nap
nap: A molecular dynamics package with parameter-optimization programs for classical and machine-learning potentials - Published in JOSS (2021)
Science Score: 95.0%
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Found 1 DOI reference(s) in JOSS metadata -
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2 of 3 committers (66.7%) from academic institutions -
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Published in Journal of Open Source Software
Keywords
Repository
Nagoya Atomistic-simulation Package (NAP). Why don't you take a NAP? ;)
Basic Info
Statistics
- Stars: 22
- Watchers: 1
- Forks: 4
- Open Issues: 0
- Releases: 38
Topics
Metadata Files
README.md
What's nap
Nagoya Atomistic-simulation Package (nap) includes the following programs and utilities: - parallel molecular dynamics simulation (pmd) - potential parameter fitting (fitpot for neural-network potential, and for other potentials, see optzer) - python modules for pre/post-processes (nappy)
The program, pmd, includes various interatomic potentials for metals and semiconductors, and uses spatial decomposition technique for the parallelization, and linked-cell method for efficient neighbor search.
Who made this?
- Ryo KOBAYASHI
- Assistant Professor in the department of mechanical engineering, Nagoya Institute of Technology.
Requirements and dependencies
To compile pmd and fitpot, the following programs/libraries are required:
- Fortran compiler
- MPI library
nappy requires the following packages:
- numpy
- scipy
- pandas
- docopt
- ASE
Compilation and usage
For the short test, whether or not you can use this program in your environment,
bash
$ git clone https://github.com/ryokbys/nap.git ./nap
$ cd nap/
$ ./configure --prefix=$(pwd)
$ make test
If it works, you can use this program in your system.
To install the python package nappy, run the following commands on nap/ top directory,
shell
$ python -m build
$ pip install -e .
Then you can use the nappy commands, napsys, in the terminal and can import nappy package in python programs.
For details, please see the documentation (in Japanese) or ask me via e-mail (kobayashi.ryo[at]nitech.ac.jp).
Acknowledgements
This program was supported in part by "Materials research by Information Integration" Initiative (MI2I) project of the Support Program for Starting Up Innovation Hub from Japan Science and Technology Agency (JST).
LICENSE
This software is released under the MIT License, see the LICENSE.
Owner
- Name: RYO KOBAYASHI
- Login: ryokbys
- Kind: user
- Location: Nagoya, JAPAN
- Company: Nagoya Institute of Technology
- Website: http://ryokbys.web.nitech.ac.jp/index.html
- Repositories: 14
- Profile: https://github.com/ryokbys
JOSS Publication
nap: A molecular dynamics package with parameter-optimization programs for classical and machine-learning potentials
Authors
Department of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555, Japan
Editor
Bruce E. Wilson
Tags
materials science molecular dynamics interatomic potential neural-network potential meta-heuristicsGitHub Events
Total
- Release event: 6
- Watch event: 1
- Push event: 27
- Create event: 6
Last Year
- Release event: 6
- Watch event: 1
- Push event: 27
- Create event: 6
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Ryo KOBAYASHI | r****s@g****m | 1,592 |
| kobayashi | k****i@n****p | 1 |
| Ryo KOBAYASHI | k****i@p****p | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 4
- Total pull requests: 0
- Average time to close issues: about 1 month
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- richardjgowers (2)
- foeroyingur (2)