https://github.com/berquist/openqcschema

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

https://github.com/berquist/openqcschema

Repository

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

https://github.com/berquist/openqcschema/blob/master/

# QCElemental

[![Build Status](https://github.com/MolSSI/QCElemental/workflows/CI/badge.svg?branch=master)](https://github.com/MolSSI/QCElemental/actions?query=workflow%3ACI)
[![codecov](https://img.shields.io/codecov/c/github/MolSSI/QCElemental.svg?logo=Codecov&logoColor=white)](https://codecov.io/gh/MolSSI/QCElemental)
[![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/MolSSI/QCElemental.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/MolSSI/QCElemental/context:python)
[![Documentation Status](https://img.shields.io/github/workflow/status/MolSSI/QCElemental/CI/master?label=docs&logo=readthedocs&logoColor=white)](http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/)
[![Chat on Slack](https://img.shields.io/badge/chat-on_slack-green.svg?longCache=true&style=flat&logo=slack)](https://join.slack.com/t/qcarchive/shared_invite/enQtNDIzNTQ2OTExODk0LTE3MWI0YzBjNzVhNzczNDM0ZTA5MmQ1ODcxYTc0YTA1ZDQ2MTk1NDhlMjhjMmQ0YWYwOGMzYzJkZTM2NDlmOGM)
![python](https://img.shields.io/badge/python-3.6+-blue.svg)

QCElemental is a resource module for quantum chemistry containing 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](raw_data/README.md)) in a renewable manner
(class around NIST-published JSON file).

This project also contains a generator, validator, and translator for [Molecule
QCSchema](https://molssi-qc-schema.readthedocs.io/en/latest/auto_topology.html).

It is intended to keep the QCElemental code compatible with Python 3.6+
as long as dependencies allow. Packages are assured for Python 3.8+.


### Periodic Table

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

```python
>>> import qcelemental as qcel
>>> qcel.periodictable.to_E('KRYPTON')
'Kr'
>>> qcel.periodictable.to_element(36)
'Krypton'
>>> qcel.periodictable.to_Z('kr84')
36
>>> qcel.periodictable.to_A('Kr')
84
>>> qcel.periodictable.to_A('D')
2
>>> qcel.periodictable.to_mass('kr', return_decimal=True)
Decimal('83.9114977282')
>>> qcel.periodictable.to_mass('kr84')
83.9114977282
>>> qcel.periodictable.to_mass('Kr86')
85.9106106269
```

### Physical Constants

Physical constants can be acquired directly from the [NIST CODATA](https://physics.nist.gov/cuu/Constants/Table/allascii.txt):

```python
>>> import qcelemental as qcel
>>> qcel.constants.Hartree_energy_in_eV
27.21138602
>>> qcel.constants.get('hartree ENERGY in ev')
27.21138602
>>> pc = qcel.constants.get('hartree ENERGY in ev', return_tuple=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](https://pint.readthedocs.io/en/latest/), 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](https://doi.org/10.1039/b801115j) ([details](qcelemental/data/alvarez_2008_covalent_radii.py.py)).
```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 tmost of the periodic table from [Mantina, J. Phys. Chem. A (2009) doi: 10.1021/jp8111556](https://pubs.acs.org/doi/10.1021/jp8111556) ([details](qcelemental/data/mantina_2009_vanderwaals_radii.py)).
```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

GitHub Events