Molecular dynamics
==================

MLatom can run molecular dynamics simulation. Here we use the trained model of KREG for H\ :sub:`2`\ . 

.. note::
    You need to have a KREG model trained in the :ref:`previous section <KREG>` before running MD. 

Now prepare the input file for MD simulation: :download:`h2_md_kreg.inp <files/h2_md_kreg.inp>`.

.. code-block::

    # h2_md_kreg.inp
    MD                             # molecular dynamics
    initXYZ=h2_md_kreg_init.xyz    # initial geometry; Unit: Angstrom
    initVXYZ=h2_md_kreg_init.vxyz  # initial velocity; Unit: Angstrom/fs
    dt=0.3                         # time step; Unit: fs 
    trun=30                        # total time; Unit: fs 
    ensemble=NVE                   # NVE ensemble 
    MLprog=KREG_API                # for KREG model implemented in KREG Python API
    MLmodelIn=energies.npz         # file that saves the model 
    #MLprog=MLatomF                # for KREG model implemented in the Fortran part of MLatom 
    #MLmodelIn=energies.unf        # file that saves the model 
    #MLmodelType=ANI               # or use an ANI model 
    #MLmodelIn=energies_ani.pt     # the ANI model file

And provide the initial XYZ coordinates (:download:`h2_md_kreg_init.xyz <files/h2_md_kreg_init.xyz>`) and initial XYZ 
velocities (:download:`h2_md_kreg_init.vxyz <files/h2_md_kreg_init.vxyz>`) of this model.

.. code-block::

    # h2_md_kreg_init.xyz
    2

    H 0.0 0.0 1.0
    H 0.0 0.0 0.0

Run the MD simulation.

.. code-block::

    mlatom h2_md_kreg.inp

The result will be saved in ``traj.xyz``. We can view it by:

.. code-block::

    cat traj.xyz

In Python, same as above, we should provide the initial XYZ coordinates ``.xyz`` and initial XYZ velocities ``.vxyz``.
The result will be saved in ``traj.xyz``.

.. code-block::

    import mlatom as ml 

    # Get initial condition
    mol = ml.data.molecule.from_xyz_file('h2_md_kreg_init.xyz')
    init_cond_db = ml.generate_initial_conditions(molecule = mol,
                                                  generation_method = 'user-defined',
                                                  file_with_initial_xyz_coordinates = 'h2_md_kreg_init.xyz',
                                                  file_with_initial_xyz_velocities  = 'h2_md_kreg_init.vxyz')
    init_mol = init_cond_db[0]

    # Initialize model
    model = ml.models.kreg(model_file='energies.npz', ml_program='KREG_API')
    # model = ml.models.kreg(model_file='energies.unf', ml_program='MLatomF') # use KREG model from MLatomF
    # model = ml.models.ani(model_file='energies_ani.pt')                     # or use an ANI model  

    # Run molecular dynamics
    dyn = ml.md(model=model,
                molecule_with_initial_conditions = init_mol,
                ensemble='NVE',
                time_step=0.3,
                maximum_propagation_time = 30.0)

    # Dump trajectory
    traj = dyn.molecular_trajectory
    traj.dump(filename='traj', format='plain_text')
    traj.dump(filename='traj.h5', format='h5md')