Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
-
✓Committers with academic emails
4 of 15 committers (26.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.2%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
A post-processing engine for particle simulations
Basic Info
- Host: GitHub
- Owner: zincware
- License: epl-2.0
- Language: Python
- Default Branch: main
- Homepage: https://mdsuite.readthedocs.io/
- Size: 52.2 MB
Statistics
- Stars: 45
- Watchers: 2
- Forks: 10
- Open Issues: 70
- Releases: 2
Topics
Metadata Files
README.md
Introduction
MDSuite is a software designed specifically for the molecular dynamics community to enable fast, reliable, and easy-to-run calculations from simulation data.
If you want to start learning about the code, you can check out the docs here.
Installation
There are several ways to install MDSuite depending on what you would like from it.
One can simply install using
shell
pip install mdsuite
If you would like to install it from source then you can clone the repository by running
shell
git clone https://github.com/SamTov/MDSuite.git
Once you have cloned the repository, depending on whether you prefer conda or straight pip, you should follow the instructions below.
Installation with pip
shell
cd MDSuite
pip install .
Installation with conda
shell
cd MDSuite
conda create -n MDSuite python=3.8
conda activate MDSuite
pip install .
Documentation
There is a live version of the documentation hosted here. If you prefer to have a local copy, that can be built using sphinx by following the instructions below.
shell
cd MDSuite/docs
make html
cd build/html
firefox index.html
HINT
Check out the MDSuite code through a jupyter notebook for a more user-friendly experience. You can take full advantage of the autocomplete features that are available for the calculators.
Disclaimer
MDSuite as far as is possible is tested against results validated by simulation engines or theoretical models. However, MDSuite or zincware are not liable for incorrect results produced when using the software.
Owner
- Name: Zincware
- Login: zincware
- Kind: organization
- Email: zincwarecode@gmail.com
- Location: Germany
- Website: zincwarecode.com
- Twitter: zincwarecode
- Repositories: 33
- Profile: https://github.com/zincware
Open source software organisation hosting software built for computational physics and chemistry.
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: MDSuite
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Samuel
family-names: Tovey
email: tovey.samuel@gmail.com
affiliation: >-
Institute for Computational Physics, University of
Stuttgart
orcid: 'https://orcid.org/0000-0001-9537-8361'
- given-names: Fabian
family-names: Zills
affiliation: >-
Institute for Computational Physics, University of
Stuttgart
orcid: 'https://orcid.org/0000-0002-6936-4692'
- given-names: Francisco
family-names: Torres-Herrador
affiliation: >-
Aeronautics and Aerospace department, von Karman
Institute for Fluid Dynamics, Rhode-St-Genese,
Belgium. Thermo and Fluid dynamics (FLOW), Vrije
Universiteit Brussel, Brussels, Belgium. Laboratory
for Chemical Technology (LCT), Ghent University,
Ghent, Belgium
orcid: 'https://orcid.org/0000-0002-3901-3461'
- given-names: Christoph
family-names: Lohrmann
affiliation: >-
Institute for Computational Physics, University of
Stuttgart
orcid: 'https://orcid.org/0000-0002-9011-2975'
identifiers:
- type: doi
value: 10.1186/s13321-023-00687-y
description: >-
MDSuite: comprehensive post-processing tool for
particle simulations
license: EPL-2.0
GitHub Events
Total
- Watch event: 9
- Delete event: 8
- Issue comment event: 4
- Push event: 73
- Pull request review event: 5
- Pull request event: 19
- Fork event: 2
- Create event: 8
Last Year
- Watch event: 9
- Delete event: 8
- Issue comment event: 4
- Push event: 73
- Pull request review event: 5
- Pull request event: 19
- Fork event: 2
- Create event: 8
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| SamTov | t****l@g****m | 657 |
| PythonFZ | f****s@w****e | 427 |
| Fran | f****e@v****e | 130 |
| Christoph Lohrmann | c****n@i****e | 64 |
| Marco Brueckner | m****7@w****e | 31 |
| Samuel Tovey | s****y@S****x | 12 |
| PythonFZ | i****a | 10 |
| tmerkt | t****t@l****e | 7 |
| ac133451 | p****s@i****e | 5 |
| dependabot[bot] | 4****] | 4 |
| Fran Torres | f****e@g****m | 3 |
| Psomers3 | 3****3 | 2 |
| Fabian Zills | 4****z | 1 |
| Kai Szuttor | k****i@i****e | 1 |
| Samuel Tovey | s****y@m****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 42
- Total pull requests: 81
- Average time to close issues: 5 months
- Average time to close pull requests: about 2 months
- Total issue authors: 8
- Total pull request authors: 7
- Average comments per issue: 2.17
- Average comments per pull request: 1.56
- Merged pull requests: 47
- Bot issues: 0
- Bot pull requests: 30
Past Year
- Issues: 0
- Pull requests: 12
- Average time to close issues: N/A
- Average time to close pull requests: 6 days
- Issue authors: 0
- Pull request authors: 4
- Average comments per issue: 0
- Average comments per pull request: 0.5
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 10
Top Authors
Issue Authors
- PythonFZ (18)
- SamTov (13)
- christophlohrmann (3)
- okunoyukihiro2 (3)
- tobiasmerkt (2)
- hguo28 (1)
- Fratorhe (1)
- Z-Rashid (1)
Pull Request Authors
- dependabot[bot] (31)
- SamTov (23)
- PythonFZ (22)
- christophlohrmann (4)
- pre-commit-ci[bot] (2)
- Fratorhe (2)
- alvarovm (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 26 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 2
- Total maintainers: 1
pypi.org: mdsuite
A postprocessing tool for molecular dynamics simulations.
- Homepage: https://github.com/zincware/MDSuite
- Documentation: https://mdsuite.readthedocs.io/
- License: Eclipse Public License 2.0 (EPL-2.0)
-
Latest release: 0.2.0
published over 3 years ago
Rankings
Maintainers (1)
Dependencies
- IPython * development
- Sphinx ==4.3.0 development
- ase * development
- black * development
- coverage * development
- coveralls * development
- isort * development
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- nbsphinx-link * development
- numpydoc * development
- pandoc * development
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- pytest * development
- sphinx-copybutton * development
- sphinx_rtd_theme * development
- sphinxcontrib.bibtex * development
- znvis * development
- PyYAML >=5.4
- bokeh *
- chemfiles *
- colorutils *
- dot4dict *
- gputil *
- h5py *
- matplotlib *
- numpy *
- pandas >=1.0.0
- psutil >=5.6.6
- pubchempy *
- pysmiles *
- scipy *
- scooby *
- sqlalchemy >=1.4
- tensorflow >=2.5
- tensorflow_probability *
- tqdm *
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