CDTK.Dynamics.SimulationBox2 module

class CDTK.Dynamics.SimulationBox2.SimulationBox(**opts)

Bases: object

Bunch of atoms given by their cartesian coordinates.

Provides functionality to follow and analyze their classical dynamics

add_observable_cntrl(ob)

Add an observable object

OB objects provide observable properties for the molecule

centerOfMassVelocity(**opts)

Compute the velocity vector of the center of mass

Optional arguments: - stepnum: step number to consider - time: time to consider

** use time OR stepnum

getKineticEnergy(**opts)

Total kinetic energy of the system of particles

Optional arguments: - stepnum: step number to consider - time: time to consider

** use time OR stepnum

getMomentum(**opts)

Return total momentum vector (in [au])

Optional arguments: - indices: tuple with indices of a group of atoms - stepnum: step number to consider - time: time to consider

** use time OR stepnum

getPotEnergy(**opts)

Return potential energy (last time or stored) of the system (a.u.)

Optional arguments: - stepnum: step number to consider - time: time to consider

** use time OR stepnum

getProperty2D_F(a_dir, a_funcX, a_filename, match=None)

Return a 2D function of the system in block form, one block per time step

Input arguments:

a_dir – directory with SimulationBox to be averaged a_filename – file where to store the data in table form

match – load only files matching a_match

On return two arrays with:

time, func_val

getPropertyTable(funcX=None, filename=None, usevel=False, **opts)

Return property as a function of time

Works on a single SimulationBox instance

Input arguments:

funcX – (optional) function of the coordinates

may have more than one return value

filename – (optional) file where to store the data in table form usevel – (optional) if True, velocities are

used instead of positions

on return the following arrays:

time, ekin, etrans, erot, evib, epot

or

time, func_val

if funcX provided

Options

finalTime – final time for property analysis over patial time domain

getPropertyTableDir_E(a_dir, filename=None, match=None, **opts)

Return ensemble averages of various energies

Input arguments:

a_dir – directory with SimulationBox to be averaged

filename – (optional) file where to store the data in table form match – load only files matching a_match

On return two arrays with:

time, func_val

Options

finalTime – final time for property analysis over patial time domain

getPropertyTableDir_F(a_dir, a_funcX, filename=None, match=None, usevel=False, **opts)

Return an ensemble average property as a function of time

Input arguments:

a_dir – directory with SimulationBox to be averaged a_funcX – function of the coordinates;

may have more than one return value

filename – (optional) file where to store the data in table form match – load only files matching match usevel – (optional) if True, velocities are used instead of positions

On return two arrays with:

time, func_val

Options

finalTime – final time for property analysis over patial time domain

getReducedMass()

Return the reduced mass of the molecule

getRotationalEnergy(**opts)

Rotational energy around the center of mass of the system of particles

Optional arguments: - stepnum: step number to consider - time: time to consider

** use time OR stepnum

getTranslationalEnergy(**opts)

Translational energy of the center of mass of the system of particles

Optional arguments: - stepnum: step number to consider - time: time to consider

** use time OR stepnum

getVibrationalEnergy(**opts)

Internal energy of the system of particles

Optional arguments: - stepnum: step number to consider - time: time to consider

** use time OR stepnum

getVibrationalMomentum(**opts)

Internal momentum of the system of particles

Optional arguments: - stepnum: step number to consider - time: time to consider

** use time OR stepnum

integrate(**opts)

Integrate up to tfinal

load(a_fname, **opts)

Load a simulationbox object from file

loadDirectory(a_dir, match=None, **opts)

Load all simulationbox objects stored in a directory

Input arguments:

a_dir – directory where to load simbox objects from match – (optional) load only files that match “match”

removeCenterMassMotion()

Remove center of mass translational motion

save(**opts)

Save object using pickle

optional arguments:

• fname: filename to save to. If not given a random

  hash will be used

traj2VTF(**opts)

Generate a trajectory in .vtf format

Useful for plots with VMD

CDTK.Dynamics.SimulationBox2.load(filename)

Load a SimulationBox from file and return it