Editing 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/


[[Image:Jmol1.png]]


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 ==

[[Image:Jmolrun.jpg]]

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