HowTo:gamess

Gamess (US)

This is an introduction to the usage of the electronic-structure code "Gamess" on the HPCVL clusters. It is meant as an initial pointer to more detailed information, and to get started. It does not replace study of the manual.

Features The "General Atomic and Molecular Electronic Structure System" (GAMESS) is a quantum chemistry software package that was assembled from various older codes (in particular, HONDO) by M. Dupuis, D. Spangler, and J. J. Wendoloski of the National Resources for Computations in Chemistry (NRCC). The code has undergone great changes since then and is maintained now by the Gordon Research Group at Iowa State University. Gamess performs a great many of standard quantum chemical calculations. These include: RHF, UHF, ROHF, GVB, or MCSCF self-consistent calculations. CI or MP2 corrections to the energy. Semi-empirical MNDO, AM1, or PM3 methods. Analytic energy gradients for SCF, MP2 or CI. Geometry optimizations, saddle point searches, and vibrational frequencies. Intrinsic reaction paths, gradient extremal curves, and dynmic reaction coordinates. Many molecular properties, such as densities, electrostatic potentials, dipole moments, etc. Modelling of solvent effects and electric fields. For a complete list of capabilities of GAMESS, consult this table or look at the Gamess documentation. Gamess is described in General Atomic and Molecular Electronic Structure System; M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.Su, T.L.Windus, M.Dupuis, J.A.Montgomery; J. Comput. Chem. 14, 1347-1363 (1993) and Advances in electronic structure theory: GAMESS a decade later; M.S.Gordon, M.W.Schmidt pp. 1167-1189 in Theory and Applications of Computational Chemistry: the first forty years; C.E.Dykstra, G.Frenking, K.S.Kim, G.E.Scuseria (editors), Elsevier, Amsterdam, 2005. Location of the program and setup The program resides in /opt/gamess and is called gamess.01.x. You also find some test examples in the program directory, which are useful to get an idea of the input format for the program. You are not allowed to copy the executable or any part of the distribution onto your local machine. However you can easily obtain the program yourself. See the GAMESS source code distribution page. Unlike other programs, no special setup is needed to run Gamess. All environment variables etc. are set with an execution script that will be described in the next section. However, it is a good idea to put the directory with the Gamess program into the path, i.e. set the PATH environment variable. This is best done through the usepackage utility, simply by typing use gamess Scratch files When you run Gamess a scratch space directory is set to /scratch/$USER and all temporary files and intermediate output will be placed in that directory. The program also requires a local temporary directory right below your home directory called $USER/scr. Make sure that you move files that you want to keep from there before running Gamess again with the same case_name. The second run requires that some temporary files be removed before re-run and will fail if they are still present in the scratch directory. For instance, if your username is "hpc9876", you will need "/scratch/hpc9876" and "/home/hpc9876/scr". Note that the former is automatically created when you obtain an account, but the latter has to be made by you explicitly.

Running Gamess from a command line To run Gamess, a script file rungms is used. This file resides in the same directory as the gamess.00.x executable. Assuming that the home of the script file and executable is in your path, all you need to do is type rungms case_name 01 n_procs where case_name is the name of the input file (file extension is assumed to be .inp and must not be specified), and n_procs stands for the number of processes to be used in a parallel Gamess run. If n_procs=1 a serial run will be performed. Note: It is absolutely essential to have a good idea about the size and complexity of your calculations before you start a Gamess job. Many of the methods have terrible scaling properties, i.e. the computational cost grows very quickly with the number of electrons, degrees of freedom, or number of basis functions used. We suggest you start with a small basis set and a cheap method, and then slowly increase those parameters. Submitting (parallel) Gaussian jobs If you want to run Gaussian on several processors on our machines, you have to include a line in your input file: %nproc=8 where we assume that you want to use 8 processors (cores, threads). It is mandatory to submit a Gaussian job script through our scheduling software (see our Scheduler Help File for details). Here is a "bare bones" sample of a Gaussian submission script: #! /bin/bash #$ -S /bin/bash #$ -q abaqus.q #$ -l qname=abaqus.q #$ -cwd #$ -V #$ -M hpcXXXX@localhost #$ -m be #$ -o STD.out #$ -e STD.err #$ -pe shm.pe 8 g09 < sample.g09 > sample.log The first 6 lines of the script make sure the right shell is used, the program executes on the correct cluster, and all necessary setup is done. An email address for notifications is specified in the #$ -M line. We suggest "hpcXXXX@localhost" (hpcXXXX stands for the username). Place a file .forward containing your actual email address into your home directory. The -o and -e lines are used to tell the system where to write "standard output" and "standard error", i.e. the screen output. The #$ -pe gaussian.pe 8 line specifies the number of processors the scheduler will allocate (8 in this example). It is crucial to choose the same number as specified in the %nrocs= line of the input file. The script (let's call it g09.sh) is submitted by the qsub command: qsub g09.sh This must be done from the working directory, i.e. the directory that contains the input file and is supposed to contain the output. Also make sure that you have set up gaussian (use g09) before you submit a job.

Licensing Gaussian is a licensed program. The license held by the Centre for Advanced Computing is limited to our computers at our main site. That means that any of our users can use the program on our machines (but nowhere else), whether they are located at Queen's or not. We require users of Gaussian to sign a statement in which they state that they are informed about the terms of the license to be included in the Gaussian user group named "g98". Please fax the completed statement to (613) 533-2015 or scan/email to cac.admin@queensu.ca. Where can I get more detailed information ? To learn the basics about Gaussian input and output, refer to the Gaussian 09 User's Reference. For templates, and to get many examples, check out /opt/gaussian/g09/bsd/examples. The Gaussian web page contains a lot of information. For hardcore computational chemists, there is the Gaussian IOPs Reference, useful if you want to tinker with default settings and internal parameters. These can be purchased from Gaussian Inc.. Send to cac.help@queensu.ca. We're happy to help.