Scidac 2015 progress: Advanced Modeling of ions in ... · PDF fileScidac 2015 progress:...
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Scidac 2015 progress: Advanced Modeling of ions in solutions, on surfaces, and in biological environments
Princeton University: Roberto Car (PI), Weinan E
Temple University: Mike Klein, Xifan Wu (presenting)
LBL: Esmond Ng, Chao Yang, Lin Lin
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Outline
Part I. Projects
Proton transfer of OH- and H3O+ in an accurately modeled H-bond network
X-ray absorption spectra in liquid water by advanced modeling
Part III. Other performed projects and introduction of our posters
Part II. Progress of our team members at LBL
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Proton Transfer through hydronium and hydroxide: Current controversy
PT in H3O+ through
structural diffusion
PT in OH- through
structural diffusion
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Proton Transfer through hydronium and hydroxide: Current controversy
Eigen cation Zundel cation
Proton Transfer mechanism in H3O+
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Proton Transfer through hydronium and hydroxide: Current controversy
Three controversial mechanisms for hydroxide OH-
Dynamical
hyper-coordination Static
hyper-coordination
Mirror image
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Proton Transfer through hydronium and hydroxide
Diffusion Coefficient
(10-9 m2/s)
MI(PW91)1 SH(HCTH) 1
DH (BLYP) 1
Exp.2, 3, 4
OH- 18.5 0.44 1.92 3.12
H3O+ 3.24 3.25 2.83 6.69
D(OH- )/D(H3O+ ) 5.88 0.14 0.68 0.47
Dynamical
hyper-coordination (DH) Static
hyper-coordination (SH)
Mirror image (MI)
Three controversial mechanisms for hydroxide OH-
Why controversial?
• All three scenarios can be theoretically obtained by GGA functional
• BLYP predicts a qualitatively correct picture, but ions diffuse too slow
• The H-bond by BLYP is known to be over-structured
1. Tuckerman, M. E.; Chandra, A.; Marx, D. J. Chem. Phys. 133, 124108 (2010) 2. Tuckerman, M. E.; Chandra, A.; Marx, D. Chem. Rev. 2010, 110, 2174 3. Milles, R. J. Phys. Chem., 1973, 77, 685 4. Halle, B.; Karlstrom, G. J. Chem. Soc., Faraday Trans. 2 1983, 70, 1031
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Proton Transfer through hydronium and hydroxide: Current controversy
0
0.5
1
1.5
2
2.5
3
3.5
2 2.5 3 3.5 4 4.5 5 5.5 6
gOO
Distance (Å)
BLYP 300KXray 295K
Joint Xray/Neutron 298K
BLYP: PRL 101, 017801 (2008)
X-ray at 295K: JCP 138, 074506 (2013)
X-ray/Neutron at 298K: PRL 101, 065502 (2008)
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Proton Transfer with accurately modeled H-bond network
Accurate modeling of H-bond is the key!!
What are missing in GGA-AIMD simulations?
• Inclusion of van der Waals interactions
• Correction of delocalization by hybrid functional
• Treatment of nuclear quantum effects
Our advanced modeling approaches:
• TS-vdW
• PBE0 hybrid functional
• Approximate treatment of nuclear quantum
effect by 30K elevated temperature
R. DiStasio et al, J. Chem. Phys. 141, 084502 (2014)
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Proton Transfer with accurately modeled H-bond network
Diffusion Coefficient
(10-9 m2/s)
BLYP1 PBE PBE vdW PBE0
vdW
Exp.2, 3, 4
OH- 1.92 16.4 14.0 3.90 3.12
H3O+ 2.83 9.78 11.4 8.15 6.69
D(OH- )/D(H3O+ ) 0.68 1.7 1.2 0.48 0.47
Diffusion
Proton Transfer rate (per picosecond)
L. Zheng, B. Santra, R. DiStasio Jr., R. Car, M. Klein, X. Wu, manuscript in preparation
1. Tuckerman, M. E.; Chandra, A.; Marx, D. J. Chem. Phys. 133, 124108 (2010) 2. Tuckerman, M. E.; Chandra, A.; Marx, D. Chem. Rev. 2010, 110, 2174 3. Milles, R. J. Phys. Chem., 1973, 77, 685 4. Halle, B.; Karlstrom, G. J. Chem. Soc., Faraday Trans. 2 1983, 70, 1031
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Three controversial mechanisms for hydroxide OH-
Dynamical
hyper-coordination Static
hyper-coordination
Mirror image
Proton Transfer with accurately modeled H-bond network
OH-
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Dynamical
hyper-coordination Presolvation structure of PT in OH-:
Complex receiving the proton
Resembling water
Must change from hypercoordination
to tetrahedral like Ready Inactive
Proton Transfer with accurately modeled H-bond network
Diffusion Coefficient
(10-9 m2/s)
BLYP1 PBE PBE vdW PBE0
vdW
Exp.2, 3, 4
OH- 1.92 16.4 14.0 3.90 3.12
L. Zheng, B. Santra, R. DiStasio Jr., R. Car, M. Klein, X. Wu, manuscript in preparation
1. Tuckerman, M. E.; Chandra, A.; Marx, D. J. Chem. Phys. 133, 124108 (2010) 2. Tuckerman, M. E.; Chandra, A.; Marx, D. Chem. Rev. 2010, 110, 2174 3. Milles, R. J. Phys. Chem., 1973, 77, 685 4. Halle, B.; Karlstrom, G. J. Chem. Soc., Faraday Trans. 2 1983, 70, 1031
OH-
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Proton Transfer of OH-: Presolvation structure
Dynamical
hyper-coordination
Diffusion Coefficient
(10-9 m2/s)
BLYP1 PBE PBE vdW PBE0
vdW
Exp.2, 3, 4
OH- 1.92 16.4 14.0 3.90 3.12
Ready Inactive
L. Zheng, B. Santra, R. DiStasio Jr., R. Car, M. Klein, X. Wu, manuscript in preparation
1. Tuckerman, M. E.; Chandra, A.; Marx, D. J. Chem. Phys. 133, 124108 (2010) 2. Tuckerman, M. E.; Chandra, A.; Marx, D. Chem. Rev. 2010, 110, 2174 3. Milles, R. J. Phys. Chem., 1973, 77, 685 4. Halle, B.; Karlstrom, G. J. Chem. Soc., Faraday Trans. 2 1983, 70, 1031
OH-
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Proton Transfer with accurately modeled H-bond network
Diffusion Coefficient
(10-9 m2/s)
BLYP1 PBE PBE vdW PBE0
vdW
Exp.2, 3, 4
OH- 1.92 16.4 14.0 3.90 3.12
Weakening of directional
H-bond strength !
L. Zheng, B. Santra, R. DiStasio Jr., R. Car, M. Klein, X. Wu, manuscript in preparation
1. Tuckerman, M. E.; Chandra, A.; Marx, D. J. Chem. Phys. 133, 124108 (2010) 2. Tuckerman, M. E.; Chandra, A.; Marx, D. Chem. Rev. 2010, 110, 2174 3. Milles, R. J. Phys. Chem., 1973, 77, 685 4. Halle, B.; Karlstrom, G. J. Chem. Soc., Faraday Trans. 2 1983, 70, 1031
OH-
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Proton Transfer with accurately modeled H-bond network
Diffusion Coefficient
(10-9 m2/s)
BLYP1 PBE PBE vdW PBE0
vdW
Exp.2, 3, 4
H3O+ 2.83 9.78 11.4 8.15 6.69
Presolvation structure of PT in H3O+:
Complex receiving the proton
Water molecule in first shell
A2D2 (inactive) to A1D2 (ready)
H3O+
L. Zheng, B. Santra, R. DiStasio Jr., R. Car, M. Klein, X. Wu, manuscript in preparation
1. Tuckerman, M. E.; Chandra, A.; Marx, D. J. Chem. Phys. 133, 124108 (2010) 2. Tuckerman, M. E.; Chandra, A.; Marx, D. Chem. Rev. 2010, 110, 2174 3. Milles, R. J. Phys. Chem., 1973, 77, 685 4. Halle, B.; Karlstrom, G. J. Chem. Soc., Faraday Trans. 2 1983, 70, 1031
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H3O+ decompose
lone pair side hydrogen side
Proton Transfer with accurately modeled H-bond network
Inactive Ready
L. Zheng, B. Santra, R. DiStasio Jr., R. Car, M. Klein, X. Wu, manuscript in preparation
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Proton Transfer with accurately modeled H-bond network
Diffusion Coefficient
(10-9 m2/s)
BLYP1 PBE PBE vdW PBE0
vdW
Exp.2, 3, 4
H3O+ 2.83 9.78 11.4 8.15 6.69
Inactive Ready
L. Zheng, B. Santra, R. DiStasio Jr., R. Car, M. Klein, X. Wu, manuscript in preparation
1. Tuckerman, M. E.; Chandra, A.; Marx, D. J. Chem. Phys. 133, 124108 (2010) 2. Tuckerman, M. E.; Chandra, A.; Marx, D. Chem. Rev. 2010, 110, 2174 3. Milles, R. J. Phys. Chem., 1973, 77, 685 4. Halle, B.; Karlstrom, G. J. Chem. Soc., Faraday Trans. 2 1983, 70, 1031
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Proton Transfer with accurately modeled H-bond network
1. Settle down the controversy on the proton transfer mechanism in OH-
2. Delocalization correction by hybrid functional
3. van der Waals interaction
4. Slow down PT in OH- towards experimental direction
5. The PT of H3O+ is much less affected due to error cancelation
L. Zheng, B. Santra, R. DiStasio Jr., R. Car, M. Klein, X. Wu, manuscript in preparation
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Outline
Part I. Projects
Proton transfer of OH- and H3O+ in an accurately modeled H-bond network
X-ray absorption spectra in liquid water by advanced modeling
Part III. Other performed projects and introduction of our posters
Part II. Progress of our team members at LBL
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• The spectral width (~ 11 eV) is the same in all spectra
• Three features (pre-edge, main-edge, post-edge) are present
in the same energy range in all spectra
• The relative intensity of the features shows a characteristic
system dependence
J. Tse et. al. Phys. Rev. Lett. 100,095502(2008)
pre-edge main-edge post-edge
X-ray absorption of liquid water and ice
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20
32-mol water, 363 K
64-mol, ice
water, 363 K vs. water, 330 K
Variation of the spectrum with T
Quasiparticle treatment based on GW
approximation is crucial in obtaining the XAS spectra
Difference in XAS between water and ice
X-ray absorption of liquid water and ice
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-10-10 -5 00 5 10100
20
40
60
80
100
120
Water
DO
S
Ice Ih
Ice Ic
Energy (eV)
X-ray absorption of liquid water and ice: the difference in main peak
Chen et al, PRL 105, 017802 (2010)
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32-mol water, 363 K
64-mol, ice
water, 363 K vs. water, 330 K
Variation of the spectrum with T Importance of of electron
excitation calculations?
GW vs. DFT method
G0W0 vs self-consistent GW
The importance of molecular
modeling of water by AIMD?
o vdW and hybrid functional
o nuclear quantum effect
o ab initio vs. classical MD
o size effect in water model
X-ray absorption of liquid water and ice
Chen et al, PRL 105, 017802 (2010) AIMD: ab initio molecular dynamics
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X-ray absorption of liquid water
Importance of of electron
excitation calculations?
GW vs. DFT method
G0W0 vs self-consistent
GW
The importance of molecular
modeling of water by AIMD?
o vdW and hybrid functional
o nuclear quantum effect
o ab initio vs. classical
o size effect in water model
AIMD: ab initio molecular dynamics
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24
X-ray absorption of liquid water : recent advanced modeling
0
2
4
6
8
10
12
14
16
532 534 536 538 540 542 544 546
Intensity (Arb. Unit)
Energy (eV)
PBE
PBEvdW
PBE0vdW
Tse-exp
Tse et al., PRL 100, 095502 (2008)
Z. Sun, et. al. in preparation
Liquid water modeled in a cubic
box of 128-mol
Importance of of electron
excitation calculations?
GW vs. DFT method
G0W0 vs self-consistent
GW
The importance of molecular
modeling of water by AIMD?
o vdW and hybrid DFT
o nuclear quantum effect
o ab initio vs. classical
o size effect in water model
AIMD: ab initio molecular dynamics
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X-ray absorption of liquid water : nuclear quantum effect
Z. Sun, et. al. in preparation
0
2
4
6
8
10
12
532 534 536 538 540 542 544 546
Intensity (Arb. Unit)
Energy (eV)
Static-GW theory
0
2
4
6
8
10
12
14
16
532 534 536 538 540 542 544 546
Intensity (Arb. Unit)
Energy (eV)
PBE0vdW 128mol
Tse-exp
Importance of of electron
excitation calculations?
GW vs. DFT method
G0W0 vs self-consistent
GW
The importance of molecular
modeling of water by AIMD?
o vdW and hybrid DFT
o nuclear quantum effect
o ab initio vs. classical MD
o size effect in water model
AIMD: ab initio molecular dynamics Classical AIMD
Quantum AIMD
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X-ray absorption of liquid water : recent advanced modeling
Importance of of electron
excitation calculations?
GW vs. DFT method
G0W0 vs self-consistent
GW
The importance of molecular
modeling of water by AIMD?
o vdW and hybrid DFT
o nuclear quantum effect
o ab initio vs. classical MD
o size effect in water model
Z. Sun, et. al. in preparation
Tse et al., PRL 100, 095502 (2008)
AIMD: ab initio molecular dynamics
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X-ray absorption of liquid water : recent advanced modeling
0
2
4
6
8
10
12
14
16
532 534 536 538 540 542 544 546
Intensity (Arb. Unit)
Energy (eV)
PBE0vdW 32mol
Tse-exp
0
2
4
6
8
10
12
14
16
532 534 536 538 540 542 544 546
Intensity (Arb. Unit)
Energy (eV)
PBE0vdW 128mol
Tse-exp
Importance of of electron
excitation calculations?
GW vs. DFT method
G0W0 vs self-consistent GW
The importance of molecular
modeling of water by AIMD?
o vdW and hybrid DFT
o nuclear quantum effect
o ab initio vs. classical MD
o size effect in water model
Tse et al., PRL 100, 095502 (2008)
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X-ray absorption of liquid water : advanced modeling
0
0.005
0.01
0.015
0.02
0.025
0.03
0.035
0.04
0.045
0 1 2 3 4 5 6 7
0
1
2
3
WF density of 128mol
gOO(r)
Distance (Å)
gOOPre−edge
Main−edgePost−edge
32-mol
box 64-mol
box
128-mol
box
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X-ray absorption of liquid water : Summary
Solve the XAS theoretical modeling in water
Electron excitation theory is crucial to go beyond the DFT approach
Self-consistent GW is important to obtain the correct transition matrix
van der Waals interaction, correction of delocalization error by PBE0,
nuclear quantum effect are all important
Size of modeling the water is also important
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PEXSI (Pole Expansion and Selected Inversion) • An efficient way to evaluate electron
density 𝜌 = diag 𝑋𝑋∗ , energies and forces without diagonalizing Kohn-Sham Hamiltonian (L. Lin, R. Car, C. Yang, J. Lu, L. Ying, W. E) in ab initio MD simulation
• Pole expansion 𝑋𝑋∗ ≈ 𝐼𝑚 𝜔𝑖 𝐻 − 𝑧𝑖𝐼
−1𝑀𝑖
• Selected Inversion: compute selected entries of 𝐻 − 𝑧𝑖𝐼
−1 using sparse matrix techniques.
• Complexity: 𝑂 𝑛𝑒 for 1D, 𝑂 𝑛𝑒3/2
for
2D, 𝑂 𝑛𝑒2 for 3D
• Work for both insulators and metals
30
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PEXSI Parallelization • Multi-level parallelism for high performance parallel computation • Embarrassing parallelization at
the pole level.
• Elimination tree level parallelism
• Asynchronous communication
• Overlap communication with computation
• Tree-based restricted collective communication
31
[Jacquelin-Lin-Yang, ACM TOMS, 2015]
Before
After
⋮ ⋮ ⋮
⋯
pselinv at pole i 𝐻 − 𝑧𝑖𝐼
−1
Processor groups
group i
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Application
• Electronic structure of large-scale graphene nanoflakes of different edges.
• SIESTA-PEXSI for large system size: 11700 atoms
[Hu-Lin-Yang-Yang, JCP, 2014]
• Integrated with SIESTA, CP2K
• On-going SciDAC collaboration for electronic structure of WTe2 layered systems.
(http://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/DFT/LS_SCF/PEXSI.html)
Monolayer graphene 6400 cores used, 256 cores per pole, 50 poles
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Poster by Fausto Martelli from Princeton University
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Poster by Hsin-Yu Ho from Princeton University
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Most recent work
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Future work
• Nuclear quantum effects on important ions solutions
• Highly parallelized RPA-GW
• OH radical in water
• Thermodynamics of water
• Interfaces of water and functional materials
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Acknowledgement
Roberto Car (Princeton)
Bsiwajit Santra (Princeton)
Fausto Martelli (Princeton)
Jimin Sun (Princeton)
Hsin-Yu Ho (Princeton, Chemistry)
Lixin Zheng (Temple Student)
Zhaoru Sun (Postdoc, Temple Physics)
Mike Klein (Temple U.)
Esmond Ng (LBL)
Chao Yang (LBL)
Lin Lin (UC Berkeley)