https://github.com/whitead/symd
N-Dimensional MD engine with symmetry group constraints written in C
Science Score: 46.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: acs.org -
✓Committers with academic emails
2 of 3 committers (66.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.1%) to scientific vocabulary
Keywords
Repository
N-Dimensional MD engine with symmetry group constraints written in C
Basic Info
- Host: GitHub
- Owner: whitead
- License: mit
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://whitead.github.io/symd
- Size: 45 MB
Statistics
- Stars: 50
- Watchers: 2
- Forks: 6
- Open Issues: 1
- Releases: 6
Topics
Metadata Files
README.md
Symmetric Molecular Dynamics Engine
This is a simple MD engine written in C that can be constrained to obey given symmetry groups at every frame. It can be compiled for any dimension, but scaffolding only exists for 2 and 3D lattices. It supports the following features:
- NVE, NVT (BAOAB, CSVR thermostats), NPT
- LJ, harmonic, cosine potentials
- Neighbor lists (use
nljinstead ofljfor potential) - Symmetry constraints and all Bravais Lattices in 2D/3D
Purpose
https://user-images.githubusercontent.com/908389/162356564-95f35117-e31b-412c-8a3a-c3a92a92ae81.mp4
This is not really intended to be a production-ready simulation engine. Instead, it is a reference implementation of symmetric MD. I hope then the algorithm can be incorporated into other engines, or this engine can be extended, for others to use the algorithm. The Python package (see below) should make implementing the method as easy as possible. With that said, the most important files are box.c and group.c, which contain the key algorithms: fold_particles and the NPT algorithms: make_box, and try_rescale.
Python Package
There is a companion python package (symd) that can be installed via:
sh
pip install symd
This does not include the MD engine, but instead includes necessary details to set-up symmetry constraints like getting affine matrices and Bravais lattice tensors.
Docs & Examples
See the docs which includes the python API, examples of running simulations, and shows how the figures from the manuscript were generated.
Compiling
sh
mkdir build && cd build
cmake ..
make && [sudo] make install
The executable is symdX where X is the number of spatial dimensions
Dependencies
- libgsl-dev (GNU Scientific Library headers)
- CMake
Python Interface
It is recommended to use the python interface, which simplifies building the input files and parsing output files. See the examples in the docs.
Example
An example can be found in the examples/lj-symm-example directory.
Citation
bibtex
@article{cox2022symmetric,
author = {Cox, Sam and White, Andrew D.},
title = {Symmetric Molecular Dynamics},
journal = {Journal of Chemical Theory and Computation},
year = {2022},
doi = {10.1021/acs.jctc.2c00401},
}
Owner
- Name: Andrew White
- Login: whitead
- Kind: user
- Location: Rochester, NY
- Company: University of Rochester
- Website: http://thewhitelab.org
- Twitter: andrewwhite01
- Repositories: 27
- Profile: https://github.com/whitead
GitHub Events
Total
- Watch event: 4
- Fork event: 1
Last Year
- Watch event: 4
- Fork event: 1
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 186
- Total Committers: 3
- Avg Commits per committer: 62.0
- Development Distribution Score (DDS): 0.016
Top Committers
| Name | Commits | |
|---|---|---|
| Andrew White | w****w@g****m | 183 |
| Sam Cox | s****0@u****u | 2 |
| Andrew White | w****d@u****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 6
- Total pull requests: 23
- Average time to close issues: 22 days
- Average time to close pull requests: 1 day
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 1.5
- Average comments per pull request: 0.0
- Merged pull requests: 22
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: 1 day
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- whitead (5)
- SamCox822 (1)
Pull Request Authors
- whitead (22)
- SamCox822 (3)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 52 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 7
- Total maintainers: 1
pypi.org: symd
Symmetric Molecular Dynamics
- Homepage: https://whitead.github.io/symd/
- Documentation: https://symd.readthedocs.io/
- License: MIT
-
Latest release: 1.1.3
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- pre-commit * development
- cairosvg *
- matplotlib *
- pandas *
- seaborn *
- skunk *
- svglib *
- matplotlib *
- myst-nb *
- pandas *
- seaborn *
- skunk *
- sphinx *
- sphinx-rtd-theme *
- sphinx_autodoc_typehints *
- svglib *
- 118 dependencies
- numpy *
- actions/checkout v2 composite
- actions/setup-python v2 composite
- pypa/gh-action-pypi-publish master composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- peaceiris/actions-gh-pages v3 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite