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https://github.com/abelcarreras/dynaphopy

Phonon anharmonicity analysis from molecular dynamics

https://github.com/abelcarreras/dynaphopy

Science Score: 49.0%

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    DOI references
    Found 2 DOI reference(s) in README
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    1 of 4 committers (25.0%) from academic institutions
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    Low similarity (12.8%) to scientific vocabulary

Keywords

anharmonicity lammps molecular-dynamics phonon phonopy vasp
Last synced: 6 months ago · JSON representation

Repository

Phonon anharmonicity analysis from molecular dynamics

Basic Info
Statistics
  • Stars: 130
  • Watchers: 17
  • Forks: 53
  • Open Issues: 4
  • Releases: 29
Topics
anharmonicity lammps molecular-dynamics phonon phonopy vasp
Created over 11 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

PyPI version Build Status Coverage Status DOI

DynaPhoPy

Software to calculate crystal microscopic anharmonic properties from molecular dynamics (MD) using the normal-mode-decomposition technique. These properties include the phonon frequency shifts and linewidths, as well as the renormalized force constanst and thermal properties by using quasiparticle theory. This code includes interfaces for MD outputs from VASP and LAMMPS. PHONOPY code is used to obtain harmonic phonon modes.

Online manual: http://abelcarreras.github.io/DynaPhoPy/

Installation instructions

  1. Requirements
    • Python 2.7.x/3.5 or higher
    • Phonopy 2.0 or higher (https://phonopy.github.io/phonopy)
    • Matplotlib
    • Scipy
    • h5py
    • pyYAML
    • (optional) pyFFTW (http://www.fftw.org/)
    • (optional) cudafunctions (https://github.com/abelcarreras/cudafunctions)

2a. Install from pypi repository pip install dynaphopy --user

2b. Install from source (requires c compiler) - Install requirements from requirements.txt: pip install -r requirements.txt --user - Run setup.py to install dynaphopy python setup.py install --user

Executing this software

  1. Command line method

    • execute dynaphopy -h for detailed description of available options dynaphopy input_file MD_file [Options]

  2. Interactive mode

    • Use -i option from command line method and follow the instructions dynaphopy input_file MD_file -i

  3. Scripting method (as a module)

    • Dynaphopy can be imported as a python module
    • In examples/apiscripts directory an example script is available (scriptsilicon.py)
    • The comments in the script makes it (hopefully) self explained.

Input files for several materials can be found in the same example/inputs directory. More information in the online manual at: http://abelcarreras.github.io/DynaPhoPy

Contact info

Abel Carreras
abelcarreras83@gmail.com

Donostia International Physics Center (DIPC)
Donostia-San Sebastian (Spain)

Owner

  • Name: Abel Carreras
  • Login: abelcarreras
  • Kind: user
  • Location: Spain
  • Company: Donostia International Physics Center (DIPC)

GitHub Events

Total
  • Issues event: 7
  • Watch event: 18
  • Issue comment event: 14
  • Push event: 11
  • Fork event: 3
  • Create event: 1
Last Year
  • Issues event: 7
  • Watch event: 18
  • Issue comment event: 14
  • Push event: 11
  • Fork event: 3
  • Create event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 1,047
  • Total Committers: 4
  • Avg Commits per committer: 261.75
  • Development Distribution Score (DDS): 0.011
Past Year
  • Commits: 13
  • Committers: 2
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.385
Top Committers
Name Email Commits
abel a****3@g****m 1,036
Chenxing Luo c****o@g****m 8
Jan Janßen j****n@m****e 2
Pynappledude 7****e 1
Committer Domains (Top 20 + Academic)
mpie.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 33
  • Total pull requests: 7
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 1 day
  • Total issue authors: 25
  • Total pull request authors: 5
  • Average comments per issue: 6.97
  • Average comments per pull request: 1.57
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 1
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 20 hours
  • Issue authors: 4
  • Pull request authors: 1
  • Average comments per issue: 3.17
  • Average comments per pull request: 3.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gabkrenzer (4)
  • ZhangMin-qq (2)
  • ziyun894 (2)
  • ZengZezhu (2)
  • Bowen-677 (2)
  • gooaah (1)
  • Lweiweij (1)
  • jxsun-netizen (1)
  • 1041176461 (1)
  • bobleesj (1)
  • Liang1Kai (1)
  • Guancred (1)
  • ballal09 (1)
  • bjmorgan (1)
  • thliu-hust (1)
Pull Request Authors
  • jan-janssen (4)
  • chazeon (2)
  • Pyneappledude (1)
  • abelcarreras (1)
  • bjmorgan (1)
Top Labels
Issue Labels
bug (1) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 544 last-month
  • Total dependent packages: 4
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 53
  • Total maintainers: 1
pypi.org: dynaphopy

dynaphopy module

  • Versions: 37
  • Dependent Packages: 3
  • Dependent Repositories: 1
  • Downloads: 544 Last month
Rankings
Dependent packages count: 4.7%
Forks count: 6.0%
Stargazers count: 7.4%
Downloads: 9.2%
Average: 9.8%
Dependent repos count: 21.8%
Maintainers (1)
abelcarreras83
Last synced: 6 months ago
conda-forge.org: dynaphopy

Software to calculate crystal microscopic anharmonic properties from molecular dynamics (MD) using the normal-mode-decomposition technique. These properties include the phonon frequency shifts and linewidths, as well as the renormalized force constanst and thermal properties by using quasiparticle theory. This code includes interfaces for MD outputs from VASP and LAMMPS. PHONOPY code is used to obtain harmonic phonon modes.

  • Versions: 16
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Forks count: 25.9%
Dependent packages count: 28.8%
Average: 30.4%
Stargazers count: 33.0%
Dependent repos count: 34.0%
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • PyYAML *
  • matplotlib *
  • numpy >=1.8.2
  • phonopy >=2.0
  • scipy *
  • seekpath *
  • windows-curses *
setup.py pypi
  • matplotlib *
  • numpy *
  • phonopy *
  • scipy *
.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/download-artifact v2 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v2 composite
  • pypa/cibuildwheel v2.4.0 composite
  • pypa/gh-action-pypi-publish v1.4.2 composite