Get started
=====================
To get started, we provide show how to use different capabilities of MLatom on an example of geometry optimization.

Using input file
----------------
You can watch a short video demonstrating how to use the command-line options or input file to run some calculations on the :doc:`XACS cloud <cloud>`.

.. raw:: html

    <video width="640" height="480" controls>
        <source src="_static/get_started_input_file.mp4" type="video/mp4">
    </video>

MLatom can be run in the command line format using the command-line options or input file.
To optimize geometry using the ANI-1ccx method, you can use the input file :download:`geomopt.inp <files/get_started/geomopt.inp>` which you can download or copy-paste from:

.. code-block:: 

    ANI-1ccx                # pre-trained model
    geomopt                 # requests geometry optimization
    xyzfile=init.xyz        # initial geometry guess
    optxyz=opt.xyz          # file with optimized geometry

This input requires you to provide :download:`init.xyz <files/get_started/init.xyz>` file (which you need to upload as *auxiliary file* on `XACS cloud <http://XACScloud.com>`__)

.. note::

    This self-contained input file without the need to provide auxiliary file also works:

    .. code-block::

        ANI-1ccx                # pre-trained model
        geomopt                 # requests geometry optimization
        xyzfile='
        8

        C             0.0000000000000           0.0000000000000           0.7608350816719
        H            -0.0000000000000           1.0182031026887           1.1438748775511
        H             0.8817897531403          -0.5091015513443           1.1438748775511
        H            -0.8817897531403          -0.5091015513443           1.1438748775511
        C            -0.0000000000000          -0.0000000000000          -0.7608350816719
        H            -0.8817897531403           0.5091015513443          -1.1438748775511
        H             0.8817897531403           0.5091015513443          -1.1438748775511
        H            -0.0000000000000          -1.0182031026887          -1.1438748775511
        '

Then run MLatom simulations using this input file as:

.. code-block:: bash

    mlatom geomopt.inp &> geomopt.out

The program will print out the relevant calculation information to the output file :code:`geomopt.out`.

Using PyAPI
-----------
You can watch a short video demonstrating how to use PyAPI on the :doc:`XACS cloud <cloud>`.

.. raw:: html

    <video width="640" height="480" controls>
        <source src="_static/get_started.mp4" type="video/mp4">
    </video>

Below is an example of Python script using MLatom to optimize geometry at ANI-1ccx -- the simulation task the same as in the above example with command-line execution:

.. code-block:: python

    import mlatom as ml                                                                         # import MLatom module.
    ani = ml.models.methods(method='ANI-1ccx')                                                  # denfine an ANI-1cxx model.
    init_mol = ml.data.molecule.from_xyz_file('init.xyz')                                       # load the molecular structure.
    final_mol = ml.optimize_geometry(model=ani, initial_molecule=init_mol).optimized_molecule   # the optimized structure can be obtained by command.
    final_mol.xyz_coordinates                                                                   # we can see the coordinates of the last molecule. 
    print(final_mol.get_xyz_string())                                                           # print the coordinates in ".xyz" format.
    final_mol.write_file_with_xyz_coordinates(filename='opt.xyz')                              # save it in "final.xyz".