NAMD using Turbomole
====================

This section briefly describes how to run nonadiabatic molecular dynamics
(NAMD) with mudslide using Turbomole as a QM engine.

.. warning::
   This is a work in progress. Expect some kinks.

Setup Turbomole
---------------
The first step will be to setup a directory that contains all the
input information you will need for a turbomole calculation.
This means run define, TmoleX, or whatever else you would normally
run to set up the calculation. Please see the Turbomole documentation
for more information on how to do this. When the directory is set up,
change to it:

.. code-block:: bash

    cd /path/to/turbomole/directory


Load TMModel class
------------------
Next, you will set up a python script that will create a TMModel
and run the simulation. An example script is shown below:

.. code-block:: python

    import mudslide

    model = mudslide.models.TMModel(states=[0, 1]) # run using ground and first excited states
    positions = model._position # read position from the coord file
    momenta = mudslide.math.boltzmann_velocities(model._mass, 300) * model._mass

    log = mudslide.YAMLTrace() # log trajectory using YAML files
    traj = mudslide.TrajectoryCum(model, # run using turbomole model
                                 positions, # start at position from coord
                                 momenta, # use boltzmann momenta
                                 1, # start on 1st excited state
                                 tracer=log, # use yaml log
                                 dt=20, # 20 a.u. time step
                                 max_time=80, # run for 80 a.u.
                                 )
    results = traj.simulate()


Advice
------

*  Make sure your control file specifies all the options you need for dynamics. For example:

   * For NAMD you will need to have

     * ``$soes`` data group with information on the excitations.
     * ``$nacme`` (for just states 0,1) or ``$nacme pseudo`` (for state-to-state)
     * weight derivatives

   * And it is recommended to have

     * ``$phaser``
     * ``$do_etf``