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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]>
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‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, caste, color, religion, or sexual
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identity and orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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## Our Standards
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Examples of behavior that contributes to a positive environment for our
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community include:
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* Demonstrating empathy and kindness toward other people
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* Being respectful of differing opinions, viewpoints, and experiences
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* Giving and gracefully accepting constructive feedback
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* Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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* Focusing on what is best not just for us as individuals, but for the overall
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community
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Examples of unacceptable behavior include:
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* The use of sexualized language or imagery, and sexual attention or advances of
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any kind
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* Trolling, insulting or derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or email address,
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without their explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Enforcement Responsibilities
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Community leaders are responsible for clarifying and enforcing our standards of
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acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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## Scope
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This Code of Conduct applies within all community spaces, and also applies when
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an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official email address,
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posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement at
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[email protected].
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All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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## Enforcement Guidelines
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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### 1. Correction
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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### 2. Warning
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**Community Impact**: A violation through a single incident or series of
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actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or permanent
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ban.
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### 3. Temporary Ban
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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### 4. Permanent Ban
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within the
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community.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 2.1, available at
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[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
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Community Impact Guidelines were inspired by
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[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
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For answers to common questions about this code of conduct, see the FAQ at
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[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
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[https://www.contributor-covenant.org/translations][translations].
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[homepage]: https://www.contributor-covenant.org
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[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
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[Mozilla CoC]: https://github.com/mozilla/diversity
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[FAQ]: https://www.contributor-covenant.org/faq
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[translations]: https://www.contributor-covenant.org/translations

‎CONTRIBUTING.md

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

‎README.md

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and applied engineering components of this effort.
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Documentation
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---------------------
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-------------
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Our documentation is hosted [here](https://geosx-geosx.readthedocs-hosted.com/en/latest/?).
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Please visit the [Main documentation for GEOS](https://geosx-geosx.readthedocs-hosted.com/en/latest/?).
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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)
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If you would like to report a bug, please submit an [issue](https://github.com/GEOS-DEV/GEOS/issues/new/choose).
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Who develops GEOS?
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-------------------

‎host-configs/apple/macOS_base.cmake

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set( BLAS_LIBRARIES ${HOMEBREW_DIR}/opt/lapack/lib/libblas.dylib CACHE PATH "" FORCE )
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set( LAPACK_LIBRARIES ${HOMEBREW_DIR}/opt/lapack/lib/liblapack.dylib CACHE PATH "" FORCE )
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set(ENABLE_DOXYGEN OFF CACHE BOOL "" FORCE)
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set(ENABLE_DOXYGEN ON CACHE BOOL "" FORCE)
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set(ENABLE_SPHINX ON CACHE BOOL "" FORCE)
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set(ENABLE_MATHPRESSO OFF CACHE BOOL "" FORCE )
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set(GEOS_BUILD_SHARED_LIBS ON CACHE BOOL "" FORCE)
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#set( DOXYGEN_EXECUTABLE /usr/local/bin/doxygen CACHE PATH "" FORCE )
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#set( SPHINX_EXECUTABLE /usr/local/bin/sphinx-build CACHE PATH "" FORCE )
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set( DOXYGEN_EXECUTABLE ${HOMEBREW_DIR}/bin/doxygen CACHE PATH "" FORCE )
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set( SPHINX_EXECUTABLE ${HOMEBREW_DIR}/opt/sphinx-doc/bin/sphinx-build CACHE PATH "" FORCE )
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if(NOT ( EXISTS "${GEOS_TPL_DIR}" AND IS_DIRECTORY "${GEOS_TPL_DIR}" ) )
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set(GEOS_TPL_DIR "${CMAKE_SOURCE_DIR}/../../thirdPartyLibs/install-${CONFIG_NAME}-release" CACHE PATH "" FORCE )

‎host-configs/quick-start-template.cmake

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set( CONFIG_NAME "quick-start" )
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# Set compilers path
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set(CMAKE_C_COMPILER "path-to-gcc/bin/gcc" CACHE PATH "") # This is typically something like /usr/bin/gcc ... or clang
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set(CMAKE_CXX_COMPILER "path-to-gcc/bin/g++" CACHE PATH "") # This is typically something like /usr/bin/g++ ... or clang++
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set(ENABLE_FORTRAN OFF CACHE BOOL "" FORCE)
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# Set paths to mpi
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set(ENABLE_MPI ON CACHE PATH "")
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set(MPI_C_COMPILER "path-to-mpi/bin/mpicc" CACHE PATH "") # This is typically something like /usr/bin/mpicc
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set(MPI_CXX_COMPILER "path-to-mpi/bin/mpicxx" CACHE PATH "") # This is typically something like /usr/bin/mpicxx
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set(MPIEXEC "path-to-mpi/bin/mpirun" CACHE PATH "") # This is typically something like /usr/bin/mpirun
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# Set paths to blas and lapack
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set( BLAS_LIBRARIES "path-to-blas" CACHE PATH "" FORCE ) # This is typically something like /usr/lib64/libblas.so
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set( LAPACK_LIBRARIES CACHE PATH "path-to-lapack" FORCE ) # This is typically something like /usr/lib64/liblapack.so
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# Cuda and openMP
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set( ENABLE_CUDA OFF CACHE PATH "" FORCE )
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set( ENABLE_OPENMP OFF CACHE PATH "" FORCE )
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# TPLs
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set( ENABLE_TRILINOS OFF CACHE PATH "" FORCE )
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set( ENABLE_CALIPER OFF CACHE PATH "" FORCE )
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set( ENABLE_DOXYGEN OFF CACHE BOOL "" FORCE)
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set( ENABLE_MATHPRESSO OFF CACHE BOOL "" FORCE )
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if(NOT ( EXISTS "${GEOS_TPL_DIR}" AND IS_DIRECTORY "${GEOS_TPL_DIR}" ) )
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set(GEOS_TPL_DIR "${CMAKE_SOURCE_DIR}/../../thirdPartyLibs/install-${CONFIG_NAME}-release" CACHE PATH "" FORCE )
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endif()
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include(${CMAKE_CURRENT_LIST_DIR}/../tpls.cmake)

‎inputFiles/compositionalMultiphaseWell/benchmarks/Egg/deadOilEgg_base_iterative.xml

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preconditionerType="mgr"
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krylovTol="1e-4"
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krylovAdaptiveTol="1"
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krylovWeakestTol="1e-2"/>
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krylovWeakestTol="1e-2"
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logLevel="1"/>
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</CompositionalMultiphaseReservoir>
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<CompositionalMultiphaseFVM

‎inputFiles/wellboreECP/ECP_Wellbore_geom01.xml

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‎inputFiles/wellboreECP/ECP_Wellbore_geom02.xml

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‎inputFiles/wellboreECP/ECP_Wellbore_geom03.xml

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‎inputFiles/wellboreECP/ECP_Wellbore_geom04.xml

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‎inputFiles/wellboreECP/ECP_Wellbore_geom05.xml

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nz="{ 25000 }"
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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 }"
15+
useCartesianOuterBoundary="2"
16+
cartesianMappingInnerRadius="0.12"
17+
cellBlockNames="{ casing, cement, rock }"
18+
/>
19+
</Mesh>
20+
21+
<Geometry>
22+
<Box
23+
name="sourceLeak"
24+
xMin="{ -0.51, -0.51, -10.00001 }"
25+
xMax="{ 0.51, 0.51, -9.99999 }"/>
26+
<Box
27+
name="output"
28+
xMin="{ -0.51, -0.51, -0.00001 }"
29+
xMax="{ 0.51, 0.51, 0.00001 }"/>
30+
</Geometry>
31+
32+
</Problem>

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