Finding the nearest atoms around a given atoms

[nguyen man]

Hi everybody,

I am new in MDAnalysis, I am trying to find the 10 atoms around Litium atom, here is a part in my code:

for ts in u.trajectory:
    box = u.dimensions[0:3]
    Li.pack_into_box(box=box)
    O.pack_into_box(box=box)
    Cl.pack_into_box(box=box)
    pos_Li = Li.positions
    pos_O = O.positions
    pos_Cl = Cl.positions
    tree = cKDTree(pos_O,pos_Li, pos_Cl,boxsize=box)

    dist, ids = tree.query(pos_Li,10)

but it did not work, the error "

TypeError: only size-1 arrays can be converted to Python scalars

"

could anyone help me with this problem?

Thanks very much.

Hong Man

[nguyen man]

[Johannes Zeman]

Hi Hong Man,

Can you provide some additional information about the implementation of cKDTree that you use?

If it's scipy.spatial.cKDTree, that explains the error (The second argument must be a scalar, see here: https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.cKDTree.html)

Apart from that, scipy.spatial.cKDTree is *not* suited for systems with periodic boundary conditions!

If you use MDAnalysis 18.0, I'd recommend something along these lines:

Finding the N closest oxygens around each lithium:

    N = 10

1. compute a distance array:

    distances = MDAnalysis.lib.distances.distance_array(Li.positions, O.positions, box=u.dimensions)

2. get the indices of the N nearest oxygen atoms:

    indices = numpy.argpartition(distances, N, axis=1)[:, :N]

3. create empty AtomGroup:

    O_around_Li = MDAnalysis.AtomGroup([], u)

4. Add oxygens to group using the indices we found:

    for idx in indices:

        O_around_Li += O[idx]

Beware: If you have multiple Li atoms, the obtained group might contain duplicate atoms (oxygen atoms that solvate two or more Li atoms)

Hope this helps!

Cheers,

Johannes

[nguyen man]

Hi Johannes,

Thank you very much for your help,

Yes, it's scipy.spatial.cKDTree

I will try what you suggested

Cheers,

Hong Man

Vào 23:55:58 UTC+2 Thứ Hai, ngày 01 tháng 10 năm 2018, Johannes Zeman đã viết: