runArgs": [

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/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -177,14 +177,6 @@ jobs:
             ENABLE_HYPRE: ON
             ENABLE_TRILINOS: OFF
 
-          - name: Sherlock CPU (centos 7.9.2009, gcc 10.1.0, open-mpi 4.1.2, openblas 0.3.10)
-            CMAKE_BUILD_TYPE: Release
-            DOCKER_REPOSITORY: geosx/sherlock-gcc10.1.0-openmpi4.1.2-openblas0.3.10-zlib1.2.11
-            ENABLE_HYPRE: ON
-            ENABLE_TRILINOS: OFF
-            GCP_BUCKET: geosx/Sherlock-CPU
-            HOST_CONFIG: host-configs/Stanford/sherlock-gcc10-ompi4.1.2-openblas0.3.10.cmake
-
     uses: ./.github/workflows/build_and_test.yml
     with:
       CMAKE_BUILD_TYPE: ${{ matrix.CMAKE_BUILD_TYPE }}
@@ -323,20 +315,6 @@ jobs:
           #   DOCKER_CERTS_UPDATE_COMMAND: "update-ca-trust"  
 
           # Below this line, jobs that deploy to Google Cloud.
-          - name: Sherlock GPU (centos 7.9.2009, gcc 10.1.0, open-mpi 4.1.2, openblas 0.3.10, cuda 11.7.1,)
-            BUILD_AND_TEST_CLI_ARGS: "--no-run-unit-tests --no-install-schema"
-            CMAKE_BUILD_TYPE: Release
-            DOCKER_REPOSITORY: geosx/sherlock-gcc10.1.0-openmpi4.1.2-cuda11.7.1-openblas0.3.10-zlib1.2.11
-            ENABLE_HYPRE_DEVICE: CUDA
-            ENABLE_HYPRE: ON
-            ENABLE_TRILINOS: OFF
-            GCP_BUCKET: geosx/Sherlock-GPU
-            HOST_CONFIG: host-configs/Stanford/sherlock-gcc10-ompi4.1.2-openblas0.3.10-cuda11.7.1-sm70.cmake
-            RUNS_ON: streak2
-            NPROC: 8
-            DOCKER_RUN_ARGS: "--cpus=8 --memory=128g --runtime=nvidia -v /etc/pki/ca-trust/source/anchors/:/etc/pki/ca-trust/source/anchors/llnl:ro"
-            DOCKER_CERTS_DIR: "/etc/pki/ca-trust/source/anchors"
-            DOCKER_CERTS_UPDATE_COMMAND: "update-ca-trust"
 
     uses: ./.github/workflows/build_and_test.yml
     with:

diff --git a/.integrated_tests.yaml b/.integrated_tests.yaml
@@ -1,6 +1,6 @@
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr3215-6396-9b43cc8
+  baseline: integratedTests/baseline_integratedTests-pr3249-6781-4998bc8
 
 allow_fail:
   all: ''

diff --git a/BASELINE_NOTES.md b/BASELINE_NOTES.md
@@ -6,6 +6,23 @@ 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 #3249 (2024-08-14)
+======================
+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. 
+
+
+PR #3202 (2024-08-03)
+======================
+Acoustic VTI tests needed rebaselining after update in source and receiver location algorithm.
+
+
 PR #3215 (2024-07-23)
 ======================
 Changed the default value for massCreation and name of the wrapper.

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 [![DOI](https://zenodo.org/badge/131810578.svg)](https://zenodo.org/badge/latestdoi/131810578)
 [![codecov](https://codecov.io/github/GEOS-DEV/GEOS/graph/badge.svg?token=0VTEHPQG58)](https://codecov.io/github/GEOS-DEV/GEOS)
-![CI](https://github.com/GEOS-DEV/GEOS/actions/workflows/ci_tests.yml/badge.svg)
+[![CI](https://github.com/GEOS-DEV/GEOS/actions/workflows/ci_tests.yml/badge.svg)](https://github.com/GEOS-DEV/GEOS/actions?query=branch%3Adevelop)
 [![docs](https://readthedocs.com/projects/geosx-geosx/badge/?version=latest)](https://geosx-geosx.readthedocs-hosted.com/en/latest/)
 
 Welcome to the GEOS project!

diff --git a/examples/ObjectCatalog/main.cpp b/examples/ObjectCatalog/main.cpp
@@ -17,7 +17,7 @@
 
 #include <iostream>
 
-#include "common/Logger.hpp"
+#include "common/logger/Logger.hpp"
 #include "Base.hpp"
 #include "Derived1.hpp"
 

diff --git a/examples/pygeosxExamples/modifyBoundaryCondition/pkn_example.xml b/examples/pygeosxExamples/modifyBoundaryCondition/pkn_example.xml
@@ -22,7 +22,6 @@
       name="hydrofracture"
       solidSolverName="lagsolve"
       logLevel="1"
-      contactRelationName="fractureContact"
       flowSolverName="SinglePhaseFlow"
       surfaceGeneratorName="SurfaceGen"      
       targetRegions="{ Domain, Fracture }">
@@ -39,8 +38,8 @@
       timeIntegrationOption="QuasiStatic"
       discretization="FE1"
       name="lagsolve"
-      contactRelationName="fractureContact"
-      targetRegions="{ Domain, Fracture }">
+      targetRegions="{ Domain, Fracture }"
+      contactPenaltyStiffness="1.0e0">
       <NonlinearSolverParameters
         newtonTol="1.0e-6"/>
       <LinearSolverParameters
@@ -77,7 +76,7 @@
     <SurfaceElementRegion
       name="Fracture"
       defaultAperture="0.02e-3"
-      materialList="{ water, rock, fractureFilling, fracturePorosity, fracturePerm, nullSolid }"/>
+      materialList="{ water, rock, fractureFilling, fracturePorosity, fracturePerm, nullSolid, hApertureTable }"/>
   </ElementRegions>
 
   <Constitutive>
@@ -112,9 +111,11 @@
       compressibility="0.0"/>
 
     <FrictionlessContact
-      name="fractureContact"
-      penaltyStiffness="1.0e0"
-      apertureTableName="apertureTable"/>
+      name="fractureContact"/>
+
+    <HydraulicApertureTable
+      name="hApertureTable"
+      apertureTableName="apertureTable"/>  
 
     <ParallelPlatesPermeability
       name="fracturePerm"/>

diff --git a/host-configs/apple/macOS_customized.cmake b/host-configs/apple/macOS_customized.cmake
diff --git a/inputFiles/almContactMechanics/ALM_stickFault_base.xml b/inputFiles/almContactMechanics/ALM_stickFault_base.xml
@@ -92,8 +92,11 @@
     <Coulomb
       name="fractureMaterial"
       cohesion="0.0"
-      frictionCoefficient="0.1"
-      apertureTableName="apertureTable"/>
+      frictionCoefficient="0.1"/>
+
+    <HydraulicApertureTable
+      name="hApertureModel"
+      apertureTableName="apertureTable"/>  
   </Constitutive>
 
   <Functions>

diff --git a/inputFiles/compositionalMultiphaseFlow/deadoil_3ph_staircase_3d_transmi_output.xml b/inputFiles/compositionalMultiphaseFlow/deadoil_3ph_staircase_3d_transmi_output.xml
@@ -0,0 +1,81 @@
+<?xml version="1.0" ?>
+
+<Problem>
+  <!-- this exemple adds a transmissibility output to "deadoilStaircase.xml".
+
+    The "cellToCellDataCollection" gather the transmissibility data at the first timestep (triggered by
+    the SoloEvents). The transmissibility could be gathered at multiple timestep to see the influence
+    of the permeability variations.
+    All fields need to be individualy packed by the PackCollection, the TimeHistory outputs them in an hdf5.
+  -->
+
+  <Included>
+    <File name="./deadoil_3ph_staircase_3d.xml"/>
+  </Included>
+
+  <Events>
+
+    <SoloEvent
+      name="cellToCellDataCollectionEvent"
+      beginTime="1e5"
+      target="/Tasks/cellToCellDataCollection" />
+    <SoloEvent
+      name="cellAGlobalIdPackCollectionEvent"
+      beginTime="1e5"
+      target="/Tasks/cellAGlobalIdPackCollection" />
+    <SoloEvent
+      name="cellBGlobalIdPackCollectionEvent"
+      beginTime="1e5"
+      target="/Tasks/cellBGlobalIdPackCollection" />
+    <SoloEvent
+      name="transmissibilityABPackCollectionEvent"
+      beginTime="1e5"
+      target="/Tasks/transmissibilityABPackCollection" />
+    <SoloEvent
+      name="transmissibilityBAPackCollectionEvent"
+      beginTime="1e5"
+      target="/Tasks/transmissibilityBAPackCollection" />
+    <SoloEvent
+      name="cellToCellDataHistoryEvent"
+      beginTime="1e5"
+      target="/Outputs/cellToCellDataHistory" />
+
+  </Events>
+
+  <Tasks>
+    <CellToCellDataCollection
+      name="cellToCellDataCollection"
+      flowSolverName="compflow"
+      meshBody="mesh"
+      logLevel="1" />
+    <PackCollection
+      name="cellAGlobalIdPackCollection"
+      objectPath="/Tasks/cellToCellDataCollection"
+      fieldName="cellAGlobalId" />
+    <PackCollection
+      name="cellBGlobalIdPackCollection"
+      objectPath="/Tasks/cellToCellDataCollection"
+      fieldName="cellBGlobalId" />
+    <PackCollection
+      name="transmissibilityABPackCollection"
+      objectPath="/Tasks/cellToCellDataCollection"
+      fieldName="transmissibilityAB" />
+    <PackCollection
+      name="transmissibilityBAPackCollection"
+      objectPath="/Tasks/cellToCellDataCollection"
+      fieldName="transmissibilityBA" />
+  </Tasks>
+
+  <Outputs>
+    <TimeHistory
+      name="cellToCellDataHistory"
+      sources="{ 
+        /Tasks/cellAGlobalIdPackCollection,
+        /Tasks/cellBGlobalIdPackCollection,
+        /Tasks/transmissibilityABPackCollection,
+        /Tasks/transmissibilityBAPackCollection
+      }"
+      filename="deadoil_3ph_staircase_3d_cellToCellData" />
+  </Outputs>
+
+</Problem>
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/efemFractureMechanics/EmbFrac_Compression_CoulombFriction_base.xml b/inputFiles/efemFractureMechanics/EmbFrac_Compression_CoulombFriction_base.xml
@@ -9,7 +9,8 @@
       initialDt="10"
       discretization="FE1"
       timeIntegrationOption="QuasiStatic"
-      logLevel="1">
+      logLevel="1"
+      contactPenaltyStiffness="1.0e12">
       <NonlinearSolverParameters
         newtonTol="1.0e-6"
         newtonMaxIter="2"
@@ -48,7 +49,7 @@
       name="Fracture"
       faceBlock="embeddedSurfaceSubRegion"
       subRegionType="embeddedElement"
-      materialList="{ fractureContact }"
+      materialList="{ frictionLaw }"
       defaultAperture="1e-3"/>
   </ElementRegions>
 
@@ -60,12 +61,10 @@
       defaultShearModulus="1.0e10"/>
 
     <Coulomb
-      name="fractureContact"
-      penaltyStiffness="1.0e12"
+      name="frictionLaw"
       shearStiffness="1.0e8"
       cohesion ="0.0"
-      frictionCoefficient = "0.8"
-      apertureTableName="apertureTable"/>
+      frictionCoefficient = "0.8"/>
   </Constitutive>
 
   <Functions>
@@ -116,13 +115,6 @@
       scale="0.0"
       setNames="{ zneg, zpos }"/>   
   </FieldSpecifications>
-
-  <Functions>
-    <TableFunction
-      name="apertureTable"
-      coordinates="{ -1.0e-3, 0.0 }"
-      values="{ 1.0e-6, 1.0e-4 }"/>
-  </Functions>
 
   <Tasks>
     <PackCollection

diff --git a/inputFiles/efemFractureMechanics/EmbFrac_Compression_Frictionless_base.xml b/inputFiles/efemFractureMechanics/EmbFrac_Compression_Frictionless_base.xml
@@ -9,7 +9,8 @@
       initialDt="10"
       timeIntegrationOption="QuasiStatic"
       discretization="FE1"
-      logLevel="1">
+      logLevel="1"
+      contactPenaltyStiffness="1.0e8">
       <NonlinearSolverParameters
         newtonTol="1.0e-6"
         newtonMaxIter="2"
@@ -48,7 +49,7 @@
       name="Fracture"
       faceBlock="embeddedSurfaceSubRegion"
       subRegionType="embeddedElement"
-      materialList="{ fractureContact }"
+      materialList="{ frictionLaw }"
       defaultAperture="1e-3"/>
   </ElementRegions>
 
@@ -60,18 +61,9 @@
       defaultShearModulus="1.0e10"/>
 
     <FrictionlessContact
-      name="fractureContact"
-      penaltyStiffness="1.0e8"
-      apertureTableName="apertureTable"/>
+      name="frictionLaw"/>
   </Constitutive>
 
-  <Functions>
-    <TableFunction
-      name="apertureTable"
-      coordinates="{ -1.0e-3, 0.0 }"
-      values="{ 0.002e-3, 0.02e-3 }"/>
-  </Functions>
-
   <FieldSpecifications>
     <Traction
       name="xload1"