workshop on hpc in india impact of hpc on chemistry and environment eluvathingal d. jemmis...
TRANSCRIPT
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 -
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 3
Experiment Theory & Computation - the third stabilizing leg of the research tripod -
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 4
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.
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 5
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
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 6
Theoretical methodologies. Software and Hardware. Problems waiting for Hardware and
Software solutions.
Issues Outside the Holy Grails of HPC
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 7
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.
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 8
Urgency
Bottlenecks: Lack of awareness, expertise, facilities of an appropriate kind.
TWO EXAMPLES
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 9
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
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 10
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
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 11
-30
-20
-10
0
10
20
30
40
50
60
70
5b(TS)
5d(TS)
5c
5d
5b
5c(TS)
5a(TS)
G
(kc
al/m
ol)
5a
X = CH3
X = H
X = SiH3
X = BH2.PH
3
4+HX
4+HX 5 5(TS) 6+XCl
RuP
P
P
PP(OH)3
H
6
[OTf]
RuP
P
P
PP(OH)3
H
H H
H
5d
[OTf]2
Nagaraja, CM; Parameswaran, P; Jemmis, ED; Jagirdar, BR, J. Am. Chem. Soc., 129, 5587, 2007.
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 12
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
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 13
Myers-Saito Cyclization of Ene-Yne-alleneProf. Amit Basak, IIT Kharagpur
Garratt-Braverman Cyclization of Conjugated Bisallenic Sulfone
Quick-Time Files
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 14
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 15
Garratt-Braverman Cyclization of Conjugated Bisallenic Sulfone
Basak, Das, Mallick, JemmisJ. Am. Chem. Soc. 131, 2009 (in press).
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 16
Periodic Table of the Elements
Group**ŹŹŹŹŹŹŹ
Period 1IA1A
18VIIIA8A
1
1
Hhydrogen
1.008
2IIA2A
13IIIA3A
14IVA4A
15VA5A
16VIA6A
17VIIA7A
2
Hehelium4.003
2
3
Lilithium 6.941
4
Beberyllium
9.012
5
Bboron 10.81
6
Ccarbon 12.01
7
Nnitrogen
14.01
8
Ooxygen 16.00
9
Ffluorine 19.00
10
Neneon 20.18
8 9 103
11
Nasodiu m 22.99
12
Mgmagnesium
24.31
3IIIB3B
4IVB4B
5VB5B
6VIB6B
7VIIB7B
------- VIII -------------- 8 -------
11IB1B
12IIB2B
13
Alaluminium
26.98
14
Sisilicon 28.09
15
Pphosphorus
30.97
16
Ssulfur 32.07
17
Clchlorine 35.45
18
Arargon 39.95
4
19
Kpotassium
39.10
20
Cacalcium 40.08
21
Scscandium
44.96
22
Tititanium
47.88
23
Vvanadium
50.94
24
Crchromium
52.00
25
Mnmanganese
54.94
26
Feiron
55.85
27
Cocobalt 58.47
28
Ninickel 58.69
29
Cucopper 63.55
30
Znzinc
65.39
31
Gagallium 69.72
32
Gegermanium
72.59
33
Asarsenic 74.92
34
Seselenium
78.96
35
Brbromine
79.90
36
Krkrypton 83.80
5
37
Rbrubi dium
85.47
38
Srstrontium
87.62
39
Yyttrium 88.91
40
Zrzirconiu m 91.22
41
Nbniobium
92.91
42
Momolybdenum
95.94
43
Tctechnetium
(98)
44
Ruruthenium
101.1
45
Rhrhod ium
102.9
46
Pdpalladium
106.4
47
Agsilver 107.9
48
Cdcadmiu m
112.4
49
Inindium 114.8
50
Sntin
118.7
51
Sbantimon y
121.8
52
Tetellurium
127.6
53
Iiodine 126.9
54
Xexenon 131.3
6
55
Cscaesium
132.9
56
Babarium 137.3
57
La*lanthanum
138.9
72
Hfhafnium
178.5
73
Tatantalum
180.9
74
Wtungsten
183.9
75
Rerhenium
186.2
76
Ososmium 190.2
77
Iriridium 190.2
78
Ptplatinum
195.1
79
Augold
197.0
80
Hgmercury
200.5
81
Tlthallium 204.4
82
Pblead
207.2
83
Bibismuth 209.0
84
Popoloniu m
(210)
85
Atastatine (210)
86
Rnradon (222)
7
87
Frfrancium
(223)
88
Raradium (226)
89
Ac~actinium
(227)
104
Rfrutherfordium
(257)
105
Dbdubn ium
(260)
106
Sgseaborgium
(263)
107
Bhbohrium
(262)
108
Hshassium
(265)
109
Mtmeitnerium
(266)
110
Dsdarmstadtium
(271)
111
Rgroentgenium
(272)
112
Uubununb ium
(285)
113
Uutunun trium
(284)
114
Uuqununqu adium
(289)
115
Uupununp entium
(288)
116
Uuhununh exium
(292)
117
Uusunun septium
(310)
118
Uuoununo ctium
(294)
Ź
Ź
Lanthanide Series*
58
Cecerium 140.1
59
Prpraseodymium
140.9
60
Ndneodymium
144.2
61
Pmpromethium
(147)
62
Smsamarium
150.4
63
Eueuropiu m
152.0
64
Gdgadol inium
157.3
65
Tbterbium 158.9
66
Dydysprosium
162.5
67
Hoholmium
164.9
68
Ererbium 167.3
69
Tmthul ium 168.9
70
Ybytterbium
173.0
71
Lulutetium
175.0
Actinide Series~
90
Ththorium 232.0
91
Paprotactinium
(231)
92
Uuranium
(238)
93
Npneptuniu m
(237)
94
Pupluton ium
(242)
95
Amamericium
(243)
96
Cmcurium (247)
97
Bkberkelium
(247)
98
Cfcalifornium
(249)
99
Eseinsteinium
(254)
100
Fmfermium
(253)
101
Mdmendelevium
(256)
102
Nonobelium
(254)
103
Lrlawrencium
(257)
Department of Inorganic and Physical Chemistry, Indian Institute of Science
Quic kTime™ and aTIFF (Unc ompres s ed) dec ompres s or
are needed to s ee this pic ture.
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 17
C C
H
HH
H
H
HH
CH
H
H
Benzenoid aromaticsgraphite
Alkanes and Diamond
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 18
What we do not knowPeriodic Table of the Elements
Group**ŹŹŹŹŹŹŹ
Period 1IA1A
18VIIIA8A
1
1
Hhydrogen
1.008
2IIA2A
13IIIA3A
14IVA4A
15VA5A
16VIA6A
17VIIA7A
2
Hehelium4.003
2
3
Lilithium 6.941
4
Beberyllium
9.012
5
Bboron 10.81
6
Ccarbon 12.01
7
Nnitrogen
14.01
8
Ooxygen 16.00
9
Ffluorine 19.00
10
Neneon 20.18
8 9 103
11
Nasodiu m 22.99
12
Mgmagnesium
24.31
3IIIB3B
4IVB4B
5VB5B
6VIB6B
7VIIB7B
------- VIII -------------- 8 -------
11IB1B
12IIB2B
13
Alaluminium
26.98
14
Sisilicon 28.09
15
Pphosphorus
30.97
16
Ssulfur 32.07
17
Clchlorine 35.45
18
Arargon 39.95
4
19
Kpotassium
39.10
20
Cacalcium 40.08
21
Scscandium
44.96
22
Tititanium
47.88
23
Vvanadium
50.94
24
Crchromium
52.00
25
Mnmanganese
54.94
26
Feiron
55.85
27
Cocobalt 58.47
28
Ninickel 58.69
29
Cucopper 63.55
30
Znzinc
65.39
31
Gagallium 69.72
32
Gegermanium
72.59
33
Asarsenic 74.92
34
Seselenium
78.96
35
Brbromine
79.90
36
Krkrypton 83.80
5
37
Rbrubi dium
85.47
38
Srstrontium
87.62
39
Yyttrium 88.91
40
Zrzirconiu m 91.22
41
Nbniobium
92.91
42
Momolybdenum
95.94
43
Tctechnetium
(98)
44
Ruruthenium
101.1
45
Rhrhod ium
102.9
46
Pdpalladium
106.4
47
Agsilver 107.9
48
Cdcadmiu m
112.4
49
Inindium 114.8
50
Sntin
118.7
51
Sbantimon y
121.8
52
Tetellurium
127.6
53
Iiodine 126.9
54
Xexenon 131.3
6
55
Cscaesium
132.9
56
Babarium 137.3
57
La*lanthanum
138.9
72
Hfhafnium
178.5
73
Tatantalum
180.9
74
Wtungsten
183.9
75
Rerhenium
186.2
76
Ososmium 190.2
77
Iriridium 190.2
78
Ptplatinum
195.1
79
Augold
197.0
80
Hgmercury
200.5
81
Tlthallium 204.4
82
Pblead
207.2
83
Bibismuth 209.0
84
Popoloniu m
(210)
85
Atastatine (210)
86
Rnradon (222)
7
87
Frfrancium
(223)
88
Raradium (226)
89
Ac~actinium
(227)
104
Rfrutherfordium
(257)
105
Dbdubn ium
(260)
106
Sgseaborgium
(263)
107
Bhbohrium
(262)
108
Hshassium
(265)
109
Mtmeitnerium
(266)
110
Dsdarmstadtium
(271)
111
Rgroentgenium
(272)
112
Uubununb ium
(285)
113
Uutunun trium
(284)
114
Uuqununqu adium
(289)
115
Uupununp entium
(288)
116
Uuhununh exium
(292)
117
Uusunun septium
(310)
118
Uuoununo ctium
(294)
Ź
Ź
Lanthanide Series*
58
Cecerium 140.1
59
Prpraseodymium
140.9
60
Ndneodymium
144.2
61
Pmpromethium
(147)
62
Smsamarium
150.4
63
Eueuropiu m
152.0
64
Gdgadol inium
157.3
65
Tbterbium 158.9
66
Dydysprosium
162.5
67
Hoholmium
164.9
68
Ererbium 167.3
69
Tmthul ium 168.9
70
Ybytterbium
173.0
71
Lulutetium
175.0
Actinide Series~
90
Ththorium 232.0
91
Paprotactinium
(231)
92
Uuranium
(238)
93
Npneptuniu m
(237)
94
Pupluton ium
(242)
95
Amamericium
(243)
96
Cmcurium (247)
97
Bkberkelium
(247)
98
Cfcalifornium
(249)
99
Eseinsteinium
(254)
100
Fmfermium
(253)
101
Mdmendelevium
(256)
102
Nonobelium
(254)
103
Lrlawrencium
(257)
Department of Inorganic and Physical Chemistry, Indian Institute of Science
Quic kTime™ and aTIFF (Unc ompres s ed) dec ompres s or
are needed to s ee this pic ture.
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 19
Beta-Rhombohedral Boron,Thermodynamically most stable allotrope
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 20
Percentage of partially substituted and interstitially occupied sites of different crystal structures of beta-rhombohedral boron
83.33 0.00
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 21
Percentage of partially substituted and interstitially occupied sites of different crystal structures of beta-rhombohedral boron
83.33 0.00
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 22
Percentage of partially substituted and interstitially occupied sites of different crystal structures of beta-rhombohedral boron
83.33 0.00
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 23
Percentage of partially substituted and interstitially occupied sites of different crystal structures of beta-rhombohedral boron
83.33 0.00
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 24
Hardness of Boron close to diamond yet lighter than Aluminium.
How to make it even harder? Applications of Boron plentiful; a lot more anticipated if it can be made even harder.
D.L.V.K. Prasad, M.M. Balakrishnarajan, E D Jemmis, Phys Rev B, 72, 195102 (2005).
83.33%
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 25
Ab initio Molecular Dynamics - eg Car-Parinello (CPMD)
Easier said than done even with moderatelyLarge HPC facility
CMSD
van Setten, Uijttewaal, de Wijs, de Groot, J. Am. Chem. Soc., 2007, 129, 2458.
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 26
2005 APS March MeetingMonday–Friday, March 21–25, 2005; Los Angeles, CASession B11:High Pressure I11:15 AM–2:15 PM, Monday, March 21, 2005
Abstract: B11.00001 : Boron a frustrated element: ab-initio study of pressure induced amorphization
Authors: Tadashi Ogitsu Francois Gygi Giulia Galli (Lawrence Livermore National Laboratory)
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.
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 27
Percentage of partially substituted and interstitially occupied sites of different crystal structures of beta-rhombohedral boron
83.33 0.00
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 28
*Here percentage of occupancy has [12] fold symmetry.
Site No [symmetry multiplicity] % of occupancy
# of e- Vol (Ao)
No Crystal structure
13[6] 16[6] A[2] E[2] D[6]
1 Li8 B103.44a 64.00 10.00 0.000 100.0 100.0 318.32 834.765 2 Cu3.72 B103.92b 61.10 20.90 6.100 50.50 22.1,10* 319.12 829.963 3 Cu4.14 B103.92c 69.00 13.00 8.000 61.00 22.0,12* 320.04 833.415 4 Fe2.12 B103.36d 72.60 0.000 50.70 0.000 18.50 316.44 826.105 5 Hf2.07 B103.42e 65.50 8.100 0.500 9.800 31.10 314.40 835.689 6 Zr2.04 B103.04f 52.80 14.50 0.000 18.10 27.90 313.20 832.377 7 Cr2.52 B103.30g 71.17 0.000 71.90 0.000 18.00 314.94 831.321 8 Li8Be3 B102h 100.0 0.000 100.0 100.0 0.000 320.00 815.339 9 Li10CB102
h 100.0 0.000 100.0 100.0 0.000 320.00 807.985
E. D. Jemmis, D. L. V. K. Prasad, J. Solid State Chemistry, 179, 2768, (2006).
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 29
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.
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 30
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
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 31
Acknowledgements
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 32
THANK YOU FOR YOUR KIND ATTENTION
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 33
2020
Cost
Year
1950 2100
ComputationExperiment
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 34
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
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 35
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)
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 36
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)
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 37
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
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 38
Collaborations
Centre for Advanced Scientific Computing and Modelling (CASCam), University of North Texas Prof. Tom Cundari G. S. Srinivasan
Computational Material Science, Metal borides
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 39
Jemmis ATIP 1st Workshop on HPC in India @ SC-09 40
INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCHHTTP://WWW.IISERTVM.AC.IN
THIRUVANANTHAPURAM