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‎CONTRIBUTING.md

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# Contributing
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# Contributing to OasisMove
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Contributions are welcome, and they are greatly appreciated! Every little bit
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helps, and credit will always be given. You can contribute in the ways listed below.
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When contributing to this repository, please first discuss the change you wish to make via issue,
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email, or any other method with the owners of this repository before making a change.
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## Report Bugs
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### Testing
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Report bugs using GitHub issues.
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Please provide unit tests for the new code you create, testing the main functionality or feature to be submitted. We can always use more test coverage!
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If you are reporting a bug, please include:
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### Submitting changes
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* Your operating system name and version.
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* Any details about your local setup that might be helpful in troubleshooting.
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* Detailed steps to reproduce the bug.
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In order to submit you changes, please send a [GitHub Pull Request to OasisMove](https://github.com/KVSlab/OasisMove/pull/new/master) with a clear list of what you've done (read more about [pull requests](http://help.github.com/pull-requests/)). Please follow our coding conventions (below) and make sure all of your commits are atomic (one feature per commit).
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## Fix Bugs
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Always write a clear commit message when submitting your changes. One-line messages are fine for small changes, but bigger changes should look like this:
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Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
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wanted" is open to whoever wants to implement it.
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> $ git commit -m "A brief summary of the commit
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>
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> A paragraph describing what changed and its impact."
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## Implement Features
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### Coding conventions
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Look through the GitHub issues for features. Anything tagged with "enhancement"
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and "help wanted" is open to whoever wants to implement it.
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#### Formatting
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* Avoid inline comments.
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* Break long lines after 120 characters.
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* Delete trailing whitespace.
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* Don't include spaces after `(`, `[` or before `]`, `)`.
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* Don't misspell.
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* Use 4 space indentation.
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* Use an empty line between methods.
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* Use spaces around operators, except for unary operators, such as `!`.
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* Use spaces after commas, after colons and semicolons, around `{` and before
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`}`.
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## Write Documentation
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#### Naming
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* Avoid abbreviations.
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* Use snake case for variables and methods.
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* Use camel case for classes.
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* Name variables, methods, and classes to reveal intent.
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OasisMove could always use more documentation, whether as part of the
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official OasisMove docs, in docstrings, or even on the web in blog posts,
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articles, and such.
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#### Organization
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* Order methods so that caller methods are earlier in the file than the methods
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they call.
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* Place methods receiving command line arguments at the bottom of the file, but above the top-level script environment check.
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* Separate local and global imports of modules.
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## Submit Feedback
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### Code of Conduct
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The best way to send feedback is to file an issue on GitHub.
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### Our Pledge
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If you are proposing a feature:
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to making participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, sex characteristics, gender identity and expression,
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level of experience, education, socio-economic status, nationality, personal
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appearance, race, religion, or sexual identity and orientation.
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* Explain in detail how it would work.
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* Keep the scope as narrow as possible, to make it easier to implement.
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* Remember that this is a volunteer-driven project, and that contributions
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are welcome :)
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### Our Standards
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## Get Started
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Examples of behavior that contributes to creating a positive environment
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include:
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Ready to contribute? Here's how to set up `OasisMove` for local development.
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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1. Fork the repo on GitHub.
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2. Clone your fork locally.
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3. Install your local copy into a virtualenv, e.g., using `conda`.
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4. Create a branch for local development and make changes locally.
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5. Commit your changes and push your branch to GitHub.
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6. Submit a pull request through the GitHub website.
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Examples of unacceptable behavior by participants include:
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## Code of Conduct
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/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 electronic
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address, without 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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Please note that the OasisMove project is released with a [Contributor Code of Conduct](CONDUCT.md). By contributing to this project you agree to abide by its terms.
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### Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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### Scope
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This Code of Conduct applies both within project spaces and in public spaces
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when an individual is representing the project or its community. Examples of
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representing a project or community include using an official project e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event. Representation of a project may be
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further defined and clarified by project maintainers.
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### Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the project team at [email protected]. All
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complaints will be reviewed and investigated and will result in a response that
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is deemed necessary and appropriate to the circumstances. The project team is
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obligated to maintain confidentiality with regard to the reporter of an incident.
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Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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### Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
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For answers to common questions about this code of conduct, see
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https://www.contributor-covenant.org/faq
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[homepage]: https://www.contributor-covenant.org

‎README.md

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# OasisMove
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_________________
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## OasisMove - Oasis for Moving Domains
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[![GPL-3.0](https://img.shields.io/github/license/hkjeldsberg/oasismove)](LICENSE)
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[Read Latest Documentation](https://hkjeldsberg.github.io/oasismove/)
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[Read Latest Documentation](https://kvslab.github.io/oasismove/)
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[![Build Status](https://travis-ci.org/mikaem/Oasis.svg?branch=master)](https://travis-ci.org/mikaem/Oasis)
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![github-CI](https://github.com/mikaem/Oasis/workflows/github-CI/badge.svg)
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_________________
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<p align="center">
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<img src="figs/moving_ventricle.gif" width="640" height="315" alt="Left ventricle flow"/>
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</p>
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<p align="center">
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Fluid velocity (left) and mesh deformation (right) of an idealized left ventricle.
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</p>
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Description
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-----------
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OasisMove is a high-level/high-performance open-source Navier-Stokes solver for fluid flow in rigid and moving domains
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written in Python/[FEniCS](https://fenicsproject.org/>), and is an extension of the computational fluid dynamics (CFD)
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solver [Oasis](https://github.com/mikaem/Oasis>). In OasisMove the Navier-Stokes equations are expressed in the
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arbitrary Lagrangian-Eulerian formulation, which is suitable for handling moving domains. This moving domain solver has
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undergone rigorous verification and validation, and results have shown that OasisMove follows theoretical convergence
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rates, begin second order accurate in time, and second and third order accurate in space with P1/P1 and P2/P1 finite
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elements. Although OasisMove was developed with cardiovascular flows in mind, it is applicable to several flow problems
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within CFD.
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<p align="center">
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<img src=figs/verification_u_p.png width="630 height="470" alt="Convergence rate analysis"/>
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</p>
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<p align="center">
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Spatial convergence study of OasisMove performed by varying the characteristic edge length Δx. On the left, the L2 error for the
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velocity, and on the right the L2 error for the pressure, both following theoretical convergence rates.
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The solid lines represent the simulation results, and the dashed lines display the theoretical convergence rates.
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A similar study was performed to address temporal convergence, resulting in second order convergence (not shown here).
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</p>
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Authors
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-------
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OasisMove is developed by
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* Henrik Aasen Kjeldsberg
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Licence
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-------
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OasisMove is licensed under the GNU GPL, version 3 or (at your option) any later version.
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OasisMove is Copyright (2022) by the author.
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Documentation
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-------------
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For detailed installation notes and an introduction to OasisMove, please refer to
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the [documentation](https://oasismove.readthedocs.io/en/latest/). For (outdated) details on vanilla Oasis, please refer
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to its [wiki](https://github.com/mikaem/oasis/wiki) or
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the [user manual](https://github.com/mikaem/Oasis/tree/master/doc/usermanual.pdf)
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If you wish to use OasisMove/Oasis for journal publications, please cite the
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following [paper](http://www.sciencedirect.com/science/article/pii/S0010465514003786).
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Installation
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------------
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OasisMove requires a compatible installation of FEniCS, which is available through Anaconda on macOS and Linux. Windows
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users may need to install FEniCS as described [here](https://fenicsproject.org/download/). Start by installing
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Anaconda/Miniconda on your computer, and add the `conda-forge` channel with:
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conda config --add channels conda-forge
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conda config --set channel_priority strict
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Then create a conda environment for `FEniCS` by executing the following command in a terminal
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conda create -n your_environment fenics
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An alternative is to run FEniCS through a [Docker](https://www.docker.com/) image. Next, you need to install OasisMove.
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You can do so with the following commands:
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git clone https://github.com/KVSlab/OasisMove
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pip install --editable OasisMove
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Now you are all set, and can start running CFD simulations in moving domains with OasisMove.
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Issues
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------
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Please report bugs and other issues through the [issue tracker](https://github.com/KVSlab/OasisMove/issues).
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