autoconnect

class libra_py.autoconnect.TestAutoconnect(methodName='runTest')

Docs

test_1()

Diatomic

test_2()

Triatomic

libra_py.autoconnect.autoconnect(R, MaxCoord, params)

Parameters

• R (list of VECTOR objects) – The atomic coordinates of the system [ units: arbitrary ]

• MaxCoord (list of ints) – Maximal coorination numbers of each atom

• params (dictionary) –

  Parameters controlling the execution of this function

  • params[“Rcut”] ( double ): The maximal radius of connectivity [ units: same as R, default: 0.0 ]

  • params[“tv1”] ( VECTOR ): unit cell translation vector a [ units: same as R ]

  • params[“tv2”] ( VECTOR ): unit cell translation vector b [ units: same as R ]

  • params[“tv3”] ( VECTOR ): unit cell translation vector c [ units: same as R ]

  • params[“pbc_opt”] ( string ): what type of periodicity to assume.

    Options: “a”, “b”, “c”, “ab”, “ac”, “bc”, “abc”, “none” [ default: None ]

  • params[“opt”] ( int ): Option to obey maximal coordination number:

    • 0: the connected atoms in a pair have to obey both the coordination numbers

      Some of the atoms may stay undercoordinated. This is the consistent scheme in the sense that if A is connected to B, then B is necessarily connected to A [default]

    • 1: treat the MaxCoord as the minimal coordination number each atom should attain.

      Some atoms may be overcoordinated.

  • params[“verbosity”] ( int ): Flag to control the amount of the printout [ default: 0 ]

Returns

( res, line, unsorted_pairs_out ), where:

• res ( list of lists [ res[i][0], res[0][1] ] ), where

  • res[i][0] ( int ): index of the atom

  • res[i][1] ( list of ints ): indices of the atoms that are connected to res[i][0]

• line ( string ): the connectivity information in the .ent format

• unsorted_pairs_out ( same type as `res`): same as `res`, but not sorted

Return type

tuple

libra_py.autoconnect.find_undercoordinated_atoms(res, MaxCoord)

Parameters

• res (list of lists [ res[i][0], res[0][1] ]) –

  • res[i][0] ( int ): index of the atom

  • res[i][1] ( list of ints ): indices of the atoms that are connected to res[i][0]

  This would typically be the first output of the `autoconnect` function

• MaxCoord (list of ints) – Maximal coorination numbers of each atom

Returns

out, such that:

out[i][0] - is the index of the i-th undercoordinated atom out[i][1] - is the number of dangling bonds on the i-th atom

Return type

(list)