pyvibdmc.simulation_utilities.initial_conditioner

Submodules

Classes

`MolFiniteDifference`	Helper to calculate derivatives of some value as a function of Cartesian displacements in a molecule.
`HarmonicAnalysis`
`InitialConditioner`	If given a minimum energy geometry of the system you are trying to run, it will generate a preliminary ensemble.

Package Contents

class pyvibdmc.simulation_utilities.initial_conditioner.MolFiniteDifference[source]

Helper to calculate derivatives of some value as a function of Cartesian displacements in a molecule.

weights_der1

weights_der2

static displace_molecule(eq_geom, atm_cd, dx, num_disps)[source]: Displace atm along cd :param eq_geom: Geometry from which you will be displaced :param atm_cd: a tuple that has a paricular atom of interest to displace in a particular dimension (x,y,or,z) :param dx: The amount each geometry will be replaced :param num_disps: int of how many displacements to do, will take the form of 3 or 5 for harmonic analysis. :return: Displaced coordinates in a 3D array (n,m,3). If displaced in two directions, then still (n,m,3)

classmethod differentiate(values, dx, num_points, der)[source]

class pyvibdmc.simulation_utilities.initial_conditioner.HarmonicAnalysis(eq_geom, atoms, potential, masses=None, dx=0.001, points_diag=5, points_off_diag=3, dipole=None)[source]

eq_geom

atoms

potential

masses = None

dx = 0.001

points_diag = 5

points_off_diag = 3

num_elems

dipole = None

generate_hessian()[source]

dipole_derivs()[source]

diagonalize(hessian)[source]

run()[source]

class pyvibdmc.simulation_utilities.initial_conditioner.InitialConditioner(coord, atoms, num_walkers, technique, technique_kwargs, masses=None)[source]

If given a minimum energy geometry of the system you are trying to run, it will generate a preliminary ensemble. In one instance, you can calculate the harmonic frequencies and normal modes, and then sample the harmonic 3N-6 ground state wave function along those normal modes. Will, in the future, handle other initial conditions.

coord

atoms

masses = None

num_walkers

technique

technique_kwargs

gen_disps(sigmas)[source]

displace_along_nms(freqz, nmz, massez, ensemble)[source]

run_harm()[source]

run_permute()[source]: Must pass in a list of lists.

run()[source]