.. _md:

================================
Molecular Dynamics
================================

This class  is an addition to the molecular dynamics module in ASE `(See ASE for details) <https://wiki.fysik.dtu.dk/ase/ase/md.html#module-md>`_. 

Anderson thermostat
----------------------
The anderson thermostat couples the dynamics of a system to a heat bath in order to simulate constant NVT simulations.  
The thermostat is imposed by stochastic collisions of randomly selected particles throughout the simulation.  Below defines the 
various options for this class:

class ``tsase.md.`` **nvtandersen** (atoms,timestep,temperature,alpha,tcol,fixcm = True,
        trajectory=None,logfile=None,loginterval=1, communicator=world,hyperplane=False,eig=None)

	**atoms** : atoms object with list of atoms

	**timestep** : the time step 

	**temperature** : the temperature in kT

	**alpha** : the collison strength in the andersen thermostat

	**tcol** : the collision period for the andersen thermostat

	**fixm** : If True, the position and momentum of the center of mass is kept constant 

	**trajectory** : file to save a movie of the MD trajectory

	**logfile** : file to save various properties throughout trajectory 

	**loginterval** : every time step information is saved in log file

	**hyperplane** : options to run dynamics in a htst hyperplane; if True no components of the velocity 
			 will be in the direction of the degree of freedom taken away 

	**eig** : required when running dynamics in hyperplane; defines the vector corresponding to the
		  degree of freedom being taken away from the system.

Usage:
======
Below is an example of how to use the thermostat: 

.. code-block:: none
	
	dyn = tsase.md.nvtandersen(atoms,1.0*units.fs,300*units.kB)
	### the function step takes a velocity verlet step and applies the andersen thermostep once
	f = atoms.get_forces()
	f = dyn.step(f)