pele.systems.BaseSystem

class pele.systems.BaseSystem(*args, **kwargs)

The base class for a System object

Notes

The following functions need to be overloaded for running the given routines

Global Optimization:

1. get_potential : required

2. get_takestep : optional

3. get_random_configuration : optional

4. get_compare_exact : optional

Connecting Minima and Transition State Searches:

1. get_potential : required

2. get_mindist : required

3. get_orthogonalize_to_zero_eigenvectors : required

4. get_compare_exact : optional, recommended

thermodynamics:

1. get_metric_tensor

GUI:

1. all of the above functions are required, plus

2. draw : required

3. smooth_path : required

4. load_coords_pymol : recommended

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.

Attributes