Undergraduate Research at UA in the Dixon Group in Chemistry David Dixon Robert Ramsay Chair Chemistry 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 2 nd semester freshman or 1 st 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: TiO 2 clusters for sensors and photocatalysts; Shape memory alloys (Nitinol) (NASA) Energy: H 2 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 CO 2 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: RC 3 & software development Science Drivers: Science across Scales in Space & Time

Computing Hardware Resources Supercomputer#ProcsArchitectureMem/NodeDisk StorageInterconnect Desktop~30Intel Pentium 3.4 GHz & Core GHz, ATI HD 4650 Pro 2 to 4 GB2x 160 or 250 GB per desktop Ethernet Graphics4Intel Quad Core 2.66 GHz, ATI FireGL V GBSystem: 2x 73 GB Data: 2x 500 GB Ethernet UAHPC (UA) 262Intel 3.2 GHz (130 nodes) 4 or 6 GBScratch: 120 GB/node Storage: 1.4 TB (NFS) Infiniband DMC (ASC/Huntsville) 1,256AMD Dual Core 3.0 GHz (20 nodes), Quad Core 2.3 GHz (40 nodes) Intel Quad Core Xeon 2.26 GHz (96 nodes) 64 GB 24 GB Scratch: 1 TB/node + 15 TB (global) Storage: 4 TB (NFS) Infiniband Altix (ASC/Huntsville) 228Intel 1.4 or 1.5 GHz Intel Dual Core 1.6 GHz 32 to 464 GB Scratch: 12 TB (global) Storage: shared with DMC Infiniband Colonel (UA) 136AMD Quad Core 2.1 GHz (16 nodes) 32 GBScratch: 2 TB/node Storage: 4 TB (NFS) Ethernet Hope (UA) 136Intel Quad Core 2.5 GHz (16 nodes) 16 or 32 GB Scratch: 2 TB/node Storage: 4 TB (NFS) Ethernet Pople (UA) 60Intel Six Core Xeon 2.66 GHz (5 nodes) 48 GBScratch: 2 TB/node Storage: 6 TB (NFS) Ethernet Chinook (EMSL/PNNL) 18,480AMD Quad Core 2.2 GHz (2310 nodes) 32 GBScratch: 365 GB/node Storage: 297 TB Infiniband

Computing Software Resources ProgramVersionCapabilityParallelScalabilityRuns On Computational Chemistry Software Gaussian09 (source) DFT, MP2, Gn, Solvation, Transition state, Opt / Freq, etc. OpenMP, Linda16All Molpro2009 (source) CCSD(T), CASSCF, CASPT2, MRCI, etc. MPI + GA128All NWChem5.1.1 (source) CCSD(T), TD-DFT, DFT (Plane wave), Molecular dynamics, etc. MPI + GA>1024All ADF2009.1DFT (Slater basis), NMR, Solvation, etc. MPI128DMC/Altix/Colonel/Hope VASP5.2 (source) DFT (plane wave), condensed phase, etc. MPI128All AGUI by AMPAC 9.2Semi-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 OrbitalsSurface Adsorption