pyvibdmc.analysis.extract_sim_info

Classes

Object that takes in a .hdf5 file (one of the outputs of the simulation) and provides tools for analysis.

class pyvibdmc.analysis.extract_sim_info.SimInfo(h5_name)[source]

Object that takes in a .hdf5 file (one of the outputs of the simulation) and provides tools for analysis.

:type str

static get_wfn(wfn_fl, ret_ang=False, get_parent_wts=False)[source]

Given a .hdf5 file, return wave function and descendant weights associated with that wave function.

Parameters:

wfn_fl – A resultant .hdf5 file from a PyVibDMC simulation
ret_ang – boolean indicating returning the coordinates in angtstroms. Bohr is the default.

Returns:

Coordinates array in angstroms (nxmx3), descendant weights array (n).

get_wfns(time_step_list, ret_ang=False, get_parent_wts=False)[source]: Extract the wave function (walker set) and descendant weights given a time step number or numbers :param time_step_list: a list of ints that correspond to the time steps you want the wfn from given the simulation you are working with :type time_step_list: int or list :param ret_ang: boolean indicating returning the coordinates in angtstroms. Bohr is the default. :param get_parent_wts: Return the continuous weights associated with the walkers at the beginning of descendant weighting.

get_pop()[source]: Returns population array, either ensemble size or sum of weights

get_atomic_nums()[source]: Returns list of atoms used in the simulation (by atomic number)

get_atom_masses()[source]: Returns masses used in the simulation in atomic units (mass electron)

get_zpe(onwards=1000, ret_cm=False)[source]: onwards is an int that tells us where to start averaging (python indexing starts at 0)

window_avg(blocks=5, ret_cm=False)[source]: Splits vref into blocks, calculates zpe in each of those blocks

static get_training(training_file, ret_ang=False, ret_cm=False)[source]: If using deb_training_every argument, read the files with this. Returns walkers in angstr and engs in cm-1