Zhengda He - He Zhengda

Compile VASP 6.3.2 with VTST on supercomputer

In this post I will introduce the steps and key points for compiling the latest VASP (version 6.3.2) with the latest VTST (190) successfully. There are some mistakes along the way, and I hope you won't repeat those mistakes like I did. Let's begin! Step 1: Download the

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First-Principle Electrocatalysis - Episode 1 - General Discussion

In this series, I will introduce and discuss the latest computational approaches for first-principle electrocatalysis (FPEC), which is the foundation for understanding electrochemical reactions at the electrified interface. This is episode 1, which is the general discussion of the question. Master question of electrocatalysis The structure of the electrochemical interface

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Compile RuNNer on Supercomputer

Intro We have discussed in detail about the high-dimensional neural network potential (HDNNP) in this post. In this post we will show how to compile the RuNNer code, which was developed by the creator of HDNNP, Prof. Jörg Behler. You can email him (via joerg.behler@uni-goettingen.de) in order

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High-Dimensional Neural Network Potential

Disclaimer: All the information in this article comes from my own understanding after reading the original literatures. If something is wrong, that is totally on my foolishness. You should use this article with the literature to learn this important method. Key References All the contents in this article came from

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Install GPU version of LAMMPS

Download the code from Github: https://github.com/lammps/lammps (develop version) Unzip it and upload to the supercomputer (e.g. our own cluster) Go into the folder you will see something like this: Compile lib/gpu Go into the lib/gpu folder: Load modules: (1) nvidia/cuda/11.2

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Compile JDFTx (CPU and GPU version)

The official website for JDFTx is: https://jdftx.org/ Packages that you need: * cmake: https://cmake.org/ * GSL (GNU Scientific Library): https://www.gnu.org/software/gsl/ * OpenMPI: https://www.open-mpi.org/software/ompi/v4.1/ * FFTW3: https://www.fftw.org/ * Intel MKL: (from your cluster) So we need to

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Compile Quantum ESPRESSO with multi-GPU parallelism (qe-7.0 + CUDA + OpenMPI)

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How to add desktop audio to OBS on macOS

Adding desktop audio on macOS to OBS is not easy, but in this post, I will give you a step-by-step procedure so that you can do it with ease. Step 1: Download BlackHole The website for blackhole is: https://existential.audio/blackhole/. After the registration, you will get an email

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How I use RoamResearch in scientific research

Roam Research should be in every researcher's toolbox. -------------------------------------------------------------------------------- Hi there, nice to see you again! In this post I will introduce my workflow of using Roam Research for scientific research. Tools that you need: (1) Roam Research (link [https://roamresearch.com/]) (2) Zotero-Roam plugin (link [https://alix-lahuec.gitbook.io/

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XML file from Quantum Espresso

In this post I will deep dive into the xml file from pw.x calculation, there are so much information that we can get from the xml file. Also the xml file can be used as the input in the next stages of our simulation. Installation In order to get

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Deep Dive into the LAMMPS input file

LAMMPS [https://lammps.sandia.gov/] is a really popular code for doing classical molecular dynamics simulations. In this post, we will dive deep into the heart of molecular dynamics and also how to construct the input file for LAMMPS. It is really important to know that when you try to

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Install and using openbabel on macOS

In this post, I will introduce how to install openbabel package and use it through python. Installation Before you install the openbabel, you need to make sure that you have: (1) Eigen package and (2) SWIG. Prerequists Eigen You can download the Eigen package through this command: git clone https:

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How do I write scientific paper

Writing scientific paper is hard, so we need a methodology for that. In the following I will share with you my strategy in writing a scientific paper (from start to finish), hope it will help you too. Logic is important Whatever we write, logic is very important. Everything in our

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My personal knowledge management system

In this blog post I want to share with you my personal knowledge management (PKM) system. I will share with you the tools that I found really helpful, and I also want to share with you my philophy in PKM. I will divide the post into three categories, which is

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How to setup the table of contents in ghost.org

We all know table of content is very important for the convenience of the reader experience. So that today I will show you how you can add table of contents like this: The red arrow represents the end result that we want to getOn the ghost.org website there is

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DeepMD

DeepMD (official website [http://www.deepmd.org/], github [https://github.com/deepmodeling/deepmd-kit], documentation [https://deepmd.readthedocs.io/en/latest/index.html]) is a powerful tool for modelling the time-evolution of a chemical system by using molecular dynamics with machine-learning force field. The theoretical foundation of DeepMD can be found

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My work flow on daily literature

Everyday we should read the latest literature in order to keep up with the scientific discovery. But this can be a daunting task because there are so many literatures to choose from. Here are how I do it, and hopefully it will provide some inspirtaions to you. -------------------------------------------------------------------------------- Step 1