docs: apply suggestions from joss review (#3296)

* Modify build documents for problems from JOSS reviewers (#3258) * add Apple MacOS build doc * quick-start-template.cmake * Update host-configs/quick-start-template.cmake * add CODE_OF_CONDUCT and CONTRIBUTING file * fix doxygen links in sphinx docs * Update src/docs/sphinx/QuickStart.rst * Doxygen for SolverBase * Update Example.rst (#3315) * add frontier scaling to documentation * add the entire physicsSolver directory to the readthedocs doxygen * add card on main documentation page for submitting issues * fix a couple of typos * Add instructions, postprocess script, and figures to WellboreECP problem --------- Co-authored-by: Randolph Settgast <[email protected]> Co-authored-by: Gerasimos Chourdakis <[email protected]> Co-authored-by: Victor A. P. Magri <[email protected]>
GEOS-DEV · Sep 17, 2024 · c88111c · c88111c
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diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -0,0 +1,133 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[email protected].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,3 @@
+To contribute to GEOS, please refer to the [Contributing](https://geosx-geosx.readthedocs-hosted.com/en/latest/docs/sphinx/developerGuide/Contributing/index_contributing.html) section in the [GEOS developer guide](https://geosx-geosx.readthedocs-hosted.com/en/latest/docs/sphinx/developerGuide/Index.html#).
+
+To report a bug please open an [issue](https://github.com/GEOS-DEV/GEOS/issues)
diff --git a/README.md b/README.md
@@ -21,10 +21,13 @@ page for more details on the HPC, numerics,
 and applied engineering components of this effort.
 
 Documentation
----------------------
+-------------
 
-Our documentation is hosted [here](https://geosx-geosx.readthedocs-hosted.com/en/latest/?).
+Please visit the [Main documentation for GEOS](https://geosx-geosx.readthedocs-hosted.com/en/latest/?).
 
+If you would like to contribute to GEOS, please see the [developer guide](https://geosx-geosx.readthedocs-hosted.com/en/latest/docs/sphinx/developerGuide/Index.html)
+
+If you would like to report a bug, please submit an [issue](https://github.com/GEOS-DEV/GEOS/issues/new/choose). 
 
 Who develops GEOS?
 -------------------

diff --git a/host-configs/apple/macOS_base.cmake b/host-configs/apple/macOS_base.cmake
@@ -25,15 +25,16 @@ set(ENABLE_CALIPER "OFF" CACHE PATH "" FORCE )
 set( BLAS_LIBRARIES ${HOMEBREW_DIR}/opt/lapack/lib/libblas.dylib CACHE PATH "" FORCE )
 set( LAPACK_LIBRARIES ${HOMEBREW_DIR}/opt/lapack/lib/liblapack.dylib CACHE PATH "" FORCE )
 
-set(ENABLE_DOXYGEN OFF CACHE BOOL "" FORCE)
+set(ENABLE_DOXYGEN ON CACHE BOOL "" FORCE)
+set(ENABLE_SPHINX ON CACHE BOOL "" FORCE)
 set(ENABLE_MATHPRESSO OFF CACHE BOOL "" FORCE )
 
 set(GEOS_BUILD_SHARED_LIBS ON CACHE BOOL "" FORCE)
 
 
 
-#set( DOXYGEN_EXECUTABLE /usr/local/bin/doxygen CACHE PATH "" FORCE )
-#set( SPHINX_EXECUTABLE /usr/local/bin/sphinx-build CACHE PATH "" FORCE )
+set( DOXYGEN_EXECUTABLE ${HOMEBREW_DIR}/bin/doxygen CACHE PATH "" FORCE )
+set( SPHINX_EXECUTABLE ${HOMEBREW_DIR}/opt/sphinx-doc/bin/sphinx-build CACHE PATH "" FORCE )
 
 if(NOT ( EXISTS "${GEOS_TPL_DIR}" AND IS_DIRECTORY "${GEOS_TPL_DIR}" ) )
    set(GEOS_TPL_DIR "${CMAKE_SOURCE_DIR}/../../thirdPartyLibs/install-${CONFIG_NAME}-release" CACHE PATH "" FORCE )

diff --git a/host-configs/quick-start-template.cmake b/host-configs/quick-start-template.cmake
@@ -0,0 +1,32 @@
+set( CONFIG_NAME "quick-start" ) 
+
+# Set compilers path
+set(CMAKE_C_COMPILER "path-to-gcc/bin/gcc" CACHE PATH "")   # This is typically something like /usr/bin/gcc ... or clang
+set(CMAKE_CXX_COMPILER "path-to-gcc/bin/g++" CACHE PATH "") # This is typically something like /usr/bin/g++ ... or clang++
+set(ENABLE_FORTRAN OFF CACHE BOOL "" FORCE)
+
+# Set paths to mpi
+set(ENABLE_MPI ON CACHE PATH "")
+set(MPI_C_COMPILER "path-to-mpi/bin/mpicc" CACHE PATH "")    # This is typically something like /usr/bin/mpicc
+set(MPI_CXX_COMPILER "path-to-mpi/bin/mpicxx" CACHE PATH "") # This is typically something like /usr/bin/mpicxx
+set(MPIEXEC "path-to-mpi/bin/mpirun" CACHE PATH "")          # This is typically something like /usr/bin/mpirun
+
+# Set paths to blas and lapack
+set( BLAS_LIBRARIES "path-to-blas" CACHE PATH "" FORCE )   # This is typically something like /usr/lib64/libblas.so 
+set( LAPACK_LIBRARIES  CACHE PATH "path-to-lapack" FORCE ) # This is typically something like /usr/lib64/liblapack.so
+
+# Cuda and openMP
+set( ENABLE_CUDA OFF CACHE PATH "" FORCE )
+set( ENABLE_OPENMP OFF CACHE PATH "" FORCE )
+
+# TPLs
+set( ENABLE_TRILINOS OFF CACHE PATH "" FORCE )
+set( ENABLE_CALIPER OFF CACHE PATH "" FORCE )
+set( ENABLE_DOXYGEN OFF CACHE BOOL "" FORCE)
+set( ENABLE_MATHPRESSO OFF CACHE BOOL "" FORCE )
+
+if(NOT ( EXISTS "${GEOS_TPL_DIR}" AND IS_DIRECTORY "${GEOS_TPL_DIR}" ) )
+   set(GEOS_TPL_DIR "${CMAKE_SOURCE_DIR}/../../thirdPartyLibs/install-${CONFIG_NAME}-release" CACHE PATH "" FORCE )
+endif()
+
+include(${CMAKE_CURRENT_LIST_DIR}/../tpls.cmake)
diff --git a/inputFiles/compositionalMultiphaseWell/benchmarks/Egg/deadOilEgg_base_iterative.xml b/inputFiles/compositionalMultiphaseWell/benchmarks/Egg/deadOilEgg_base_iterative.xml
@@ -23,7 +23,8 @@
         preconditionerType="mgr"
         krylovTol="1e-4"
         krylovAdaptiveTol="1"
-        krylovWeakestTol="1e-2"/>
+        krylovWeakestTol="1e-2"
+        logLevel="1"/>
     </CompositionalMultiphaseReservoir>
 
     <CompositionalMultiphaseFVM

diff --git a/inputFiles/wellboreECP/ECP_Wellbore_geom01.xml b/inputFiles/wellboreECP/ECP_Wellbore_geom01.xml
@@ -0,0 +1,32 @@
+<Problem>
+  <Mesh>
+    <InternalWellbore
+      name="mesh1"
+      elementTypes="{ C3D8, C3D8, C3D8 }"
+      radius="{0.057, 0.063, 0.1, 0.2}"
+      theta="{0, 180}"
+      zCoords="{-1.25,0}"
+      trajectory="{ { -0.0, 0.0, 0.0 },
+                    {  0.0, 0.0, -1.0 } }"
+      nr="{ 1, 18, 14 }"
+      nt="{ 64 }"
+      nz="{ 391 }"
+      hardRadialCoords="{ 0.057, 0.063, 0.0646667, 0.0663333, 0.068, 0.0696667, 0.0713333, 0.073, 0.075594, 0.0782794, 0.0810593, 0.083937, 0.0869161, 0.09, 0.0916667, 0.0933333, 0.095, 0.0966667, 0.0983333, 0.1, 0.101667, 0.103333, 0.105, 0.106667, 0.108333, 0.11, 0.118447, 0.127574, 0.137435, 0.14809, 0.159602, 0.17204, 0.185479, 0.2 }"
+      useCartesianOuterBoundary="2"
+      cartesianMappingInnerRadius="0.12"
+      cellBlockNames="{ casing, cement, rock }"
+      />
+  </Mesh>
+
+  <Geometry>
+    <Box
+      name="sourceLeak"
+      xMin="{ -0.51, -0.51, -1.25001 }"
+      xMax="{  0.51,  0.51, -1.24999 }"/>
+    <Box
+      name="output"
+      xMin="{ -0.51,  -0.51, -0.00001 }"
+      xMax="{  0.51,   0.51,  0.00001 }"/>
+  </Geometry>
+
+</Problem>
diff --git a/inputFiles/wellboreECP/ECP_Wellbore_geom02.xml b/inputFiles/wellboreECP/ECP_Wellbore_geom02.xml
@@ -0,0 +1,32 @@
+<Problem>
+  <Mesh>
+    <InternalWellbore
+      name="mesh1"
+      elementTypes="{ C3D8, C3D8, C3D8 }"
+      radius="{0.057, 0.063, 0.1, 0.2}"
+      theta="{0, 180}"
+      zCoords="{-10,0}"
+      trajectory="{ { -0.0, 0.0, 0.0 },
+                    {  0.0, 0.0, -1.0 } }"
+      nr="{ 1, 18, 14 }"
+      nt="{ 64 }"
+      nz="{ 3125 }"
+      hardRadialCoords="{ 0.057, 0.063, 0.0646667, 0.0663333, 0.068, 0.0696667, 0.0713333, 0.073, 0.075594, 0.0782794, 0.0810593, 0.083937, 0.0869161, 0.09, 0.0916667, 0.0933333, 0.095, 0.0966667, 0.0983333, 0.1, 0.101667, 0.103333, 0.105, 0.106667, 0.108333, 0.11, 0.118447, 0.127574, 0.137435, 0.14809, 0.159602, 0.17204, 0.185479, 0.2 }"
+      useCartesianOuterBoundary="2"
+      cartesianMappingInnerRadius="0.12"
+      cellBlockNames="{ casing, cement, rock }"
+      />
+  </Mesh>
+
+  <Geometry>
+    <Box
+      name="sourceLeak"
+      xMin="{ -0.51, -0.51, -10.00001 }"
+      xMax="{  0.51,  0.51, -9.99999 }"/>
+    <Box
+      name="output"
+      xMin="{ -0.51,  -0.51, -0.00001 }"
+      xMax="{  0.51,   0.51,  0.00001 }"/>
+  </Geometry>
+
+</Problem>
diff --git a/inputFiles/wellboreECP/ECP_Wellbore_geom03.xml b/inputFiles/wellboreECP/ECP_Wellbore_geom03.xml
@@ -0,0 +1,32 @@
+<Problem>
+  <Mesh>
+    <InternalWellbore
+      name="mesh1"
+      elementTypes="{ C3D8, C3D8, C3D8 }"
+      radius="{0.057, 0.063, 0.1, 0.2}"
+      theta="{0, 180}"
+      zCoords="{-10,0}"
+      trajectory="{ { -0.0, 0.0, 0.0 },
+                    {  0.0, 0.0, -1.0 } }"
+      nr="{ 2, 36, 28 }"
+      nt="{ 128 }"
+      nz="{ 6250 }"
+      hardRadialCoords="{ 0.057, 0.06, 0.063, 0.0638333, 0.0646667, 0.0655, 0.0663333, 0.0671667, 0.068, 0.0688333, 0.0696667, 0.0705, 0.0713333, 0.0721667, 0.073, 0.0742862, 0.0755948, 0.0769261, 0.0782806, 0.0796587, 0.0810607, 0.0824871, 0.0839383, 0.0854148, 0.0869169, 0.0884452, 0.09, 0.0908333, 0.0916667, 0.0925, 0.0933333, 0.0941667, 0.095, 0.0958333, 0.0966667, 0.0975, 0.0983333, 0.0991667, 0.1, 0.100833, 0.101667, 0.1025, 0.103333, 0.104167, 0.105, 0.105833, 0.106667, 0.1075, 0.108333, 0.109167, 0.11, 0.114215, 0.118587, 0.123122, 0.127825, 0.132705, 0.137766, 0.143015, 0.14846, 0.154109, 0.159967, 0.166044, 0.172348, 0.178886, 0.185668, 0.192703, 0.2 }"
+      useCartesianOuterBoundary="2"
+      cartesianMappingInnerRadius="0.12"
+      cellBlockNames="{ casing, cement, rock }"
+      />
+  </Mesh>
+
+  <Geometry>
+    <Box
+      name="sourceLeak"
+      xMin="{ -0.51, -0.51, -10.00001 }"
+      xMax="{  0.51,  0.51, -9.99999 }"/>
+    <Box
+      name="output"
+      xMin="{ -0.51,  -0.51, -0.00001 }"
+      xMax="{  0.51,   0.51,  0.00001 }"/>
+  </Geometry>
+
+</Problem>
diff --git a/inputFiles/wellboreECP/ECP_Wellbore_geom04.xml b/inputFiles/wellboreECP/ECP_Wellbore_geom04.xml
@@ -0,0 +1,32 @@
+<Problem>
+  <Mesh>
+    <InternalWellbore
+      name="mesh1"
+      elementTypes="{ C3D8, C3D8, C3D8 }"
+      radius="{0.057, 0.063, 0.1, 0.2}"
+      theta="{0, 180}"
+      zCoords="{-10,0}"
+      trajectory="{ { -0.0, 0.0, 0.0 },
+                    {  0.0, 0.0, -1.0 } }"
+      nr="{ 4, 72, 56 }"
+      nt="{ 256 }"
+      nz="{ 12500 }"
+      hardRadialCoords="{ 0.057, 0.0585, 0.06, 0.0615, 0.063, 0.0634167, 0.0638333, 0.06425, 0.0646667, 0.0650833, 0.0655, 0.0659167, 0.0663333, 0.06675, 0.0671667, 0.0675833, 0.068, 0.0684167, 0.0688333, 0.06925, 0.0696667, 0.0700833, 0.0705, 0.0709167, 0.0713333, 0.07175, 0.0721667, 0.0725833, 0.073, 0.0736405, 0.0742864, 0.074938, 0.0755952, 0.0762581, 0.0769267, 0.0776011, 0.0782813, 0.0789674, 0.0796594, 0.0803574, 0.0810615, 0.0817716, 0.0824879, 0.0832103, 0.083939, 0.084674, 0.0854154, 0.0861631, 0.0869174, 0.0876781, 0.0884454, 0.0892194, 0.09, 0.0904167, 0.0908333, 0.09125, 0.0916667, 0.0920833, 0.0925, 0.0929167, 0.0933333, 0.09375, 0.0941667, 0.0945833, 0.095, 0.0954167, 0.0958333, 0.09625, 0.0966667, 0.0970833, 0.0975, 0.0979167, 0.0983333, 0.09875, 0.0991667, 0.0995833, 0.1, 0.100417, 0.100833, 0.10125, 0.101667, 0.102083, 0.1025, 0.102917, 0.103333, 0.10375, 0.104167, 0.104583, 0.105, 0.105417, 0.105833, 0.10625, 0.106667, 0.107083, 0.1075, 0.107917, 0.108333, 0.10875, 0.109167, 0.109583, 0.11, 0.112065, 0.114169, 0.116313, 0.118499, 0.120726, 0.122996, 0.125309, 0.127667, 0.13007, 0.132519, 0.135014, 0.137558, 0.14015, 0.142791, 0.145483, 0.148227, 0.151023, 0.153873, 0.156778, 0.159737, 0.162754, 0.165828, 0.168961, 0.172154, 0.175409, 0.178725, 0.182105, 0.18555, 0.18906, 0.192638, 0.196284, 0.2  }"
+      useCartesianOuterBoundary="2"
+      cartesianMappingInnerRadius="0.12"
+      cellBlockNames="{ casing, cement, rock }"
+      />
+  </Mesh>
+
+  <Geometry>
+    <Box
+      name="sourceLeak"
+      xMin="{ -0.51, -0.51, -10.00001 }"
+      xMax="{  0.51,  0.51, -9.99999 }"/>
+    <Box
+      name="output"
+      xMin="{ -0.51,  -0.51, -0.00001 }"
+      xMax="{  0.51,   0.51,  0.00001 }"/>
+  </Geometry>
+
+</Problem>
diff --git a/inputFiles/wellboreECP/ECP_Wellbore_geom05.xml b/inputFiles/wellboreECP/ECP_Wellbore_geom05.xml
@@ -0,0 +1,32 @@
+<Problem>
+  <Mesh>
+    <InternalWellbore
+      name="mesh1"
+      elementTypes="{ C3D8, C3D8, C3D8 }"
+      radius="{0.057, 0.063, 0.1, 0.2}"
+      theta="{0, 180}"
+      zCoords="{-10,0}"
+      trajectory="{ { -0.0, 0.0, 0.0 },
+                    {  0.0, 0.0, -1.0 } }"
+      nr="{ 8, 144, 112 }"
+      nt="{ 512 }"
+      nz="{ 25000 }"
+      hardRadialCoords="{ 0.057, 0.05775, 0.0585, 0.05925, 0.06, 0.06075, 0.0615, 0.06225, 0.063, 0.0632083, 0.0634167, 0.063625, 0.0638333, 0.0640417, 0.06425, 0.0644583, 0.0646667, 0.064875, 0.0650833, 0.0652917, 0.0655, 0.0657083, 0.0659167, 0.066125, 0.0663333, 0.0665417, 0.06675, 0.0669583, 0.0671667, 0.067375, 0.0675833, 0.0677917, 0.068, 0.0682083, 0.0684167, 0.068625, 0.0688333, 0.0690417, 0.06925, 0.0694583, 0.0696667, 0.069875, 0.0700833, 0.0702917, 0.0705, 0.0707083, 0.0709167, 0.071125, 0.0713333, 0.0715417, 0.07175, 0.0719583, 0.0721667, 0.072375, 0.0725833, 0.0727917, 0.073, 0.0733191, 0.0736396, 0.0739615, 0.0742848, 0.0746095, 0.0749356, 0.0752631, 0.0755921, 0.0759225, 0.0762544, 0.0765877, 0.0769225, 0.0772587, 0.0775964, 0.0779356, 0.0782762, 0.0786184, 0.078962, 0.0793072, 0.0796538, 0.080002, 0.0803517, 0.0807029, 0.0810556, 0.0814099, 0.0817658, 0.0821232, 0.0824821, 0.0828427, 0.0832048, 0.0835685, 0.0839337, 0.0843006, 0.0846691, 0.0850391, 0.0854108, 0.0857842, 0.0861591, 0.0865357, 0.086914, 0.0872939, 0.0876754, 0.0880586, 0.0884435, 0.0888301, 0.0892184, 0.0896083, 0.09, 0.0902083, 0.0904167, 0.090625, 0.0908333, 0.0910417, 0.09125, 0.0914583, 0.0916667, 0.091875, 0.0920833, 0.0922917, 0.0925, 0.0927083, 0.0929167, 0.093125, 0.0933333, 0.0935417, 0.09375, 0.0939583, 0.0941667, 0.094375, 0.0945833, 0.0947917, 0.095, 0.0952083, 0.0954167, 0.095625, 0.0958333, 0.0960417, 0.09625, 0.0964583, 0.0966667, 0.096875, 0.0970833, 0.0972917, 0.0975, 0.0977083, 0.0979167, 0.098125, 0.0983333, 0.0985417, 0.09875, 0.0989583, 0.0991667, 0.099375, 0.0995833, 0.0997917, 0.1, 0.100208, 0.100417, 0.100625, 0.100833, 0.101042, 0.10125, 0.101458, 0.101667, 0.101875, 0.102083, 0.102292, 0.1025, 0.102708, 0.102917, 0.103125, 0.103333, 0.103542, 0.10375, 0.103958, 0.104167, 0.104375, 0.104583, 0.104792, 0.105, 0.105208, 0.105417, 0.105625, 0.105833, 0.106042, 0.10625, 0.106458, 0.106667, 0.106875, 0.107083, 0.107292, 0.1075, 0.107708, 0.107917, 0.108125, 0.108333, 0.108542, 0.10875, 0.108958, 0.109167, 0.109375, 0.109583, 0.109792, 0.11, 0.111031, 0.112072, 0.113123, 0.114184, 0.115254, 0.116335, 0.117426, 0.118527, 0.119638, 0.12076, 0.121893, 0.123036, 0.12419, 0.125355, 0.126531, 0.127718, 0.128916, 0.130125, 0.131346, 0.132578, 0.133822, 0.135077, 0.136345, 0.137624, 0.138915, 0.140219, 0.141535, 0.142863, 0.144204, 0.145557, 0.146923, 0.148302, 0.149694, 0.151099, 0.152517, 0.153949, 0.155394, 0.156852, 0.158325, 0.159811, 0.161311, 0.162826, 0.164354, 0.165897, 0.167455, 0.169027, 0.170614, 0.172216, 0.173833, 0.175466, 0.177113, 0.178777, 0.180456, 0.18215, 0.183861, 0.185588, 0.187331, 0.18909, 0.190866, 0.192659, 0.194468, 0.196295, 0.198139, 0.2 }"
+      useCartesianOuterBoundary="2"
+      cartesianMappingInnerRadius="0.12"
+      cellBlockNames="{ casing, cement, rock }"
+      />
+  </Mesh>
+
+  <Geometry>
+    <Box
+      name="sourceLeak"
+      xMin="{ -0.51, -0.51, -10.00001 }"
+      xMax="{  0.51,  0.51, -9.99999 }"/>
+    <Box
+      name="output"
+      xMin="{ -0.51,  -0.51, -0.00001 }"
+      xMax="{  0.51,   0.51,  0.00001 }"/>
+  </Geometry>
+
+</Problem>
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		To contribute to GEOS, please refer to the [Contributing](https://geosx-geosx.readthedocs-hosted.com/en/latest/docs/sphinx/developerGuide/Contributing/index_contributing.html) section in the [GEOS developer guide](https://geosx-geosx.readthedocs-hosted.com/en/latest/docs/sphinx/developerGuide/Index.html#).

		To report a bug please open an [issue](https://github.com/GEOS-DEV/GEOS/issues)