Cholesky decomposition based methods.

Alfredo M.J. Snchez de Mers Institut de Cincia Molecular Universitat de Valncia

Model systems QM part of QM/MM calculation

Oslo, August 17 07

Outline
1. Introduction 2. Background
a) Cholesky CCSD(T) b) Cholesky decomposed two-electron integrals

3. Present work
a) Interaction between oligopeptides b) Method-specific decomposition

4. Our expectations
Oslo, August 17 07

Introduction
Scaling of ab initio methods is not convenient: N4 - N7

#CPU impact Too expensive !! $ " %Storage requirements

Cholesky decomposition can do the job: Decompose a (semi)positive definite matrix M

H. Beebe and J. Lindenberg, Int. J. Quantum Chem. 12 (1977) 683
Oslo, August 17 07

Introduction
Sensibly less ' ! + ! "1 + q than the total ) p ) dimension of )(#$|%&) = M#$,%& ) n ) ) J J M pq = ( the matrix , = .Lp Lq )D#$ (#$|%&) D%& = M#$,%& ) J=1 ) ) )(#% |$&) D%& = M#%,$& ) * Posive (semi)definite matrix " M(i) % " M(i) % p,J i q,J i i+1 (i) J J M(pq ) = M(i) ! $ '$ ' = M pq ! L pi L qi pq $ M(i) ' $ M(i) ' J i ,J i & # J i ,J i & #

Oslo, August 17 07

Cholesky CCSD(T)
Dabc = M aij,bck ijk
$ 1 = = = % dn dn aij bck ! a " ! i " ! j + (! b + ! c " ! k ) # aij + # bck n

# ! p " ! Jm & n n d aij = d p = )$ ! p + ! Jn m =1 % ! p + ! Jm ( ' 2! Jn

n "1

# ! p " ! Jm & 1 n Dpp = )$ 2! p m =1 % ! p + ! Jm ( '

n

Oslo, August 17 07

Cholesky CCSD(T): coronene-(H2)2

D2h symmetry avdz+2mb basis (772 bf) 82.2 million t2-amplitudes

E (kcal/mol) MP2 CCSD CCSD(T)

Oslo, August 17 07

-2.58 -1.60 -2.00

SCF repulsive!

2-e integrals decomposition

M!",#$ = (!"| #$)

Rounding errors make M, to be not exactly semipositive definite Non analytical expression Strict pivoting is not possible to avoid recalculations Full decomposition of an integral batch unstable

Out-of-core numerical algorithm with empirically optimized parameters.

Oslo, August 17 07

Cholesky SCF & MP2

HF : - J & 1 ) / 2 J J J / F!" = % .2L !" ( % D#$ L #$ + , % L !k L "k 2 ' #$ * k / J / 0 3 MP2 : N 2O ) (

(ai | bj) = ! L
J
Oslo, August 17 07

J ai

J bj

(V O )
2 2

Cholesky DFT & CC2

DFT: Add contribution from Kohn-Sham vXC to modified Fock matrix
(Salek & Helgaker DFT conventional code)

CC2: Doubles-direct algorithm identical to RI-CC2

(C. Httig et al., JCP 113 (2000) 5154)
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Energy : errors in benzene

Basis avdz avtz avqz av5z av6z
Oslo, August 17 07

SCF =10-6 0.35 0.05 0.20 0.81 0.10 =10-8 0.12 0.64 0.74 0.01 0.50

MP2 =10-10 =10-6 =10-8 2.17 0.08 1.27 0.06 2.9 6.3 10.3 53.9 31.2 3.2 8.2 12.1 10.4 76.2

Energy: a pseudorotaxane
E kcal/mol 6-31G 6-31GH 6-311G

HF MP2 LDA

-16.04 -11.94 -16.11 -20.71 -26.78 -22.85 -31.82 -31.52 -34.28

B3LYP -14.55 -15.29 -15.21

Oslo, August 17 07

Energy: a nano-ring

Electrostatic effects?
Oslo, August 17 07

Energy: a nano-ring
6-CPPA (10-2 a.u.)

Charge transfer? Electron density

HMB (10-2 a.u.)

Complex (10-2 a.u.)

Difference between complex and fragments (10-4 a.u.)

Oslo, August 17 07

Energy: a nano-ring
Method B3LYP HC407 PBE PW91 B971 VSXC E 5.46 0.34 -0.25 -1.44 -2.93 -82.27

Oslo, August 17 07

Energy: a nano-ring
Method B3LYP HC407 PBE PW91 B971 VSXC E 5.46 0.34 -0.25 -1.44 -2.93 -82.27

Oslo, August 17 07

Energy : Others nano-compounds

Oslo, August 17 07

Molecular properties
Energy derivatives
#2 W ! ij = " #E i #E j & #2 W ) [!] % Tr ( + ' #E i #B j * #2 W $ ij = " #Bi #B j #2 W ,K = " ij #m K,i #B j

Oslo, August 17 07

Molecular properties
Linear response function formalism
! i j (") = # ri ,rj
"

[!]" # $ Im
0

Tr r , L 6%
0

! ij = " L i ,L j

" #jkl p k ,rlL i

! A,ij = "
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! A,i rA
3

,L j
0

" #jkl

pk ,

rO,l! A,i rA
3 0

Polarizability: annulenes

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Optical rotation
CONFH2 av6z CC2 1010 MDMA avtz CC2 989 Dyn-A 6-31++G** 834 B3LYP 81.04 -29.82 0.29*

Oslo, August 17 07

Magnetic susceptibility: annulenes

nC 6 10 14 18 22 26 30 B3LYP 53,52 116,66 204,98 350,75 540,71 813,08 1195,75 CC2 54,32 82,76 216,44 368,39 564,77 840,86 1224,67
aug-cc-pVDZ exp6 55 cgs

Oslo, August 17 07

Magnetic susceptibility: timings

o

Benzene (HF / 666 bf) 52.61 ppm cm3 mol-1 Energy & wavefunction 7133 sec (x 13/2) Properties 134406 sec Total 39 hr 19 min 4 sec
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Magnetic susceptibility: timings

Energy & wavefunction 7133 sec (x 13/2) Properties 134406 sec Total 39 hr 19 min 4 sec
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Decomposition 6203 sec Energy & wavefunction 51 sec Properties 1263 sec Total 2 hr 5 min 17 sec

H-NMR: Dimethyl-dihydropyrene
H1 H5

H7
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H-NMR shieldings: DMDHP

510 824 1036 1940 exp
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HF KT3 HF KT3 HF KT3 HF KT3

H1 20.1 20.2 20.2 20.4 21.5 21.8 21.9 22.2 8.23

H5 20.7 20.8 20.9 21.0 22.2 22.4 22.5 22.7 8.14

H7 20.0 20.1 20.1 20.3 21.3 21.7 21.8 22.1 8.67

Hm 36.2 34.7 36.3 34.9 37.7 36.5 38.0 36.7 -4.25

m5

15.5 13.9 15.4 13.9 15.5 14.1 15.5 14.0 12.4

Parity violation in RNA

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Current density streamlines

Current density streamlines.
X [2,3-b] X

|J|

In a plane 0.8 a.u. above the molecule

Oslo, August 17 07

Present applications: Prion protein

NNQQY -sheet 200 atoms 824 electrons 6-31G*(0.25) basis

Dimer (a.u.)

Monomer (a.u.) -2771.523 -2778.138

E kcal/mol

SCF MP2
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-5543.088 -5556.361

25.5 53.5

Tyrosine dimer
Comparison MP2 / CCSD(T) Final goal: Role of -stacking in amyloid formation
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Specific decompositions

In many cases, we do too much not necessary work

E = 2 % D!" (!"|#$) D#$

!"#$

Use density for more efficient screening

& ) J = 2 % ( % L !" + * J ' !"

Oslo, August 17 07

Coulomb energy

Oslo, August 17 07

Coulomb energy
basis vdz vtz vqz v5z avdz avtz avqz av5z nbas 24 58 115 201 41 92 172 287 H2O
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#vec 59 65 73 69 66 66 75 73

The number of vectors is basically constant

Coulomb energy
8 amino acids fragment of a synthetic endorphine in -helix Basis
6-31G*

# bf 952 1964 4278 7860

# vec 3428 3766 3399 5649

avdz avtz avqz

Oslo, August 17 07

Exchange contribution
X

E=

!"#$

% D (!# |"$) D
!"

X
#$

F!" = % (!# |"$) D#$

#$

& & k k) k , k ,) = % ( % L ! L " + (!# |"$) ( % L # L $ + * ' k, * !"#$ ' k = % % Lk Lk#, (!# |"$) Lk Lk , ! " $
k k , !"#$

' k k* = % (!# |"$) ) % L # L $ , ( k& + #$ = % % L (!# |"$) L

k #$ k # k $

& ) J,kk , = % ( % L !# + * k k , ' J,!#

Oslo, August 17 07

= % % LJ,k LJ,k !# "$

k J,#$

Exchange energy

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Exchange Fock matrix

Oslo, August 17 07

Exchange Fock matrix

Oslo, August 17 07

Exchange Fock matrix

Oslo, August 17 07

Summary
Better scaling of CCSD(T) Substantial saving in calculation and storage of two-electron integrals. Significant speed-up of HF, MP2, DFT and CC2. Linear scaling in SCF methods Calculations on large systems are feasible.

.
Oslo, August 17 07

The calcium pump project

Theoretical developments Ab-initio applications in model systems

Oslo, August 17 07

The calcium pump project

Theoretical developments Ab-initio applications QM-MM methods Entropy contributions

Oslo, August 17 07

Cholesky decomposition based methods.

Institut de Cincia Molecular Universitat de Valncia