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Step1: grep f/i OUTCAR  To get the wave number of imaginary frequencies
Step1: grep f/i OUTCAR   
Step2: jmol.sh OUTCAR    Open OUTCAR with Jmol package
 
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
Step3: Click Tools and click AtomSetChooser
Step4: Select the modes
Step4: Select the modes
Step5: Click the Arrow button in the bottom to start visualizing.
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
'''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.
Then, you will get the wave number of imaginary frequencies and visualize the vibration modes by comparing the wave numbers.




"Note2:"
'''Note2:'''


In the  step2 in the figure, I used the command:  jmol.sh OUTCAR_jmol  
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.
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.
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.
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:
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.
'''Method-1)''' Use NWRITE = 2 and  run jmol.sh OUTCAR


Enjoy.


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


i) '''grep TIT POTCAR  > title''' 


1)  
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!




uncompress it and compile it: ''f77 Cell.f -o x.Cell'' or ''ifort Cell.f -o x.Cell'' or ''gfortran Cell.f -o x.Cell''. Place it in your ~/bin folder.
Qiang
 
2) Download the script and uncompress it. Make it executable with the command: ''chmod ug+x nfreq.sh'':
[[Image:nfreq.tgz]]
 
 
 
3) Change in line of''nfreq.sh'': ''path=/home/lbellarosa/bin/exe/Cell'' with the path of the directory where you put the executable (i.e. ''path=/home/yourusername/bin'').
 
4) Now you can run the script typing:
nfreq.sh OUTCAR
 
Be sure you are using standard pseudopotentials (not soft nor hard). Otherwise change the name of the pseudopotentials in OUTCAR (i.e O_h ==> O)

Latest revision as of 11:27, 16 May 2018

go back to Main Page, Computational Resources, Scripts, Scripts for VASP

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

Installation steps[edit]

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[edit]

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

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