Top 10 algorthims in 20 centry
Very interesting series on the top 10 algorithms with the greatest influence on the development and practice of science and engineering in the 20th century. Metropolis Algorithm for Monte Carlo...
GROMACS gmx dump
Gromacs trr file Files with the trr file extension contain the trajectory of a simulation. In this file all the coordinates, velocities, forces and energies are printed as you told GROMACS in your...
Tips for Linux
Basis Compare two folders, 比較兩個目錄內檔案的差異，列出所有差異處 1 diff -bur folder1/ folder2/ 比較兩個目錄內檔案的差異，只列出有差異的檔案名稱 1 diff -qr folder1/ folder2/ 1 diff -qr folder1/ folder2/ | sort Handle files with patter...
Convert file format from GROMACS to xyz
Convert g96 to xyz 1 gmx editconf -f input.g96 -o output.gro 1 obabel input.gro -O output.xyz
SPACK Basic
SPACK Showing installed version of a package 1 2 spack find [option] <package name> $ spack find -v gromacs load package 1 spack load <package name> Compiler 1 2 3 4 spack find -p g...
CP2K
Basis sets and pseudopotentials Which basis sets and/or pseudopotentials should I use? When in doubt, always use the DZVP-MOLOPT-GTH basis set and the GTH-PBE pseudopotential. use OT for non-m...
Git Basic
Git Create a Branch List all your branches: 1 $ git branch -a Create a New Branch 1 git checkout -b new-branch-name Or, checkout the branch you want to use: 1 $ git checkout <feature_branch&g...
Atomsk - The Swiss-army knife of atomic simulations
Unwrap atom coordinates To calculate diffusion coefficient from the mean-square-displacement, we need to unwrap the atom coordinates. https://atomsk.univ-lille.fr/doc/en/mode_unwrap.html Ref: A...
Porous Media
Basic Concepts Contact Angle Pore Size Distribution fdsfdsfds fdsfdsfds fdsfdsf \ nnnnnnnn nnnnnn aaaaa fdsfdsfds fdsfds Ref: Quick start guide MDAnalysis Examples
Update GitHub Token
Show current origin 1 git remote -v Remove your current, expired, remote URL: 1 git remote remove origin Github token Using an Access Token for the first time Follow the instructions on Github ...
Conda Environments
list environments 1 conda env list creat and remove environments 1 2 # creat the environment named ENV_NAME conda create --name ENV_NAME python==3.9 1 2 # remove the environment named ENV_NAME c...
Phase diagram and free energy
Free energy Represent phase diagram
Multiple accounts on GitHub
Set up SSH keys 1 ssh-keygen -t rsa -b 4096 -C "work.emailid" 1 Enter file in which to save the key (/Users/mark/.ssh/id_rsa): ./id_rsa_freecafe Add the SSH (public) ...
Forcefield for Ionic Liquids
Forcefield Bis(fluorosulfonyl)amide, [N(SO2F)2]-, FSI (OPLS) References: Molecular Force Field for Ionic Liquids Ionic liquid force field parameters (OPLS-2009IL and OPLS-VSIL)
VMD
Changes display defaults 1 2 3 4 5 6 # Changes display defaults display resize 600 600 axes location off display projection orthographic color Display Background white color Name {L} silver Set t...
Matplot in Python
Ref: mathplotlib: mathematical expressions Making better plots with matplotlib.pyplot in Python3 Improve matplotlib
Analogies in Physics
This comprehensive paragraph by Dieter Forster1 ” Physics is a field that thrives on analogies. We can understand, partially at least, superfluid Helium on the basis of concepts borroed from sup...
Google Colab
Mount (unmount) Google Drive 1 2 from google.colab import drive drive.mount('/content/drive') 1 drive.mount('/drive', force_remount=True)
Bell Inequality
The Bell Inequalities: Identifying What Is Testable and What Is Not
The Matrix Exponential
If a matrix A is diagonalizable, then there exists an invertible P so that $A = PDP^{−1}$, where D is a diagonal matrix of eigenvalues of A, and P is a matrix having eigenvectors of A as its column...
Gaussian
Memory Requirements for Parallel Calculations 1 2 3 %Mem=128MW Memory required by each multiprocessor. %NProcShared=2 Use two shared memory processor...
Story: no one knows what entropy really is
In the case of Shannon’s measure the naming was not accidental. In 1961 one of us (Tribus) asked Shannon what he had thought about when he had finally confirmed his famous measure. Shannon replied:...
Lars Onsager (1903–1976)
兩位飄浮在耶魯校園的寂寞天才(下) 陽春白雪又何妨 by 高崇文
Transport equations
### Onsager’s regression hypothesis states that fluctuations evolve according to the laws that govern macroscopic variations. Boltzmann equation the derivation of Euler, Navier–Stokes, Burnett, a...
ORCA
ORCA ORCA is an ab initio, DFT, and semi-empirical SCF-MO package developed by Frank Neese et al. at the Max Planck Institut für Kohlenforschung. Orbital and density plots If you run a calculation...
Ab initio molecular dynamics (AIMD)
AIMD ORCA Molecular Dynamics Module Here is a nice example given by Dr. Martin Brehm. Also the metadynamics on top of AIMD.
References of quantum computing
BCG: The Race to Quantum Advantage Depends on Benchmarking McKinsey: Quantum computing use cases are getting real—what you need to know
GROMACS
Gromacs File formats tpr file tpr file extension stands for portable binary run input file. This file contains the starting structure of your simulation, the molecular topology and all the simula...
Debye-Hückel Theory
Electrolyte Debye-Hückel Theory (only valid for dilute solutions) In electrolyte, the ions are surrounded by clouds of charge opposite their own, due to the attractive forces of the opposing char...
MDAnalysis
MDAnalysis Atoms, residules, and segments The data structure in MDAnalysis Source: https://userguide.mdanalysis.org/stable/groups_of_atoms.html Selecting atoms Numerical ranges can be written ...
Rclone (Transferring Files Using rclone)
Ref: Rclone on Sherlock 使用 Rclone 串接雲端空間 Rclone Load module : 1 $ ml load system rclone Checkout the branch you want to use: 1 $rclone lsd gdrive: --max-depth 1 sync folder from Sherlock to G...
Branch of GitHub
Git List all your branches: 1 $ git branch -a Create a New Branch 1 git checkout -b new-branch-name Or, checkout the branch you want to use: 1 $ git checkout <feature_branch> Confirm yo...
Overleaf + GitHub
Regular Workflow Make some changes on Overleaf On your computer (while in the local repo directory), run 1 2 git pull overleaf master git push github master Any changes you ...
Jekyll Server on local host
To start Jekyll with Bundler 1 bundle exec jekyll serve
Math and Code
Footnote Click the hook will locate the footnote1, and here is another footnote2. Mathematics The mathematics powered by MathJax: [\sum_{n=1}^\infty 1/n^2 = \frac{\pi^2}{6}] When $a \ne 0$, th...
Search files by command Line
Search file/搜尋檔案 (Linux Tips) Find oldest files 1 find /home/sk/ostechnix/ -type f -printf '%T+ %p\n' | sort | head -n 5 找出大於Gigabyte 的資料夾： 1 2 3 4 # du -h -d 1 /var | grep '[0-9]G\>' sudo f...
Customize the Favicon
The favicons of Chirpy are placed in the directory assets/img/favicons/. You may want to replace them with your own. The following sections will guide you to create and replace the default favicons...
Getting Started
Prerequisites Follow the instructions in the Jekyll Docs to complete the installation of Ruby, RubyGems, Jekyll, and Bundler. In addition, Git is also required to be installed. Installation Crea...
Writing a New Post
To start Jekyll with Bundler 1 bundle exec jekyll serve This post will guide you how to write a post on Chirpy theme. Even if you have previous experience with Jekyll, this article is worth rea...
Text and Typography
This post is to show Markdown syntax rendering on Chirpy, you can also use it as an example of writing. Now, let’s start looking at text and typography. Titles H1 - heading H2 - heading H3 - h...