Modifying a POSCAR File: Scaling, Supercells, and Defects#

In this example, we’ll demonstrate several modifications on a POSCAR file using the pyprocar package:

Scaling the lattice vectors to reduce vacuum space.
Generating a supercell.
Introducing defects by changing atom types.

Let’s get started!

import os
from itertools import product
import pyprocar.pyposcar as p
import numpy as np
import pyvista as pv
from pyprocar.utils import ROOT

data_dir=os.path.join(ROOT,'data','examples','PyPoscar','01-poscar_utils')
# You do not need this. This is to ensure an image is rendered off screen when generating exmaple gallery.
pv.OFF_SCREEN = True

Utility function for creating GIF visualizations#

def create_gif(atoms, labels, unit_cell, save_file):
    plotter = pv.Plotter()
    title = save_file.split(os.sep)[-1].split('.')[0]
    plotter.add_title(title)
    plotter.add_mesh(unit_cell.delaunay_3d().extract_feature_edges(), color='black', line_width=5, render_lines_as_tubes=True)
    plotter.add_point_labels(points=atoms.points, labels=labels, show_points=False, always_visible=True)
    plotter.add_mesh(atoms, scalars='atoms', point_size=30, render_points_as_spheres=True, show_scalar_bar=False)
    path = plotter.generate_orbital_path(n_points=36)
    plotter.open_gif(os.path.join(data_dir, save_file))
    plotter.orbit_on_path(path, write_frames=True, viewup=[0, 0, 1], step=0.05)
    plotter.close()

Scaling Vacuum Space in the Lattice#

a = p.poscarUtils.poscar_modify(os.path.join(data_dir, "POSCAR-9AGNR.vasp"), verbose=False)
print('the lattice has too much vacuum space\n', a.p.lat)
print('I will shrink these vector by 1/3')

scaling = np.array([1, 1/3, 1/3])
a.scale_lattice(factor=scaling, keep_cartesian=True)
a.write(os.path.join(data_dir,'POSCAR-9AGNR-smaller.vasp'))
print('New lattice\n', a.p.lat)

tmp_a = p.Poscar(os.path.join(data_dir, "POSCAR-9AGNR.vasp"))
tmp_a.parse()

# Convert positions to Cartesian coordinates for visualization
atoms_before = pv.PolyData(np.dot(tmp_a.dpos, tmp_a.lat))
atoms_before['atoms'] = tmp_a.elm
labels_before = [elm for elm, point in zip(tmp_a.elm, tmp_a.dpos)]
# Define the unit cell using lattice vectors
unit_cell_comb = list(product([0, 1], repeat=3))
unit_cell = np.array([comb[0]*tmp_a.lat[0] + comb[1]*tmp_a.lat[1] + comb[2]*tmp_a.lat[2] for comb in unit_cell_comb])
unit_cell_before = pv.PolyData(unit_cell)

tmp_a = p.Poscar(os.path.join(data_dir, "POSCAR-9AGNR-smaller.vasp"))
tmp_a.parse()

# Convert positions to Cartesian coordinates for visualization
atoms_after = pv.PolyData(np.dot(tmp_a.dpos, tmp_a.lat))
atoms_after['atoms'] = tmp_a.elm
labels_after = [elm for elm, point in zip(tmp_a.elm, tmp_a.dpos)]
# Define the unit cell using lattice vectors
unit_cell_comb = list(product([0, 1], repeat=3))
unit_cell = np.array([comb[0]*tmp_a.lat[0] + comb[1]*tmp_a.lat[1] + comb[2]*tmp_a.lat[2] for comb in unit_cell_comb])
unit_cell_after = pv.PolyData(unit_cell)

create_gif(atoms=atoms_before, labels=labels_before, unit_cell=unit_cell_before, save_file='atoms_before_scaling.gif')
create_gif(atoms=atoms_after, labels=labels_after, unit_cell=unit_cell_after, save_file='atoms_after_scaling.gif')

the lattice has too much vacuum space
 [[ 4.3878  0.      0.    ]
 [ 0.     60.      0.    ]
 [ 0.      0.     71.726 ]]
I will shrink these vector by 1/3
New lattice
 [[ 4.3878  0.      0.    ]
 [ 0.     20.      0.    ]
 [ 0.      0.     23.9087]]

Creating a Supercell#

print('\n\nNow I will make an supercell 3x1x1')
b = p.poscarUtils.poscar_supercell(os.path.join(data_dir, "POSCAR-9AGNR-smaller.vasp"), verbose=False)
size = np.array([[3,0,0],[0,1,0],[0,0,1]])
b.supercell(size = size)
b.write(os.path.join(data_dir, 'POSCAR-9AGNR-311.vasp'))
print('It was saved as POSCAR-9AGNR-311.vasp')


tmp_a = p.Poscar(os.path.join(data_dir, "POSCAR-9AGNR-smaller.vasp"))
tmp_a.parse()

# Convert positions to Cartesian coordinates for visualization
atoms_before = pv.PolyData(np.dot(tmp_a.dpos, tmp_a.lat))
atoms_before['atoms'] = tmp_a.elm
labels_before = [elm  for elm, point in zip(tmp_a.elm, tmp_a.dpos)]
# Define the unit cell using lattice vectors
unit_cell_comb = list(product([0, 1], repeat=3))
unit_cell = np.array([comb[0]*tmp_a.lat[0] + comb[1]*tmp_a.lat[1] + comb[2]*tmp_a.lat[2] for comb in unit_cell_comb])
unit_cell_before = pv.PolyData(unit_cell)

tmp_a = p.Poscar(os.path.join(data_dir, "POSCAR-9AGNR-311.vasp"))
tmp_a.parse()

# Convert positions to Cartesian coordinates for visualization
atoms_after = pv.PolyData(np.dot(tmp_a.dpos, tmp_a.lat))
atoms_after['atoms'] = tmp_a.elm
labels_after = [elm for elm, point in zip(tmp_a.elm, tmp_a.dpos)]
# Define the unit cell using lattice vectors
unit_cell_comb = list(product([0, 1], repeat=3))
unit_cell = np.array([comb[0]*tmp_a.lat[0] + comb[1]*tmp_a.lat[1] + comb[2]*tmp_a.lat[2] for comb in unit_cell_comb])
unit_cell_after = pv.PolyData(unit_cell)

create_gif(atoms=atoms_before, labels=labels_before, unit_cell=unit_cell_before, save_file='atoms_before_supercell.gif')
create_gif(atoms=atoms_after, labels=labels_after, unit_cell=unit_cell_after, save_file='atoms_after_supercell.gif')

Now I will make an supercell 3x1x1
It was saved as POSCAR-9AGNR-311.vasp

Introducing Defects#

print('\n\nFinally I want to create a defect by changing atoms #28, #29 to B and N, respectively')
c = p.poscarUtils.poscar_modify(os.path.join(data_dir, "POSCAR-9AGNR-311.vasp"), verbose=False)
c.change_elements(indexes = [28,29],
                  newElements = ['B', 'N'],
                  human = True) # Mind, without `human`, first is 0, second is 1, ...
c.write(os.path.join(data_dir, 'POSCAR-AGNR-defect.vasp'))
print('It was saves as POSCAR-AGNR-defect.vasp')


tmp_a = p.Poscar(os.path.join(data_dir, "POSCAR-9AGNR-311.vasp"))
tmp_a.parse()

# Convert positions to Cartesian coordinates for visualization
atoms_before = pv.PolyData(np.dot(tmp_a.dpos, tmp_a.lat))
atoms_before['atoms'] = tmp_a.elm
labels_before = [elm for elm, point in zip(tmp_a.elm, tmp_a.dpos)]
# Define the unit cell using lattice vectors
unit_cell_comb = list(product([0, 1], repeat=3))
unit_cell = np.array([comb[0]*tmp_a.lat[0] + comb[1]*tmp_a.lat[1] + comb[2]*tmp_a.lat[2] for comb in unit_cell_comb])
unit_cell_before = pv.PolyData(unit_cell)

tmp_a = p.Poscar(os.path.join(data_dir, "POSCAR-AGNR-defect.vasp"))
tmp_a.parse()

# Convert positions to Cartesian coordinates for visualization
atoms_after = pv.PolyData(np.dot(tmp_a.dpos, tmp_a.lat))
atoms_after['atoms'] = tmp_a.elm
labels_after = [elm for elm, point in zip(tmp_a.elm, tmp_a.dpos)]
# Define the unit cell using lattice vectors
unit_cell_comb = list(product([0, 1], repeat=3))
unit_cell = np.array([comb[0]*tmp_a.lat[0] + comb[1]*tmp_a.lat[1] + comb[2]*tmp_a.lat[2] for comb in unit_cell_comb])
unit_cell_after = pv.PolyData(unit_cell)

create_gif(atoms=atoms_before, labels=labels_before, unit_cell=unit_cell_before, save_file='atoms_before_defect.gif')
create_gif(atoms=atoms_after, labels=labels_after, unit_cell=unit_cell_after, save_file='atoms_after_defect.gif')


print('')

print('Loading an AGNR with a defects in the last two entries')
a = p.poscar.Poscar(os.path.join(data_dir,"POSCAR-AGNR-defect.vasp"), verbose=False)
a.parse()

print('The nearest neighbors of the defects are:')
nn=p.latticeUtils.Neighbors(a)
print(a.elm[-2], ':', a.Ntotal-2, '-->', nn.nn_list[-2])
print(a.elm[-1], ':', a.Ntotal-1, '-->', nn.nn_list[-1])

Finally I want to create a defect by changing atoms #28, #29 to B and N, respectively
It was saves as POSCAR-AGNR-defect.vasp

Loading an AGNR with a defects in the last two entries
The nearest neighbors of the defects are:
B : 64 --> [22, 26, 65]
N : 65 --> [25, 27, 64]

Total running time of the script: (0 minutes 23.325 seconds)

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