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https://github.com/barbagroup/PetIBM

PetIBM - toolbox and applications of the immersed-boundary method on distributed-memory architectures
https://github.com/barbagroup/PetIBM

computational-fluid-dynamics gpu-computing immersed-boundary-method nvidia-amgx petsc

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PetIBM - toolbox and applications of the immersed-boundary method on distributed-memory architectures

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# PetIBM - toolbox and applications of the immersed-boundary method on distributed-memory architectures



[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://github.com/barbagroup/PetIBM/raw/master/LICENSE)

[![Travis](https://img.shields.io/travis/barbagroup/PetIBM/develop.svg?logo=travis)](https://travis-ci.org/barbagroup/PetIBM)

[![Docs](https://img.shields.io/badge/docs-0.4-brightgreen.svg)](https://barbagroup.github.io/PetIBM)

[![DOI](https://img.shields.io/badge/JOSS-10.21105%2Fjoss.00558-brightgreen.svg)](https://doi.org/10.21105/joss.00558)

[![CITE_BIB](https://img.shields.io/badge/Cite%20PetIBM-bibtex-blue.svg)](https://www.doi2bib.org/bib/10.21105/joss.00558)



PetIBM implements immersed-boundary methods to solve 2D and 3D incompressible Navier-Stokes on stretched Cartesian grids using a projection approach.



Currently, two immersed boundary methods are implemented:



* Immersed Boundary Projection Method (IBPM; Taira and Colonius, 2007);

* decoupled version of the IBPM (Li et al., 2016).



With object-oriented design, the objects and classes in PetIBM can be re-used to develop other solvers easily, as long as the numerical methods used can fit into Perot's framework (Perot, 1993; Chang et. al, 2002).

See [Doxygen pages](https://barbagroup.github.io/PetIBM/modules.html) for API manual.



PetIBM relies on the [PETSc](http://www.mcs.anl.gov/petsc/) library for data structures and parallel routines.

Linear systems can be solved either on CPUs using PETSc KSP objects or on multiple CUDA-capable GPU devices using the NVIDIA [AmgX](https://github.com/NVIDIA/AMGX) library.

Data transfers between PETSc and AmgX are handled by [AmgXWrapper](https://github.com/barbagroup/AmgXWrapper).



PetIBM runs only on Unix-based systems (no support on Windows) and was last tested on Ubuntu 16.04, MacOS Sierra 10.12.6, and Arch Linux.

PetIBM was also tested on the following HPC systems: [GW ColonialOne](https://colonialone.gwu.edu/) and [Titan at ORNL](https://www.olcf.ornl.gov/titan/).



Please see [Documentation](#documentation) for more details.



---



## Features



PetIBM supports:



* multiple immersed bodies,

* moving bodies with prescribed kinematics,

* 2D and 3D stretched Cartesian meshes,

* distributed-memory architectures,

* multiple GPUs on a single node,

* GPU clusters, and

* HDF5 I/O.



---



## Documentation



* [Quick Start](doc/markdowns)

  * [Dependencies and Installation](doc/markdowns/installation.md)

  * [Run PetIBM](doc/markdowns/runpetibm.md)

  * [Input files](doc/markdowns/inputs.md)

  * [Output files](doc/markdowns/outputs.md)

  * [2D Examples](doc/markdowns/examples2d.md)

  * [3D Examples](doc/markdowns/examples3d.md)

  * [Use PetIBM API](doc/markdowns/usepetibmapi.md)

* [Online API manual](https://barbagroup.github.io/PetIBM)

* [Change Log](CHANGELOG.md)

* [Contributing](CONTRIBUTING.md)



Offline API manual can be generated with [Doxygen](http://www.stack.nl/~dimitri/doxygen/).



---



## Papers published using PetIBM



* Mesnard, O., & Barba, L. A. (2017). _Reproducible and Replicable Computational Fluid Dynamics: It's Harder Than You Think_. Computing in Science & Engineering, 19(4), 44-55, https://doi.org/10.1109/MCSE.2017.3151254.



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## Contact



Please e-mail [Olivier Mesnard](mailto:[email protected]) or [Pi-Yueh Chuang](mailto:[email protected]) if you have any questions, suggestions, or feedback.



To report bugs, please use the GitHub issue tracking system.

We are also open to pull-requests.



---



## References



* Chang, W., Giraldo, F., & Perot, B. (2002). *Analysis of an exact fractional step method*. Journal of Computational Physics, 180(1), 183-199.

* Li, R. Y., Xie, C. M., Huang, W. X., & Xu, C. X. (2016). *An efficient immersed boundary projection method for flow over complex/moving boundaries*. Computers & Fluids, 140, 122-135.

* Perot, J. B. (1993). *An analysis of the fractional step method*. Journal of Computational Physics, 108(1), 51-58.

* Taira, K., & Colonius, T. (2007). *The immersed boundary method: a projection approach*. Journal of Computational Physics, 225(2), 2118-2137.



---



## How to cite PetIBM



If PetIBM contributes to a project that leads to a scientific publication, please cite the project.

You can use this citation or the BibTeX entry below.



> Pi-Yueh Chuang, Olivier Mesnard, Anush Krishnan, Lorena A. Barba (2018). PetIBM: toolbox and applications of the immersed-boundary method on distributed-memory architectures. _Journal of Open Source Software_, **3**(25), 558, [doi:10.21105/joss.00558](https://doi.org/10.21105/joss.00558)



```console

@article{chuang2018petibm,

  doi = {10.21105/joss.00558},

  url = {https://doi.org/10.21105/joss.00558},

  year = {2018},

  month = {may},

  publisher = {The Open Journal},

  volume = {3},

  number = {25},

  pages = {558},

  author = {Pi-Yueh Chuang and Olivier Mesnard and Anush Krishnan and Lorena A. Barba},

  title = {{PetIBM}: toolbox and applications of the immersed-boundary method on distributed-memory architectures},

  journal = {The Journal of Open Source Software}

}

```