Tool - Summary

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  1. 0. Write the first. Interesting Tools (see Endnote: DFT-HCP-Au/Tools)
  2. 1. High-through electronic calculations
    1. 1.1 Automatic Flow, AFLOW/ACONVASP
    2. 1.2 PASP
  3. 2 Design material
    1. 2.1 MLMD
    2. 2.2 AtomGPT 程序：用于正向和逆向材料设计的原子生成预训练转换器
  4. 3. Surface calculation
    1. 3.1 SurFlow
    2. 3.2 Surfkit
    3. 3.3 CLEAVING 程序：用于计算表面自由能的 LAMMPS 软件包
  5. 4. Mechanics
    1. 4.1 SMATool
    2. 4.2 ElasTool (update to 3.0)
    3. 4.3 VELAS
    4. 4.3 MyElas
  6. 5. Building heterostructure
    1. 5.1 Hetbuilder
    2. 5.2 Hetero2D
    3. 5.3 VASPKIT_CUP
    4. 5.4 Structure Tool (maybe useless)
    5. 5.5 Interface_master
    6. 5.6 OgreInterface
    7. 5.7 ASE / Pymatgen
    8. 5.8 Pymatgen
    9. 5.9 InterMatch
  7. 6. About heterostructure (see Tool-Find-heterostructure)
    1. 6.1 Epitaxy
    2. 6.2 2D Elastic Properties
  8. 7. Python and DFT/MD
    1. 7.1 QMC DFT Python
    2. 7.2 FCP-vasp-ase
    3. 7.3 PyL3dMD: Python LAMMPS 3D molecular descriptors package
    4. 7.4 eNEB
    5. 7.5 PyLAT 程序：基于 Python 代码的 LAMMPS 数据处理工具
    6. 7.6 VTAnDeM 程序：用于同时可视化材料的相稳定性、缺陷能量学和载流子浓度的 python 工具包
    7. 7.7 PyCDT 程序：用于对半导体和绝缘体中的点缺陷进行建模的 Python 工具包
  9. 8. Re-compile VASP
    1. 8.1 VASP OPT AXIS
  10. 9. Model tools / Pre / Post process
    1. 9.1 VASPKIT
    2. 9.2 ATOMKIT
    3. 9.3 Atomsk
    4. 9.4 ASE
    5. 9.5 AACSD
    6. 9.6 Pyprocar
    7. 9.7 IFermi
    8. 9.8 Aimsgb: 生成周期性晶界
    9. 9.9 原子结构识别
    10. 9.10 MDANSE
    11. 9.11 Pymatgen
    12. 9.12 VoroTop 程序 + Vorotis 程序 + ParVoro++ 程序结合 OVITO 程序
    13. 9.13 ScaleLat 程序：一种用于绘制多相体系和高熵合金原子结构的化学结构匹配算法
  11. 10. Space group
    1. 10.1 Spglib
    2. 10.2 CrystKit
    3. 10.3 SeeK-path
    4. 10.4 Brillouin.jl 程序：k-空间路径和布里渊区可视化软件包
  12. 11. Phase diagram
    1. 11.1 Phasego
  13. 12. Test of the convergence
    1. 12.1 vaspup2.0
  14. 13. Machine learning
    1. 13.1 CrySPY

Knowledge starts with practice.

实践出真知

Updated time: 08/02 2024.

0. Write the first. Interesting Tools (see Endnote: DFT-HCP-Au/Tools)

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

Not only software, also some GitHub stars.

1. High-through electronic calculations

1.1 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.

1.2 PASP

2 Design material

2.1 MLMD

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

2.2 AtomGPT 程序：用于正向和逆向材料设计的原子生成预训练转换器

  • Article: AtomGPT: Atomistic Generative Pretrained Transformer for Forward and Inverse Materials Design (see Endnote)
  • Description: WeiXin

3. Surface calculation

3.1 SurFlow

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

3.2 Surfkit

  • Article: Surfkit: An atomic toolkit for surface modelling with molecular adsorption (see Endnote)
  • Source code: Github

3.3 CLEAVING 程序：用于计算表面自由能的 LAMMPS 软件包

  • Article: CLEAVING: a LAMMPS package to compute surface free energies (see Endnote)

4. Mechanics

4.1 SMATool

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

4.2 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

4.3 VELAS

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

4.3 MyElas

  • Article:
    • MyElas: An automatized tool-kit for high-throughput calculation, post-processing and visualization of elasticity and related properties of solids (see Endnote)
  • Source code: GitHub
  • Description: WeiXin

5. Building heterostructure

5.1 Hetbuilder

5.2 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

5.3 VASPKIT_CUP

5.4 Structure Tool (maybe useless)

5.5 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

5.6 OgreInterface

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

5.7 ASE / Pymatgen

5.8 Pymatgen

  • Nice tool

5.9 InterMatch

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

6. About heterostructure (see Tool-Find-heterostructure)

6.1 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

6.2 2D Elastic Properties

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

7. Python and DFT/MD

7.1 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).

7.2 FCP-vasp-ase

  • Source code: Github
  • Article: Grand Canonical Ensemble Modeling of Electrochemical Interfaces Made Simple (see Endnote)

7.3 PyL3dMD: Python LAMMPS 3D molecular descriptors package

  • Source code: Github
  • Article: PyL3dMD: Python LAMMPS 3D molecular descriptors package (see Endnote)

7.4 eNEB

  • Article: Simulation of Potential-Dependent Activation Energies in Electrocatalysis: Mechanism of O–O Bond Formation on RuO2 (see Endnote)

  • Source code: Github

7.5 PyLAT 程序：基于 Python 代码的 LAMMPS 数据处理工具

  • Article: PyLAT: Python LAMMPS Analysis Tools (see Endnote)
  • Source code: Github
  • Description: WeiXin

7.6 VTAnDeM 程序：用于同时可视化材料的相稳定性、缺陷能量学和载流子浓度的 python 工具包

  • Article: VTAnDeM: A python toolkit for simultaneously visualizing phase stability, defect energetics, and carrier concentrations of materials (see Endnote)

7.7 PyCDT 程序：用于对半导体和绝缘体中的点缺陷进行建模的 Python 工具包

  • Description: WeiXin
  • Article: PyCDT: A Python toolkit for modeling point defects in semiconductors and insulators (see Endnote)

8. Re-compile VASP

8.1 VASP OPT AXIS

9. Model tools / Pre / Post process

9.1 VASPKIT

9.2 ATOMKIT

9.3 Atomsk

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

9.4 ASE

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

9.5 AACSD

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

9.6 Pyprocar

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

9.7 IFermi

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

9.8 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

9.9 原子结构识别

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

9.10 MDANSE

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

9.11 Pymatgen

  • Article: Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis. (see Endnote)
  • Source code: Github

9.12 VoroTop 程序 + Vorotis 程序 + ParVoro++ 程序结合 OVITO 程序

9.13 ScaleLat 程序：一种用于绘制多相体系和高熵合金原子结构的化学结构匹配算法

  • Source code: Github
  • Description: WeiXin
  • Article: ScaleLat: A chemical structure matching algorithm for mapping atomic structure of multi-phase system and high entropy alloys (see Endnote)

10. Space group

10.1 Spglib

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

10.2 CrystKit

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

10.3 SeeK-path

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

10.4 Brillouin.jl 程序：k-空间路径和布里渊区可视化软件包

11. Phase diagram

11.1 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

12. Test of the convergence

12.1 vaspup2.0

13. Machine learning

13.1 CrySPY

  • Article: CrySPY: a crystal structure prediction tool accelerated by machine learning (see Endnote)

  • Source code: Github

  • Description: WeiXin

Please indicate the source when reprinting. Please verify the citation sources in the article and point out any errors or unclear expressions.

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