leaflet-dask-array.py 文件源码

def Leaflet_finder(block, traj, cutoff, len_atom, len_chunks, block_id=None):
    id_0 = block_id[0]
    id_1 = block_id[1]

    block[:,:] = cdist(np.load(traj, mmap_mode='r')[id_0*len_chunks:(id_0+1)*len_chunks], np.load(traj, mmap_mode='r')[id_1*len_chunks:(id_1+1)*len_chunks]) <= cutoff 
    adj_list = np.where(block[:,:] == True)        
    adj_list = np.vstack(adj_list)

    adj_list[0] = adj_list[0]+id_0*len_chunks
    adj_list[1] = adj_list[1]+id_1*len_chunks

    if adj_list.shape[1] == 0:
        adj_list=np.zeros((2,1))

    graph = nx.Graph()
    edges = [(adj_list[0,k],adj_list[1,k]) for k in range(0,adj_list.shape[1])]
    graph.add_edges_from(edges)
    l = np.array({i: item for i, item in enumerate(sorted(nx.connected_components(graph)))}, dtype=np.object).reshape(1,1)

    return l