September 2014

How to plot the polarizability of the cluster using jmol

To process charge of polarizability; that is, show the color of each atom in the molecule in the structure according to its polararizability .

For this we need:
1.- The adious.out file which contain the polarizability of the molecule which is listed according to the contribution due to each atom.
2.- The gemoetry (.xyz) file
3.- A python script called , it can be downloaded here

Now we can put these three files in a directory then we have to run:

./ Sc3NC68_6140_adious.out -4 7

Performing vibrational analysis

To perform vibrational analysis, first you must obtain the specsym code from the repository, compile it by typing 'make', then take the following files from the converged ground state calculation (this means CONVEGRE TRUE in the GEOCNVRG file) and put them in a separate directory with the specsym binary:


once there, run the specsym code, which will produce the following new files: