Package schrodinger :: Package application :: Package matsci :: Package nano :: Module xtal :: Class PBCBond

Class PBCBond

object --+
         |
        PBCBond

Class to manage a PBC bond, i.e. a long bond connecting two real atoms on opposite sides of a unit cell that is used in lieu of the bond between the real and image atoms.

Instance Methods

[hide private]

__init__(self, atom1, atom2, order, also_reg_bond)
Create an instance.

str

__repr__(self)
Define a class representation.

setDeltasToNeighboringCells(self, atom1_vec, atom2_vec, spanning_vectors)
Set two dictionaries, one for moving to neighboring cells ahead and one for moving behind.

tuple

getNeighborPBCBond(self, cell_indices, ncella, ncellb, ncellc, cell_size, cell_delta, tail_head)
Return a (tail, head) ordered tuple of atom indices for the neighboring PBC bond in the cell given by the cell delta.

offsetAtomData(self, offset)
Offset the atom data of this instance.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

PBC_BOND_THRESHOLD = 1e-3

PBC_BOND_KEY = 'b_matsci_PBC_bond'

ALSO_REG_BOND_KEY = 'b_matsci_also_reg_bond'

PBC_BOND_COLOR_KEY = 'i_m_color'

PBC_BOND_COLOR = 4

AHEAD = 'ahead'

BEHIND = 'behind'

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, atom1, atom2, order, also_reg_bond)
(Constructor)

Create an instance.

Parameters:

atom1 (int) - the first atom index of the bond
atom2 (int) - the second atom index of the bond
order (int) - the bond order
also_reg_bond (bool) - indicates whether this PBC bond is also a regular bond, meaning that one of the atoms of the PBC bond is covalently bound to two copies of the other atom, one inside the cell and one outside the cell

Overrides: object.__init__

repr(self)
(Representation operator)

Define a class representation.

Returns: str: string representation of the class
Overrides: object.__repr__

setDeltasToNeighboringCells(self, atom1_vec, atom2_vec, spanning_vectors)

Set two dictionaries, one for moving to neighboring cells ahead and one for moving behind. Keys are tuples of integer cell deltas and values are (tail, head) tuples giving a directionality of this PBC bond along the given direction.

Parameters:

atom1_vec (numpy.array) - vector to the first atom of the PBC bond
atom2_vec (numpy.array) - vector to the second atom of the PBC bond
spanning_vectors (dict) - keys are tuples of cell index triples, values are tuples of normalized spanning vectors for the cell and their original lengths

getNeighborPBCBond(self, cell_indices, ncella, ncellb, ncellc, cell_size, cell_delta, tail_head)

Return a (tail, head) ordered tuple of atom indices for the neighboring PBC bond in the cell given by the cell delta. If this cell is the first or last cell then it will wrap around to the ending or beginning cell, respectively.

Parameters:

cell_indices (tuple) - a triple of cell indices
ncella (int) - the number of cells along a
ncellb (int) - the number of cells along b
ncellc (int) - the number of cells along c
cell_size (int) - the number of atoms in a cell
cell_delta (tuple) - a triple of cell deltas which provide the neighboring cells location
tail_head (tuple) - provides the tail and head atom indices for this PBC bond given the cell delta

Returns: tuple

atom indices for the neighboring PBC bond

offsetAtomData(self, offset)

Offset the atom data of this instance.

Parameters:

offset (int) - the offset to use

Class PBCBond

__init__(self, atom1, atom2, order, also_reg_bond) (Constructor)

__repr__(self) (Representation operator)

setDeltasToNeighboringCells(self, atom1_vec, atom2_vec, spanning_vectors)

getNeighborPBCBond(self, cell_indices, ncella, ncellb, ncellc, cell_size, cell_delta, tail_head)

offsetAtomData(self, offset)

init(self, atom1, atom2, order, also_reg_bond)
(Constructor)

repr(self)
(Representation operator)