Workshop on HPC in India Impact of HPC on Chemistry and Environment Eluvathingal D. Jemmis Department of Inorganic and Physical Chemistry Indian Institute of Science, Bangalore 560 012 And Indian Institute of Science Education and Research Thiruvananthapuram CET Campus, Thiruvananthapuram 695 016 Kerala ATIP 1 st Workshop on HPC in India @ SC-09
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Workshop on HPC in India Impact of HPC on Chemistry and Environment Eluvathingal D. Jemmis Department of Inorganic and Physical Chemistry Indian Institute.
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Workshop on HPC in India
Impact of HPC on Chemistry and EnvironmentEluvathingal D. Jemmis
Department of Inorganic and Physical ChemistryIndian Institute of Science, Bangalore 560 012
AndIndian Institute of Science Education and Research
ThiruvananthapuramCET Campus, Thiruvananthapuram 695 016 Kerala
ATIP 1st Workshop on HPC in India @ SC-09
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 2
Experiment Theory & Computation - the third leg of the research tripod -
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Experiment Theory & Computation - the third stabilizing leg of the research tripod -
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Experiment Theory & Computation - the third stabilizing leg of the research tripod -
Not stabilizing enough in practice.
The third leg reaches the theoretician’s ground often, but not of the experimentalist.
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Urgency. Awareness of the possibilities. Benchmarking of capabilities, not
in terms of cpu-time but in terms of solvable problems and accessibility.
Availability of the hardware and software.
Issues Outside the Holy Grails of HPC
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Theoretical methodologies. Software and Hardware. Problems waiting for Hardware and
Software solutions.
Issues Outside the Holy Grails of HPC
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Urgency
Advances in HPC that are currently available are not applied for various reasons to decide what is the next reaction to be carried out and whether it is going to work.
The current level of development will not give answers to all questions, but what is within the realm of the possible is not attempted.
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Urgency
Bottlenecks: Lack of awareness, expertise, facilities of an appropriate kind.
TWO EXAMPLES
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A Case History
RuP
P
P
P
P(OH)3
RuP
P
P
P
P(OH)3
H
SiRR'R"
RuP
P
P
P
P(OH)3
H
+
1
2
CD2Cl2RR'R"SiH
+RR'R"SiOTf
R = Et, R' = R" = MeR = R' = R" = Et
[OTf] 2 [OTf] 2
[OTf]
RuP
P
P
P
P(OH)3
RuP
P
P
P
P(OH)3
H
B
L
H
H
RuP
P
P
P
P(OH)3
H
[H2(OTf)B.L]
+
1
2
T > 303 K
THF
+
L = PMe3, PPh3
[OTf]2 [OTf]2
[OTf]
H3B.L
Reaction goes with Si-H, B-H and H-H bonds,But not with C-H bonds where it is needed most.4 months of the graduate student’s time and volumes of Chemicals later…
Prof. Balaji Jagirdar, IISc
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Activation of Small Molecules - CH4,SiH4,BH3-NH3
Important - in view of the dwindling Petrochemical feedstocks.
Transition state for SiH4
~40.4 kcal/mol
Transition state for CH4
Ru complex activatesSiH4, not CH4.Strategy is to reduceActivation barrier for C-HBond activation, using clues from electronic structure calculations
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Two week’s CPU time of a 32 Processor Regatta or equivalent and some expertise to do this could have saved time and chemicals. If it can be reduced to a day, it is even better!
NOT AN ISOLATED EXAMPLE. IMPORTANT IN SYNTHESIS OF DRUGS AND MATERIALS
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Myers-Saito Cyclization of Ene-Yne-alleneProf. Amit Basak, IIT Kharagpur
Garratt-Braverman Cyclization of Conjugated Bisallenic Sulfone
Quick-Time Files
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Jemmis ATIP 1st Workshop on HPC in India @ SC-09 15
Garratt-Braverman Cyclization of Conjugated Bisallenic Sulfone
2006 APS March MeetingMonday–Friday, March 13–17, 2006; Baltimore, MDSession H31: Simulation of Complex Materials II11:15 AM–1:51 PM, Tuesday, March 14, 2006
Abstract: H31.00004 : Boron: do we know the ground state structure?
Authors: Tadashi Ogitsu (Lawrence Livermore National Laboratory, Berkeley)
2007 APS March MeetingMonday–Friday, March 5–9, 2007; Denver, ColoradoSession J19: Frontiers in Electronic Structure Theory I
Abstract: J19.00009 : Bonding in elemental boron: a view from electronic structure calculations using maximally localized Wannier functions1:39 PM–1:51 PMAuthors: Tadashi Ogitsu (Lawrence Livermore National Laboratory) Francois Gygi(University of California, Davis)John Reed (L L N L)Eric Schwegler (L L N L)Giulia Galli(University of California, Davis)
Blue Gene of several thousands of processorsOgitsu, Galli et al J. Am. Chem. Soc. 2009, 131.
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Percentage of partially substituted and interstitially occupied sites of different crystal structures of beta-rhombohedral boron
83.33 0.00
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*Here percentage of occupancy has [12] fold symmetry.
E. D. Jemmis, D. L. V. K. Prasad, J. Solid State Chemistry, 179, 2768, (2006).
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Conclusions
Advances in many fronts: Awareness of the possibilities. Availability of the hardware and software. Theoretical methodologies. Software and Hardware. Benchmarking of capabilities, not in terms of
time but in terms of solvable problems.
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Acknowledgements
ATIP R. GOVINDARAJAN
Department of Science and TechnologyCentre for Modelling, Simulation and Design,University of HyderabadSupercomputer Education and ResearchCentre, Indian Institute of ScienceIndian Institute of Science Education and Research Thiruvananthapuram
Prof. Balaji Jagirdar, Prof. Amit BasakParameswaran, Prasad, Mallick
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Acknowledgements
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THANK YOU FOR YOUR KIND ATTENTION
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2020
Cost
Year
1950 2100
ComputationExperiment
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From the PWSCF.ORG site
To. Prof. Nicola Marzari Department of Materials Science and Engineering13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USAtel 617.4522758 fax 2586534 [email protected] http://quasiamore.mit.eduFrom [email protected] Wed Aug 23 19:24:28 2006Date: Wed, 23 Aug 2006 11:24:28 -0700Subject: [Wannier] parameter to control convergenceIn-Reply-To: <[email protected]>References: <[email protected]> <[email protected]>Message-ID: <[email protected]>
Dear Nicola,
Thanks for your quick reply. I'd like to develop chemical intuition of boron crystal from Wannier functions.…. I'm trying to analyze the bonding nature of beta-boron crystal with this way and to compare with known empirical rule for boron chemistry such as mno rule…
Tadashi Ogitsu
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2006 APS March MeetingMonday–Friday, March 13–17, 2006; Baltimore, MD
Session H31: Simulation of Complex Materials II11:15 AM–1:51 PM, Tuesday, March 14, 2006
Abstract: H31.00004 : Boron: do we know the ground state structure?
Abstract: by Tadashi Ogitsu (Lawrence Livermore National Laboratory, Berkeley)
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2007 APS March MeetingMonday–Friday, March 5–9, 2007; Denver, ColoradoSession J19: Frontiers in Electronic Structure Theory I
Abstract: J19.00009 : Bonding in elemental boron: a view from electronic structure calculations using maximally localized Wannier functions1:39 PM–1:51 PMAuthors: Tadashi Ogitsu (Lawrence Livermore National Laboratory) Francois Gygi (University of California, Davis) John Reed (L L N L) Eric Schwegler (L L N L) Giulia Galli (University of California, Davis)
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An experimental problem would demand computational work to get better design strategies, but this will not be attempted if the computation itself is going to involve enormous waiting.
Holy Grails
Collaborations
Centre for Computational Chemistry, University of Georgia Prof. Fritz Schaefer
Metal carbonyls, Nanoclusters
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Collaborations
Centre for Advanced Scientific Computing and Modelling (CASCam), University of North Texas Prof. Tom Cundari G. S. Srinivasan
Computational Material Science, Metal borides
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INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCHHTTP://WWW.IISERTVM.AC.IN