Interaction#
The interaction module contains functions for generating interaction matrices.
- anisotropy(dx, dy, dz)[source]#
Easy axes components.
- Parameters:
- dx, dy, dz2d array
Separation distance vector.
- Returns:
- uxx, uyy, uzz, uyz, uxz, uxy2d array
Components of easy axes.
- atom_pairs_distance(rx, ry, rz, nu, nv, nw, n_atm, A, tol=0.001)[source]#
Atom pairs.
- Parameters:
- rx, ry, rz1d array
Atomic positions.
- nu, nv, nwint
Supercell size.
- n_atmint
Number of unit cell atoms.
- A2d array, 3x3
Real space crystal axis to Cartesian transformation matrix.
- tolfloat, optional
Tolerance of distances for unique pairs. Default is
1e-3.
- Returns:
- dx, dy, dz1d array
Separation distance vector.
- i, j1d array, int
Coordinate pairs.
- inverse1d array, int
Indices of the unique pair distances array that reconstruct all pairs.
- bonds(pair_info, u, v, w, A, tol=0.001)[source]#
Generate bond pairs.
- Parameters:
- pair_infodict
Pair information for constructing bonds.
- u, v, w1d array
Fractional coordinates.
- atm1d array, str
Atoms, ions, or isotopes.
- A2d array, 3x3
Real space crystal axis to Cartesian transformation matrix.
- tolfloat, optional
Tolerance of distances for unique pairs. The default is
1e-3.
- Returns:
- dx, dy, dz2d array
Separation distance vector.
- img_i, img_j, img_k2d array, int
Indices of cell-pairs.
- atm_ind2d array, int
Indices of atom-pairs.
- pair_inv2d array, int
Indices of inverse-pairs.
- pair_ind2d array, int
Indices of bond-pairs.
- pair_trans2d array, int
Indices of transpose-pairs.
- charge_charge_matrix(rx, ry, rz, nu, nv, nw, n_atm, A, B, R, tol=0.001)[source]#
Charge-charge matrix.
- Parameters:
- rx, ry, rz1d array
Atomic positions.
- nu, nv, nwint
Supercell size.
- n_atmint
Number of unit cell atoms.
- A2d array, 3x3
Real space crystal axis to Cartesian transformation matrix.
- B2d array, 3x3
Reciprocal-space crystal axis to Cartesian transformation matrix.
- R2d array, 3x3
Rotation matrix between real and reciprocal-space Cartesian axes.
- tolfloat, optional
Tolerance of distances for unique pairs. Default is
1e-3.
- Returns:
- Qij1d array
Charge-charge matrix. Array of size
n*(n+1)//2.
- charge_dipole_matrix(rx, ry, rz, nu, nv, nw, n_atm, A, B, R, tol=0.001)[source]#
Charge-dipole matrix.
- Parameters:
- rx, ry, rz1d array
Atomic positions.
- nu, nv, nwint
Supercell size.
- n_atmint
Number of unit cell atoms.
- A2d array, 3x3
Real space crystal axis to Cartesian transformation matrix.
- B2d array, 3x3
Reciprocal-space crystal axis to Cartesian transformation matrix.
- R2d array, 3x3
Rotation matrix between real and reciprocal-space Cartesian axes.
- tolfloat, optional
Tolerance of distances for unique pairs. Default is
1e-3.
- Returns:
- Qijk2d array
Charge-dipole matrix. Array of shape
n*(n+1)//2x3.
- dipole_dipole_matrix(rx, ry, rz, nu, nv, nw, n_atm, A, B, R, tol=0.001)[source]#
Dipole-dipole matrix.
- Parameters:
- rx, ry, rz1d array
Atomic positions.
- nu, nv, nwint
Supercell size.
- n_atmint
Number of unit cell atoms.
- A2d array, 3x3
Real space crystal axis to Cartesian transformation matrix.
- B2d array, 3x3
Reciprocal-space crystal axis to Cartesian transformation matrix.
- R2d array, 3x3
Rotation matrix between real and reciprocal-space Cartesian axes.
- tolfloat, optional
Tolerance of distances for unique pairs. Default is
1e-3.
- Returns:
- Qijkl2d array,
Dipole-dipole matrix. Array of shape
n*(n+1)//2x6.
- pairs(u, v, w, atm, A, extend=False)[source]#
Generate pairs.
- Parameters:
- u, v, w1d array
Fractional coordinates.
- atm1d array, str
Atoms, ions, or isotopes.
- A2d array, 3x3
Real space crystal axis to Cartesian transformation matrix.
- extendbool, optional
Extend beyond one unit cell. The default is
False.
- Returns:
- pair_infodict
Pair information for constructing bonds.
- spatial_wavevector(nu, nv, nw, n_atm, B, R)[source]#
Spatial wavevector.
- Parameters:
- nu, nv, nwint
Supercell size.
- n_atmint
Number of unit cell atoms.
- B2d array, 3x3
Reciprocal-space crystal axis to Cartesian transformation matrix.
- R2d array, 3x3
Rotation matrix between real and reciprocal-space Cartesian axes.
- Returns:
- Gx, Gy, Gz1d array
Wavevector components.