Upload
amie
View
43
Download
0
Embed Size (px)
DESCRIPTION
Undergraduate Research at UA in the Dixon Group in Chemistry David Dixon Robert Ramsay Chair Chemistry 205-348-8441 [email protected]. Hydrogen Storage Grand Challenge, Solicitation No. DE-PS36-03GO93013. Robert Ramsay Chair Fund. - PowerPoint PPT Presentation
Citation preview
Undergraduate Research at UA in the Dixon Group in ChemistryDavid DixonRobert Ramsay [email protected]
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