overlap module

class overlap.mode_overlap(nmode, orbital_space, directory='../cube_files.1/', cube_prefix='wf')

Bases: object

This class computes the overlap integral between displaced structures along each normal modes. This code is parallelized with MPI4Py. Therefore, MPI4Py is needed.

Warning

Parallelization is done over normal modes. The chosen number of MPI tasks should not be within 1/2 of nmode and nmode. For example if there are 9 normal modes, the number of chosen MPI tasks should not be 5 to 8. Otherwise the calculation would crash due to improper load distribution.

Arguments:

nmode = Total number of normal modes; an integer.

orbital_space = A python list of lists. Each inside list must contain a set of orbital indices.

Example: orbital_space=[[66,67,68],[69,70]] would create 2 orbital(band) spaces. In the first space orbitals with indices 66-68 would be included, while in the second space 69-70 would be included. Usually, the orbitals which are degenerate in the undistorted structure should be kept in the same space.

directory = Directory path where wave function cube files are located.

cube_prefix = String Prefix of the cube files.

Returns:

Files with names orbital-0.overlap, orbital-1.overlap, … containing overlap matrices for 1st, 2nd,… orbital spaces, respectively.

class overlap.frame_overlap(ref_frame=1, start_frame=2, last_frame=5, inc_frame=1, directory='./', orbital_space=[[126, 127, 128]], cube_prefix='wf')

Bases: object

This class computes the overlap integral for a set of orbitals (defined by indices, file type: cube files) at a structure (usually from MD or Frozen phonon) and a reference structure (usually optimized structure)

Arguments:

ref_frame = Integer. Index of the reference frame within the cube files

start_frame = Integer. Index of the first frame whose overlap to be computed

last_frame = Integer. Index of the last frame whose overlap to be computed

inc_frame = Integer. Increment of frame indices

directory = String. Directory path where cube files are located.

cube_prefix = String Prefix of the cube files.

orbital_space = Same as mode_overlap class.

Returns:

Files with names orbital-0.overlap, orbital-1.overlap, … containing overlap matrices for 1st, 2nd,… orbital spaces, respectively.