The base class for a System object
Notes
The following functions need to be overloaded for running the given routines
Global Optimization:
Connecting Minima and Transition State Searches:
thermodynamics:: 1. get_metric_tensor
GUI:
additionally, it’s a very good idea to specify the accuracy in the database using self.params.database.accuracy
See the method documentation for more information and relevant links
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(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() | object that returns True if two structures 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) | return (mass-weighted) metric tensor for given coordinates |
| get_mindist() | return a function that structurally aligns two configurations |
| 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() | return None or a function which makes a vector orthogonal to the known zero eigenvectors |
| 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(images, **kwargs) | return a smoothed path between two configurations. |