leaflet-dask-delayed.py 文件源码

def Leaflet_finder(traj, i, j,len_atom, cutoff):
    atom = np.load(traj)
    g1 = atom[i:i+len_chunks]
    g2 = atom[j:j+len_chunks]
    block = np.zeros((len(g1),len(g2)),dtype=float)
    block[:,:] = cdist(g1, g2) <= cutoff
    S = scipy.sparse.dok_matrix((len_atom, len_atom))
    S[i:i+len_chunks, j:j+len_chunks] = block
    leaflet = sorted(nx.connected_components(nx.Graph(S>0)), key=len, reverse=True)
    l_connected = [] # Keep only connected components
    for lng in range(len(leaflet)):
        if(len(leaflet[lng])>1):l_connected.append(leaflet[lng])

    return list(l_connected)