Topics Map > SCS Computing > How-To

Quantum Chemistry - Intro to Gaussian I

This is part one of a two part series of using Gaussian at SCS. Topics that are covered include: Generating an input file using Avogadro, Running a single-point Energy calculation, Calculation molecular orbitals, and Visualizing orbitals. Update: to submit Gaussian jobs on triton please use new script submit-g09

 QUANTUM CHEMISTRY WITH GUASSIAN: A VERY BRIEF INTRODUCTION

TARAS V. POGORELOV AND MIKE HALLOCK
SCHOOL OF CHEMICAL SCIENCES, UIUC

This tutorial is designed to help getting started with Gaussian. Single point energy calculation is performed on a single water molecule. Molecular orbitals are calculated. Basic knowledge of Unix/Linux is assumed. Estimated time to complete this tutorial is 50 min.

1. SOFTWARE

One will need: text editor, ssh client, and molecule builder. 
Suggestions: 
Molecule builder: Avogadro (http://sourceforge.net/projects/avogadro/files/)
Mac
Text editors: TextEdit, Vim
SSH client: built in Terminal, scp or Fugu for file transfers
PC
Text editor: Notepad, Vim
SSH client: putty, WinSCP for file transfer

2. PREPARE GAUSSIAN INPUT FILE FOR A WATER MOLECULE USING AVOGADRO

Install Avogadro on your computer, if needed. 
Open Avogadro and Select Element: Oxygen(8)
Click once anywhere is the main window and watch hydrogens being added making a water molecule. 
Prepare Gaussian input file: Open Extensions, Gaussian. 
Note: the coordinates are already listed in the Gaussian Input plugin. 
Enter title: water SP
Select: Calculation: Single Point Energy, Theory level: RHF, Basis: 6-31G(d), Charge: 0, Multiplicity: 1. 
Click: Generate button. 
Save as: water.com

3. Gaussian SINGLE POINT CALCULATION: INTERACTIVELY ON TRITON (SCS' LINUX CLUSTER)

Copy Gaussian input file to triton using scp command. 
> ssh triton
Make a directory waterSP in your home directory. 
Copy Gaussian input file to triton using scp command. 
Note: please see the Unix/Linux Primer if you need to refresh your knowledge of the OS. 
Setup your environment: 
> setenv g09root /share/apps/gaussian
> source $g09root/g09_login.csh
Start Gaussian job with prepared files: 
> g09 < water.com
Note: < is the "pipe" flag to direct the input file to Gaussian
Output will be printed on the screen. 
To direct output into a file add > water.log in the end. 
Note: proceed to Appendix for an example of submitting a Gaussian calculation in queue. Please make sure to understand each line of the script. 

4. Gaussian OUTPUT: BASIC FEATURES

Open water.log in a text editor and locate the following: Input data, Standard orientation, Number of basis functions used, Single point energy, Symmetry, Mulliken charges.
Note: the energy is reported in A.U. please estimate how many significant digits are needed to guarantee sufficient accuracy. Define sufficient. 

4.1. Find data in the output without opening. Close the output file and use grep to find the energy value, without opening the file. This can become important for larger systems, as the size of the output file will grow very fast. 

5. USE Gaussian TO CALCULATE MOLECULAR ORBITALS

Copy water.com into waterMD.com and add in the end of the first line, after SP the following Pop=Reg formcheck. The former requests the data on molecular orbitals to be included into the output and the former asks to print what is called checkpoint file. It is used to restart calculations and to graph molecular orbitals. 
Run the new calculation. Locate in the output file the following: the data mentioned above, molecular orbital coefficients, symmetries and energies of the MO's and HOMO/LUMO orbitals. 
Note: the checkpoint Test.FChk was produced. This is an ASCII file which has MO information. 

5.1. Display molecular orbitals using Avogadro. Copy Test.FChk to your computer where Avogadro is installed. 
Start Avogadro. File->OpenTest.FChk. Tow show surfaces go to Extensions->Create Surfaces
To plot electrostatic potential select menu flags as shown on figure 1. 

The result will look similar to figure 2.



Plot HOMO for water molecule. Select menu flags as shown on figure 3.



HOMO is shown on figure 4.



Use Avogardo to graph LUMO of a water molecule.

6. SUMMARY

This tutorial covered material to have one started using Gaussian for single point energy calculation, analyze the output, graph electrostatic potentials and molecular orbitals.

7. CONTACT

If you found errors/typos or have suggestions or comments on material in this tutorial please contact us at the SCS Computer Center. We are looking forward to hearing from you.

8. APPENDIX: RUNNING Gaussian IN QUEUE ON TRITON (LINUX CLUSTERS)

Please make sure to understand each line of the shell script below. Edit it to match your file names.
Submit the queue script to the queue:
> qsub g09 qjob
Note: The following is probably not needed for the fast test job.
Check the status of your job:
> qstat
Delete the job if need:
> qdel
Study the shell script for queue submission open g09 gjob:
#!/bin/tcsh
#$ -cwd
#$ -pe default 1
#$ -q general
source /share/apps/gaussian/g09 login.csh
g09 input.com

______________
Date: February 10, 2010.




Keywords:quantum chemistry, gaussian, intro   Doc ID:103204
Owner:Taras P.Group:University of Illinois School of Chemical Sciences
Created:2020-06-18 22:52 CDTUpdated:2020-06-30 19:53 CDT
Sites:University of Illinois School of Chemical Sciences
Feedback:  0   0