Define an atomic cluster.
This is a system of point particles with global rotational and translational symmetry and some form of permutational symmetry.
Methods
| __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_nzero_modes() | |
| get_orthogonalize_to_zero_eigenvectors() | the zero eigenvectors correspond to 3 global translational |
| get_permlist() | |
| get_pgorder(coords) | |
| get_potential() | |
| get_random_configuration() | |
| 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) |