I was trying to analyze the result obtained by using pymatgen.analysis.local_env
module by using min_dist approach by using following script:
from pymatgen.analysis.local_env import
structure_from_cif = Structure.from_file("mp-685151TiO.cif")
neighbor_list = []
for i in range(len(structure_from_cif.species)):
neighbors = get_neighbors_of_site_with_index(structure_from_cif, i, approach = "min_dist", delta = 0.3, cutoff= 3)
neighbor_list.append([str(structure_from_cif.species[i])+str(i), str(neighbors)])
I get the following output a part of which is shown below. I understand that the first coordinates in () are the Cartesian coordinates. I thought the coordinates in [] are of periodic image but I am in doubt when I analyze them. Could any one please help me to understand the actual meaning and significance of those coordinates in [], for example [-0.3863, -0.2759, 1.3863] in first case and so on.
['Ti0', '[PeriodicSite: O (-0.8310, -0.7224, 22.9070) [-0.3863, -0.2759, 1.3863], PeriodicSite: O (-1.3193, 1.8955, 23.8405) [-0.3863, 0.7241, 0.3863], PeriodicSite: O (1.6691, -0.7224, 24.2132) [0.6137, -0.2759, 1.3863], PeriodicSite: O (1.1809, 1.8955, 25.1466) [0.6137, 0.7241, 0.3863]]'], ['Ti1', '[PeriodicSite: O (-1.3145, -0.7079, 26.8777) [-0.5786, -0.2704, 1.5786], PeriodicSite: O (-1.8028, 1.9100, 27.8111) [-0.5786, 0.7296, 0.5786], PeriodicSite: O (1.1856, -0.7079, 28.1838) [0.4214, -0.2704, 1.5786], PeriodicSite: O (0.6974, 1.9100, 29.1173) [0.4214, 0.7296, 0.5786], PeriodicSite: O (-1.0443, -0.0383, 29.4055) [-0.4205, -0.0146, 1.4205]]'], ['Ti2', '[PeriodicSite: O (-1.4562, 0.0380, 33.2391) [-0.5796, 0.0145, 1.5796], PeriodicSite: O (-1.9444, 2.6559, 34.1725) [-0.5796, 1.0145, 0.5796], PeriodicSite: O (1.0440, 0.0380, 34.5452) [0.4204, 0.0145, 1.5796], PeriodicSite: O (0.5557, 2.6559, 35.4787) [0.4204, 1.0145, 0.5796], PeriodicSite: O (-1.1854, 0.7081, 35.7657) [-0.4213, 0.2705, 1.4213]]'],
The second set of co-ordinates in square brackets are the fractional co-ordinates of that site with respect to the Structure's Lattice. Fractional co-ordinates wrap around periodic boundaries, so:
[-0.3863, -0.2759, 1.3863]
is equivalent to these co-ordinates in the [0,1) range:
[0.6137, 0.7241, 0.3863]
For technical reasons, fractional co-ordinates are not wrapped to [0, 1) by default however, since this information is meaningful for some simulation code. For practical purposes however, the easiest way to interpret them is in the [0, 1) range.