Diary - Log

Knowledge starts with practice.

实践出真知

Updated time: 04/16 2024.

Write the first

It’s for add some interesting tools that I interested in but not used.

Not only software, also some GitHub stars.

Interesting Tools (see Endnote: DFT-HCP-Au/Tools)

High-through electronic calculations

Automatic Flow, AFLOW/ACONVASP

• Article: High-throughput electronic band structure calculations: Challenges and tools (see Endnote)
• Function:
  • The article give some example of momentum space for lots of bravais lattice.

Design material

NLMD

• Article: MLMD: a programming-free AI platform to predict and design materials (see Endnote)
• Source code:
  • NLMD
  • Bgolearn - Active learning package
• Description: WeiXin

Surface calculation

SurFlow

• Article: SurfFlow: High-throughput surface energy calculations for arbitrary crystals (see Endnote)
• Source code: GitHub
• Description: WeiXin

Mechanics

SMATool

• Article: SMATOOL: Strength of materials analysis toolkit (see Endnote)
• Source code: Github
• Description: WeiXin

ElasTool (update to 3.0)

• Article:
  • ElasTool: An automated toolkit for elastic constants calculation (see Endnote)
  • ELASTOOL V3.0: Efficient computational and visualization toolkit for elastic and mechanical properties of materials (see Endnote)
• Source code: GitHub
• Description: WeiXin

VELAS

• Article:
  • VELAS: An open-source toolbox for visualization and analysis of elastic anisotropy (see Endnote)
• Source code: GitHub
• Description: WeiXin

Building heterostructure

Hetbuilder

• Algorithm: Coincidence lattices

• Source code: Github, revised version

• Document: Page

Hetero2D

• Article: Computational synthesis of 2D materials: A high-throughput approach to materials design (see Endnote)
• Source code: Github

• Document: Page

• Description: low-lattice mismatched hetero-structures for arbitrary 2D materials and substrate surfaces

VASPKIT_CUP

• Source code: Github

Structure Tool (maybe useless)

• Source code: Github

Interface_master

• Source code: Github
• Article: A brute-force code searching for cell of non-identical displacement for CSL grain boundaries and interfaces (see Endnote)
• Description: Find heterostructure and shift in plane to search a minimal energy configuration

OgreInterface

• Source code: Github
• Description: Package for creating and optimizing lattice matched and domain matched epitaxial interfaces.

ASE / Pymatgen

• Issues: Github

Pymatgen

• Nice tool

InterMatch

• Article: High-throughput ab initio design of atomic interfaces using InterMatch (see Endnote)
• Description: WeiXin

About heterostructure

Epitaxy

• Source code: Github

• Description: The objective of this project is to write a Python code for identifying a suitable crystal substrate which shows least lattice mismatch for a film crystal

2D Elastic Properties

• Source code: Github
• Description: Computational Design and Analysis of Mechanical Properties of 2D Materials & Heterostructures

Python and DFT

QMC DFT Python

• Source code: Github
• Description: QMC-DFT-Python is a lightweight open-source code for scientists and enthusiasts to understand the basic concepts behind the implementations of most popular electronic structure calculation method: Density Functional Theory (DFT) and also quantum Monte carlo (QMC).

Re-compile VASP

VASP OPT AXIS

• Source code: Github

Model tools / Pre / Post process

VASPKIT

• Source code: VASPKIT

ATOMKIT

• Source code: ATOMKIT

atomsk

• Source code: Github
• Description: For metal, alloy, poly, dislocation, cenvert cell

ASE

• Article: The atomic simulation environment-a Python library for working with atoms (see Endnote)
• Website: ASE

AACSD

• Article: AACSD: An atomistic analyzer for crystal structure and defects (see Endnote)
• Description: Weixin

Pyprocar

• Article: PyProcar: A Python library for electronic structure pre/post-processing (see Endnote)
• Description: WeiXin

IFermi

• Article: IFermi - A python library for Fermi surface generation and analysis (see Endnote)

aimsgb: 生成周期性晶界

• Article: Aimsgb: An algorithm and open-source python library to generate periodic grain boundary structures (see Endnote)
• Description: Weixin

原子结构识别

• Article: Structure identification methods for atomistic simulations of crystalline materials (see Endnote)
• Description: WeiXin

MDANSE

• Article: MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations (see Endnote)
• Description: WeiXin

Space group

Spglib

• Article: Spglib: a software library for crystal symmetry search (see Endnote)
• Functions:
  • Could convert between primitive <<==>> conventional cell

CrystKit

• Source code: Github
• Description: CrystKit is a GAP package designed to manipulate and analyze crystallographic groups

SeeK-path

• Article: Band structure diagram paths based on crystallography (see Endnote)
• Functions:
  • the k-path finder and visualizer

Brillouin.jl 程序：k-空间路径和布里渊区可视化软件包

• https://zhuanlan.zhihu.com/p/621112008

• https://thchr.github.io/Brillouin.jl/stable/kpaths/

• Description: Weixin

Phase diagram

Phasego

• Article:
  • [1] Phasego: A toolkit for automatic calculation and plot of phase diagram
  • [2] Phasego 2.0: Counting full anharmonic effects from high-temperature phonon density of states
  • [3] Phasego 3.0: Automatic analysis of synthesis and decomposition conditions for compounds
• Description: WeiXin

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