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https://github.com/abelcarreras/pyqchem
Python interface for Q-Chem
https://github.com/abelcarreras/pyqchem
interface python q-chem qchem quantum-chemistry
Last synced: 15 days ago
JSON representation
Python interface for Q-Chem
- Host: GitHub
- URL: https://github.com/abelcarreras/pyqchem
- Owner: abelcarreras
- License: mit
- Created: 2018-10-26T09:19:50.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2024-10-31T10:35:16.000Z (2 months ago)
- Last Synced: 2024-11-25T18:39:22.974Z (about 1 month ago)
- Topics: interface, python, q-chem, qchem, quantum-chemistry
- Language: Python
- Homepage: https://pyqchem.readthedocs.io/
- Size: 19.3 MB
- Stars: 21
- Watchers: 3
- Forks: 7
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://github.com/abelcarreras/PyQchem/actions/workflows/test-publish.yaml)
[](https://coveralls.io/github/abelcarreras/PyQchem?branch=master)
[](https://badge.fury.io/py/pyqchem)
[](https://pyqchem.readthedocs.io/en/master/?badge=master)
PyQchem
=======
Python wrapper for Q-Chem (https://www.q-chem.com)
Online manual: https://pyqchem.readthedocs.io/
Main features
-------------
- Easy to use clean python interface for Q-Chem
- No special q-chem installation needed (reads Q-Chem environment)
- Output parsers for different type of calculations
- Custom basis set and guess support using high level interface
- Calculation Cache system powered by SQLite database
- python 2.7.x/3.5+ compatibility
Installation instructions
-------------------------
1. Requirements
- numpy
- scipy
- matplotlib
- requests
- lxml
- wfnsympy (optional)
- paramiko (optional)
- pymatgen (optional)
2a. From pypi repository (recommended)
```shell
pip install pyqchem --user
```
2b. Installation from source
```shell
python setup.py install --user
```
Examples
--------
**Simple pythonic API to define your input**
```python
from pyqchem import Structure, QchemInput, get_output_from_qchem
from pyqchem.parsers.basic import basic_parser_qchem
molecule = Structure(coordinates=[[0.0, 0.0, 0.0],
[0.0, 0.0, 0.9]],
symbols=['H', 'H'],
charge=0,
multiplicity=1)
qc_input = QchemInput(molecule,
jobtype='sp',
exchange='hf',
basis='6-31G')
data = get_output_from_qchem(qc_input,
processors=4,
parser=basic_parser_qchem)
# obtain a python dictionary
print('Energy: ', data['scf_energy'])
```
**Link calculations in powerful workflows**
```python
from pyqchem import QchemInput, get_output_from_qchem
from pyqchem.parsers.parser_optimization import basic_optimization
from pyqchem.parsers.parser_frequencies import basic_frequencies
from pyqchem.tools import get_geometry_from_pubchem
molecule = get_geometry_from_pubchem('aspirin')
qc_input = QchemInput(molecule,
jobtype='opt',
exchange='hf',
basis='sto-3g',
geom_opt_tol_gradient=300,
geom_opt_tol_energy=100,
geom_opt_tol_displacement=1200)
parsed_data, electronic_structure = get_output_from_qchem(qc_input,
processors=4,
parser=basic_optimization,
read_fchk=True)
qc_input = QchemInput(parsed_data['optimized_molecule'],
jobtype='freq',
exchange='hf',
basis='sto-3g',
scf_guess=electronic_structure['coefficients'])
parsed_data = get_output_from_qchem(qc_input,
processors=4,
parser=basic_frequencies)
for i, mode in enumerate(parsed_data['modes']):
print('mode: {}'.format(i+1))
print('frequency (cm-1): {:10.2f}'.format(mode['frequency']))
print('force constant (mdyne/A): {:10.5f}\n'.format(mode['force_constant']))
```
**Custom basis support**
```python
from pyqchem import QchemInput, Structure
from pyqchem.basis import get_basis_from_BSE
molecule = Structure(coordinates=[[0.0, 0.0, 0.0000],
[0.0, 0.0, 1.5811]],
symbols=['Se', 'H'],
charge=-1,
multiplicity=1)
basis_custom = get_basis_from_BSE(molecule, 'cc-pVTZ')
qc_input = QchemInput(molecule,
jobtype='sp',
exchange='hf',
basis=basis_custom)
```
**Handle qchem errors**
```python
from pyqchem import get_output_from_qchem
from pyqchem.errors import OutputError, ParserError
from pyqchem.parsers.parser_rasci import parser_rasci
try:
parsed_data = get_output_from_qchem(qc_input,
processors=4,
parser=parser_rasci,
)
except OutputError as e:
print('Calculation ended with errors. Error lines:')
print(e.error_lines)
# Try to parse your output anyway
try:
parsed_data = parser_rasci(e.full_output)
except ParserError:
print('Failed parsing')
exit()
print('Energy: ', parsed_data['scf_energy'])
```
Additional example scripts are found at the [examples folder](/examples)
Contact info
------------
Abel Carreras
[email protected]
Donostia International Physics Center (DIPC)
Donostia-San Sebastian (Spain)