My blog - Literature summary

Please the eye and plague the heart

贪图-时快活, 必然留下隐患

Updated time: 06/24 2024.

Find the heterostructure

Tools

see Tool - Summary

Some talks / advices

• Issue

ASE/Pymatgen

• stack/interface function - only used for some similar structure (lattice type, constant, orientation), but could found a minimal force on the interface with specified interlayer space

VASPKIT

When I use VASPKIT to generate a heterostructure, I found some interesting thing.

1. VASPKIT can’t fix the lattice constant of upper or lower material.
2. I found over-distorted material in some model of extremely small angle, causing lose its original lattice information like HCP/FCC/… I think it’s because the VASPKIT didn’t set a tolerance of angle mismatch, and it has important influence in this extremely small angle model.

VASPKIT First-Cup

Because I want to fix the lattice constant of substrates, the VASPKIT couldn’t meet this requirement.

The code of The First Prize - LUOJUN maybe could do it.

Dependency

1. VASPKIT = 0.73
2. Python3
3. some python packages

Error

1. VASPKIT must ~0.73, because the bash command has run VASPKIT 406. This command is 406 Converte POSCAR to other format -> POSCAR -> 4061 POSCAR with Cartesian Coordinates in 0.73 version, but has been changed now.

1. The POSCAR can’t has 0.00000000 direct coordinate, if it has, this procedure will output some unexpected value errors.

Parameters

1. v is controlling the shifting basic vector, maybe could be using to search more heterostructures.

Hetbuilder

It has been installed !!!!

Installation

% python3 3.11.2
python3 -m venv /../../env
% activate
source /../../env/bin/activate
% get root
sudo apt-get update && sudo apt install -y build-essential cmake git python3-dev python3-tk libsymspg-dev
git clone https://github.com/hongyi-zhao/hetbuilder.git && cd hetbuilder
pip install -r requirements.txt
pip install .

The Coincidence lattices theory maybe too strict for high mismatched film/substrate system to search a minimal configuration (like vaspkit, ~45 atoms).

The most output has > 200 atoms, although we enlarge the t parameter - space in Angstrom unit.

usage (see more mymetal/build/findhetero.py)

hetbuilder --help
hetbuilder build --help
hetbuilder -N 2 -t 2 -w 0 CONTCAR_SiO_film CONTCAR_FCC_film

from hetbuilder.algorithm import CoincidenceAlgorithm
from hetbuilder.plotting import InteractivePlot
from ase.io.vasp import read_vasp, write_vasp

bottom = read_vasp('CONTCAR_SiO_film')
top = read_vasp('CONTCAR_FCC_film')
# we set up the algorithm class
alg = CoincidenceAlgorithm(bottom, top)
# we run the algorithm for a choice of parameters
results = alg.run(Nmax = 5, Nmin = 0, 
                  tolerance = 2, weight = 0.5)

#for j in results:
#    print(j)

#%matplotlib widget
import matplotlib
matplotlib.use('Qt5Agg') # if failed,  pip install PyQt5  PySide2
iplot = InteractivePlot(bottom=bottom, top=top, results=results, weight=0)
iplot.plot_results()

j = results[1]
print(type(j))
print(j.bottom)
print(j.top)
print(j.stack)
print(j.strain)
# view(bottom)
# view(j.stack)

construct heterostructure

from ase import Atoms
from ase.build import make_supercell
from ase.build.tools import sort
from numpy import array, zeros, concatenate
from ase.visualize import view

def build_supercells(primitive_bottom: Atoms = None, 
                         primitive_top: Atoms = None,
                         M: array = None,
                         N: array = None,
                         angle_z: float = None, 
                         weight: float = 0.5,
                         distance: float = 3.5,
                         vacuum: float = 15,
                         pbc: list = [True, True, False], 
                         reorder=True ) -> Atoms:
    """
    For construct supercell for two primitive cell known transition matrix and rotation angle of top layer around z-dir\n
    Input: must be primitive cell\n
           M, N: bottom, top matrix\n
           angle_z: units: degree, +z direction\n
           distance, vacuum: units: Angstron\n
           weight: must be 0~1, fixing bottom~top\n
           pbc, reorder: the default value is good\n
    Output: 
           heterostructure
    Usage:
           For output of hetbuilder, results is a list contained many structures.
           defined: j = results[0] or any index
                    build_supercells(j.bottom, j.top, j.M, j.N, j.angle, j._weight) # note: _weight
           For general situation,
                    build_supercells(bottom, top, M, N, angle, weight)
    """
    bottom = primitive_bottom.copy()
    top = primitive_top.copy()
    #print(top)
    # make_supercell
    bottom_sup = make_supercell(bottom, M)
    top_sup = make_supercell(top, N)
    #print(bottom_sup)

    # rotate top layer around z, units: degree
    top_sup.rotate(angle_z, 'z', rotate_cell=True)
    #print(top_sup)
    # translate from hetbuilder (atom_functions.cpp/.h) stack_atoms function
    stack = stack_atoms(bottom_sup, top_sup, weight, distance, vacuum, pbc, reorder)
    #print(1)
    return stack

def stack_atoms(bottom_sup: Atoms = None, top_sup: Atoms = None, weight: float = 0.5, distance: float = 3.5, vacuum: float = 15, 
                pbc: list = [True, True, False], reorder: bool=True, shift_tolerance: float = 1e-5) -> Atoms:
    """
    After searching the coincidenced supecell, we get the transition matrix(M for bottom, N for top), and make two supercells, and then try to match them.\n
    Additionally, bottom, top, weight, distance, vacuum.\n
    usage: updating...
    Noted: the cell C = A + weight * [B - A], A - bottom, B - top
    """
    # get the max, min z-position 
    bottom = bottom_sup.copy()
    top = top_sup.copy()
    min_z1, max_z1 = bottom.positions[:,2].min(), bottom.positions[:,2].max()
    min_z2, max_z2 = top.positions[:,2].min(), top.positions[:,2].max()
    bottom_thickness = max_z1 - min_z1
    top_thickness = max_z2 - min_z2
    #print(bottom_thickness)
    #print(distance)
    shift = bottom_thickness + distance

    # add distance
    bottom.positions[:,2] -= min_z1
    bottom.positions[:,2] += shift_tolerance
    top.positions[:,2] -= min_z2
    top.positions[:,2] += shift
    top.positions[:,2] += shift_tolerance

    # generate lattice
    new_lattice = zeros((3,3))

    # C = A + weight * [B - A]
    for i in range(2):  
        for j in range(2):
            #print(i,j)
            new_lattice[i, j] = bottom.cell[i, j] + weight * (top.cell[i, j] - bottom.cell[i, j])
    new_lattice[2,2] = bottom_thickness + distance + top_thickness + vacuum

    # combine the position and symbols information
    all_positions = concatenate([bottom.positions, top.positions], axis=0)
    all_symbols = bottom.get_chemical_symbols() + top.get_chemical_symbols()

    # create new Atoms
    stack = Atoms(symbols=all_symbols, positions=all_positions, cell=new_lattice, pbc=pbc)
    stack.center()
    if reorder:
        stack = sort(stack)
    return stack

print(build_supercells(bottom, top, j.M, j.N, j.angle, j._weight))
print(build_supercells(bottom, top, j.M, j.N, j.angle, 0.5))
print(build_supercells(bottom, top, j.M, j.N, j.angle, 0))
print(build_supercells(bottom, top, j.M, j.N, j.angle, 1))

Strain, Stress

• issue

Some bugs

Fixed by change cli.py, it lose weight parameter when the run function are executed.

Next step

Zur algorithm

see Endnote/DFT-HCP-Au/Construct-Heterostructure/Lattice match: An application to heteroepitaxy

see Endnote/DFT-HCP-Au/Construct-Heterostructure/Computational Approach for Epitaxial Polymorph Stabilization through Substrate Selection

Interface-master

see Endnote/DFT-HCP-Au/Construct-Heterostructure/A brute-force code searching for cell of non-identical displacement for CSL grain boundaries and interfaces

InterMatch

see Endnote/DFT-HCP-Au/Construct-Heterostructure/High-throughput ab initio design of atomic interfaces using InterMatch

Coincidence-lattice

see Endnote/DFT-HCP-Au/Construct-Heterostructure/Coincidence Lattices of 2D Crystals: Heterostructure Predictions and Applications

Further thinking

• Het2D maybe useful!

• interface_master

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