Undergraduate Research at UA in the Dixon Group in Chemistry David Dixon Robert Ramsay Chair

Undergraduate Research at UA in the Dixon Group in ChemistryDavid DixonRobert Ramsay ChairChemistry205-348-8441dadixon@bama.ua.edu

Robert Ramsay Chair Fund

Hydrogen Storage Grand Challenge, Solicitation No. DE-PS36-03GO93013

• 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

• 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

Science Drivers: Science across Scales in Space & Time

Computing Hardware ResourcesSupercomputer #Procs Architecture Mem/Node Disk Storage InterconnectDesktop ~30 Intel Pentium 4 @ 3.4 GHz &

Core 2 Duo @ 2.93 GHz, ATI HD 4650 Pro

2 to 4 GB 2x 160 or 250 GB per desktop

Ethernet

Graphics 4 Intel Quad Core Xeon @ 2.66 GHz, ATI FireGL V7700

8 GB System: 2x 73 GB

Data: 2x 500 GB

Ethernet

UAHPC

(UA)

262 Intel Xeon @ 3.2 GHz (130 nodes)

4 or 6 GB Scratch: 120 GB/node

Storage: 1.4 TB (NFS)

Infiniband

DMC

(ASC/Huntsville)

1,256 AMD Dual Core Opteron @ 3.0 GHz (20 nodes), Quad Core Opteron @ 2.3 GHz (40 nodes)

Intel Quad Core Xeon (Nehalem) @ 2.26 GHz (96 nodes)

64 GB

64 GB

24 GB

Scratch: 1 TB/node + 15 TB (global)

Storage: 4 TB (NFS)

Infiniband

Altix

(ASC/Huntsville)

228 Intel Itanium2 @ 1.4 or 1.5 GHz

Intel Dual Core Itanium2 @ 1.6 GHz

32 to 464 GB

Scratch: 12 TB (global)

Storage: shared with DMC

Infiniband

Colonel

(UA)

136 AMD Quad Core Opteron @ 2.1 GHz (16 nodes)

32 GB Scratch: 2 TB/node

Storage: 4 TB (NFS)

Ethernet

Hope

(UA)

136 Intel Quad Core Xeon @ 2.5 GHz (16 nodes)

16 or 32 GB

Scratch: 2 TB/node

Storage: 4 TB (NFS)

Ethernet

Pople

(UA)

60 Intel Six Core Xeon (Nehalem) @ 2.66 GHz (5 nodes)

48 GB Scratch: 2 TB/node

Storage: 6 TB (NFS)

Ethernet

Chinook

(EMSL/PNNL)

18,480 AMD Quad Core Opteron @ 2.2 GHz (2310 nodes)

32 GB Scratch: 365 GB/node

Storage: 297 TB

Infiniband

Computing Software ResourcesProgram Version Capability Parallel Scalability Runs OnComputational Chemistry Software

Gaussian 09 (source)

DFT, MP2, Gn, Solvation, Transition state, Opt / Freq, etc.

OpenMP, Linda 16 All

Molpro 2009 (source)

CCSD(T), CASSCF, CASPT2, MRCI, etc.

MPI + GA 128 All

NWChem 5.1.1 (source)

CCSD(T), TD-DFT, DFT (Plane wave), Molecular dynamics, etc.

MPI + GA >1024 All

ADF 2009.1 DFT (Slater basis), NMR, Solvation, etc.

MPI 128 DMC/Altix/Colonel/Hope

VASP 5.2 (source)

DFT (plane wave), condensed phase, etc.

MPI 128 All

AGUI by AMPAC

9.2 Semi-empirical methods, graphical user interface, etc.

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

• 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.

3D Reaction Surface PlotManage Molecular Orbitals Surface Adsorption