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phonolammps

LAMMPS interface for phonon calculations using phonopy

https://github.com/abelcarreras/phonolammps

Science Score: 23.0%

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
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
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    Scientific vocabulary similarity
    Low similarity (13.2%) to scientific vocabulary

Keywords

lammps lammps-python-interface phonon phonopy python-api

Keywords from Contributors

molecular-dynamics
Last synced: 6 months ago · JSON representation

Repository

LAMMPS interface for phonon calculations using phonopy

Basic Info
Statistics
  • Stars: 87
  • Watchers: 7
  • Forks: 26
  • Open Issues: 1
  • Releases: 6
Topics
lammps lammps-python-interface phonon phonopy python-api
Created about 8 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

PyPI version Downloads DOI

phonoLAMMPS

Calculate the harmonic interatomic force constants using phonopy and LAMMPS.
Online manual: https://phonolammps.readthedocs.io

Main features

  • Command line interface (phonopy like style)
  • Python API fully compatible with phonopy
  • Use of official LAMMPS python interface
  • Simple and easy to use
  • Finite temperature force constants using DynaPhoPy

Requirements

  • python 2.7.x/3.x
  • numpy
  • phonopy (https://atztogo.github.io/phonopy/)
  • LAMMPS python interface (https://lammps.sandia.gov/doc/Python_library.html)

Optional requirements for phonon band structure preview

  • matplotlib
  • seekpath (https://github.com/giovannipizzi/seekpath)

Optional requirements for finite temperature FC calculations

  • DynaPhoPy (https://github.com/abelcarreras/DynaPhoPy)

Optional requirements for tinker

  • Tinker testgrad (https://dasher.wustl.edu/tinker/)

Installation instructions

1) From source code ```

python setup.py install --user --prefix=

```

2) From PyPI repository

```

pip install phonoLAMMPS --user

```

For convenience, you may want to copy (or link) the files inside scripts folder to a location included in $PATH environment variable

Command line interface

phonoLAMMPS has a similar interface to phonopy to allow to easily calculate the 2nd order force constants and generate the crystal unitcell from a LAMMPS input file in VASP/POSCAR format. All outputs are fully compatible and ready to use in phonopy calculations. Also features a quick preview of the phonon band structure (requires seekpath).

```

phonolammps in.lammps --dim 2 2 2 -c POSCAR_unitcell -p

Additionally phonoLAMMPS allows to easily calculate finite temperature force constants from molecular dynamics by quasiparticle theory (requires dynaphopy).

phonolammps in.lammps --dim 2 2 2 -c POSCAR_unitcell -p -t 300 (at 300 K)

The obtained *FORCE_CONSTANTS* and *POSCAR_unitcell* can be used in phonopy using **--readfc** option for more advanced calculations.

phonopy --dim="2 2 2" --readfc -c POSCAR_unitcell band.conf

```

Python API

Simple python API fully compatible with phonopy.

``` from phonolammps import Phonolammps from phonopy import Phonopy

phlammps = Phonolammps('in.lammps', supercell_matrix=[[3, 0, 0], [0, 3, 0], [0, 0, 3]])

unitcell = phlammps.getunitcell() forceconstants = phlammps.getforceconstants() supercellmatrix = phlammps.getsupercell_matrix()

phonon = Phonopy(unitcell, supercell_matrix)

phonon.setforceconstants(forceconstants) phonon.setmesh([20, 20, 20])

phonon.settotalDOS() phonon.plottotalDOS().show()

phonon.setthermalproperties() phonon.plotthermalproperties().show() ```

Contact info

Abel Carreras
abelcarreras83@gmail.com

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

GitHub Events

Total
  • Issues event: 1
  • Watch event: 4
Last Year
  • Issues event: 1
  • Watch event: 4

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 157
  • Total Committers: 4
  • Avg Commits per committer: 39.25
  • Development Distribution Score (DDS): 0.025
Past Year
  • Commits: 11
  • Committers: 3
  • Avg Commits per committer: 3.667
  • Development Distribution Score (DDS): 0.273
Top Committers
Name Email Commits
abel a****3@g****m 153
yuhldr y****r@q****m 2
Jan Janßen j****n@m****e 1
Pablo Piaggi p****i@g****m 1
Committer Domains (Top 20 + Academic)
mpie.de: 1 qq.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 17
  • Total pull requests: 3
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 23 hours
  • Total issue authors: 16
  • Total pull request authors: 3
  • Average comments per issue: 2.53
  • Average comments per pull request: 0.67
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • 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
View more stats
Top Authors
Issue Authors
  • zhangxiaoyu2046 (2)
  • Movaffaq (1)
  • antonf-ekb (1)
  • ChengyangYuan (1)
  • yuzc22 (1)
  • Appalakondaiah (1)
  • JWCheys (1)
  • wilsonnieto (1)
  • alexgorfer (1)
  • yuhldr (1)
  • YuuuXie (1)
  • JTaozhang (1)
  • TerryHangLyu (1)
  • maverick422 (1)
  • LANHNU (1)
Pull Request Authors
  • jan-janssen (1)
  • shangling3 (1)
  • PabloPiaggi (1)
  • yuhldr (1)
Top Labels
Issue Labels
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Packages

  • Total packages: 2
  • Total downloads:
    • pypi 205 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 36
  • Total maintainers: 1
pypi.org: phonolammps

phonoLAMMPS module

  • Versions: 24
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 205 Last month
Rankings
Forks count: 8.0%
Stargazers count: 8.3%
Downloads: 9.7%
Dependent packages count: 10.0%
Average: 20.7%
Dependent repos count: 67.6%
Maintainers (1)
abelcarreras83
Last synced: 6 months ago
conda-forge.org: phonolammps

Calculate the 2nd order force constants using phonopy and LAMMPS.

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Forks count: 36.1%
Stargazers count: 38.0%
Average: 39.8%
Dependent packages count: 51.2%
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • numpy >=1.8.2
requirements.txt pypi
  • dynaphopy *
  • matplotlib *
  • numpy >=1.8.2
  • phonopy *
  • seekpath *
setup.py pypi
  • dynaphopy *
  • matplotlib *
  • numpy *
  • phonopy *
  • seekpath *
.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • pypa/gh-action-pypi-publish 27b31702a0e7fc50959f5ad993c78deac1bdfc29 composite