Running Gaussian

This page describes the operating system commands required to execute Gaussian on Unix-based computer systems. See the additional instructions accompanying the program for the equivalent information for other operating systems. This discussion assumes that the program has already been installed. The final section lists the component links of the Gaussian 03 program.

Running Gaussian involves the following activities:

• Creating Gaussian input describing the desired calculation.

• Specifying the locations of the various scratch files.

• Specifying resource requirements.

• Initiating program execution, in either interactive or batch mode.

In this page, we will assume that a basic Gaussian input file has been created, and our discussion will examine the remaining three items on the list.

Specifying Scratch File Handling and Location

Gaussian uses several scratch files in the course of its computation. They include:

• The Checkpoint file: name.chk

• The Read-Write file: name.rwf

• The Two-Electron Integral file: name.int

• The Two-Electron Integral Derivative file: name.d2e

By default, these files are given a name generated from the process ID of the Gaussian process, and they are stored in the scratch directory, designated by the GAUSS_SCRDIR environment variable (UNIX). You may also see files of the form name.inp in this directory. These are the internal input files used by the program. If the environment variable is unset, the location defaults to the current working directory of the Gaussian process.

By default, these files are deleted at the end of a successful run. However, you may wish to save the checkpoint file for later use in another Gaussian job, for use by a visualization program, to restart a failed job, and so on. This may be accomplished by naming the checkpoint file, providing an explicit name and/or location for it, via a %Chk command within the Gaussian input file. Here is an example:

%Chk=water 

This command, which is placed at the beginning of the input file (before the route section-see chapter 3 for details), gives the checkpoint file the name water.chk, overriding the usual generated name and causing the file to be saved at job conclusion. In this case, the file will reside in the current directory. However, a command like this one will specify an alternate directory location as well as filename:

%Chk=/chem/scratch2/water 

If disk space in the scratch directory is limited, but space is available elsewhere on the system, you may want to split the scratch files among several disk locations. The following commands allow you to specify the names and locations of the other scratch files:

%RWF=path              Read-Write file 
%Int=path              Integral file 
%D2E=path              Integral Derivative file

In general, the read-write file is by far the largest, and so it is the one for which an alternate location is most often specified.

Splitting Scratch Files Across Disks

An alternate syntax is provided for splitting the Read-Write file, the Integral file, and/or the Integral Derivative file among two or more disks (or file systems). Here is the syntax for the %RWF command:

%RWF=loc1,size1,loc2,size2, ...

where each loc is a directory location or a file pathname, and each size is the maximum size for the file segment at that location. Gaussian will automatically generate unique filenames for any loc which specifies a directory only. On UNIX systems, directory specifications (without filenames) must include a terminal slash.

By default, the sizes are in units of words; the value may be followed by KB, MB or GB (without intervening spaces) to designate KB, MB or GB, respectively, or by KW, MW or GW to indicate units of kilowords, megawords or gigawords, respectively. Note that 1 MB = 1024² bytes = 1,048,576 bytes (not 1,000,000 bytes).

A value of -1 for any size parameter indicates that any and all available space may be used, and a value of 0 says to use the current size of an existing segment. -1 is useful only for the last file specified, for which it is the default.

For example, the following directive splits the Read-Write file across three disks:

%RWF=/dalton/s0/,60MW,/scratch/,800MB,/temp/s0/my_job,-1 

The maximum sizes for the file segments are 480 MB, 800 MB, and unlimited, respectively. Gaussian will generate names for the first two segments, and the third will be given the name my_job. Note that the directory specifications include terminal slashes.

Due to limitations in current UNIX implementations, -1 should be used with caution, as it will attempt to extend a file segment beyond all remaining disk capacity on these systems; using it will also have the side effect of keeping any additional file segments included in the list from ever being used.

Saving and Deleting Scratch Files

By default, unnamed scratch files are deleted at the end of the Gaussian run, and named files are saved. The %NoSave command may be used to change this default behavior. When this directive is included in an input file, named scratch files whose directives appear in the input file before %NoSave will be deleted at the end of a run (as well as all unnamed scratch files). However, if the % directive naming the file appears after the %NoSave directive, the file will be retained. For example, these commands specify a name for the checkpoint file, and an alternate name and directory location for the read-write file, and cause only the checkpoint file to be saved at the conclusion of the Gaussian job:

%RWF=/chem/scratch2/water          Files to be deleted go here. 
%NoSave 
%Chk=water                         Files to be saved go here. 

Initialization Files

The Gaussian system includes initialization files to set up the user environment for running the program. These files are:

$g03root/g03/bsd/g03.login                C shell 
$g03root/g03/bsd/g03.profile              Bourne shell 

Note that the g03root environment variable must be set up by the user. Thus, it is customary to include lines like the following within the .login or .profile file for Gaussian users:

.login  files: 
setenv g03root location 
source $g03root/g03/bsd/g03.login 

.profile files: 
g03root=location 
export g03root 
. $g03root/g03/bsd/g03.profile 

Once things are set up correctly, the g03 command is used to execute Gaussian 03 (see below).

Controlling Memory Usage

The %Mem command controls the amount of dynamic memory to be used by Gaussian. By default, 6 megawords are used. This can be changed to n double-precision words by specifying:

%Mem=n 

For example, the following command sets memory use to 64 million bytes:

%Mem=8000000 

The value given to %Mem may also be followed by KB, KW, MB, MW, GB or GW (no intervening spaces) to denote other units. For example, the following command also sets the amount of dynamic memory to 64 MB:

%Mem=64MB 

Even larger allocations may be needed for very large direct SCF calculations-at least 3N² words, where N is the number of basis functions. Frequency and post-SCF calculations involving f functions should be given 6 MWords if possible. Using more than 6 million words for moderate-sized calculations (i.e., a direct SCF with less than 500 basis functions) does not improve performance on most systems.

Warning: Requesting more memory than the amount of physical memory actually available on a computer system will lead to very poor performance.

If Gaussian is being used on a machine with limited physical memory, so that the default of 48 MB is not available, the default algorithms as well as the default memory allocation should be set appropriately during installation. See this page for more details on using Gaussian efficiently.

Gaussian 03 Links

The following table lists the component programs of Gaussian 03—known as links—along with their primary functions: