class*args, **kwargs)[source]

The base class for a System object


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


  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


__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.

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