Undergraduate Research at UA in the Dixon Group

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-PS 36 -03 GO 93013 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 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 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: Ti. O 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

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 Fire. GL V 7700 Mem/Node Disk Storage 2 to 4 GB 2 x 160 or 250 GB per desktop Interconnect Ethernet 8 GB System: 2 x 73 GB Ethernet UAHPC 4 or 6 GB Data: 2 x 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 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 Itanium 2 @ 1. 4 or 1. 5 GHz 32 to 464 Intel Dual Core Itanium 2 @ 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: 6 TB (NFS) Scratch: 365 GB/node Infiniband Storage: 297 TB

Computing Software Resources Program Version Capability Computational Chemistry Software Gaussian 09 (source) Molpro 2009 (source) Parallel Scalability DFT, MP 2, Gn, Solvation, Open. MP, Linda 16 Transition state, Opt / Freq, etc. CCSD(T), CASSCF, CASPT 2, MPI + GA 128 MRCI, etc. Runs On 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 (Slater basis), NMR, Solvation, etc. 5. 2 DFT (plane wave), condensed (source) phase, etc. 9. 2 Semi-empirical methods, graphical user interface, etc. All Other computational chemistry programs – For quantum chemistry: ACES 3, CFour, Columbus, Dalton, GAMESS, Molcas, MPQC, PSI 3, 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 • • 3 D Reaction Surface Plot Surface Adsorption Ampac for fast semi-empirical calculations – Fast and reliable – Many methods: AM 1, MNDO, MINDO 3, PM 3, MNDO/d, RM 1, PM 6, SAM 1, 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, Mol 2, SDF, PDB, CIF – Support many platforms: Windows, Linux, Mac OS X, etc.