CDTK.Dynamics.Trajectory module

class CDTK.Dynamics.Trajectory.Trajectory(NDof=1, **opts)

Bases: object

Born-Oppenheimer trajectory on a single PES

self.NDof – int, Number of degrees of freedom self.R – np.array, positions self.V – np.array, velocities self.M – np.array float, masses self.dt – float, time-step for nuclear displacements self.rseed – int, default None, random seed to be set before 1st step self.NAME – Identification string of this trajectory. It is uniquely

generated at the initialization

self.f_Egrad – function, provides energy and gradient on PES of state S

e,g = f(R,S)

self.ES – electronic state for large hop electron dynamics self.MM – MM region instance

getCOM(atomlist, step=0)

This function returns the center of mass of a set of atoms given by their index.

Input: atomlist — list of indices for the atoms

Output: center of mass

init_log()

integrate(tfinal=None, **opts)

Integrate trajectory until tfinal

tfinal – final time to be reached by the integrator in steps of dt.

**opts:

dt – delta time used in this segment.

It is not a good idea to change this when continuing from a previous integration

kinetic_energy(step=None, atomlist=None)

Calculates the kinetic energy for a certain timestep and a given set of atoms.

Input: step — timestep for which kinetic energy should be calculated given as integer.

default is None and gives the current timestep

atomlist — list of indices for the atoms to be included, default is None and gives all.

Output: kin — kinetic energy

log()

log_to_file(**opts)

Write all log information to a set of files

restart()

Function to restart trajectory. Reads in all important values from log-files.

set_constraints(f_constraints)