pele.systems.LJCluster

class pele.systems.LJCluster(natoms)

define the System class for a Lennard-Jones cluster

Parameters:

natomsint

See also

BaseSystem, AtomicCluster

Methods

__call__()	calling a system returns itself
createNEB(coords1, coords2, **kwargs)	return an NEB object to find a minimum energy path from coords1 to coords2
create_database(*args, **kwargs)	return a new database object
draw(coordslinear, index[, subtract_com])	tell the gui how to represent your system using openGL objects
get_basinhopping([database, takestep, ...])	construct a basinhopping object with takestep and accept step already implemented
get_compare_exact(**kwargs)	this function quickly determines whether two clusters are identical given translational, rotational and permutational symmeties
get_compare_exact_without_perms(**kwargs)
get_compare_minima()	a wrapper for compare exact so in input can be in Minimum Form
get_double_ended_connect(min1, min2, ...)	return a DoubleEndedConnect object
get_log_product_normalmode_freq(coords[, ...])	return the log product of the squared normal mode frequencies
get_metric_tensor(coords)	metric tensor for all masses m_i=1.0
get_mindist(**kwargs)	return a function which puts two structures in best alignment.
get_minimizer(**kwargs)	return a function to minimize the structure
get_ndof()	return the number of degrees of freedom
get_normalmodes(coords)	return the squared normal mode frequencies and eigenvectors
get_nzero_modes()	return the number of vibration modes with zero frequency
get_orthogonalize_to_zero_eigenvectors()	the zero eigenvectors correspond to 3 global translational degrees of freedom and 3 global rotational degrees of freedom
get_permlist()
get_pgorder(coords)	return the point group order of the configuration
get_potential()	return the potential object
get_random_configuration()	return starting point for basinhopping, etc.
get_random_minimized_configuration(**kwargs)	return a random configuration that is already minimized
get_system_properties()	return a dictionary of system specific properties.
get_takestep(**kwargs)	return the takestep object for use in basinhopping, etc.
load_coords_pymol(coordslist, oname[, index])	load the coords into pymol
smooth_path(path, **kwargs)	return a smoothed path between two configurations.

Attributes