qcelemental

Periodic table, physical constants, and molecule parsing for quantum chemistry.

https://github.com/molssi/qcelemental

Science Score: 77.0%

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CITATION.cff file
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DOI references
Found 7 DOI reference(s) in README
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Academic publication links
Links to: acs.org
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Committers with academic emails
8 of 39 committers (20.5%) from academic institutions
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Scientific vocabulary similarity
Low similarity (11.5%) to scientific vocabulary

Keywords

chemistry codata computational-chemistry nist periodic-table physical-constant python quantum-chemistry standards

Keywords from Contributors

molecular-dynamics

Last synced: 6 months ago · JSON representation ·

Repository

Periodic table, physical constants, and molecule parsing for quantum chemistry.

Basic Info

Host: GitHub
Owner: MolSSI
License: bsd-3-clause
Language: Python
Default Branch: master
Homepage: https://molssi.github.io/QCElemental/
Size: 35 MB

Statistics

Stars: 167
Watchers: 9
Forks: 71
Open Issues: 49
Releases: 49

Topics

chemistry codata computational-chemistry nist periodic-table physical-constant python quantum-chemistry standards

Created over 7 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Citation

README.md

QCElemental

Documentation: GitHub Pages

Core data structures for Quantum Chemistry. QCElemental also contains physical constants and periodic table data from NIST and molecule handlers.

Periodic Table and Physical Constants data are pulled from NIST srd144 and srd121, respectively (details) in a renewable manner (class around NIST-published JSON file).

This project also contains a generator, validator, and translator for Molecule QCSchema.

✨ Getting Started

Installation. QCElemental supports Python 3.7+. Starting with v0.50 (aka "next", aka "QCSchema v2 available"), Python 3.8+ will be supported.

sh python -m pip install qcelemental

To install QCElemental with molecule visualization capabilities (useful in iPython or Jupyter notebook environments):

sh python -m pip install 'qcelemental[viz]`

To install QCElemental with various alignment capabilities using networkx

sh python -m pip install 'qcelemental[align]`

Or install both:

sh python -m pip install 'qcelemental[viz,align]`

See documentation

Periodic Table

A variety of periodic table quantities are available using virtually any alias:

```python

import qcelemental as qcel qcel.periodictable.toE('KRYPTON') 'Kr' qcel.periodictable.toelement(36) 'Krypton' qcel.periodictable.toZ('kr84') 36 qcel.periodictable.toA('Kr') 84 qcel.periodictable.toA('D') 2 qcel.periodictable.tomass('kr', returndecimal=True) Decimal('83.9114977282') qcel.periodictable.tomass('kr84') 83.9114977282 qcel.periodictable.to_mass('Kr86') 85.9106106269 ```

Physical Constants

Physical constants can be acquired directly from the NIST CODATA:

```python

import qcelemental as qcel qcel.constants.HartreeenergyineV 27.21138602 qcel.constants.get('hartree ENERGY in ev') 27.21138602 pc = qcel.constants.get('hartree ENERGY in ev', returntuple=True) pc.label 'Hartree energy in eV' pc.data Decimal('27.21138602') pc.units 'eV' pc.comment 'uncertainty=0.000 000 17' ```

Alternatively, with the use of the Pint unit conversion package, arbitrary conversion factors can be obtained:

```python

qcel.constants.conversion_factor("bohr", "miles") 3.2881547429884475e-14 ```

Covalent Radii

Covalent radii are accessible for most of the periodic table from Alvarez, Dalton Transactions (2008) doi:10.1039/b801115j (details).

```python

import qcelemental as qcel qcel.covalentradii.get('I') 2.626719314386381 qcel.covalentradii.get('I', units='angstrom') 1.39 qcel.covalentradii.get(116) Traceback (most recent call last): ... qcelemental.exceptions.DataUnavailableError: ('covalent radius', 'Lv') qcel.covalentradii.get(116, missing=4.0) 4.0 qcel.covalentradii.get('iodine', return_tuple=True).dict() {'numeric': True, 'label': 'I', 'units': 'angstrom', 'data': Decimal('1.39'), 'comment': 'e.s.d.=3 n=451', 'doi': 'DOI: 10.1039/b801115j'} ```

van der Waals Radii

Van der Waals radii are accessible for most of the periodic table from Mantina, J. Phys. Chem. A (2009) doi: 10.1021/jp8111556 (details).

```python

import qcelemental as qcel qcel.vdwradii.get('I') 3.7416577284064996 qcel.vdwradii.get('I', units='angstrom') 1.98 qcel.vdwradii.get(116) Traceback (most recent call last): ... qcelemental.exceptions.DataUnavailableError: ('vanderwaals radius', 'Lv') qcel.vdwradii.get('iodine', return_tuple=True).dict() {'numeric': True, 'label': 'I', 'units': 'angstrom', 'data': Decimal('1.98'), 'doi': 'DOI: 10.1021/jp8111556'} ```

Owner

Name: The Molecular Science Software Institute
Login: MolSSI
Kind: organization
Email: info@molssi.org

Website: http://molssi.org
Repositories: 37
Profile: https://github.com/MolSSI

A nexus for science, education, and cooperation serving the worldwide community of computational molecular scientists. [MolSSI]

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: QCElemental
message: >-
  Periodic table, physical constants, molecule parsing, and
  QCSchema implementation for quantum chemistry
type: software
authors:
  - given-names: Lori A.
    family-names: Burns
    affiliation: >-
      Center for Computational Molecular Science and
      Technology, Georgia Institute of Technology
    orcid: 'https://orcid.org/0000-0003-2852-5864'
  - given-names: Daniel G. A.
    family-names: Smith
    affiliation: The Molecular Sciences Software Institute
    orcid: 'https://orcid.org/0000-0001-8626-0900'
  - given-names: Levi N.
    family-names: Naden
    affiliation: The Molecular Sciences Software Institute
    orcid: 'https://orcid.org/0000-0002-3692-5027'
  - given-names: Matthew
    family-names: Welborn
    affiliation: The Molecular Sciences Software Institute
identifiers:
  - type: doi
    value: 10.1002/wcms.1491
    description: QCArchive article
  - type: doi
    value: 10.1063/5.0059356
    description: QCEngine article
repository-code: 'https://github.com/MolSSI/QCElemental/'
url: 'https://molssi.github.io/QCElemental/'
repository-artifact: 'https://anaconda.org/conda-forge/qcelemental/files'
keywords:
  - nist
  - chemistry
  - standards
  - computational-chemistry
  - quantum-chemistry
  - periodic-table
  - codata
  - physical-constant
  - schema
license: BSD-3-Clause
version: 0.28.0
date-released: '2024-06-21'

GitHub Events

Total

Create event: 7
Release event: 1
Issues event: 8
Watch event: 23
Delete event: 5
Issue comment event: 24
Push event: 46
Pull request review comment event: 15
Pull request event: 22
Pull request review event: 17
Fork event: 3

Last Year

Create event: 7
Release event: 1
Issues event: 8
Watch event: 23
Delete event: 5
Issue comment event: 24
Push event: 46
Pull request review comment event: 15
Pull request event: 22
Pull request review event: 17
Fork event: 3

Committers

Last synced: about 2 years ago

All Time

Total Commits: 749
Total Committers: 39
Avg Commits per committer: 19.205
Development Distribution Score (DDS): 0.587

Past Year

Commits: 21
Committers: 8
Avg Commits per committer: 2.625
Development Distribution Score (DDS): 0.429

Top Committers

Name	Email	Commits
Lori A. Burns	l**s@g**m	309
Daniel Smith	m**n@m**m	208
Levi Naden	l**n@v**u	52
Daniel G. A. Smith	d**h@v**u	46
Matthew Welborn	m**n@g**m	45
Sebastian Lee	s**3@g**m	13
Daniel Smith	d**h@i**m	11
Logan Ward	w**t@g**m	6
Rollin King	r**g@b**u	6
Muammar El Khatib	m**b@g**m	5
Sebastian Ehlert	2****k	4
Johannes Steinmetzer	j**8@a**m	4
David Dotson	d**l@g**m	3
Benjamin Pritchard	b**n@b**g	3
Colton Hicks	g**b@c**m	3
stvogt	s**e@g**m	3
Janos Sarka	j**a@t**u	2
Zhi Wang	o**e@g**m	2
Fang Liu	f**c@g**m	2
Roberto Di Remigio	r****r	2
Roberto Di Remigio	r**o@g**m	2
Josh Horton	J**n@n**k	1
Rohit Goswami	r**0@g**m	1
Giuseppe Barbalinardo	g**o@g**m	1
Andrew Abi-Mansour	a**m@g**m	1
Jennifer A Clark	j**k@g**m	1
sgreene8	s**e@u**u	1
Matthew W. Thompson	m**n@p**m	1
SinaMostafanejad	m**d@h**m	1
SimonBoothroyd	s**d@h**m	1
and 9 more...

Committer Domains (Top 20 + Academic)

vt.edu: 2 choderalab.org: 1 umich.edu: 1 stonybrook.edu: 1 uchicago.edu: 1 gnarlyoak.com: 1 newcastle.ac.uk: 1 ttu.edu: 1 coltonhicks.com: 1 bennyp.org: 1 aol.com: 1 bethel.edu: 1 me.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 39
Total pull requests: 105
Average time to close issues: 2 months
Average time to close pull requests: about 1 month
Total issue authors: 23
Total pull request authors: 24
Average comments per issue: 2.54
Average comments per pull request: 2.43
Merged pull requests: 75
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 5
Pull requests: 7
Average time to close issues: about 10 hours
Average time to close pull requests: about 1 month
Issue authors: 4
Pull request authors: 2
Average comments per issue: 0.2
Average comments per pull request: 0.57
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

awvwgk (10)
loriab (4)
mbanck (3)
susilehtola (2)
coltonbh (2)
shehan807 (2)
philipmnel (1)
WardLT (1)
mattwthompson (1)
LecrisUT (1)
VHchavez (1)
alongd (1)
jaclark5 (1)
dotsdl (1)
yurivict (1)

Pull Request Authors

loriab (81)
coltonbh (8)
awvwgk (5)
bennybp (4)
mattwthompson (2)
TyBalduf (2)
dgasmith (2)
anabiman (2)
berquist (2)
jthorton (2)
Lnaden (2)
WardLT (2)
SinaMostafanejad (1)
dr-marsmm (1)
mattwelborn (1)

Top Labels

Issue Labels

Enhancement (2) invalid (1)

Pull Request Labels

wontfix (2) Documentation (2) Enhancement (2) Bug (2) Feature (1) hacktoberfest-accepted (1)

Packages

Total packages: 2
Total downloads:
- pypi 25,837 last-month
Total docker downloads: 2,926

Total dependent packages: 29
(may contain duplicates)
Total dependent repositories: 66
(may contain duplicates)
Total versions: 86
Total maintainers: 4

pypi.org: qcelemental

Core data structures for Quantum Chemistry.

Homepage: https://github.com/MolSSI/QCElemental
Documentation: http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/
License: BSD-3-Clause
Latest release: 0.29.0
published about 1 year ago

Versions: 47
Dependent Packages: 20
Dependent Repositories: 37
Downloads: 25,837 Last month
Docker Downloads: 2,926

Rankings

Dependent packages count: 0.7%

Docker downloads count: 1.4%

Downloads: 2.0%

Dependent repos count: 2.4%

Average: 3.0%

Forks count: 5.2%

Stargazers count: 6.5%

Maintainers (4)

bennybp lnaden molssi loriab

Last synced: 6 months ago

conda-forge.org: qcelemental

Homepage: https://github.com/MolSSI/QCElemental
License: BSD-3-Clause
Latest release: 0.25.1
published over 3 years ago

Versions: 39
Dependent Packages: 9
Dependent Repositories: 29

Rankings

Dependent packages count: 6.4%

Dependent repos count: 6.8%

Average: 16.8%

Forks count: 22.3%

Stargazers count: 31.7%

Last synced: 6 months ago

Dependencies

setup.py pypi

numpy *

.github/workflows/CI.yml actions

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.github/workflows/Lint.yml actions

actions/checkout v1 composite
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.github/workflows/QCSchema.yml_wip actions

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