.. MLatom PyAPI manual documentation master file, created by
   sphinx-quickstart on Fri Sep  1 09:28:40 2023.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

===============================================
Welcome to MLatom documentation!
===============================================

MLatom is a program package for AI-enhanced computational chemistry. It is designed to leverage the power of ML to speed up and make more accurate common :ref:`simulations <overview_simulations>` and to create complex workflows.

The users can run simulations with input files, Python script, and command-line options.

MLatom is an :ref:`open-source <source_code>` package that can be installed via ``pip`` and cloned from GitHub. Additional advanced features can be obtained via the `Aitomic <http://mlatom.com/aitomic>`__ add-ons. The calculations with MLatom can be performed on the `Aitomistic Hub <https://www.aitomistic.xyz>`__  and `XACS cloud computing service <https://XACScloud.com>`__.

.. `Online courses <https://xacs.xmu.edu.cn/course>`__ *Modern computational chemistry and AI with MLatom\@XACS* by Pavlo O. Dral.

.. image:: _static/mlatom3paper/toc.png
    :width: 250
    :align: center

A video overview of the MLatom capabilities:

.. raw:: html

    <iframe src="https://player.bilibili.com/player.html?isOutside=true&bvid=BV1Sv421C7tn&p=1&autoplay=0" scrolling="no" border="0" frameborder="no" framespacing="0" allowfullscreen="true" height=500 width=800></iframe>

To get quickly started, please check a :doc:`simple example <get_started>` illustrating the use of MLatom.

See a :ref:`detailed overview <overview>` of capabilities of MLatom for more information.

.. toctree::
    :maxdepth: 1
    :caption: Overview

    overview
    license
    releases
    about
    contact


.. toctree::
    :maxdepth: 1
    :caption: Setup

    installation
    source_code
    use
    cloud

.. toctree::
    :maxdepth: 1
    :caption: Tutorials: Introduction

    get_started
    tutorial_data
    tutorial_workshops


.. toctree::
    :maxdepth: 1
    :caption: Tutorials: Methods

    tutorial_uaiqm
    tutorial_aiqm1
    tutorial_aiqm2
    tutorial_omnip2x
    tutorial_universalml
    tutorial_dft
    tutorial_dens

.. toctree::
    :maxdepth: 1
    :caption: Tutorials: (ML) models

    tutorial_user_defined_models
    tutorial_mlp
    tutorial_al
    tutorial_tl
    tutorial_delta
    tutorial_4d
    tutorial_mdtrajnet
    tutorial_krr_julia

.. toctree::
    :maxdepth: 1
    :caption: Tutorials: Simulations

    tutorial_sp
    tutorial_geomopt
    tutorial_ts
    tutorial_re_explore
    tutorial_freq
    tutorial_ir
    tutorial_raman
    tutorial_md
    tutorial_qct
    tutorial_md2vibr
    tutorial_pbc

.. toctree::
    :maxdepth: 1
    :caption: Tutorials: Excited states

    tutorial_es_methods
    tutorial_es_sp
    tutorial_es_data
    tutorial_es_ml
    tutorial_uvvis
    tutorial_namd
    tutorial_tsh_al
    tutorial_gampd

.. toctree::
    :maxdepth: 2
    :caption: Manual for input file/CLI

    cl_manual_overview
    cl_manual_simulations
    cl_manual_learning
    cl_manual_data

.. toctree::
    :maxdepth: 2
    :caption: Manual for API

    api


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`