.. SITH documentation master file, created by
   sphinx-quickstart on Fri Aug 26 12:18:30 2022.

SITH
####

citation: coming soon.
~~~~~~~~~~~~~~~~~~~~~~

.. figure:: tutorials/stretching/G-distribution.png
  :align: center

SITH is a novel method that decomposes the total electronic energy change of a
stretched molecule into contributions from individual degrees of freedom —such
as bond lengths, angles, and dihedrals— using numerical integration of the
work-energy theorem,

.. math::
   :label: eq:numerical_integration

   \Delta E_i = - \int_{0}^{k} F_i \, dq_i
   \approx - \sum_{j=0}^{k} \frac{F^j_i + F^{j+1}_i}{2} \Delta_j^{j+1} q_i,

where :math:`\Delta_j^{j+1} q_i` is the change of the value of the :math:`i`-th degree of
freedom between two consecutive configurations in the COGEF path. :math:`F^j_i` is
the force associated to the i-th degree of freedom for the j-th configuration
in the path,

.. math::
   :label: eq:force_i

   F^j_i = -\frac{\partial E^{DFT}}{\partial q_i}\bigg|_{\{q\}^j}.

SITH software is organized as follows:

.. include:: flowchart.rst


Contents
========

.. toctree::
   :maxdepth: 3
   :name: contents

   install
   workflow/workflow
   modules/sith
   tutorials/tutorials


* :ref:`genindex`