Merge branch 'develop' of https://github.com/GEOS-DEV/GEOS into develop

GEOS-DEV · Nov 4, 2024 · 0e81bed · 0e81bed
2 parents 065a9a1 + d19bdd7
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diff --git a/.integrated_tests.yaml b/.integrated_tests.yaml
@@ -1,6 +1,6 @@
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr3364-7912-d967424
+  baseline: integratedTests/baseline_integratedTests-pr2909-8386-3a7b08d
 
 allow_fail:
   all: ''

diff --git a/BASELINE_NOTES.md b/BASELINE_NOTES.md
@@ -6,6 +6,22 @@ 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 #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.
+
+PR #3364( 2024-10-15)
+=====================
+Enable reservoir+wells+contact mechanics. Rebaseline needed because of 'allowNegativePressure' flag added for wells.
+
 PR #3364( 2024-10-01)
 =====================
 Separate mass and volume residuals for output in compositional flow solver. Baseline update because of minor numerical diffs.
@@ -40,7 +56,7 @@ 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)
 ======================
@@ -56,11 +72,11 @@ 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)
 ======================

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,5 +1,6 @@
 cff-version: 1.2.0
-message: "Publications that present GEOSX simulations and/or results should cite as follows:"
+message: If you use this software, please cite this repository and our article in the
+  Journal of Open Source Software.
 authors:
 - family-names: "Settgast"
   given-names: "Randolph Richard"
@@ -166,3 +167,167 @@ version: 1.1.0
 doi: "10.5281/zenodo.7151031"
 date-released: 2024-09-14
 url: "https://github.com/GEOS-DEV/GEOS"
+preferred-citation:
+  authors:
+  - family-names: Settgast
+    given-names: Randolph R.
+    orcid: "https://orcid.org/0000-0002-2536-7867"
+  - family-names: Aronson
+    given-names: Ryan M.
+    orcid: "https://orcid.org/0009-0004-0785-5084"
+  - family-names: Besset
+    given-names: Julien R.
+  - family-names: Borio
+    given-names: Andrea
+    orcid: "https://orcid.org/0000-0003-2016-5403"
+  - family-names: Bui
+    given-names: Quan M.
+    orcid: "https://orcid.org/0000-0003-2648-0586"
+  - family-names: Byer
+    given-names: Thomas J.
+  - family-names: Castelletto
+    given-names: Nicola
+    orcid: "https://orcid.org/0000-0001-6816-6769"
+  - family-names: Citrain
+    given-names: Aurélien
+    orcid: "https://orcid.org/0009-0006-3742-1425"
+  - family-names: Corbett
+    given-names: Benjamin C.
+    orcid: "https://orcid.org/0009-0008-7108-9651"
+  - family-names: Corbett
+    given-names: James
+  - family-names: Cordier
+    given-names: Philippe
+    orcid: "https://orcid.org/0000-0002-6439-9263"
+  - family-names: Cremon
+    given-names: Matthias A.
+    orcid: "https://orcid.org/0000-0001-7458-6401"
+  - family-names: Crook
+    given-names: Cameron M.
+    orcid: "https://orcid.org/0000-0002-5366-6418"
+  - family-names: Cusini
+    given-names: Matteo
+    orcid: "https://orcid.org/0000-0002-6024-861X"
+  - family-names: Fei
+    given-names: Fan
+    orcid: "https://orcid.org/0000-0001-7273-4458"
+  - family-names: Frambati
+    given-names: Stefano
+    orcid: "https://orcid.org/0000-0003-0683-1203"
+  - family-names: Franc
+    given-names: Jacques
+    orcid: "https://orcid.org/0000-0002-8833-9425"
+  - family-names: Franceschini
+    given-names: Andrea
+    orcid: "https://orcid.org/0000-0003-4395-5125"
+  - family-names: Frigo
+    given-names: Matteo
+    orcid: "https://orcid.org/0000-0001-8150-1090"
+  - family-names: Fu
+    given-names: Pengcheng
+    orcid: "https://orcid.org/0000-0002-7408-3350"
+  - family-names: Gazzola
+    given-names: Thomas
+    orcid: "https://orcid.org/0000-0002-6103-4605"
+  - family-names: Gross
+    given-names: Herve
+    orcid: "https://orcid.org/0000-0002-1747-2018"
+  - family-names: Hamon
+    given-names: Francois
+    orcid: "https://orcid.org/0000-0001-8229-963X"
+  - family-names: Han
+    given-names: Brian M.
+    orcid: "https://orcid.org/0009-0002-8549-7644"
+  - family-names: Hao
+    given-names: Yue
+    orcid: "https://orcid.org/0000-0002-4543-8618"
+  - family-names: Hasanzade
+    given-names: Rasim
+  - family-names: Homel
+    given-names: Michael
+    orcid: "https://orcid.org/0000-0002-0399-0092"
+  - family-names: Huang
+    given-names: Jian
+    orcid: "https://orcid.org/0000-0002-5380-2563"
+  - family-names: Jin
+    given-names: Tao
+    orcid: "https://orcid.org/0000-0001-6658-8941"
+  - family-names: Ju
+    given-names: Isaac
+    orcid: "https://orcid.org/0000-0003-4110-7472"
+  - family-names: Kachuma
+    given-names: Dickson
+  - family-names: Karimi-Fard
+    given-names: Mohammad
+    orcid: "https://orcid.org/0000-0001-5707-165X"
+  - family-names: Kim
+    given-names: Taeho
+  - family-names: Klevtsov
+    given-names: Sergey
+    orcid: "https://orcid.org/0000-0001-9044-1827"
+  - family-names: Lapene
+    given-names: Alexandre
+  - family-names: Magri
+    given-names: Victor A. P.
+    orcid: "https://orcid.org/0000-0002-3389-523X"
+  - family-names: Mazuyer
+    given-names: Antoine
+    orcid: "https://orcid.org/0000-0002-0329-3385"
+  - family-names: N'diaye
+    given-names: Mamadou
+  - family-names: Osei-Kuffuor
+    given-names: Daniel
+    orcid: "https://orcid.org/0000-0002-6111-6205"
+  - family-names: Povolny
+    given-names: Stefan
+  - family-names: Ren
+    given-names: Guotong
+    orcid: "https://orcid.org/0000-0002-5821-9158"
+  - family-names: Semnani
+    given-names: Shabnam J.
+  - family-names: Sherman
+    given-names: Chris S.
+    orcid: "https://orcid.org/0000-0003-3550-0657"
+  - family-names: Rey
+    given-names: Melvin
+  - family-names: Tchelepi
+    given-names: Hamdi A.
+    orcid: "https://orcid.org/0000-0002-3084-6635"
+  - family-names: Tobin
+    given-names: William R.
+    orcid: "https://orcid.org/0009-0001-3960-6064"
+  - family-names: Tomin
+    given-names: Pavel
+    orcid: "https://orcid.org/0000-0003-4862-4288"
+  - family-names: Untereiner
+    given-names: Lionel
+    orcid: "https://orcid.org/0000-0002-8025-2616"
+  - family-names: Vargas
+    given-names: Arturo
+    orcid: "https://orcid.org/0000-0001-8001-5517"
+  - family-names: Waziri
+    given-names: Sohail
+  - family-names: Wen
+    given-names: Xianhuan
+    orcid: "https://orcid.org/0000-0002-6055-4553"
+  - family-names: White
+    given-names: Joshua A.
+    orcid: "https://orcid.org/0000-0003-3491-142X"
+  - family-names: Wu
+    given-names: Hui
+    orcid: "https://orcid.org/0000-0002-9575-3886"
+  date-published: 2024-10-10
+  doi: 10.21105/joss.06973
+  issn: 2475-9066
+  issue: 102
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 6973
+  title: "GEOS: A performance portable multi-physics simulation
+    framework for subsurface applications"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.06973"
+  volume: 9
+title: "GEOS: A performance portable multi-physics simulation framework
+  for subsurface applications"
diff --git a/examples/GPU/beamBending.xml b/examples/GPU/beamBending.xml
@@ -77,7 +77,7 @@
   <ElementRegions>
     <CellElementRegion
       name="Region2"
-      cellBlocks="{ cb1 }"
+      cellBlocks="{ * }"
       materialList="{ shale }"/>
   </ElementRegions>
 

diff --git a/examples/advanced_xml_features/included/included_b.xml b/examples/advanced_xml_features/included/included_b.xml
@@ -30,7 +30,7 @@
   <ElementRegions>
     <CellElementRegion
       name="Region1"
-      cellBlocks="{ block1 }"
+      cellBlocks="{ * }"
       materialList="{ water, rock }"/>
   </ElementRegions>
 

diff --git a/examples/advanced_xml_features/parameters_example.xml b/examples/advanced_xml_features/parameters_example.xml
@@ -96,7 +96,7 @@ XML Units:
   <ElementRegions>
     <CellElementRegion
       name="Region1"
-      cellBlocks="{ block1 }"
+      cellBlocks="{ * }"
       materialList="{ water, rock }"/>
   </ElementRegions>
 

diff --git a/examples/advanced_xml_features/symbolic_math_example.xml b/examples/advanced_xml_features/symbolic_math_example.xml
@@ -106,7 +106,7 @@ XML Symbolic Math:
   <ElementRegions>
     <CellElementRegion
       name="Region1"
-      cellBlocks="{ block1 }"
+      cellBlocks="{ * }"
       materialList="{ water, rock }"/>
   </ElementRegions>
 

diff --git a/examples/pygeosxExamples/modifyBoundaryCondition/pkn_example.xml b/examples/pygeosxExamples/modifyBoundaryCondition/pkn_example.xml
@@ -70,7 +70,7 @@
   <ElementRegions>
     <CellElementRegion
       name="Domain"
-      cellBlocks="{ cb1 }"
+      cellBlocks="{ * }"
       materialList="{ water, rock }"/>
 
     <SurfaceElementRegion

diff --git a/examples/pygeosxExamples/parametricSurfaceMapping/parametricMesh.xml b/examples/pygeosxExamples/parametricSurfaceMapping/parametricMesh.xml
@@ -58,7 +58,7 @@
   <ElementRegions>
     <CellElementRegion
       name="Region2"
-      cellBlocks="{ cb1 }"
+      cellBlocks="{ * }"
       materialList="{ shale }"/>
   </ElementRegions>
 

diff --git a/examples/sedovKernelTest.xml b/examples/sedovKernelTest.xml
@@ -68,7 +68,7 @@
   <ElementRegions>
     <CellElementRegion
       name="Region2"
-      cellBlocks="{ cb1 }"
+      cellBlocks="{ * }"
       materialList="{ shale }"/>
   </ElementRegions>
 

diff --git a/inputFiles/compositionalMultiphaseFlow/2ph_cap_1d_ihu.xml b/inputFiles/compositionalMultiphaseFlow/2ph_cap_1d_ihu.xml
@@ -69,7 +69,7 @@
   <ElementRegions>
     <CellElementRegion
         name="Region1"
-        cellBlocks="{ block1 }"
+        cellBlocks="{ * }"
         materialList="{ fluid1, rock, relperm, cappres }"/>
   </ElementRegions>
 

diff --git a/inputFiles/compositionalMultiphaseFlow/4comp_2ph_1d.xml b/inputFiles/compositionalMultiphaseFlow/4comp_2ph_1d.xml
@@ -72,7 +72,7 @@
   <ElementRegions>
     <CellElementRegion
       name="Region1"
-      cellBlocks="{ block1 }"
+      cellBlocks="{ * }"
       materialList="{ fluid1, rock, relperm }"/>
   </ElementRegions>
 

diff --git a/inputFiles/compositionalMultiphaseFlow/4comp_2ph_cap_1d.xml b/inputFiles/compositionalMultiphaseFlow/4comp_2ph_cap_1d.xml
@@ -85,7 +85,7 @@
   <ElementRegions>
     <CellElementRegion
       name="Region1"
-      cellBlocks="{ block1 }"
+      cellBlocks="{ * }"
       materialList="{ fluid1, rock, relperm, capPressure }"/>
   </ElementRegions>
 

diff --git a/...iles/compositionalMultiphaseFlow/benchmarks/SPE10/deadOilSpe10Layers84_85_base_direct.xml b/...iles/compositionalMultiphaseFlow/benchmarks/SPE10/deadOilSpe10Layers84_85_base_direct.xml
@@ -67,7 +67,7 @@
   <ElementRegions>
     <CellElementRegion
       name="reservoir"
-      cellBlocks="{ block }"
+      cellBlocks="{ * }"
       materialList="{ fluid, rock, relperm }"/>
   </ElementRegions>
   <!-- SPHINX_TUT_DEAD_OIL_BOTTOM_SPE10_ELEMENT_REGIONS_END -->

diff --git a/...s/compositionalMultiphaseFlow/benchmarks/SPE10/deadOilSpe10Layers84_85_base_iterative.xml b/...s/compositionalMultiphaseFlow/benchmarks/SPE10/deadOilSpe10Layers84_85_base_iterative.xml
@@ -66,7 +66,7 @@
   <ElementRegions>
     <CellElementRegion
       name="reservoir"
-      cellBlocks="{ block }"
+      cellBlocks="{ * }"
       materialList="{ fluid, rock, relperm }"/>
   </ElementRegions>
   <!-- SPHINX_TUT_DEAD_OIL_BOTTOM_SPE10_ELEMENT_REGIONS_END -->

diff --git a/...es/compositionalMultiphaseFlow/benchmarks/buckleyLeverettProblem/buckleyLeverett_base.xml b/...es/compositionalMultiphaseFlow/benchmarks/buckleyLeverettProblem/buckleyLeverett_base.xml
@@ -37,7 +37,7 @@
   <ElementRegions>
     <CellElementRegion
       name="region"
-      cellBlocks="{ cellBlock }"
+      cellBlocks="{ * }"
       materialList="{ fluid, rock, relperm }"/>
   </ElementRegions>
   <!-- SPHINX_ELEMENTREGIONS_END -->

diff --git a/inputFiles/compositionalMultiphaseFlow/c1-ppu/grav_seg_c1ppu_base.xml b/inputFiles/compositionalMultiphaseFlow/c1-ppu/grav_seg_c1ppu_base.xml
@@ -44,7 +44,7 @@
   <ElementRegions>
     <CellElementRegion
       name="region"
-      cellBlocks="{ cellBlock }"
+      cellBlocks="{ * }"
       materialList="{ fluid, rock, relperm }"/>
   </ElementRegions>
   <!-- SPHINX_ELEMENTREGIONS_END -->

diff --git a/inputFiles/compositionalMultiphaseFlow/co2_flux_3d.xml b/inputFiles/compositionalMultiphaseFlow/co2_flux_3d.xml
@@ -112,7 +112,7 @@
   <ElementRegions>
     <CellElementRegion
       name="region"
-      cellBlocks="{ cellBlock }"
+      cellBlocks="{ * }"
       materialList="{ fluid, rock, relperm, cappres }"/>
   </ElementRegions>
 

diff --git a/inputFiles/compositionalMultiphaseFlow/co2_hybrid_1d.xml b/inputFiles/compositionalMultiphaseFlow/co2_hybrid_1d.xml
@@ -75,7 +75,7 @@
   <ElementRegions>
     <CellElementRegion
       name="region"
-      cellBlocks="{ cb }"
+      cellBlocks="{ * }"
       materialList="{ fluid, rock, relperm }"/>
   </ElementRegions>
 

diff --git a/inputFiles/compositionalMultiphaseFlow/dbc/bottom_layer_SPE10/bottom_layer_SPE10_base.xml b/inputFiles/compositionalMultiphaseFlow/dbc/bottom_layer_SPE10/bottom_layer_SPE10_base.xml
@@ -11,7 +11,7 @@
   <ElementRegions>
     <CellElementRegion
       name="region"
-      cellBlocks="{ cellBlock }"
+      cellBlocks="{ * }"
       materialList="{ fluid, rock, relperm }"/>
   </ElementRegions>
 

diff --git a/inputFiles/compositionalMultiphaseFlow/dbc/buckleyLeverett_1d/buckleyLeverett_1d.xml b/inputFiles/compositionalMultiphaseFlow/dbc/buckleyLeverett_1d/buckleyLeverett_1d.xml
@@ -41,7 +41,7 @@
   <ElementRegions>
     <CellElementRegion
       name="region"
-      cellBlocks="{ cellBlock }"
+      cellBlocks="{ * }"
       materialList="{ fluid, rock, relperm }"/>
   </ElementRegions>
   <!-- SPHINX_ELEMENTREGIONS_END -->