Preparing, Running a GAMESS Experiment Locally
and Displaying the Results Visually
Authors: Wibke Sudholt, Ilkay Altintas, Kim Baldridge
Major Revision Date: April 10, 2005
1. Problem
In this workflow, we try to run high-throughput calculations of several
molecules with GAMESS quantum chemistry application. When completed,
this will enable us to obtain physical properties of all the molecules involved.
We’ll also be able to display the final(optimized) structures of these molecules
using QMView visualization software..
2. Conceptual Workflow
Select
Molecules
Prepare
GAMESS Input
Run
GAMESS
Display
Results
Figure 1. Conceptual workflow
Figure 2. Local GAMESS Experiment in Kepler
3. Computational Structure
Since this workflow involves running executable programs, it needs actors to run
command line executables. There are two actors in Kepler that can be applied to
do this. The CommandLine actor and the Exec actor. These two actors were
used to run GAMESS, Open Babel, Babel and QMView in the workflow in
Figure2.
The rest of the actors that are used are file system related for directory creation,
file selection, text file creation and writing, etc.
Since a major part of the workflow deals with creating executable scripts and file
name changes, it also depends heavily on Kepler’s string manipulation actors.
4. Executable Workflow
The main interface to the executable workflow for this problem is given in
Figure2.
All the actors that one sees in Figure2, and within the hierarchical levels below
them, are meant to be general for computational chemistry. These are the
parameterized interfaces to run widely used chem. applications.
MoleculeSelector actors is used to select the molecule directory from the file
system.
Babel and Open Babel are molecular file format transformation programs. These
composite actors use Open Babel or Babel to convert between file formats
generated and required as input by different computational chemistry software.
The GAMESS Input Generator actor takes the converted molecule file from Open
Babel and creates a GAMESS input file from it.
GAMESS Local Run actor is a parameterized version of GAMESS execution.You
can double-click to see the parameters and customize when you open the
workflow. This part of the workflow can further be customized to run locally,
through Nimrod, remotely using SSH and/or Globus technologies. These are
planned as future work.
QMView is a graphical chemistry program with features including:
* Viewing of molecular configurations
* Animation of molecular vibrations
* GAMESS interface
* Building and Comparing Structures
* Viewing of molecular electron density data
This workflow is technically different from many other Kepler workflows in the
way that it uses a lot of generic MOML classes. These classes were generated
using very little Java code, mainly by using Kepler as a visual programming
interface to generate composite generic Kepler classes for the related domain.
The workflow is parameterized to allow for molecule selection, for setting the
main scientific parameters, and for parsing the underlying program codes.
5. Running the Workflow
The example input molecules for this workflow are given under your
‘$KEPLER/lib/testdata/resurgence/cml’ directory. The default in the workflow is
also set to this directory.
To run the workflows, you need to have GAMESS, Open Babel, Babel, QMView
installed. The information on how to install and use these are given in the
‘ResurgenceWorkflowPrerequisites.doc’ file under this directory.
After installing the required software applications, you need to set the paths for
each application using the parameters of the actors in the main level.