Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

Package for investigation of 2D van der Waals heterostructures' lattices

Project description

supercell-core

Package for investigation of mulitlayer 2D heterostructures lattices

Author: Tomasz Necio, University of Warsaw

Copyright (C) 2019 University of Warsaw

Installation:

pip3 install supercell-core --user

Documentation

https://readthedocs.org/projects/supercell-core/

Usage example

# Load supercell_core
import supercell_core as sc

# Read NiPS3 data from a POSCAR file into `nips3` Lattice object
# We need to provide names of chemical elements because they don't have to
# appear in POSCAR, but supercell-core needs them
# This will only work if you actually have a file named "POSCAR_nips3",
# you can copy it from /supercell_core/resources/vasp/NiPS3 directory
nips3 = sc.read_POSCAR("POSCAR_nips3", ["Ni", "P", "S"])

# Let's create `graphene` Lattice object by hand
graphene = sc.lattice()
graphene.set_vectors([2.133, -1.23], [2.133, 1.23])
# atom "C" at position (0, 0, 0)
graphene.add_atom("C", (0, 0, 0))

# Methods can be chained
nips3_with_a_rouge_atom = sc.lattice().set_vectors(*nips3.vectors()) \
                            .add_atom("U", (0, 0, 1), spin=(0, 0, 1))

# Define heterostructure
h = sc.heterostructure().set_substrate(graphene).add_layer(nips3)

# Calculate strain tensor for particular supercell configuration
# (see help(sc.heterostructure()) for details)
M = [[1, -9], [8, 1]]
theta = 21.9 * sc.DEGREE
res = h.calc(M=M, thetas=[theta])
print(res.strain_tensors()) # Use help(res) to see all public methods of `Result`

# Optimise strain to find best supercell, with max repetition along any
# axis <= 12 substrate unit cells, and relative angle only from 0 to 7 degrees
# with resolution 0.1 deg
res = h.opt(max_el=12, thetas=[np.arange(0, 7*sc.DEGREE, 0.1*sc.DEGREE)])
superlattice = res.superlattice() # Lattice object
superlattice.save_POSCAR("POSCAR_sc") # save to file

fig, ax = superlattice.draw()
fig.show() # Show unit cell using matplotlib library

# To learn more use built-in documentation, e.g.:
help(nips3) # shows help on Lattice object when Python is in interactive mode (use 'q' to quit)
print(help(nips3)) # prints to stdout

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for supercell-core, version 0.0.3
Filename, size File type Python version Upload date Hashes
Filename, size supercell_core-0.0.3-py3-none-any.whl (48.2 kB) File type Wheel Python version py3 Upload date Hashes View hashes
Filename, size supercell_core-0.0.3.tar.gz (30.6 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page