Using bash variables in sed command

Bash commands such as awk and sed are very handy tools when dealing with text files. For example, if line 30~70 in a pw.out file are the atom coordinates, we can simply type in the terminal: $ sed -n '30,70' pw.out and line 30~70 will show up on the terminal. Things get tricker when the line numbers are variables. Often times we want to use sed in a bash script,...

[VMD] Run vmd from Mac terminal

Our work can be done faster and more efficiently if we do everything through the terminal. To ask vmd to open a file through MacOS X terminal, just type in: $/Applications/VMD\ 1.9.1.app/Contents/Resources/VMD.app/Contents/MacOS/VMD One-liner! Of course, I prefer a shorter version of the command vmd. Add the alias...

[LAMMPS] Visualizing log file

(About how to use Pizza.py, please refers to previous post of How to use Pizza.py for LAMMPS or the official Pizza.py Toolkit page. Instead of asking pizza.py to get all the "Temp", "TotEng" .. by typing in each variable, and then do g.plot (a lot of repetitive keyboard work!), there's a much faster way to visualize the thermo-type data....

[awk] using shell variable

Shell variable can be ported into awk command by using "-v" flag: #!/bin/bash var=100 awk -v var=$var '{print $1*var}' file.dat An important note here is that within the awk command, calling the var does not require the '$' sign. If there are more than one shell variable to call, use -v again and put space in between: awk -v var=$var -v var2=$var2...

How to converge ecut and kpoint in a DFT calculation?

Finding the energy cutoff and k-point is like the fundamental of doing DFT calculations. However there doesn't seem to be an universal way to do it. I found on the quantum-espresso forum a very informative and thorough explanation. Thank Stefano for a such detailed post. Below is my notes on the procedures: 1. First test ecutwfc and ecutrho Ecutwfc and ecutrho are properties related...

[Mac] Set double-sided printing as default

I recently migrated from Windows to OSX. As a kinda-happy windows user for 20+ years, I was interested in knowing what's the charisma of Apple products. --- Above is a totally unrelated preface ---------- In the System preference, there's no option to set duplex printing as default. Instead, Apple uses the Common Unix Printing System...

[LAMMPS] Read/Observe Log File

Although we could always write our own scripts to process LAMMPS output files, LAMMPS has this awesome package, Pizza.py , which already contains many powerful tools to allow quick observations on the simulation results. At the beginning of a simulation, you might want to check how energies and temperature drift, get averages over blocks...

[GNUPLOT] Hide axis range

In gnuplot, a handy way to turn off the axis is to use: unset ytics This will remove all the tics and associated labels on the y axis. Sometimes we like to have the tics there, but hide just the numbers (i.e. when using arbitrary unit). A more complicated way is to use the set ytics ("〈label〉" 〈position〉,) command. This...