HyperdynamicsBondFormingDistortion

Included in QATK.Dynamics

class HyperdynamicsBondFormingDistortion(first_atom_tag, second_atom_tag, bond_minimum=None, bond_maximum=None, fuzz_factor=None, atom_search_radius=None, ignore_bonded_atoms_depth=None, first_atom_max_coordination=None, second_atom_max_coordination=None)

Class for calculating bond forming distortions used in a hyperdynamics simulation.

Parameters:

• first_atom_tag (str) – Tag giving the set of atoms which are possibly breaking other bonds to form a new bond.

• second_atom_tag (str) – Tag giving the set of atoms that are forming a new bond.

• bond_minimum (PhysicalQuantity of type length) – The minimum length of the bond.
  Default: 1.5 Angstrom

• bond_maximum (PhysicalQuantity of type length) – The maximum length of the bond.
  Default: 4 Angstrom

• fuzz_factor (float) – The fuzz factor used in detecting bonds in the configuration.
  Default: 1.1

• atom_search_radius (PhysicalQuantity of type length) – The radius within which to search for connecting atoms.
  Default: 4 Angstrom

• ignore_bonded_atoms_depth (int) – Number of bonds to traverse in finding atoms to ignore in searching for atoms. A value of 1 means that just atoms bonded to the leaving atom are ignored, 2 also ignores atoms that form angles with the leaving atom, ect. A value of 0 means that no atoms are ignored regardless of their bonding.
  Default: 2

• first_atom_max_coordination (int | None) – The maximum coordination number of the first atom. When the atom reaches this coordination number it is not considered for forming and initial bond. None turns off this check and always includes atoms regardless of their coordination number.
  Default: None

• second_atom_max_coordination (int | None) – The maximum coordination number of the first atom. When the atom reaches this coordination number it is not considered for forming and initial bond. None turns off this check and always includes atoms regardless of their coordination number.
  Default: None

atomSearchRadius()

Returns:

The atom search radius.

Return type:

PhysicalQuantity of type length

bondMaximum()

Returns:

The maximum bond length.

Return type:

PhysicalQuantity of type length

bondMinimum()

Returns:

The minimum bond length.

Return type:

PhysicalQuantity of type length

firstAtomMaxCoordination()

Returns:

The coordination number of a saturated first atom that cannot act as a bonded atom.

Return type:

int | None

firstAtomTag()

Returns:

The first atom tag.

Return type:

str

fuzzFactor()

Returns:

The fuzz factor.

Return type:

float

ignoreBondedAtomsDepth()

Returns:

Number of bonds to traverse in finding atoms to ignore in searching for atoms.

Return type:

int

numberOfVariables()

Returns:

The number of indexed geometric coordinates being accelerated

Return type:

int

secondAtomMaxCoordination()

Returns:

The coordination number of a saturated second atom that cannot act as a bonded atom.

Return type:

int | None

secondAtomTag()

Returns:

The second atom tag.

Return type:

str

uniqueString()

Return a unique string representing the state of the object.