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distance_matrix

esta.general.distance_matrix

distance_matrix_pbc(filename=None)

find distance matrix for poscar file with PBC along all?? directions

distance_matrix_pbc_(atm_position, cell)

find distance matrix for given atom coord and cell vectors atm_position: array of rank 2 cell: array of rank 2; e.g. np.array([ [1., 2., 3.0], # lv1 [23, 32, 5.0], # lv2 [10.43, 1.32, 43.0]]) # lv3

distance_matrix_xyz(filename=None)

find distance matrix for the xyz file data

distance_matrix_xyz_(atm_position)

find distance matrix for the given atomic coords

connection_matrix(atm_position, atm_syml, scale=None, dist_add=None)

given atomic positions, atomic symobls, and atomic radii scale, find the connectivy matrix for atomic system

distance_atom_pairs(filename=None)

find distance between atom pairs given poscar data file

Warning: 
better MIC ..need to be done (already done ..see py files in general dir or externalBag or aseBag ...streamline things****)

Returns:

  • dist: ndarry –

    distance matrix or rank 2 tensor or rank2 array

  • note ( : ) –

    BEtter see ... stefano curtalo paper on lattice and space gps ..GOOD..SK!! ... on other molecular dynamics book .. ??

  • note ( : ) –

    see basics of min imgae conventions ... paper of Efficient Coding of the Minimum Image Convention By Ulrich K. Deiters ∗ Institute of Physical Chemistry, University of Cologne, Luxemburger Str. 116, 50939 Köln, Germany