workshop on hpc in india impact of hpc on chemistry and environment eluvathingal d. jemmis...

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 -


Experiment Theory & Computation - the third stabilizing leg of the research tripod -


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.


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


Theoretical methodologies. Software and Hardware. Problems waiting for Hardware and

Software solutions.

Issues Outside the Holy Grails of HPC


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.


Urgency

Bottlenecks: Lack of awareness, expertise, facilities of an appropriate kind.

TWO EXAMPLES


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


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


-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.


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


Myers-Saito Cyclization of Ene-Yne-alleneProf. Amit Basak, IIT Kharagpur

Garratt-Braverman Cyclization of Conjugated Bisallenic Sulfone

Quick-Time Files


Garratt-Braverman Cyclization of Conjugated Bisallenic Sulfone

Basak, Das, Mallick, JemmisJ. Am. Chem. Soc. 131, 2009 (in press).


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.


C C

H

HH

H

H

HH

CH

H

H

Benzenoid aromaticsgraphite

Alkanes and Diamond


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.


Beta-Rhombohedral Boron,Thermodynamically most stable allotrope


Percentage of partially substituted and interstitially occupied sites of different crystal structures of beta-rhombohedral boron

83.33 0.00



83.33 0.00


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%


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.


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.



83.33 0.00


*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).


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.


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


Acknowledgements


THANK YOU FOR YOUR KIND ATTENTION


2020

Cost

Year

1950 2100

ComputationExperiment


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


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)


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)


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


Collaborations

Centre for Advanced Scientific Computing and Modelling (CASCam), University of North Texas Prof. Tom Cundari G. S. Srinivasan

Computational Material Science, Metal borides



INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCHHTTP://WWW.IISERTVM.AC.IN

THIRUVANANTHAPURAM

workshop on hpc in india impact of hpc on chemistry and environment eluvathingal d. jemmis...

Documents

india impact of hpc

holy grails of hpc slide

materials slide

iisc slide

research tripod slide

hh bonds

stabilizing leg

ch bonds