CDTK.Dynamics.IniConSampler module

class CDTK.Dynamics.IniConSampler.IniConSampler(x0, funcE, **opts)

Bases: object

Samples initial conditions according to some statistical distribution

The object produces a bunch of files, each one containing a simulationbox object ready for propagation.

burnin(**opts)

Run the sampler without collecting data and adjust acceptance rate to target

Options

steps – number of steps to be taken in this burin phase (1000)

default: 1000

increment – number of steps used to compute rate (50)

default: 50

targetRate – target acceptance rate (0.4)

default: 0.4

startnorm – initial norm of MonteCarlo steps

default: 0.1

init_samplewigner(hessian, m, is_linear, modes=None)

Return harmonic modes

init_wigner()

Return harmonic modes

nm2x_coord(qp_nmode)

Transform from normal mode coordinates to cartesian coordinates

sample(**opts)

Sample initial conditions and produce a list of files ready for use

Options

stepnorm – norm of the MonteCarlo steps to be taken. NSAMPLES – int, number of samples to collect savefiles – bool, True, save new simulationbox objects to disk

sampleR(**opts)

Sample pure rotational initial conditions and produce a list of files ready for use

Options

stepnorm – norm of the MonteCarlo steps to be taken. NSAMPLES – int, number of samples to collect savefiles – bool, True, save new simulationbox objects to disk

sampleW(hessian, is_linear, modes, **opts)

Sample Wigner initial conditions and produce a list of files ready for use

Options

stepnorm – norm of the MonteCarlo steps to be taken. NSAMPLES – int, number of samples to collect savefiles – bool, True, save new simulationbox objects to disk

sampleWigner(hessian, nmfreq, nmcoord, is_linear, m, is_1d=False, **opts)

Sample Wigner initial conditions and produce a list of files ready for use. WARNING: THIS ONLY WORKS FOR 1D AND NEEDS TO BE UPDATED TO WORK FOR GENERAL CASES!!!

Options.

NSAMPLES – int, number of samples to collect

sampler_boltzmann(hessian=None, is_linear=None, modes=None, **opts)

Sample initial conditions according to exp(-betaH) and produce a list of files ready for use

Options stepnorm – norm of the MonteCarlo steps to be taken. NSAMPLES – int, number of samples to collect savefiles – bool, True, save new simulationbox objects to disk

CDTK.Dynamics.IniConSampler.bwd_fft(modes, nb)

Transform from normal mode representation to bead representation using FFT.

Input: modes — current position/velocity values in normal mode representation nb — number of beads

Output: beads — positions/velocities in bead representation

CDTK.Dynamics.IniConSampler.get_omega(x0, m, hessian, quantum_numbers=None, is_linear=False, modes=None)

CDTK.Dynamics.IniConSampler.rotation(x0, v0, phi=None)

Isotropically sample one rotaional degree of freedom. Currently limited to rotations about the y-axis.

Input: x0 - list of input cartesian coordinates. v0 - list of input cartesian velocities. phi - optional list of given rotation angles; for testing purposes. Output: x - list of cartesian coordinates with added sampling. v - list of cartesian velocities rotated correctly.

CDTK.Dynamics.IniConSampler.sampleRotation(xref, mass, temp, nsample, **opts)

xref – reference geometry to sample rotations [[x1,y1,z1,],[x2,y2,z2,],…], a.u. mass – atom masses [m1,m2,…] assume a.u. temp – rotational temperature nsample – number of initial conditions to generate

CDTK.Dynamics.IniConSampler.sampler_zero_point_energy(nsample, x0, m, hessian, quantum_numbers=None, is_linear=False, modes=None, rpmd=False)

Sample independent normal modes according to quantum state energies

nsample – int, number of positions and velocities to generate x0 – np array, Cartesian coordinates of the reference geometry m – np array, Mass of each Cartesian coordinate hessian – np array, Hessian matrix quan… – list, quantum number of each mode increasing in energy is_linear – bool, True if linear (e.g. diatomic) system

CDTK.Dynamics.IniConSampler.sampler_zero_point_energy_rpmd(nsample, x0, m, hessian, nb, beta, quantum_numbers=None, is_linear=False, modes=None)

Sample independent normal modes according to quantum state energies

nsample – int, number of positions and velocities to generate x0 – np array, Cartesian coordinates of the reference geometry m – np array, Mass of each Cartesian coordinate hessian – np array, Hessian matrix quan… – list, quantum number of each mode increasing in energy is_linear – bool, True if linear (e.g. diatomic) system