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colvars

Collective variables library for molecular simulation and analysis programs

https://github.com/colvars/colvars

Science Score: 36.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 19 committers (10.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.2%) to scientific vocabulary

Keywords

collective-variables enhanced-sampling free-energy gromacs lammps molecular-dynamics namd simulation tinkerhp vmd
Last synced: 6 months ago · JSON representation

Repository

Collective variables library for molecular simulation and analysis programs

Basic Info
  • Host: GitHub
  • Owner: Colvars
  • License: lgpl-3.0
  • Language: C++
  • Default Branch: master
  • Homepage: http://colvars.github.io/
  • Size: 51 MB
Statistics
  • Stars: 231
  • Watchers: 18
  • Forks: 59
  • Open Issues: 53
  • Releases: 0
Topics
collective-variables enhanced-sampling free-energy gromacs lammps molecular-dynamics namd simulation tinkerhp vmd
Created over 12 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README-c++11.md

Availability of Colvars features depending on C++ language versions

The majority of the Colvars module can be built with all major versions of the C++ language. In general, the accepted standard is C++11, which is supported by all major OSes and compilers currently in use. Any future exceptions to this will be listed here, as well as in the "Compilation notes" section of the Colvars doc.

Because Colvars relies on the build system of each engine, there is nothing for you to do, whether you are using a precompiled build or making your own. The only exception to this is VMD, whose build system requires some patching in order to work on modern architectures (details below).

Backward compatibility notes

If you are reading this page following an error message from Colvars, you are probably using an earlier version of the code, which at the time was supporting C++11 as an option but not requiring it yet. Consider upgrading your engine and/or Colvars, as you will also get new features and improvements.

We no longer support using extremely old compilers and OSes that are well past their end of life (for example, GCC 4.4 and CentOS 6).

Status of C++ language support in MD engines (as of 2023-06-22)

  • GROMACS follows the C++17 standard.

  • LAMMPS follows the C++11 standard.

  • NAMD follows the C++11 standard.

  • VMD precompiled builds do not use C++11 yet, and the optional CXX11 flag in VMD's configure script does not work yet. Please apply the c++11 patch from this repository to allow building VMD with C++11 whenever supported.

Building VMD is quite complicated: could you just provide a working VMD build?

In theory we could, but due to UIUC's restrictive license we are curently unable to distribute any version of VMD, modified or not. We hope that this restriction is lifted in the future, through the adoption of best practices for research software sharing.

Owner

  • Name: Colvars development team
  • Login: Colvars
  • Kind: organization

GitHub Events

Total
  • Create event: 51
  • Commit comment event: 3
  • Issues event: 44
  • Watch event: 22
  • Delete event: 36
  • Issue comment event: 294
  • Push event: 309
  • Gollum event: 10
  • Pull request review comment event: 80
  • Pull request event: 119
  • Pull request review event: 105
  • Fork event: 4
Last Year
  • Create event: 51
  • Commit comment event: 3
  • Issues event: 44
  • Watch event: 22
  • Delete event: 36
  • Issue comment event: 294
  • Push event: 309
  • Gollum event: 10
  • Pull request review comment event: 80
  • Pull request event: 119
  • Pull request review event: 105
  • Fork event: 4

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 3,877
  • Total Committers: 19
  • Avg Commits per committer: 204.053
  • Development Distribution Score (DDS): 0.379
Past Year
  • Commits: 617
  • Committers: 4
  • Avg Commits per committer: 154.25
  • Development Distribution Score (DDS): 0.22
Top Committers
Name Email Commits
Giacomo Fiorin g****n@g****m 2,407
Jérôme Hénin h****j@g****m 1,038
hanatok s****3@g****m 166
Axel Kohlmeyer a****y@g****m 106
Hubert h****z@g****m 91
Andrew White w****w@g****m 16
Fabrizio Marinelli f****i@g****m 12
jeffcomer j****r@g****m 9
Andrew Jewett j****j@g****m 8
Josh Vermaas v****2@i****u 8
Alejandro Bernardin b****o@g****m 5
fhh2626 f****6@g****m 3
Josh Vermaas j****s@a****u 2
Alejo BS a****b 1
Eisuke Kawashima e****m 1
Josh Vermaas j****s 1
ReneHamburger1993 4****3 1
Josh Vermaas j****s@n****v 1
Michael von Domaros m****s@g****m 1
Committer Domains (Top 20 + Academic)
nrel.gov: 1 asu.edu: 1 illinois.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 112
  • Total pull requests: 219
  • Average time to close issues: 8 months
  • Average time to close pull requests: 28 days
  • Total issue authors: 32
  • Total pull request authors: 11
  • Average comments per issue: 2.71
  • Average comments per pull request: 2.52
  • Merged pull requests: 163
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 29
  • Pull requests: 78
  • Average time to close issues: 22 days
  • Average time to close pull requests: 8 days
  • Issue authors: 10
  • Pull request authors: 6
  • Average comments per issue: 0.52
  • Average comments per pull request: 1.82
  • Merged pull requests: 52
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • giacomofiorin (27)
  • jhenin (25)
  • HanatoK (15)
  • fhh2626 (7)
  • Praveen-2k21 (5)
  • zwpku (3)
  • EzryStIago (2)
  • groponp (2)
  • wisecashew (2)
  • fabsugar (2)
  • gitkol (1)
  • balazsfabian (1)
  • satyajitkhatua09 (1)
  • naliio (1)
  • ljh433 (1)
Pull Request Authors
  • giacomofiorin (92)
  • jhenin (56)
  • HanatoK (52)
  • HubLot (7)
  • zwpku (4)
  • fabsugar (2)
  • EzryStIago (2)
  • PolyachenkoYA (1)
  • akohlmey (1)
  • alphataubio (1)
  • OmriShf (1)
Top Labels
Issue Labels
bug (10) NAMD (10) documentation (9) question (9) GROMACS (5) non-urgent (4) important (4) maintenance (3) quick (3) optimization (3) parser (3) minor bug (2) testing (2) stability (1)
Pull Request Labels
maintenance (37) bugfix (23) GROMACS (16) NAMD (10) documentation (7) LAMMPS (5) testing (4) script_API (3) VMD (3) Lepton (2) tools (2) stability (2) optimization (2) minor bug (1) important (1)

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 1
  • Total maintainers: 1
pypi.org: colvars

Collective variables module for molecular simulation and analysis programs

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
Rankings
Dependent packages count: 10.1%
Average: 15.9%
Dependent repos count: 21.6%
Maintainers (1)
giacomofiorin
Last synced: 6 months ago

Dependencies

.github/workflows/backend-template.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
.github/workflows/test-library.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • github/codeql-action/analyze v2 composite
  • github/codeql-action/init v2 composite
.github/workflows/test-backends.yml actions