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Build Perovskite Structures from Ions
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Building Perovskite Structures from their Ions Components with pyrovskite.

This notebook demonstrates how to use the python package pyrovskite to build hypothetical structures using the ions components. We will create a hypothetical Dion-Jacobson perovskite structure using the cations extracted from the Halide Perovskite Ions database.

Let's start by installing the package and importing the necessary libraries.

In [1]:
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! pip install pyrovskite
! pip install pyrovskite
Requirement already satisfied: pyrovskite in /home/pepe_marquez/NOMAD/nomad/.pyenv/lib/python3.11/site-packages (1.0.0)
Requirement already satisfied: pymatgen in /home/pepe_marquez/NOMAD/nomad/.pyenv/lib/python3.11/site-packages (from pyrovskite) (2024.5.1)
Requirement already satisfied: ase in /home/pepe_marquez/NOMAD/nomad/.pyenv/lib/python3.11/site-packages (from pyrovskite) (3.22.1)
Requirement already satisfied: matplotlib>=3.1.0 in /home/pepe_marquez/NOMAD/nomad/.pyenv/lib/python3.11/site-packages (from ase->pyrovskite) (3.10.0)
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Requirement already satisfied: certifi>=2017.4.17 in /home/pepe_marquez/NOMAD/nomad/.pyenv/lib/python3.11/site-packages (from requests->pymatgen->pyrovskite) (2024.12.14)
Requirement already satisfied: mpmath<1.4,>=1.1.0 in /home/pepe_marquez/NOMAD/nomad/.pyenv/lib/python3.11/site-packages (from sympy->pymatgen->pyrovskite) (1.3.0)

[notice] A new release of pip is available: 24.0 -> 24.3.1
[notice] To update, run: pip install --upgrade pip
In [2]:
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import os

import ase.io
import os import ase.io

In this notebook we will be using already downloaded data from the Halide Perovskite Ions database. We will use a Methilammonium (MA) cation, 2-(2-azaniumylethyldisulfanyl)ethylazanium (AESE) as a separator, a Bromide (Br) anion, and a Tin (Sn) cation to build a Dion-Jacobson perovskite structure.

You can also retrieve further structures using the NOMAD API.

In [9]:
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if not os.path.isdir('builder_outputs'):
    os.mkdir('builder_outputs')

from pyrovskite.builder import *

A = ase.io.read('CNH6.xyz')
Ap = ase.io.read('C2NH7S.xyz')
if not os.path.isdir('builder_outputs'): os.mkdir('builder_outputs') from pyrovskite.builder import * A = ase.io.read('CNH6.xyz') Ap = ase.io.read('C2NH7S.xyz')
In [ ]:
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from ase.visualize import view
from pyrovskite.builder import make_dj

dion_jacobson = make_dj(
    Ap=Ap,
    A=A,
    B='Sn',
    X='Br',
    n=2,
    BX_dist=2.8,
    Ap_Rx=0,
    Ap_Ry=90,
    Ap_Rz=0,
    penet=-0.2,
    Bp='Sn',
)
from ase.visualize import view from pyrovskite.builder import make_dj dion_jacobson = make_dj( Ap=Ap, A=A, B='Sn', X='Br', n=2, BX_dist=2.8, Ap_Rx=0, Ap_Ry=90, Ap_Rz=0, penet=-0.2, Bp='Sn', )

Let's increase the system size and visualize the structure.

In [8]:
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large_dion_jacobson = dion_jacobson.repeat((4, 2, 2))
view(large_dion_jacobson, viewer='x3d')
large_dion_jacobson = dion_jacobson.repeat((4, 2, 2)) view(large_dion_jacobson, viewer='x3d')
Out[8]:
ASE atomic visualization

Great! Save your structure and feel free to bring it to the next step to relax the structure with your favorite DFT code or your or machine learning model. Explore the pyrovskite package and build your own structures using the ions components from the Halide Perovskite Ions database.

In [ ]:
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dion_jacobson.write('builder_outputs/dion_jacobson.cif')
dion_jacobson.write('builder_outputs/dion_jacobson.cif')
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