https://github.com/schneiderfelipe/pyrrole
A Python package for solving chemical problems with computational modelling
https://github.com/schneiderfelipe/pyrrole
chemistry computational-chemistry library python quantum-chemistry research science
Last synced: 9 months ago
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A Python package for solving chemical problems with computational modelling
- Host: GitHub
- URL: https://github.com/schneiderfelipe/pyrrole
- Owner: schneiderfelipe
- License: mit
- Created: 2018-06-13T13:50:34.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2023-04-16T20:37:43.000Z (about 3 years ago)
- Last Synced: 2025-04-05T11:42:29.339Z (about 1 year ago)
- Topics: chemistry, computational-chemistry, library, python, quantum-chemistry, research, science
- Language: Python
- Homepage: https://pypi.org/project/pyrrole/
- Size: 381 KB
- Stars: 2
- Watchers: 0
- Forks: 0
- Open Issues: 7
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
README
**WARNING**: this project has been retired.
Please migrate to
`geem-lab/overreact `_.
pyrrole
=======
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A Python package for solving chemical problems with computational modeling.
Usage example
-------------
As a usage example, let's calculate the energy barrier involved in `nitrogen inversion in ammonia `_.
.. figure:: https://upload.wikimedia.org/wikipedia/commons/2/2d/Nitrogen-inversion-3D-balls.png
:alt: Nitrogen inversion in ammonia
:align: center
When ammonia turns "inside out", it passes through a planar transition state (`image in public domain `_).
We do this in three simple steps (only eight lines of code):
1. **Get the data**
We first obtain the raw data, which will later be fed to our chemical model.
Below we read computational chemistry logfiles of both ground and transition states [#level-of-theory]_.
>>> from pyrrole.atoms import read_cclib, create_data
>>> gs = read_cclib("data/ammonia/ammonia.out", name="NH3(g)")
>>> ts = read_cclib("data/ammonia/invers.out", name="NH3(g)#")
>>> data = create_data(gs, ts)
Pyrrole uses `cclib `_ for reading logfiles, which is `compatible with all major computational chemistry packages `_.
You could also want to read tabular data `from a file `_ (or even `from the web `_) using `pandas `_.
2. **Specify the model**
We now describe our model.
This is accomplished through chemical equations:
>>> from pyrrole import ChemicalEquation
>>> equation = ChemicalEquation("NH3(g) -> NH3(g)#", data)
While model above consists of a single `ChemicalEquation`, you could create complex models with multiple chemical equations with `ChemicalSystem` objects.
You might want to store your complex models in text files too.
3. **Obtain the results**
Simply let pyrrole calculate the energy barrier:
>>> results = equation.to_series()
>>> results["freeenergy"] * 2625.4996382852164 # Hartree to kJ/mol
19.30952589472923
(As a side note, the reference value is 21.162 kJ/mol [#experimental-freeenergy-ammonia-inversion]_.)
Interested? `Have another example `_.
.. [#level-of-theory] Optimizations and frequency calculations of both ammonia and the planar transition state were performed at `PBEh-3c`_ using the `ORCA`_ electronic structure package (version 4.0.1.2). Logfiles can be found in the `project's repository `_.
.. _`PBEh-3c`: https://doi.org/10.1063/1.4927476
.. _`ORCA`: https://orcaforum.cec.mpg.de/
.. [#experimental-freeenergy-ammonia-inversion] *Chem. Phys. Lett.*, **2003**, *370* (3), pp 360-365 DOI: `10.1016/S0009-2614(03)00107-6 `_.
Installation
------------
You can get the library directly from `PyPI `_:
.. code-block:: console
$ pip install pyrrole