md.simulation_hooks.GLEThermostat

class md.simulation_hooks.GLEThermostat(*args: Any, **kwargs: Any)[source]

Stochastic generalized Langevin colored noise thermostat by Ceriotti et. al. as described in [1]. This thermostat requires specially parametrized matrices, which can be obtained online from: http://gle4md.org/index.html?page=matrix

The additional degrees of freedom added to the system are defined via the matrix dimensions. This could in principle be used for ring polymer dynamics by providing a normal mode transformation.

Parameters:

  • temperature_bath (float) – Temperature of the external heat bath in Kelvin.

  • gle_file (str) – File containing the GLE matrices

  • free_particle_limit (bool) – Initialize momenta according to free particle limit instead of a zero matrix (default=True).

References