Neighborlist building routine for molecular dynamics

This routine returns interaction pairs for a given set of atoms in 3D space.

Linked cell algorithm is used, therefore, the computational cost is linear vs. the number of atoms.

Periodic boundary condition can be activated as an option.

A cubic region should be defined for generating the neighborlist.

Atomic coordinates can be ONLY in 3D format, as row vectors.

% [nebrTab, nebrLen] = md_neighlist_cube( x, nx, rc, srgdat, bctyp, frc) %
% ----------------------------------------------------------------------
% Create neighbor list for atomic system in a cubic %region
% WZ. Shan
%-----------------------------------------------------------------------
% input:
% x : atom coords, [ px, py, pz]
% nx : num. of atoms, = size( x, 1)
% rc : cutoff radius
% srgdat : region data [ srg_o(1:3), W, H, D]
% : [ srg_o(1:3), W, H, D, x, y, z] if bctyp == 2,
% srgdat defines the cubic region, where
% srg_o: coordinates of the lower-left-back corner
% [W, H, D]: dimension of the cube in x,y,z-direction.
%
% bctyp : types of boundary, 1: free, 2: periodic
% frc : cell size factor( optional)
% output:
% nebrTab : interaction pairs, [p1, p2]
% nebrLen : size( nebrTab, 1)
% ncell : global cell coordinates
% id_cell : cell coordinates