calphy

A Python library and command line interface for automated free energy calculations

https://github.com/icams/calphy

Science Score: 77.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
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DOI references
Found 9 DOI reference(s) in README
✓
Academic publication links
Links to: aps.org
✓
Committers with academic emails
2 of 8 committers (25.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (11.6%) to scientific vocabulary

Keywords

free-energy free-energy-calculations interatomic-potentials lammps molecular-dynamics thermodynamic-calculations

Last synced: 4 months ago · JSON representation ·

Repository

A Python library and command line interface for automated free energy calculations

Basic Info

Host: GitHub
Owner: ICAMS
License: other
Language: Python
Default Branch: main
Homepage:
Size: 4.13 MB

Statistics

Stars: 81
Watchers: 3
Forks: 23
Open Issues: 16
Releases: 39

Topics

free-energy free-energy-calculations interatomic-potentials lammps molecular-dynamics thermodynamic-calculations

Created over 4 years ago · Last pushed 5 months ago

Metadata Files

Readme License Citation

calphy

calphy(pronounced cal-phee) is a Python library and command line tool for calculation of free energies. It uses LAMMPS as the molecular dynamics driver to enable calculation of free energies using thermodynamic integration in a completely automated and efficient manner. The various methods that calphy can perform are:

$F(V_i,T_i)$ and $G(P_i,T_i)$ for both solid and liquid phases at the given thermodynamic conditions using non-equilibrium Hamiltonian interpolation.
$F(T_i \to T_f)$ and $G(T_i \to T_f)$ , temperature dependence of Gibbs and Helmholtz free energies using the reversible scaling approach.
Calculation of solid-solid or solid-liquid phase transition temperatures.
Calculation of coexistence lines using dynamic Clausius-Clapeyron integration.
Calculation of specific heat $c_P(T)$ as a function of temperature.
Calculation of $F(x, T)$ and $G(x, T)$ for multicomponent systems using alchemical transformations.
Upsampling calculations.

Calphy works with all interatomic potentials implemented in LAMMPS and can obtain reliable results with low error bars in as low as 50 ps of simulation time with less than 3000 atoms. More information about the methods in calphy can be found in the associated publication.

Installation, examples and documentation

Read the calphy installation instructions and documentation including examples here.
For a description of the methods and algorithms implemented in calphy, please see the associated publication.
For a set of examples presented in the calphy publication, please see here.

Citing calphy

If you find calphy useful, please consider citing:
Menon, Sarath, Yury Lysogorskiy, Jutta Rogal, and Ralf Drautz.
“Automated Free Energy Calculation from Atomistic Simulations.” Physical Review Materials 5(10), 2021
DOI: 10.1103/PhysRevMaterials.5.103801

Download bibtex here

Owner

Name: ICAMS
Login: ICAMS
Kind: organization
Location: Germany

Website: http://www.icams.de
Repositories: 9
Profile: https://github.com/ICAMS

Interdisciplinary Centre for Advanced Materials Simulation, Ruhr University Bochum

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  Automated free-energy calculation from atomistic
  simulations
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Sarath
    family-names: Menon
    email: sarath.menon@rub.de
    affiliation: >-
      Interdisciplinary Centre for Advanced Materials
      Simulation, Ruhr-Universität Bochum, 44801
      Bochum, Germany
    orcid: 'https://orcid.org/0000-0002-6776-1213'
  - given-names: Yury
    family-names: Lysogorskiy
    affiliation: >-
      Interdisciplinary Centre for Advanced Materials
      Simulation, Ruhr-Universität Bochum, 44801
      Bochum, Germany
    orcid: 'https://orcid.org/0000-0003-4617-3188'
  - given-names: Jutta
    family-names: Rogal
    affiliation: >-
      Fachbereich Physik, Freie Universität Berlin,
      14195 Berlin, Germany
    orcid: 'https://orcid.org/0000-0002-6268-380X'
  - given-names: Ralf
    family-names: Drautz
    email: ralf.drautz@rub.de
    affiliation: >-
      Interdisciplinary Centre for Advanced Materials
      Simulation, Ruhr-Universität Bochum, 44801
      Bochum, Germany
    orcid: 'https://orcid.org/0000-0001-7101-8804'
identifiers:
  - type: doi
    value: 10.1103/PhysRevMaterials.5.103801
    description: Physical Review Materials 5(10) 2021
repository-code: 'https://github.com/ICAMS/calphy'
url: 'https://calphy.org'
abstract: >-
  We devise automated workflows for the calculation
  of Helmholtz and Gibbs free energies and their
  temperature and pressure dependence and provide the
  corresponding computational tools. We employ
  nonequilibrium thermodynamics for evaluating the
  free energy of solid and liquid phases at a given
  temperature and reversible scaling for computing
  free energies over a wide range of temperatures,
  including the direct integration of P−T coexistence
  lines. By changing the chemistry and the
  interatomic potential, alchemical and upscaling
  free energy calculations are possible. Several
  examples illustrate the accuracy and efficiency of
  our implementation.
license: GPL-2.0

GitHub Events

Total

Create event: 14
Release event: 4
Issues event: 10
Watch event: 13
Delete event: 12
Issue comment event: 17
Push event: 17
Pull request event: 22
Fork event: 1

Last Year

Create event: 14
Release event: 4
Issues event: 10
Watch event: 13
Delete event: 12
Issue comment event: 17
Push event: 17
Pull request event: 22
Fork event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 696
Total Committers: 8
Avg Commits per committer: 87.0
Development Distribution Score (DDS): 0.447

Past Year

Commits: 184
Committers: 4
Avg Commits per committer: 46.0
Development Distribution Score (DDS): 0.147

Top Committers

Name	Email	Commits
Sarath Menon	s**n@m**g	385
srmnitc	s**n@g**m	281
Niklas Leimeroth	l**h@m**e	22
Sarath Radhakrishnan Menon	s**n@r**e	4
Sebastian Havens	5**s@u**m	1
Marvin Poul	p**r@c**e	1
Sarath Menon	m**l@s**e	1
Jan Janssen	j**n@u**m	1

Committer Domains (Top 20 + Academic)

sarathmenon.me: 1 creshal.de: 1 ruhr-uni-bochum.de: 1 mm.tu-darmstadt.de: 1 mailbox.org: 1

Issues and Pull Requests

Last synced: 5 months ago

All Time

Total issues: 71
Total pull requests: 101
Average time to close issues: 2 months
Average time to close pull requests: 1 day
Total issue authors: 24
Total pull request authors: 7
Average comments per issue: 2.49
Average comments per pull request: 0.24
Merged pull requests: 98
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 13
Pull requests: 22
Average time to close issues: 3 days
Average time to close pull requests: about 1 hour
Issue authors: 8
Pull request authors: 3
Average comments per issue: 3.08
Average comments per pull request: 0.09
Merged pull requests: 21
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

srmnitc (20)
Leimeroth (8)
stefanhiemer (5)
gswylq (5)
jhung12 (4)
pmrv (3)
ibrsam (3)
ZAhra-Rjz (3)
chtchelkatchev (2)
ireaml (2)
SebastianHavens (2)
wuziqi-cmu (2)
iainbest (1)
bjn123 (1)
lnnbig (1)

Pull Request Authors

srmnitc (113)
pmrv (9)
SebastianHavens (7)
stefanhiemer (4)
Leimeroth (3)
niklassiemer (2)
jan-janssen (1)

Top Labels

Issue Labels

bug (7) enhancement (4) wontfix (1)

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- pypi 248 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 3
(may contain duplicates)
Total versions: 51
Total maintainers: 2

pypi.org: calphy

free energy calculation for python

Homepage: https://github.com/ICAMS/calphy
Documentation: https://calphy.readthedocs.io/
License: GNU General Public License v3
Latest release: 1.4.3
published 6 months ago

Versions: 39
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 248 Last month

Rankings

Forks count: 9.9%

Dependent packages count: 10.0%

Stargazers count: 11.0%

Average: 14.3%

Downloads: 18.8%

Dependent repos count: 21.8%

Maintainers (2)

srmnitc yury.lysogorskiy

Last synced: 5 months ago

conda-forge.org: calphy

A Python library and command line interface for automated free energy calculations

Homepage: https://github.com/ICAMS/calphy
License: GPL-2.0-only
Latest release: 1.2.4
published about 3 years ago

Versions: 12
Dependent Packages: 0
Dependent Repositories: 2

Rankings

Dependent repos count: 20.2%

Average: 40.2%

Forks count: 42.7%

Stargazers count: 46.1%

Dependent packages count: 51.6%

Last synced: 5 months ago

calphy

Science Score: 77.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

calphy

Installation, examples and documentation

Citing calphy

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: calphy

Rankings

Maintainers (2)

conda-forge.org: calphy

Rankings