Undergraduate Research at UA in the
Dixon Group in Chemistry
David Dixon
Robert Ramsay Chair
Chemistry
205-348-8441
dadixon@bama.ua.edu
Hydrogen Storage Grand
Challenge, Solicitation
No. DE-PS36-03GO93013
Robert Ramsay Chair Fund
• Mostly CBHP students – strong math and computing backgrounds
• Many Honors Chemistry CH-117
• Use computational chemistry to solve real problems
• No actual research cost due to presence of computational resources in the Dixon
group, at UA, and at Alabama Supercomputing Center including desktop
computers, servers, massively parallel computers, and software.
• Usually assign student to individual project that meets group research interest
and the student’s interest. If the student wants an individual project, arrange for
that.
• Usually try to get students involved as 2nd semester freshman or 1st semester
sophomores. Try to get students into REU program during the summer if funds
available.
• Pick projects based on students length of stay.
• Assign student to graduate student or postdoctoral mentor.
• Encourage peer-to-peer mentoring
• Try to visit with students in the lab on a regular basis
• Focus on letting students learn how to do research by allowing failure. Acceptable
due to low cost of computer cycles.
• Work with students for publications. Focus on real publications not student ones.
• Work with students on awards.
• Pick projects students can do. If a project requires students to come in and work
every day for a week for 5 to 6 hours a day to get it going, it will not succeed.
Example molecular dynamics of biomolecules. Too hard to get calculations initiated.
• Have excellent GUIs and software.
• Provide students with place to work not only on research.
• Try not to overlap projects.
• Give student independent project.
• Either use CBHP or Departmental effort for formal research training – literature
searching, equipment use, writing.
• Research presentations – CBHP, REU, Department, UA Research Day
Science Drivers: Science across Scales in Space & Time
• Catalysis: Computational catalysis – transition metal oxides, homogeneous catalysts, metal
clusters, site isolated catalysts
• Nanoscience: TiO2 clusters for sensors and photocatalysts; Shape memory alloys (Nitinol)
(NASA)
• Energy: H2 storage in chemical systems – organic & inorganic
• Energy: Advanced Fuel Cycle Initiative – Metal oxide clusters in solution for new fuels and
environmental cleanup
• Energy: New sources of energy (solar)
• Geochemistry: Geological CO2 sequestration
• The Environment: Atmosphere, Clean Water, Subsurface & Cleanup
• Biochemistry: Peptide and amino acid negative ion chemistry
• Computational main group chemistry – fluorine chemistry, acids and bases, other
elements
• Computational thermodynamics and kinetics – high accuracy, solvation effects.
• Chemical End Station: RC3 & software development
Computing Hardware Resources
Supercomputer #Procs Architecture
Desktop
~30
Intel Pentium 4 @ 3.4 GHz &
Core 2 Duo @ 2.93 GHz, ATI
HD 4650 Pro
Graphics
4
Intel Quad Core Xeon @ 2.66
GHz, ATI FireGL V7700
Mem/Node Disk Storage
2 to 4 GB 2x 160 or 250 GB per
desktop
Interconnect
Ethernet
8 GB
System: 2x 73 GB
Ethernet
UAHPC
4 or 6 GB
Data: 2x 500 GB
Scratch: 120 GB/node Infiniband
(UA)
DMC
262
1,256
(ASC/Huntsville)
Altix
228
(ASC/Huntsville)
Colonel
(UA)
Hope
(UA)
Pople
(UA)
Chinook
(EMSL/PNNL)
136
136
60
Intel Xeon @ 3.2 GHz (130
nodes)
AMD Dual Core Opteron @ 3.0 64 GB
GHz (20 nodes), Quad Core
64 GB
Opteron @ 2.3 GHz (40 nodes)
24 GB
Intel Quad Core Xeon
(Nehalem) @ 2.26 GHz (96
nodes)
Intel Itanium2 @ 1.4 or 1.5 GHz 32 to 464
Intel Dual Core Itanium2 @ 1.6 GB
GHz
AMD Quad Core Opteron @ 2.1 32 GB
GHz (16 nodes)
Intel Quad Core Xeon @ 2.5
GHz (16 nodes)
16 or 32
GB
Intel Six Core Xeon (Nehalem)
@ 2.66 GHz (5 nodes)
48 GB
18,480 AMD Quad Core Opteron @ 2.2 32 GB
GHz (2310 nodes)
Storage: 1.4 TB (NFS)
Scratch: 1 TB/node + Infiniband
15 TB (global)
Storage: 4 TB (NFS)
Scratch: 12 TB (global) Infiniband
Storage: shared with
DMC
Scratch: 2 TB/node
Ethernet
Storage: 4 TB (NFS)
Scratch: 2 TB/node
Ethernet
Storage: 4 TB (NFS)
Scratch: 2 TB/node
Ethernet
Storage: 6 TB (NFS)
Scratch: 365 GB/node Infiniband
Storage: 297 TB
Computing Software Resources
Program Version Capability
Computational Chemistry Software
Parallel
Gaussian 09
(source)
Molpro
2009
(source)
OpenMP, Linda 16
All
MPI + GA
128
All
NWChem 5.1.1
CCSD(T), TD-DFT, DFT (Plane MPI + GA
(source) wave), Molecular dynamics, etc.
>1024
All
ADF
MPI
128
DMC/Altix/Colonel/Hope
MPI
128
All
2009.1
VASP
AGUI by
AMPAC
•
•
DFT, MP2, Gn, Solvation,
Transition state, Opt / Freq, etc.
CCSD(T), CASSCF, CASPT2,
MRCI, etc.
DFT (Slater basis), NMR,
Solvation, etc.
5.2
DFT (plane wave), condensed
(source) phase, etc.
9.2
Semi-empirical methods,
graphical user interface, etc.
Scalability
Runs On
All
Other computational chemistry programs
– For quantum chemistry: ACES3, CFour, Columbus, Dalton, GAMESS, Molcas,
MPQC, PSI3, etc.
– For molecular dynamics: CPMD, Espresso, NAMD, Tinker, ZORI, etc.
– Khimera – interface to Gaussian to do kinetics modeling
Software for program development
– Intel C/C++/Fortran compilers, MKL/IPP/TBB libraries;
– PGI C/C++/Fortran compilers, ACML libraries
Ampac / Agui from Semichem
Manage Molecular Orbitals
•
•
3D Reaction Surface Plot
Surface Adsorption
Ampac for fast semi-empirical calculations
– Fast and reliable
– Many methods: AM1, MNDO, MINDO3, PM3, MNDO/d, RM1, PM6,
SAM1, MNDOC
– Geometry optimization, frequencies, transition state, IRC, solvation,
etc.
Agui for molecular visualization
– Support most features of Gaussian 09 including periodic systems,
ONIOM, etc.
– Support many file formats including Mol, Mol2, SDF, PDB, CIF
– Support many platforms: Windows, Linux, Mac OS X, etc.