Transcript Slide 1

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 Workshop
1st Workshop on
on HPC
India
@ SC-09
HPCin in
India
Experiment
Theory
&
Computation - the third leg of the research tripod -
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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Experiment
Theory
&
Computation - the third stabilizing leg of the research tripod -
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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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.
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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Issues Outside the
Holy Grails of HPC
 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.
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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Issues Outside the
Holy Grails of HPC
 Theoretical methodologies.
 Software and Hardware.
 Problems waiting for Hardware and
Software solutions.
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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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.
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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Urgency
 Bottlenecks: Lack of awareness,
expertise, facilities of an appropriate
kind.
TWO EXAMPLES
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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A Case History
L
H
B
SiRR'R"
P
P
Ru
P
P
P(OH) 3
1
H
[OTf] 2
+
CD 2 Cl2
P
RR'R"SiH
P
[OTf] 2
P
Ru
P
P
P(OH ) 3
R = Et, R' = R" = Me
R = R' = R" = Et
H
P
P
P
Ru
P
P
P(OH)3
1
[OTf]2
+
.
H3B L
THF
P
P
P
P(OH)3
L = PMe3, PPh3
T > 303 K
[OTf]
H
P
P
[OTf]
Ru
P
P(OH ) 3
[OTf]2
Ru
P
Ru
P
H
H
P
P
P(OH)3
2
2
+
RR'R"SiOTf
+
.
[H2(OTf)B 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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ATIP 1st Workshop on HPC in India @ SC-09
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Activation of Small Molecules - CH4,SiH4,BH3-NH3
Important - in view of the dwindling Petrochemical feedstocks.
Ru complex activates
SiH4, not CH4.
Strategy is to reduce
Activation barrier for C-H
Bond activation, using clues
from electronic structure
calculations
Transition state for CH4
~40.4 kcal/mol
Transition state for SiH4
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ATIP 1st Workshop on HPC in India @ SC-09
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70
5d(TS)
60
H
 G (kcal/mol)
50
H
40
30
20
H
P
P
H
5d
4+HX
-10
5b
5a
5c(TS)
5a(TS)
P
P(OH)3
6
X = CH3
5b(TS)
X= H
5c
X = SiH
3
X = BH2.PH3
-20
-30
[OTf]
Ru
P
P
P(OH)3
5d
P
P
[OTf]2
Ru
P
10
0
H
4+HX
5
5(TS)
6+XCl
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
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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
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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Quick-Time Files
Myers-Saito Cyclization
of Ene-Yne-allene
Prof. Amit Basak, IIT Kharagpur
Jemmis
Garratt-Braverman
Cyclization of Conjugated
Bisallenic Sulfone
ATIP 1st Workshop on HPC in India @ SC-09
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Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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Garratt-Braverman Cyclization
of Conjugated Bisallenic Sulfone
Basak, Das, Mallick, Jemmis
J. Am. Chem. Soc. 131, 2009 (in press).
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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Periodic Table of the Elements
Group**
ŹŹŹŹŹŹ
Ź
Period
1
1
IA
1A
1
H
hydrogen
1.008
2
3
4
5
6
7
Qu i c k T i m e ™ a n d a
T I F F (Un c o m p re s s e d ) d e c o m p re s s o r
a re n e e d e d t o s e e t h i s p i c tu re .
2
IIA
2A
13
IIIA
3A
14
IVA
4A
15
VA
5A
16
VIA
6A
17
VIIA
7A
18
VIIIA
8A
2
He
helium
4.003
3
4
5
6
7
8
9
10
Li
Be
B
C
N
O
F
Ne
lithium
6.941
beryllium
9.012
boron
10.81
carbon
12.01
nitrogen
14.01
oxygen
16.00
fluorine
19.00
neon
20.18
11
12
13
14
15
16
17
18
Na
Mg
sodium
22.99
magnesium
24.31
3
IIIB
3B
4
IVB
4B
5
VB
5B
6
VIB
6B
7
VIIB
7B
8
9
10
------- VIII ------------- 8 -------
11
IB
1B
12
IIB
2B
Al
Si
P
S
Cl
Ar
aluminium
26.98
silicon
28.09
phosphorus
30.97
sulfur
32.07
chlorine
35.45
argon
39.95
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
K
Ca
Sc
Ti
V
Cr
Mn
Fe
Co
Ni
Cu
Zn
Ga
Ge
As
Se
Br
Kr
potassium
39.10
calcium
40.08
scandium
44.96
titanium
47.88
v anadium
50.94
chromium
52.00
manganese
54.94
iron
55.85
cobalt
58.47
nickel
58.69
copper
63.55
zinc
65.39
gallium
69.72
germanium
72.59
arsenic
74.92
selenium
78.96
bromine
79.90
krypton
83.80
37
38
39
Rb
Sr
Y
rubidium
85.47
strontium
87.62
yttrium
88.91
40
Zr
zirconium 91.22
41
42
43
44
45
46
47
48
49
50
51
52
53
Nb
Mo
Tc
Ru
Rh
Pd
Ag
Cd
In
Sn
Sb
Te
I
niobium
92.91
molybdenum
95.94
technetium
(98)
ruthenium
101.1
rhodium
102.9
palladium
106.4
silver
107.9
cadmium
112.4
indium
114.8
tin
118.7
antimony
121.8
tellurium
127.6
iodine
126.9
54
Xe
xenon 131.3
55
56
57
72
73
74
75
76
77
78
79
80
81
82
83
84
Cs
Ba
La*
Hf
Ta
W
Re
Os
Ir
Pt
Au
Hg
Tl
Pb
Bi
Po
caesium
132.9
barium
137.3
lanthanum
138.9
hafnium
178.5
tantalum
180.9
tungsten
183.9
rhenium
186.2
osmium
190.2
iridium
190.2
platinum
195.1
gold
197.0
mercury
200.5
thallium
204.4
lead
207.2
bismuth
209.0
polonium
(210)
astatine (210)
radon
(222)
87
88
89
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
Fr
Ra
Ac~
Rf
Db
Sg
Bh
Hs
Mt
Ds
Rg
Uuq
Uup
Uuh
francium
(223)
radium
(226)
actinium
(227)
rutherfordium
(257)
dubnium
(260)
seaborgium
(263)
bohrium
(262)
hassium
(265)
meitnerium
(266)
darmstadtium
(271)
roentgenium
(272)
ununquadium
(289)
ununpentium
(288)
ununhexium
(292)
Uub Uut
ununbium
(285)
ununtrium
(284)
85
At
86
Rn
Uus Uuo
ununseptium
(310)
ununoctium
(294)
Ź
Ź
Lanthanide Series*
Actinide Series~
58
59
60
61
62
63
64
65
66
67
68
69
70
71
Ce
Pr
Nd
Pm
Sm
Eu
Gd
Tb
Dy
Ho
Er
Tm
Yb
Lu
cerium
140.1
praseodymium
140.9
neodymium
144.2
promethium
(147)
samarium
150.4
europium
152.0
gadolinium
157.3
terbium
158.9
dysprosium
162.5
holmium
164.9
erbium
167.3
thulium
168.9
ytterbium
173.0
lutetium
175.0
95
96
90
91
92
93
94
Th
Pa
U
Np
Pu
thorium
232.0
protactinium
(231)
uranium
(238)
neptunium
(237)
plutonium
(242)
Am Cm
americium
(243)
curium
(247)
97
98
99
100
101
102
103
Bk
Cf
Es
Fm
Md
No
Lr
berkelium
(247)
californium
(249)
einsteinium
(254)
fermium
(253)
mendelevium
(256)
nobelium
(254)
lawrencium
(257)
Department of Inorganic and Physical Chemistry, Indian Institute of Science
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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Benzenoid aromatics
graphite
Alkanes and Diamond
H
H
H
H
H
C
C
H
H
Jemmis
H
ATIP 1st Workshop on HPC in India @ SC-09
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C
H
17
What we do not know
Periodic Table of the Elements
Group**
ŹŹŹŹŹŹ
Ź
Period
1
1
IA
1A
1
H
hydrogen
1.008
2
3
4
5
6
7
Qu i c k T i m e ™ a n d a
T I F F (Un c o m p re s s e d ) d e c o m p re s s o r
a re n e e d e d t o s e e t h i s p i c tu re .
2
IIA
2A
13
IIIA
3A
14
IVA
4A
15
VA
5A
16
VIA
6A
17
VIIA
7A
18
VIIIA
8A
2
He
helium
4.003
3
4
5
6
7
8
9
10
Li
Be
B
C
N
O
F
Ne
lithium
6.941
beryllium
9.012
boron
10.81
carbon
12.01
nitrogen
14.01
oxygen
16.00
fluorine
19.00
neon
20.18
11
12
13
14
15
16
17
18
Na
Mg
sodium
22.99
magnesium
24.31
3
IIIB
3B
4
IVB
4B
5
VB
5B
6
VIB
6B
7
VIIB
7B
8
9
10
------- VIII ------------- 8 -------
11
IB
1B
12
IIB
2B
Al
Si
P
S
Cl
Ar
aluminium
26.98
silicon
28.09
phosphorus
30.97
sulfur
32.07
chlorine
35.45
argon
39.95
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
K
Ca
Sc
Ti
V
Cr
Mn
Fe
Co
Ni
Cu
Zn
Ga
Ge
As
Se
Br
Kr
potassium
39.10
calcium
40.08
scandium
44.96
titanium
47.88
v anadium
50.94
chromium
52.00
manganese
54.94
iron
55.85
cobalt
58.47
nickel
58.69
copper
63.55
zinc
65.39
gallium
69.72
germanium
72.59
arsenic
74.92
selenium
78.96
bromine
79.90
krypton
83.80
37
38
39
Rb
Sr
Y
rubidium
85.47
strontium
87.62
yttrium
88.91
40
Zr
zirconium 91.22
41
42
43
44
45
46
47
48
49
50
51
52
53
Nb
Mo
Tc
Ru
Rh
Pd
Ag
Cd
In
Sn
Sb
Te
I
niobium
92.91
molybdenum
95.94
technetium
(98)
ruthenium
101.1
rhodium
102.9
palladium
106.4
silver
107.9
cadmium
112.4
indium
114.8
tin
118.7
antimony
121.8
tellurium
127.6
iodine
126.9
54
Xe
xenon 131.3
55
56
57
72
73
74
75
76
77
78
79
80
81
82
83
84
Cs
Ba
La*
Hf
Ta
W
Re
Os
Ir
Pt
Au
Hg
Tl
Pb
Bi
Po
caesium
132.9
barium
137.3
lanthanum
138.9
hafnium
178.5
tantalum
180.9
tungsten
183.9
rhenium
186.2
osmium
190.2
iridium
190.2
platinum
195.1
gold
197.0
mercury
200.5
thallium
204.4
lead
207.2
bismuth
209.0
polonium
(210)
astatine (210)
radon
(222)
87
88
89
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
Fr
Ra
Ac~
Rf
Db
Sg
Bh
Hs
Mt
Ds
Rg
Uuq
Uup
Uuh
francium
(223)
radium
(226)
actinium
(227)
rutherfordium
(257)
dubnium
(260)
seaborgium
(263)
bohrium
(262)
hassium
(265)
meitnerium
(266)
darmstadtium
(271)
roentgenium
(272)
ununquadium
(289)
ununpentium
(288)
ununhexium
(292)
Uub Uut
ununbium
(285)
ununtrium
(284)
85
At
86
Rn
Uus Uuo
ununseptium
(310)
ununoctium
(294)
Ź
Ź
Lanthanide Series*
Actinide Series~
58
59
60
61
62
63
64
65
66
67
68
69
70
71
Ce
Pr
Nd
Pm
Sm
Eu
Gd
Tb
Dy
Ho
Er
Tm
Yb
Lu
cerium
140.1
praseodymium
140.9
neodymium
144.2
promethium
(147)
samarium
150.4
europium
152.0
gadolinium
157.3
terbium
158.9
dysprosium
162.5
holmium
164.9
erbium
167.3
thulium
168.9
ytterbium
173.0
lutetium
175.0
95
96
90
91
92
93
94
Th
Pa
U
Np
Pu
thorium
232.0
protactinium
(231)
uranium
(238)
neptunium
(237)
plutonium
(242)
Am Cm
americium
(243)
curium
(247)
97
98
99
100
101
102
103
Bk
Cf
Es
Fm
Md
No
Lr
berkelium
(247)
californium
(249)
einsteinium
(254)
fermium
(253)
mendelevium
(256)
nobelium
(254)
lawrencium
(257)
Department of Inorganic and Physical Chemistry, Indian Institute of Science
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
18
Beta-Rhombohedral Boron,
Thermodynamically most stable allotrope
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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Percentage of partially substituted and
interstitially occupied sites of different crystal
structures of beta-rhombohedral boron
83.33
Jemmis
0.00
ATIP 1st Workshop on HPC in India @ SC-09
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Percentage of partially substituted and
interstitially occupied sites of different crystal
structures of beta-rhombohedral boron
83.33
Jemmis
0.00
ATIP 1st Workshop on HPC in India @ SC-09
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Percentage of partially substituted and
interstitially occupied sites of different crystal
structures of beta-rhombohedral boron
83.33
Jemmis
0.00
ATIP 1st Workshop on HPC in India @ SC-09
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Percentage of partially substituted and
interstitially occupied sites of different crystal
structures of beta-rhombohedral boron
83.33
Jemmis
0.00
ATIP 1st Workshop on HPC in India @ SC-09
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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.
83.33%
D.L.V.K. Prasad, M.M. Balakrishnarajan, E D Jemmis, Phys Rev B, 72, 195102 (2005).
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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Ab initio Molecular Dynamics eg Car-Parinello (CPMD)
Easier said than done even with moderately
Large 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
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2005 APS March Meeting
Monday–Friday, March 21–
25, 2005; Los Angeles, CA
Session B11:
High Pressure I
11:15 AM–2:15 PM, Monday,
March 21, 2005
2006 APS March Meeting
Monday–Friday, March 13–
17, 2006; Baltimore, MD
Session H31: Simulation of
Complex Materials II
11:15 AM–1:51 PM, Tuesday,
March 14, 2006
2007 APS March Meeting
Monday–Friday, March 5–9,
2007; Denver, Colorado
Session J19: Frontiers in
Electronic Structure Theory I
Abstract: J19.00009 : Bonding in
elemental boron: a view from
Abstract: B11.00001 : Boron a Abstract: H31.00004 : Boron: do electronic structure calculations
frustrated element: ab-initio
we know the ground state
using maximally localized Wannier
study of pressure induced
structure?
functions
amorphization
1:39 PM–1:51 PM
Authors:
Authors:
Authors:
Tadashi Ogitsu
Tadashi Ogitsu
Tadashi Ogitsu
(Lawrence Livermore
(Lawrence Livermore National
Francois Gygi
National Laboratory,
Laboratory)
Giulia Galli
Berkeley)
Francois Gygi
(Lawrence Livermore
(University of California, Davis)
National Laboratory)
John Reed (L L N L)
Eric Schwegler (L L N L)
Giulia Galli
(University of California, Davis)
Blue Gene of several thousands of processors
Ogitsu, Galli et al J. Am. Chem. Soc. 2009, 131.
Jemmis
ATIP 1st Workshop on HPC in India @ SC-09
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Percentage of partially substituted and
interstitially occupied sites of different crystal
structures of beta-rhombohedral boron
83.33
Jemmis
0.00
ATIP 1st Workshop on HPC in India @ SC-09
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No
Crystal structure
Site No [symmetry multiplicity] % of
occupancy
13[6] 16[6] A[2]
E[2]
D[6]
1
Li8 B103.44a
64.00 10.00 0.000 100.0
b
2
Cu3.72 B103.92
61.10 20.90 6.100 50.50
c
3
Cu4.14 B103.92
69.00 13.00 8.000 61.00
d
4
Fe2.12 B103.36
72.60 0.000 50.70 0.000
e
5
Hf2.07 B103.42
65.50 8.100 0.500 9.800
f
6
Zr2.04 B103.04
52.80 14.50 0.000 18.10
g
7
Cr2.52 B103.30
71.17 0.000 71.90 0.000
h
8
Li8Be3 B102
100.0 0.000 100.0 100.0
h
9
Li10CB102
100.0 0.000 100.0 100.0
*
Here percentage of o ccupancyhas [12] fold symmetry.
100.0
22.1,10*
22.0,12*
18.50
31.10
27.90
18.00
0.000
0.000
# of e-
Vol
(Ao)
318.32
319.12
320.04
316.44
314.40
313.20
314.94
320.00
320.00
834.765
829.963
833.415
826.105
835.689
832.377
831.321
815.339
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
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Conclusions
 Advances in many fronts:





Jemmis
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.
ATIP 1st Workshop on HPC in India @ SC-09
29
Acknowledgements
ATIP
R. GOVINDARAJAN
Department of Science and Technology
Centre for Modelling, Simulation and Design,
University of Hyderabad
Supercomputer Education and Research
Centre, Indian Institute of Science
Indian Institute of Science Education and Research
Thiruvananthapuram
Prof. Balaji Jagirdar, Prof. Amit Basak
Parameswaran, Prasad, Mallick
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Acknowledgements
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THANK YOU FOR YOUR
KIND ATTENTION
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Experiment
Computation
Cost
1950
2020
2100
Year
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From the PWSCF.ORG site
To. Prof. Nicola Marzari
Department of Materials Science and Engineering
13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 [email protected] http://quasiamore.mit.edu
From [email protected] Wed Aug 23 19:24:28 2006
Date: Wed, 23 Aug 2006 11:24:28 -0700
Subject: [Wannier] parameter to control convergence
In-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 Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session H31: Simulation of Complex Materials II
11:15 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 Meeting
Monday–Friday, March 5–9, 2007;
Denver, Colorado
Session J19: Frontiers in Electronic
Structure Theory I
Abstract: J19.00009 : Bonding in
elemental boron:
a view from electronic structure
calculations using
maximally localized Wannier functions
1:39 PM–1:51 PM
Authors:
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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Holy Grails
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.
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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 RESEARCH
HTTP://WWW.IISERTVM.AC.IN
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