PYCV
PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python - Published in JOSS (2019)
Science Score: 95.0%
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Found 6 DOI reference(s) in README and JOSS metadata -
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20 of 84 committers (23.8%) from academic institutions -
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✓JOSS paper metadata
Published in Journal of Open Source Software
Scientific Fields
Repository
PYCV module for PLUMED2. See the src/pycv directory.
Basic Info
- Host: GitHub
- Owner: giorginolab
- License: lgpl-3.0
- Language: C++
- Default Branch: v2.8-pycv
- Homepage: https://giorginolab.github.io/plumed2-pycv/
- Size: 151 MB
Statistics
- Stars: 8
- Watchers: 0
- Forks: 0
- Open Issues: 1
- Releases: 6
Metadata Files
README.md
The PYCV module for PLUMED 2
[!WARNING]
This repository accompanies an early version of PyCV (v1), described in the paper in JOSS. A newer version of PyCV (v2) is now included in plumed's main repository, as a plugin; the new version has the same scope but a slightly different syntax and installation procedure. This repository remains for historical preservation.
Note: this is a fork of the official PLUMED repository. Please see PLUMED's homepage for information on the PLUMED library.
The PYCV module enables PLUMED2 Collective Variables (CVs) and arbitrary functions to be defined and auto-differentiated in the Python language.
Advantages of using PYCV over standard development of CVs in C++ are: 1. functions may be prototyped in high-level code, using extensive mathematical libraries, and no boilerplate; 2. just-in-time compilation occurs transparently: there are no compilation and link delays for code changes; 3. CVs may be automatically differentiated in common cases.
Please see the project's homepage, paper, and regression tests for detailed instructions.
Citation
Giorgino T. PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python. The Journal of Open Source Software 4(42):1773
Last tested with
Software | Version ---------|--------- PLUMED | 2.8.0 Python | 3.7.7 (Homebrew) Jax | 0.2.17 Jaxlib | 0.1.69 Numpy | 1.19.5
Copyright
PYCV is distributed under the LGPL terms: see COPYRIGHT.
PYCV includes the pybind11 library, distributed under its own license terms (BSD-3).
Owner
- Name: Giorgino Laboratory
- Login: giorginolab
- Kind: organization
- Location: Milan, Italy
- Website: www.giorginolab.it
- Repositories: 63
- Profile: https://github.com/giorginolab
Computational Biophysics
JOSS Publication
PYCV: a PLUMED 2 Module Enabling the Rapid Prototyping of Collective Variables in Python
Authors
Institute of Biophysics (IBF-CNR), National Research Council of Italy
Editor
Arfon Smith
Tags
PLUMED molecular dynamics collective variables biased sampling gradientGitHub Events
Total
- Issues event: 2
- Issue comment event: 1
- Push event: 2
Last Year
- Issues event: 2
- Issue comment event: 1
- Push event: 2
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Giovanni Bussi | g****i@g****m | 4,217 |
| Carlo Camilloni | c****i@g****m | 1,600 |
| Gareth Tribello | g****o@g****m | 987 |
| Massimiliano Bonomi | m****i@g****m | 607 |
| Michele Invernizzi | i****e@g****m | 268 |
| Benjamin Pampel | p****l@m****e | 191 |
| Omar Valsson | o****n@g****m | 159 |
| Gareth Tribello | gt@e****k | 154 |
| Davide Branduardi | d****i@g****m | 141 |
| hanatok | s****3@g****m | 115 |
| Toni G | t****o@g****m | 71 |
| gilgigilgil | t****r@g****m | 46 |
| Andrew White | w****w@g****m | 41 |
| Jan Domanski | j****m@g****m | 37 |
| Glen Hocky | g****2@m****y | 35 |
| Thomas Löhr | t****s@l****k | 32 |
| Travis CI User | t****s@e****g | 27 |
| Carlo Camilloni | c****o@c****k | 21 |
| Gareth Tribello | gt@e****g | 20 |
| Toni G | t****o@i****t | 17 |
| andrea-arsiccio | a****2@g****m | 16 |
| h2nch2co2h | d****o@g****m | 16 |
| Pablo Piaggi | p****i@g****m | 12 |
| Massimiliano Bonomi | m****i@b****u | 8 |
| Drobot Viktor | l****6@g****m | 8 |
| Marco | m****a@g****m | 8 |
| alejogiley | a****y@s****t | 7 |
| Glen Hocky | h****g@g****m | 7 |
| ThorbenFroehlking | t****g@w****e | 7 |
| sandipde | 1****e@g****m | 6 |
| and 54 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 4
- Total pull requests: 0
- Average time to close issues: 15 days
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 1.25
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: about 1 month
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- amritagos (2)
- a-ws-m (2)
Pull Request Authors
Top Labels
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Dependencies
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- actions/checkout v2 composite
- ubuntu 17.04 build
- breathe ==4.34.0
- furo ==2022.6.21
- sphinx ==5.0.2
- sphinx-copybutton ==0.5.0
- sphinxcontrib-moderncmakedomain ==3.21.4
- sphinxcontrib-svg2pdfconverter ==1.2.0
- build ==0.8.0 test
- numpy ==1.21.5 test
- numpy ==1.19.3 test
- numpy ==1.22.2 test
- pytest ==7.0.0 test
- pytest-timeout * test
- scipy ==1.5.4 test
- scipy ==1.8.0 test