do_binning#
- diffsims.utils.discretise_utils.do_binning(x, loc, Rmax, d, GPU)[source]#
Utility function which takes in a mesh, atom locations, atom radius and minimal grid-spacing and returns a binned array of atom indices.
- Parameters:
x (list [np.ndarray [float]], of shape [(nx,), (ny,), ...]) – Dictates the range of the box over which to bin atoms.
loc (np.ndarray, (n, 3)) – Atoms to bin.
Rmax (float > 3) – Maximum radius of an atom (rounded up to 3).
d (list of float > 0) – The finest permitted binning.
GPU (bool) – If True then constrains to memory of GPU rather than RAM.
- Returns:
subList (np.ndarray [int]) – subList[i0,i1,i2] is a list of indices [j0, j1, …, jn, -1,…] such that the only atoms which are contained in the box: [x[0].min()+i0*r,x[0].min(),+(i0+1)*r] x [x[1].min()+i1*r,x[1].min(),+(i1+1)*r]…
r (np.ndarray [float]) – Size of each bin.
mem (int) – Upper limit of memory in bytes.