GAUSSIAN

Gaussian 03 is the latest in the Gaussian series of electronic structure programs. Gaussian 03 is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.

Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures.

Gaussian 03, Revision C.01 and Gaussian 09, A.02 are currently supported at PSC. Gaussian 98 is no longer supported.

Access is restricted. Complete and return the PSC Gaussian User Agreement (.pdf) to obtain access.

Installed on pople, salk and warhol.

Usage

Gaussian 09, Revision A.02 is available on pople.

Gaussian 03, Revision C.01 is available on pople, salk and warhol.

Gaussian creates checkpoint files while it is running, which can be quite large and can exceed the $HOME directory quota. To avoid this, it is best to run Gaussian from your $SCRATCH directory so that the checkpoint files are created there. $SCRATCH is only temporary storage, so files that need to be kept long-term should be moved to the archiver. Copying checkpoint files to $HOME automatically in the job script may exceed the quota on $HOME. Review the usage policies for:

To run Gaussian:

  • Edit your .login or .profile file to define some necessary environment variables. Choose one of the following ways:

    1. Insert these lines: 
      setenv g03root /usr/local/packages
source $g03root/g03/bsd/g03.login

      or, to use Gaussian 09:

      setenv g09root /usr/local/packages
source $g09root/g09/bsd/g09.login
    2. Insert these lines: 
      module load gaussian03

      or, to use Gaussian09:

      module load gaussian09

      Note: Only one of the gaussian modules should be loaded at any time. For more information about the module package, see the PSC module documentation.

  • Make sure that your .login or .profile file is writable by you. To check the protection on either of these files, type 
    ls -l .login

    For more information on understanding unix file permissions, see the PSC UNIX file protection page.

    To change the permission on a file, use the chmod command.

    chmod u+w .login

    For more information see the PSC page for the chmod command or type man chmod on any unix system.

  • Insert the following as the first line in your Gaussian input file: 
    %nproc = x
    where x is the number of processors to use. Choose the value that gives your program the best performance.

  • Override the (small) amount of memory allocated by default by requesting memory equal to 2*nprocs -1 GB in the input file. For example: 
    %nproc=4
%mem=7gb
  • Invoke Gaussian with: 
    g03 < inputfile >& outputfile
    or 
    g09 < inputfile >& outputfile

Performance

Please check the section on efficiency considerations in the Gaussian 03 Online Manual for ways to improve your particular job's performance.

Checkpoint files

You can use the chkchk utility to check what the content of a checkpoint file is. This can also tell you if a checkpoint file is corrupted.

For example, this checkpoint file is corrupted:

joeuser@tg-login1:~/gaussian> chkchk /usr/users/8/joeuser/gaussian/water.chk Checkpoint file /usr/users/8/joeuser/water.chk: No title or route information found. AO basis is present. SCF restart data present.

As you can see there is no title or route info found. Compare this to the ouput from another checkpoint file. You can see what the output should be like if all the information is there:

joeuser@tg-login1:~/gaussian> chkchk /usr/users/8/joeuser/gaussian/methance.chk Checkpoint file /usr/users/8/joeuser/gaussian/methane.chk: Title: DFT Calculation of (10,0) NT at B3LYP/6-31G(d) from B3LYP/3-21 G starting point Route: #P opt B3LYP/6-31g(d) geom=check guess=read scf=(maxcyc=200) Atomic coordinates present. AO basis is present. SCF restart data present. MO coefficients present. This file appears to be from the middle of a restartable job. Internal force constants may be present.

See the chkchk page of the Gaussian 03 Online Manual for details on chkchk.

Utilities

Gaussian provides other utilities. For more information, see the Utility Programs page from the Gaussian 03 Online Manual.

Example jobs

See some example jobs.