ctlee / gamer

Geometry-preserving Adaptive Mesher
https://gamer.readthedocs.io
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Geometry-preserving Adaptive MeshER

DOI PyPI Main Build Status Documentation Status

GAMer is a surface mesh improvement library developed to condition surface meshes derived from noisy biological imaging data. Using Tetgen, GAMer can generate tetrahedral meshes suitable for finite elements simulations of reaction-diffusion systems among others. GAMer has the following main features:

Technical Features:

Acknowledging your use of GAMer

Thanks for using GAMer! The developers would love to hear how you are using the tool. Please send us an email or post on GitHub letting us know.

Please cite the above Zenodo DOI to acknowledge the software version and cite the following papers:
Lee, C. T.; Laughlin, J. G.; Moody, J. B.; Amaro, R. E.; McCammon, J. A.; Holst, M.; Rangamani, P. An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophysical Journal 2020, 118 (5), 1003–1008.

Lee, C. T.; Laughlin, J. G.; Beaumelle, N. A. de L.; Amaro, R. E.; McCammon, J. A.; Ramamoorthi, R.; Holst, M.; Rangamani, P. 3D Mesh Processing Using GAMer 2 to Enable Reaction-Diffusion Simulations in Realistic Cellular Geometries. PLOS Computational Biology 2020, 16 (4), e1007756.

Installation

The following instructions are to build the base GAMer library. If you wish to additionally compile the Blender GAMer addon, GAMer documentation, or other features please refer to the Additional Options section prior to building.

First, download a copy of the source from releases or clone the master branch.

git clone https://github.com/ctlee/gamer.git
cd gamer

Linux and Mac:

mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr -DGAMER_TESTS=on -DCMAKE_BUILD_TYPE=Release ..
make

For Windows, we support building using Microsoft Visual Studio (MSVS) through the use of CMake generators:

mkdir build64
cd build64
cmake -DBUILD_BLENDGAMER=TRUE -G "Visual Studio 15 2017 Win64" -A x64 ..
cmake --build . --config Release

For a complete guide to installation, including configuration of PyGAMer and BlendGAMer please checkout the online installation documentation.

External libraries bundled/downloaded with/by GAMer

Development Build Status

Development Build Status Documentation Status