Jmol.sh

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This is a brief tutorial to use Jmol to visualize the vibration modes.

Installation steps

1) Install Java Runtime Environment: sudo apt-get install default-jre

2) Download the Jmol package: https://sourceforge.net/projects/jmol/files/Jmol/

3) Extract the file and you will get a folder named jmol-14.29.14(the numbers are depend on the versions your download), get into this folder's path in the terminal and run:

chmod u+x jmol.sh

4) In my case, I extract the file to the ~/Documents folder:

cd ~/Documents/jmol-14.29.14

chmod u+x jmol.sh

5) Edit your ~/.bashrc file:

export PATH=$PATH:~/Documents/jmol-14.29.14

6) Source your ~/.bashrc file: source ~/.bashrc or . ~/.bashrc

Visualization Steps

In terminal, go to your frequency calculation path and run the steps as shown in the figure:

Step1: grep f/i OUTCAR

To get the wave number of imaginary frequencies

Step2: jmol.sh OUTCAR

Open OUTCAR with Jmol package. (for OUTCAR_jmol file, see Note 2)

Step3: Click Tools and click AtomSetChooser

Step4: Select the modes

Step5: Click the Arrow button in the bottom to start visualizing.

Note1:

For the imaginary frequencies. In the interface of Jmol, the minus symbol is not displayed. So you need to check them firstly with the command: grep f/i OUTCAR

Then, you will get the wave number of imaginary frequencies and visualize the vibration modes by comparing the wave numbers.

Note2:

In the step2 in the figure, I used the command: jmol.sh OUTCAR_jmol This is because of the bug of Jmol when it reads OUTCAR in frequency calculations with NWRITE = 0.

When we use NWRITE = 0, the important tags for jmol to read the element information from OUTCAR is not written.

So, if you use NWRITE = 0 and run jmol.sh OUTCAR directly, you will find that all your atoms are in the same color.

To solve this bug, there are two options:

Method-1) Use NWRITE = 2 and run jmol.sh OUTCAR

Method-2) Add more information to the OUTCAR by hand.

i) grep TIT POTCAR > title

ii) copy the outputs of above commands and paste them to the OUTCAR:

cat title OUTCAR >> OUTCAR_jmol

iii) jmol.sh OUTCAR_jmol

If you have any problems in visualizing the frequencies, do not hesitate to tell me. Enjoy!

Qiang