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Tutorial - 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 the cluster lop please use new script submit-g16.
QUANTUM CHEMISTRY WITH GUASSIAN: A VERY BRIEF INTRODUCTION
TARAS V. POGORELOV AND MIKE HALLOCK
SCHOOL OF CHEMICAL SCIENCES, UIUC
Created 2011. Updated/reviewed August 4, 2022.
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.
To download and save this tutorial to your computer, print this page ('Command + P' or 'Ctrl + P') and save the document as a PDF.
One will need: text editor, ssh client, and molecule builder.
Molecule builder: Avogadro (http://sourceforge.net/projects/avogadro/files/)
Text editors: TextEdit, Vim
SSH client: built in Terminal, scp or Fugu for file transfers
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 SCS' LINUX CLUSTER
Copy Gaussian input file to the cluster you are using using scp command.
> ssh email@example.com
Make a directory waterSP in your home directory.
Copy Gaussian input file to cluster using scp command. (scp water.com firstname.lastname@example.org:~/waterSP)
Note: please see the Unix/Linux Primer if you need to refresh your knowledge of the OS.
Load Gaussian module :
> module load gaussian/g16
Start Gaussian job with prepared files:
> g16 < 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.
This tutorial covered material to have one started using Gaussian for single point energy calculation, analyze the output, graph electrostatic potentials and molecular orbitals.
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 LOP (SCS LINUX CLUSTER)
Please make sure to understand each line of the shell script below. Edit it to match your file names.
Load Gaussian module:
>module load gaussian
Submit the queue script to the queue:
> submit-g16 water.com
Note: The following is probably not needed for the fast test job.
Check the status of your job:
Delete the job if need:
> qdel jobID
where jobID is your job ID in the queue.