Gaussian 03 Calculations using
GridNexus
Ned H. Martin
Department of Chemistry and Biochemistry
University of North Carolina at Wilmington
Grid Computing
Rationale for Grid Computing
The recent proliferation* of fast, interconnected underutilized cpus
14000
12000
10000
8000
MIPS
6000
ts/104
Series2
4000
2000
0
1960 1970
1980 1990
2000 2010
* over 150,000,000 pcs are sold each year!
Grid Computing
A computing Grid is
analogous to an electrical
power grid. The user
simply “taps” into the
resource (with permission),
but is usually unaware of
the origin of the resource.
Grid Computing at UNCW
Current efforts by a group of UNCW computer
science faculty and undergraduate students, plus
faculty and students in several “application areas”
are focused on developing a graphical user interface
(GUI) called GridNexus as a front-end to simplify
data manipulations, searching or calculations of
various types performed on remote computers over
a Grid.
This project has grant support from the UNC Office
of the President
GridNexus
GridNexus is based on JXPL, a new graphical
programming language developed by UNCW
computer science faculty and students.
GridNexus allows users to link modules that perform
various operations into a usable ‘workflow’, then
save these for later use. Once a ‘workflow’ has been
created, one only need to specify the path/filename of
the data set to be operated on and the path/filename
for the output file.
This greatly simplifies repetitive operations, and
takes much of the mystery out of computing for
non-computer science users.
File Interconversion in GridNexus
One of the limitations of
most computational chemistry
software packages is that they
do not read or write many
different (proprietary) file types,
so it is difficult to transfer data
from one program to another.
GridNexus allows users to
input the most common types of
geometry specification, such as
.pdb (.ent) and .mol files, and
use a default set of options (or
select from a list) to write a
Gaussian input file (.dat). The
structure can be oriented in
XYZ coordinates as desired.
Gaussian 03 under GridNexus
Molecule Orientation in GridNexus
One module allows a molecule to be oriented in Cartesian space
in a specified way, then writes a proper Gaussian03 input file.
Gaussian 03 Input File
%chk=tmp/martinn/phenanthreneNH2.chk
# HF/6-31G(d,p) opt freq
Note C & N along the Y axis, the
midpoint of their bond at the origin
phenanthreneNH2
0 1
H
C
H
C
C
N
C
C
C
C
H
H
C
(etc.)
-1.963715
-1.127512
-0.184242
-0.149560
0.000000
0.000000
0.908090
-1.036579
0.971979
1.943981
-1.800364
1.238823
2.993024
-3.198017
-2.730904
-4.593909
-3.501921
-0.715690
0.715690
-2.892498
-1.338948
-1.491079
-3.742718
-0.744862
1.070292
-3.223318
1.280991
0.750482
0.244859
0.166986
0.000000
0.000000
-0.536779
0.691052
-0.702775
-1.057698
1.210005
-1.769705
-1.730309
Gaussian 03 under GridNexus
Submitting a Gaussian job can be as
simple as selecting the input file name
(from a variety of file types) and the
desired output file name.
What’s next for GridNexus?
Develop more “filters” to transform data.
Enhance the graphics for appearance and usability.
Include more software applications.
Extend Grid services to other disciplines.
Include industry and businesses as users and
developers.
Add more computational nodes to the Grid. The goal
is to include all NC institutions of higher learning
Acknowledgements
• UNC-Office of the President
• UNCW College of Arts and Sciences
• UNCW Division of Academic Affairs
•UNCW Department of Chemistry and Biochemistry
• UNCW Information Technology Systems Division (ITSD)
• Microelectronics Center of North Carolina (MCNC)