Electronic Structure Lab


General interests of the group are understanding the electronic structure of materials using density functional theory. Current interests include charge transfer excitations in donor acceptor complexes (organic photovolatics), linear and non linear polarizabilities of molecules.

Plotting using POVray

POVray is a program for creating graphics output (in our case of atomic structures) for publications.

You can export graphics output from our GUI, the JSmol viewer in this webpage or directly from Jmol. It doesn't actually require to have povray installed in the system to export in this format (unless you have checked the box that says "Run POV-Ray directly" in Jmol) .

Using the JSmol applet

If you need plotting capabilities but the current computer where you are in does not have Jmol or Molekel installed, you can run JSmol, a javascript version of Jmol from our website. Just go to the Utilities tab in the top menu and select "General Jmol Viewer". It will load a sample molecule by default.

In the graphics area, you can click the right-hand side mouse button and goto File->Load->Open local file to open a file from your computer, it works with the files we usually handle in the lab (.xyz, .cube, .MOLDEN).

Compiling using Cray Compilers on Hopper

To compile using Cray compilers on Hopper, first swap the programming environment by typing:
swap PrgEnv-pgi PrgEnv-cray

the CrayFtn compiler has a problem with the string ACCESS='APPEND' so these all need to be replaced with POSITION='APPEND'

you can use this command to modify them all
sed -i “s/ACCESS=’APPEND’/POSITION=’APPEND’/” *

Post doctoral positions available

The electronic structure group at the University of Texas at El Paso is seeking to fill two postdoctoral positions in the area of electronic structure calculations using density functional theory with focus on the applications related to nanomaterials and organic photovoltaic complexes. The projects involve both the theoretical and computational components. The theoretical components involve further development of the excited state method, description of van der Waal interactions etc.

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:

  • GRPMAT
  • VIBINP
  • ISYMGEN
  • SYMBOL
  • INPUT

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

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 process_charge.py , it can be downloaded here

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

./process_charge.py Sc3NC68_6140.xyz Sc3NC68_6140_adious.out -4 7 out.xyz

Fatemeh dedenfed her MS Thesis

Fatemeh Amerikheirabadi successfully defended her physics MS thesis Aug. 7 at 11:00AM

Her thesis is entitled: "ELECTRONIC STRUCTURE AND CHARGE TRANSFER EXCITED STATES OF ENDOHEDRAL FULLERENES CONTAINING ELECTRON DONOR-ACCEPTOR COMPLEXES UTILIZED IN ORGANIC PHOTOVOLTAICS"

Congratulations Fatemeh!!

Shusil defended his MS thesis

Shusil Bhusal successfully defended his Physics master's thesis Aug. 7 at 2:00PM

His thesis is entitled:"STUDY OF DIELECTRIC PROPERTIES OF ENDOHEDRAL FULLERENES"

Congratulations Shusil!!

Starting calculation from SYMBOL changes

We recently did some changes to the code, if you need to restart your calculation from the SYMBOL file read this.

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