Pair Analysis Calculation

A pair analysis calculator was implemented where the atom position can be read from a POSCAR file or entered manually. The neighbor list and binning are calculated to build up the pairs list.

Example

>>> from debyetools.pairanalysis import pair_analysis
>>> formula = 'AaAaBbAa'
>>> cutoff = 10
>>> basis_vectors = np.array([[0,0,0], [.5,.5,0], [.5,0,.5], [0,.5,.5]])
>>> primitive_cell = np.array([[4,0,0] ,[0,4,0] ,[0,0,4]])
>>> pa_result = pair_analysis(formula, cutoff, basis_vectors, primitive_cell)
>>> distances , num_pairs_per_formula , combs_types = pa_result
>>> print('distances | # of pairs per type')
>>> print('          | '+'  '.join(['%s' for _ in combs_types])%tuple(combs_types))
>>> for d, n in zip( distances , num_pairs_per_formula ):
...    print(' %.6f ' % (d) + '| ' + ' '.join([' %.2f' for _ in n])%tuple(n))
...
distances | # of pairs per type
          | Aa-Aa  Aa-Bb  Bb-Bb
 2.828427 |  6.00  6.00  0.00
 4.000000 |  4.50  0.00  1.50
 4.898979 |  12.00  12.00  0.00
 5.656854 |  9.00  0.00  3.00
 6.324555 |  12.00  12.00  0.00
 6.928203 |  6.00  0.00  2.00
 7.483315 |  24.00  24.00  0.00
 8.000000 |  4.50  0.00  1.50
 8.485281 |  18.00  18.00  0.00
 8.944272 |  18.00  0.00  6.00
 9.380832 |  12.00  12.00  0.00
 9.797959 |  18.00  0.00  6.00

Source code

debyetools.pairanalysis.neighbor_list(size: ndarray, basis: ndarray, cell: ndarray, cutoff: float) → Tuple[ndarray, ndarray, ndarray, ndarray, ndarray][source]

calculate a list i, j, dij where i and j are a pair of atoms of indexes i and j, respectively, and dij is the distance between them.

Parameters

  • size (np.ndarray) – Number of times we are replicating the primitive cel

  • basis (np.ndarray) – atoms position within a single primitive cell

  • cell (np.ndarray) – the primitive cell

  • cutoff (float) – cut-off distance

Returns

D, I , J

Return type

Tuple[np.ndarray, np.ndarray, np.ndarray]

debyetools.pairanalysis.pair_analysis(atom_types, cutoff, basis, cell, prec=10, full=False)[source]

run a pair analysis of a crystal structure of almost any type of symmetry.

Parameters

  • atom_types (str) – the types of each atom in the primitive cell in the same order as the basis vectors.

  • cutoff (float) – cut-off distance

  • basis (np.ndarray) – atoms position within a single primitive cell

  • cell (np.ndarray) – the primitive cell

  • prec (int) – precision.

  • full (boolean) – if True, returns also data of ghost cells.

Returns

pair distance, pair number, pair types

Return type

Tuple[np.ndarray,np.ndarray,np.ndarray]