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https://github.com/bio-phys/trimem

Monte Carlo sampling of the Helfrich bending energy.

https://github.com/bio-phys/trimem

Science Score: 39.0%

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Repository

Monte Carlo sampling of the Helfrich bending energy.

Basic Info
Statistics
  • Stars: 7
  • Watchers: 2
  • Forks: 5
  • Open Issues: 2
  • Releases: 0
Created about 4 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

Trimem

Trimem is a python package for the Monte Carlo simulation of lipid membranes according to the Helfrich theory [^Helfrich1973].

[^Helfrich1973]: Helfrich, W. (1973) Elastic properties of lipid bilayers: Theory and possible experiments. Zeitschrift für Naturforschung C, 28(11), 693-703

Installation

Trimem can be installed using pip:

bash git clone --recurse-submodules https://github.com/bio-phys/trimem.git pip install trimem/

We suggest the installation using the --user flag to pip. Alternatively, we recommend to consider the usage of virtual environments to isolate the installation of trimem, see, e.g., here.

Dependencies

Trimem builds upon the generic mesh data structure OpenMesh, which is included as a submodule that is pulled in upon git clone via the --recurse-submodules flag.

For the efficient utilization of shared-memory parallelism, trimem makes use of the OpenMP application programming model (>= v4.5) and modern C++. It thus requires relatively up-to-date compilers (supporting at least C++17).

If not already available, the following python dependencies will be automatically installed:

  • numpy
  • scipy
  • h5py
  • meshio

Documentation and tests further require:

  • autograd
  • trimesh
  • sphinx
  • sphinx-copybutton
  • sphinxcontrib-programoutput

Development installation

Unit-tests can be run with

bash pip install trimem/[tests] pytest -v tests/

The documentation can be generated with sphinx by

bash pip install trimem/[docs] cd doc; make html

Usage

For an introduction to the usage of trimem please refer to the documentation.

Citation

If you use trimem for your scientific work, please consider the citation of Siggel, M. et al[^Siggel2022].

[^Siggel2022]: Siggel, M. et al. (2022) TriMem: A Parallelized Hybrid Monte Carlo Software for Efficient Simulations of Lipid Membranes. J. Chem. Phys. (in press) (2022); https://doi.org/10.1063/5.0101118

References

Owner

  • Name: bio-phys
  • Login: bio-phys
  • Kind: organization

GitHub Events

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Last Year
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  • Member event: 1
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Dependencies

.github/workflows/test.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
pyproject.toml pypi
setup.py pypi