Dailybin

Programs used almost everday. Update every now and then.

Install

git clone git@github.com:HuangJiaLian/dailybin.git
./install

Install scipt will add some lines to your default shell evironment file. eg. .bashrc, .bash_profile, .zshrc, etc.

Upgrade

./upgrage

CP2K tools

• cpex: cp2k data extract from out file.
• plot_dynamics: a fast plotting tool to plot the time dependence of the energies and temperature of the system one studied. NOTE: This command is based on dplot, and it should be run under the directory ExtractData.

Usage:

(tf20) hj@node20:~/Jack/64H2O$ cpex 64H2O_298.15K.out
******************************************
A tool to extract data from cp2k outfile.
File Name:  64H2O_298.15K.out
Done. Files saved at ./ExtractData/
******************************************
(tf20) hj@node20:~/Jack/64H2O$ ls ./ExtractData/
******************************************
$ plot_dynamics
$ ls
AllDat.csv  KineticEnergy.csv  KineticEnergy.png  PotentialEnergy.csv  PotentialEnergy.png  StepNumber.csv  TempChange.csv  Temperature.png

$ enerChange out.log text saved in /home/jack/Step_Energy.png

• extractLast To extractLast frame of xyz trajectory

• keepOpt Keep optimization process; Use like this: keepOpt In_GBL.xyz FAPbI3-pos-1.xyz

Visualization

• dplot: plot csv data easily

Usage:

dplot -F AllDat.csv  -X 0 -Y 1 2 --dlabels "Tem" "Mean Tem" --xlabel Steps --ylabel "Temperature (K)" -T "Temperature Changes Over Step"

Alias

• open : alias open=\"xdg-open" Open folder in Linux Terminal like MacOS open command.

Usage:

open .

Will open current folder with your file manager.

Useful tools

• trans: Translate Shell (formerly Google Translate CLI) is a command-line translator

Usage:

>trans "學而不思則罔，思而不學則殆"
>學而不思則罔，思而不學則殆
(Xué ér bù sī zé wǎng, sī ér bù xué zé dài)

Learning without thinking is nothing, thinking without learning is perishable

Translations of 學而不思則罔，思而不學則殆
[ 简体中文 -> English ]

學而不思則罔，思而不學則殆
    Learning without thinking is nothing, thinking without learning is perishable, Learning without thought is labor lost, thought without learning is perilous

• npy2txt: a command line tool to convert .npy file to .txt file

Usage:

npy2txt data.npy

• dat2csv: a command line tool to convert .txt (.dat) file to a .csv file

Usage:

For single file, use

dat2csv data.txt

for multiple files, use

dat2csv data1.txt dat2.txt

If you want to convert all .txt files to .csv files, use

dat2csv *.txt

128w_bk_n.dat

• tp2oh: a commamd line to convert number type in .xyz file to HO type.

tp2oh example.xyz

Which convert

384
Atoms. Timestep: 0
1 4.41243 4.75955 13.3162
2 4.79362 5.1631 14.1479
2 3.68986 5.35163 12.9593
1 8.31719 4.93377 1.3229
2 8.02236 4.45941 0.493411
2 7.66956 5.66513 1.53668

to

384
Atoms. Timestep: 0
O 4.41243 4.75955 13.3162
H 4.79362 5.1631 14.1479
H 3.68986 5.35163 12.9593
O 8.31719 4.93377 1.3229
H 8.02236 4.45941 0.493411
H 7.66956 5.66513 1.53668
O 14.5847 13.2403 11.3342

• reoh: a commamd line to convert number type in .xyz file to HO type and rerange like cp2k

• aveg: A command line program to calculate average value of a given list

Example:

(tf20) mac@Macbook:~/Desktop$ cat test.txt
5.9779103
5.9810555
5.9745009
5.9779188
5.9763435
5.9829963
(tf20) mac@Macbook:~/Desktop$ cat test.txt | aveg
5.97845
(tf20) mac@Macbook:~/Desktop$ aveg test.txt
5.97845

• exthermo: A command line program to extract thermo data from LAMMPS log file.

Example:

exthermo log.lammps

• sampleevery: A command line programs to sample .xyz file.

Example:

This command will sample text.xyz every 2 dumps.

sampleevery test.xyz 2

• aimd-process: plot the Pot. and Temp. along with time
• dump2xyz: convert dumpfile format of water to xyz format

ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
192
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 1.2417126637745589e+01
0.0000000000000000e+00 1.2417126637000001e+01
0.0000000000000000e+00 1.2417126637000001e+01
ITEM: ATOMS id type xu yu zu
1 1 12.2789 12.2862 11.7326
2 2 11.7624 0.64626 12.0511
3 2 12.1577 12.1129 10.7506
4 1 12.2003 2.96671 12.3428
5 2 12.1672 1.98944 0.133342

to

192
Atoms. Timestep: 0
O 12.2789 12.2862 11.7326
H 11.7624 0.64626 12.0511
H 12.1577 12.1129 10.7506
O 12.2003 2.96671 12.3428
H 12.1672 1.98944 0.133342
H 12.0581 3.07358 11.4205
O 12.3321 6.21356 12.2795
H 11.7348 5.53013 11.9297

• kantu: show image in terminal

• get_traj.sh: Extract a LAMMPS dump file from VASP output. Author: Bowen Wang

• finkey: Finnish keyboard layout

• ccapture: Capture image from builtin camera.

• channelNumOf: Get the channel number of an image

• ele2anum: Change the element name in xyz file to atomic number

• color2gray: Convert a color image into a gray scale image.

• randomDelPNG: Delete PNG files randomly.