class*args, **kwargs)[source]

Define an atomic cluster.

This is a system of point particles with global rotational and translational symmetry and some form of permutational symmetry.


__call__() calling a system returns itself
createNEB(coords1, coords2, **kwargs)
create_database(*args, **kwargs) return a new database object
draw(coords, index) 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
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_orthogonalize_to_zero_eigenvectors() the zero eigenvectors correspond to 3 global translational
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)

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