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FHI-vibes

FHI-vibes: Ab Initio Vibrational Simulations - Published in JOSS (2020)

https://gitlab.com/vibes-developers/vibes

Science Score: 89.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: aps.org
  • ✓
    Committers with academic emails
    10 of 17 committers (58.8%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Scientific Fields

Earth and Environmental Sciences Physical Sciences - 87% confidence
Materials Science Physical Sciences - 63% confidence
Computer Science Computer Science - 60% confidence
Last synced: 4 months ago · JSON representation

Repository

[FHI-vibes](https://vibes-developers.gitlab.io/vibes/): Vibrational simulations with python powered by ASE and FHI-aims.

Basic Info
  • Host: gitlab.com
  • Owner: vibes-developers
  • License: mit
  • Default Branch: master
Statistics
  • Stars: 18
  • Forks: 12
  • Open Issues: 48
  • Releases: 0
Created over 5 years ago

https://gitlab.com/vibes-developers/vibes/blob/master/ 

FHI-vibes
===

Welcome to `FHI-vibes`, a `python` package for calculating, analyzing, and understanding the vibrational properties of solids from first principles. `FHI-vibes` is intended to seamlessly bridge between the harmonic approximation and fully anharmonic molecular dynamics simulations. To this end, `FHI-vibes` builds on several [existing packages](https://vibes-developers.gitlab.io/vibes/Credits/) and interfaces them in a consistent and user-friendly fashion.

In the documentation and tutorials, knowledge of first-principles electronic-structure theory as well as proficiency with _ab initio_ codes such as [FHI-aims](https://aimsclub.fhi-berlin.mpg.de/) and high-performance computing are assumed. Additional experience with python, the [Atomic Simulation Environment (ASE)](https://wiki.fysik.dtu.dk/ase/), or [Phonopy](https://atztogo.github.io/phonopy/) is helpful, but not needed.

`FHI-vibes` provides the following features:

- Geometry optimization via [ASE](https://wiki.fysik.dtu.dk/ase/ase/optimize.html#module-ase.optimize),
- harmonic phonon calculations via [Phonopy](https://atztogo.github.io/phonopy/),
- molecular dynamics simulations in [NVE](https://wiki.fysik.dtu.dk/ase/ase/md.html#constant-nve-simulations-the-microcanonical-ensemble), [NVT](https://wiki.fysik.dtu.dk/ase/ase/md.html#module-ase.md.langevin), and [NPT](https://wiki.fysik.dtu.dk/ase/ase/md.html#module-ase.md.nptberendsen) ensembles,
- [harmonic sampling](https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.96.115504),
- [anharmonicity quantification](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.4.083809), and
- thermal transport with [ab initio Green-Kubo](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.107.224304) and [Phono3py](Documentation/phono3py.md)

Most of the functionality is high-throughput ready via [fireworks](https://materialsproject.github.io/fireworks/#).


## Overview

- [Installation](https://vibes-developers.gitlab.io/vibes/Installation)
- [Tutorial](https://vibes-developers.gitlab.io/vibes/Tutorial/0_intro)
- [Documentation](https://vibes-developers.gitlab.io/vibes/Documentation/0_intro)
- [Credits](https://vibes-developers.gitlab.io/vibes/Credits)
- [References](https://vibes-developers.gitlab.io/vibes/References)

## Changelog

#### v1.1.0

- Update ab initio Green Kubo method and [tutorials](https://vibes-developers.gitlab.io/vibes/Tutorial/7_green_kubo/). [(!100)](https://gitlab.com/vibes-developers/vibes/-/merge_requests/100)
- Update Phono3py interface and [documentations](https://vibes-developers.gitlab.io/vibes/Documentation/phono3py/).
- Heatflux unit updated from `eV/AA^2/ps` to `eV/AA^2/fs`.

#### v1.0.5

- bugfix

#### v1.0.4

- looser dependencies
- [various bug fixes](https://gitlab.com/vibes-developers/vibes/-/merge_requests?scope=all&state=merged)

#### v1.0.3

- update dependencies to allow `phonopy` versions up to 2.8

#### v1.0.2

- First official release after passing the [JOSS review](https://github.com/openjournals/joss-reviews/issues/2671).
- Several additions to the documentation.

#### v1.0.0a10

- Enable conversion of trajectories to `ase.io.Trajectory` files for viewing with ASE [(!37)](https://gitlab.com/vibes-developers/vibes/-/merge_requests/37)
- Important fix for running NPT dynamics [(!36)](https://gitlab.com/vibes-developers/vibes/-/merge_requests/36)
- We have a changelog now!

JOSS Publication

FHI-vibes: Ab Initio Vibrational Simulations
Published
December 02, 2020
DOI
Volume 5, Issue 56, Page 2671
Authors
Florian Knoop ORCID
Fritz Haber Institute of the Max Planck Society, Berlin, Germany
Thomas A. r. Purcell ORCID
Fritz Haber Institute of the Max Planck Society, Berlin, Germany
Matthias Scheffler
Fritz Haber Institute of the Max Planck Society, Berlin, Germany
Christian Carbogno ORCID
Fritz Haber Institute of the Max Planck Society, Berlin, Germany
Editor
Jeff Gostick ORCID
Tags
Physics Phonons Transport
View PDF Review Thread Software Archive

Committers

Last synced: 4 months ago

All Time
  • Total Commits: 2,590
  • Total Committers: 17
  • Avg Commits per committer: 152.353
  • Development Distribution Score (DDS): 0.494
Past Year
  • Commits: 66
  • Committers: 3
  • Avg Commits per committer: 22.0
  • Development Distribution Score (DDS): 0.212
Top Committers
Name Email Commits
Florian Knoop k****p@f****e 1,310
Thomas Purcell p****l@f****e 593
Florian Knoop f****p@g****e 464
Surefire618 z****8@g****m 64
Florian Knoop f****p@l****e 52
Tom Purcell p****t@a****u 42
Marcel Langer me@s****m 31
Marcel Hülsberg m****g@g****m 13
Marcel Huelsberg h****g@f****e 5
Christian Carbogno c****o@f****e 3
Marcel g****b@s****m 3
Thomas Purcell t****l@d****e 2
Thomas Purcell t****l@d****e 2
Tom Purcell t****8@u****u 2
daniel speckhard s****d@f****e 2
Christian Carbogno c****o@f****e 1
Minye Zhang m****m@g****m 1
Committer Domains (Top 20 + Academic)
fhi-berlin.mpg.de: 6 sirmarcel.com: 2 u.northwestern.edu: 1 draco02.mpcdf.mpg.de: 1 draco01.mpcdf.mpg.de: 1 arizona.edu: 1 liu.se: 1 gmx.de: 1

Issues and Pull Requests

Last synced: 4 months ago

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 343 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 14
  • Total maintainers: 2
pypi.org: fhi-vibes

Fritz Haber Institute Vibrational Simulations

  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 343 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 11.9%
Stargazers count: 15.6%
Dependent repos count: 21.6%
Average: 21.8%
Downloads: 49.6%
Maintainers (2)
tpurcell90 shuozhao
Last synced: 12 months ago

Dependencies

pyproject.toml pypi
  • black ^19.10b0 develop
  • flake8 ^3.7 develop
  • flake8-bugbear ^19.8 develop
  • flake8-comprehensions ^3.1 develop
  • isort ^4.3 develop
  • mkdocs ^1.2 develop
  • mkdocs-material ^7.3 develop
  • mkdocs-minify-plugin ^0.5.0 develop
  • pytest >=6.0 develop
  • pytest-cov ^2.8 develop
  • pytest-xdist ^1.31 develop
  • rope ^0.14.0 develop
  • ase ^3.20.0,<3.23
  • attrs >=19.1
  • click >=8.0
  • click_aliases >=1.0
  • click_completion >=0.5.2
  • dataclasses *
  • fabric ^2.4
  • fireworks ^1.9
  • hiphive ^0.5.0
  • importlib_resources *
  • jconfigparser ^0.1.2
  • jinja2 >=2.10
  • matplotlib ^3.1
  • netCDF4 >=1.5
  • numpy ^1.17.5
  • pandas >=1.0
  • paramiko ^2.4
  • phono3py ^1.21
  • phonopy ^2.6
  • psycopg2 ^2.8.0
  • pymongo ^3.8
  • python ^3.6.1, <4.0
  • python-gssapi ^0.6.4
  • requests ^2.25
  • scipy ^1.1.1
  • seaborn >=0.11.0
  • son ^0.4.1
  • spglib ^1.12
  • tables ^3.5
  • xarray >=0.13