# Find neighbors of an atom and calculating coordination numbers¶

In this example, we will read in a configuration from an MD simulation and then calculate the coordination number distribution. This example assumes that you read the basic example.

import pyscal.core as pc
import numpy as np
import matplotlib.pyplot as plt


The first step is setting up a system. We can create atoms and simulation box using the crystal_structures module. Let us start by importing the module.

import pyscal.crystal_structures as pcs

atoms, box = pcs.make_crystal('bcc', lattice_constant= 4.00, repetitions=[6,6,6])


The above function creates an bcc crystal of 6x6x6 unit cells with a lattice constant of 4.00 along with a simulation box that encloses the particles. We can then create a System and assign the atoms and box to it.

sys = pc.System()
sys.atoms = atoms
sys.box = box


## Calculating neighbors¶

We start by calculating the neighbors of each atom in the system. There are two ways to do this, using a cutoff method and using a voronoi polyhedra method. We will try with both of them. First we try with cutoff system - which has three sub options. We will check each of them in detail.

### Cutoff method¶

Cutoff method takes cutoff distance value and finds all atoms within the cutoff distance of the host atom.

sys.find_neighbors(method='cutoff', cutoff=4.1)


Now lets get all the atoms.

atoms = sys.atoms


let us try accessing the coordination number of an atom

atoms[0].coordination

14


As we would expect for a bcc type lattice, we see that the atom has 14 neighbors (8 in the first shell and 6 in the second). Lets try a more interesting example by reading in a bcc system with thermal vibrations. Thermal vibrations lead to distortion in atomic positions, and hence there will be a distribution of coordination numbers.

sys = pc.System()
sys.find_neighbors(method='cutoff', cutoff=3.6)
atoms = sys.atoms


We can loop over all atoms and create a histogram of the results

coord = [atom.coordination for atom in atoms]


Now lets plot and see the results

nos, counts = np.unique(coord, return_counts=True)
plt.ylabel("density")
plt.xlabel("coordination number")
plt.title("Cutoff method")


pyscal also has adaptive cutoff methods implemented. These methods remove the restriction on having a global cutoff. A distinct cutoff is selected for each atom during runtime. pyscal uses two distinct algorithms to do this - sann and adaptive. Please check the documentation for a explanation of these algorithms. For the purpose of this example, we will use the adaptive algorithm.

sys.find_neighbors(method='cutoff', cutoff='adaptive', padding=1.5)
atoms = sys.atoms
coord = [atom.coordination for atom in atoms]


Now let us plot

nos, counts = np.unique(coord, return_counts=True)
plt.ylabel("density")
plt.xlabel("coordination number")


The adaptive method also gives similar results!

## Voronoi method¶

Voronoi method calculates the voronoi polyhedra of all atoms. Any atom that shares a voronoi face area with the host atom are considered neighbors. Voronoi polyhedra is calculated using the Voro++ code. However, you do not need to install this specifically as it is linked to pyscal.

sys.find_neighbors(method='voronoi')


Once again, let us get all atoms and find their coordination

atoms = sys.atoms
coord = [atom.coordination for atom in atoms]


And visualise the results

nos, counts = np.unique(coord, return_counts=True)