Metadata-Version: 2.4
Name: strainjedi
Version: 1.1.0
Summary: Judgement of Energy DIstribution - quantum chemical strain analysis
License-Expression: MIT
Project-URL: Homepage, https://github.com/neudecker-group/jedi
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Requires-Python: >=3.10
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: ase>=3.28.0
Requires-Dist: matplotlib>=3.10.9
Requires-Dist: numpy>=2.2.6
Requires-Dist: typing-extensions>=4.15.0
Dynamic: license-file

Judgement of Energy DIstribution
--------------------------------

JEDI is a quantum chemical strain analysis tool working with the Atomic Simulation Environment (ASE).

Requirements
------------

* Python_ 3.12 or later
* NumPy_ (base N-dimensional array package)
* ase_ 3.23 (functions to determine atomic structures' geometries and quantum chemical calculators)

Installation
------------

JEDI can be installed by running ``pip install strainjedi``. When using the ``git`` version, add ``~/jedi`` to your $PYTHONPATH environment variable. 

Development
-----------

This project uses uv_ to manage dependencies; ensure it is installed on your system.

.. code-block::

   uv sync  # install dependencies
   uv build # build the python wheel

To run tests, install the `test` dependency group:

.. code-block::

   uv sync --group=test
   uv run pytest

To build the documentation, ensure that the ``docs`` dependency group is installed.

.. code-block::

   uv sync --group=docs
   uv run sphinx-build -a -b html docs docs/_build/

this will rebuild all documentation files and generate HTML output to ``docs/_build``.

    [!TIP]

    Run ``uv sync --all-groups`` to install all dependencies for all the above scenarios.

See also our `contributing guidelines <https://neudecker-group.github.io/jedi/development.html>`_ in our documentation for more detail.

Tutorial
------------

A tutorial is available here: https://neudecker-group.github.io/jedi/

Citation
--------

When using JEDI, please cite the following papers:

* Wang, H.; Benter, S.; Dononelli, W.; Neudecker, T.; JEDI: A versatile code for strain analysis of molecular and periodic systems under deformation, J. Chem. Phys. **2024**, 160, 152501. https://doi.org/10.1063/5.0199247

* Stauch, T.; Dreuw, A.; A quantitative quantum-chemical analysis tool for the distribution of mechanical force in molecules, J. Chem. Phys. **2014**, 140, 134107. https://doi.org/10.1063/1.4870334

Additional information on the theoretical background of the JEDI analysis can be found in the following papers:

* Stauch, T.; Dreuw, A.; On the use of different coordinate systems in mechanochemical force analyses, J. Chem. Phys. **2015**, 143, 074118. https://doi.org/10.1063/1.4928973

* Stauch, T.; Dreuw, A.; Predicting the Efficiency of Photoswitches Using Force Analysis, J. Phys. Chem. Lett. **2016**, 7, 1298-1302. https://doi.org/10.1021/acs.jpclett.6b00455

* Stauch, T.; Dreuw, A.; Quantum Chemical Strain Analysis For Mechanochemical Processes, Acc. Chem. Res. **2017**, 50, 1041-1048. https://doi.org/10.1021/acs.accounts.7b00038

.. _Python: http://www.python.org/
.. _NumPy: http://docs.scipy.org/doc/numpy/reference/
.. _ase: https://wiki.fysik.dtu.dk/ase/
.. _uv: https://docs.astral.sh/uv/getting-started/installation/
