Molecular Dynamics

This class is an addition to the molecular dynamics module in ASE (See ASE for details).

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

hyperplaneoptions 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

eigrequired 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:

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)