Calculators¶

A mapped potential is a tabulated 2- or 3-body interatomic potential created from a Gaussian process using a 2- or 3-body kernel. To use a mapped potential created with this python package within the ASE environment, it is necessary to setup a calculator using the mff.calculators class.

Theory/Introduction¶

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Example¶

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Running the Calculator¶

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Configurations¶

Module used to create ase calculators using interpolators constructed with the models module of the mff package. These calculators can yield forces and energies for atoms objects at a very low computational cost.

WARNING: The atoms object must be such that the atoms are ordered with increasing atomic number for the two species calculator to work.

Example

>>> calc = calculators.CombinedTwoSpecies(
        r_cut, element0, element1,  grid_2b, grid_3b, rep_alpha=1.4)
>>> atoms = atoms[np.argsort(atoms.get_atomic_numbers())]
>>> atoms.set_calculator(calc)

class mff.calculators.CombinedSingleSpecies(r_cut, grid_2b, grid_3b, rep_alpha=0.0, **kwargs)

class mff.calculators.CombinedTwoSpecies(r_cut, element0, element1, grids_2b, grids_3b, rep_alpha=0.0, **kwargs)

class mff.calculators.MappedPotential(r_cut, **kwargs)

calculate(atoms=None, properties=('energy', 'forces'), system_changes=['positions', 'numbers', 'cell', 'pbc', 'initial_charges', 'initial_magmoms'])

Do the calculation.

properties: list of str: List of what needs to be calculated. Can be any combination of ‘energy’, ‘forces’, ‘stress’, ‘dipole’, ‘charges’, ‘magmom’ and ‘magmoms’.
system_changes: list of str: List of what has changed since last calculation. Can be any combination of these six: ‘positions’, ‘numbers’, ‘cell’, ‘pbc’, ‘initial_charges’ and ‘initial_magmoms’.

Subclasses need to implement this, but can ignore properties and system_changes if they want. Calculated properties should be inserted into results dictionary like shown in this dummy example:

self.results = {'energy': 0.0,
                'forces': np.zeros((len(atoms), 3)),
                'stress': np.zeros(6),
                'dipole': np.zeros(3),
                'charges': np.zeros(len(atoms)),
                'magmom': 0.0,
                'magmoms': np.zeros(len(atoms))}

The subclass implementation should first call this implementation to set the atoms attribute.

set(**kwargs)

Set parameters like set(key1=value1, key2=value2, …).

A dictionary containing the parameters that have been changed is returned.

Subclasses must implement a set() method that will look at the chaneged parameters and decide if a call to reset() is needed. If the changed parameters are harmless, like a change in verbosity, then there is no need to call reset().

The special keyword ‘parameters’ can be used to read parameters from a file.

exception mff.calculators.SingleSpecies

class mff.calculators.ThreeBodySingleSpecies(r_cut, grid_3b, **kwargs)

A mapped 3-body calculator for ase

grid_3b¶: object – 3D Spline interpolator for the 3-body mapped grid

results¶: dict – energy and forces calculated on the atoms object

calculate(atoms=None, properties=('energy', 'forces'), system_changes=['positions', 'numbers', 'cell', 'pbc', 'initial_charges', 'initial_magmoms']): Do the calculation.

find_triplets()

Function that efficiently finds all of the valid triplets of atoms in the atoms object.

Returns:

array containing the indices of atoms belonging to any valid triplet.: Has shape T by 3 where T is the number of valid triplets in the atoms object
distances (array): array containing the relative distances of every triplet of atoms.: Has shape T by 3 where T is the number of valid triplets in the atoms object
positions (dictionary): versor of position w.r.t. the central atom of every atom indexed in indices.: Has shape T by 3 where T is the number of valid triplets in the atoms object

Return type: indices (array)

class mff.calculators.ThreeBodyTwoSpecies(r_cut, element0, element1, grids_3b, **kwargs)

A mapped 3-body 2-species calculator for ase

elements¶: list – List of ordered atomic numbers of the mapped two species system.

grids_3b¶: dict – contains the four 3D Spline interpolators relative to the 3-body mapped grids for element0-element0-element0, element0-element0-element1, element0-element1-element1 and element1-element1-element1 interactions.

results¶: dict – energy and forces calculated on the atoms object

calculate(atoms=None, properties=('energy', 'forces'), system_changes=['positions', 'numbers', 'cell', 'pbc', 'initial_charges', 'initial_magmoms']): Do the calculation.

find_triplets(atoms)