qtpie and water (part 2)
DESCRIPTION
Slides for group meeting presentation, Spring 2008.TRANSCRIPT
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QTPIE and waterJiahao Chen2008-05-20
"We can't solve problems by using the same kind of thinking we used when we created them." - attributed to Albert Einstein
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Since last time...
• QTPIE has become much faster
• We now know why dipole moments and polarizabilities previously weren’t translationally invariant, and why they aren’t size extensive.
• We have (some) parameters for a new water model
• We’ve shown that QTPIE gets the correct direction of intermolecular charge transfer
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What is QTPIE: a scientific POV
• A way to model polarization and intermolecular charge transfer in molecular mechanics
• One of the simplest electronic structure methods, except without electrons
• Give me a geometry, and I will give you a charge distribution
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• Give me a geometry, and I will give you a charge distribution
• Minimize the quadratic form
• subject to the constraint
What is QTPIE? A numerical POV
E(q1, . . . , qN ;R) =!
i
qivi(R) +12
!
ij
qiqjJij(R)
f : R =!
!R1, . . . , !RN
"! (q1, . . . , qN )
!
i
qi = 0
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How to make QTPIE faster
• Using GTOs in place of STOs
• Integral prescreening
• Sparse matrix data structure for overlap matrix
• Conjugate gradients to solve linear problem (vs GMRES)
• Initial guess from previous solution
• Fast multipole methods (future work)
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Optimizing GTOs for STOs
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Unlike GTOs, STOs are really, really nasty to work with.
dK2
dR= !2m + 1
R2+
2m
RK2 +
(2!R)2m
(2m)!!2m (1 + 2m! 2!R) A2m!1 (2!R) + (1 + 2m) e!2!R
"
!"!2m+1R2m
2n (2m)!
2n!1#
"=0
2n! # ! 1#!
("R)"2m+"#
p=0
D2m!1,"+1p Bp (R (!! "))A2m+"!p (R (! + "))
+!2m+1R2m
2n (2m)!
2n#
"=0
2n! #
#!("R)"
2m!1+"#
p=0
D2m!1,"p "
[(!! ")Bp+1 (R (!! "))A2m+"!1!p (R (! + ")) + (! + ") Bp (R (!! "))A2m+"!p (R (! + "))]
K2 (!,", m, n, R) =1R
+(2!)2m R2m!1
(2m)!!(2!R! 2m) A2m!1 (2!R)! e!2!R
"
!!2m+1R2m
2n (2m)!
2n#
"=0
2n! #
#!("R)"
2m!1+"#
p=0
D2m!1,"p Bp (R (!! "))A2m+"!1!p (R (! + "))
An (!) =n!e!!
!n+1
n!
"=0
!"
"!
Bn (!) =n!e!!
!n+1
n!
"=0
(!!)" ! !"
"!
Dmnp =
!
k
(!1)k"
mp! k
# "nk
#
p =!
ab
a + bdK2
dR=
2p
R!
!e!p2R2
" erf (pR)R2
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STO-nG orbitals were defined by fitting an orbital of n contracted Gaussian primitives to an STO to reproduce
the orbital in a least-squares sense. The conventional wisdom is n > 2 for some kind of useful, reasonable fit.
STO-1Gs suck when used in QEq/QTPIE.
However, there is a way to get accurate results with just primitive Gaussians...
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Instead of maximizing overlap in a least-squares sense, minimize the deviation in the Coulomb integrals.
min!
!!JSTO ! JGTO (!)!!
! !
0
"JGTO (R;!)! JSTO (R)
# 1"!"
e"!R2= 0
which is minimized by the exponent such that
!JGTO " JSTO!22 =
!JGTO, JGTO
"" 2
!JGTO, JSTO
"+
!JSTO, JSTO
"
=!JGTO,
#JGTO " 2JSTO
$"+
!JSTO, JSTO
"
This is equivalent to minimizing
0 =!
!"
!JGTO (") ,
"JGTO (")! 2JSTO
#$
=%
!
!"JGTO (") ,
"JGTO (")! 2JSTO
#&+
%JGTO (") ,
!
!"JGTO (")
&
=%"
2JGTO (")! 2JSTO#,
!
!"JGTO (")
&
i.e.
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Element Best Coulomb Least-squaresH 0.5343 0.3101Li 0.1668 0.0440C 0.2069 0.1853N 0.2214 0.2088O 0.2240 0.2400F 0.2312 0.2142
Na 0.0959 0.0399Si 0.1032 0.1256P 0.1085 0.1430S 0.1156 0.1584Cl 0.1137 0.1758K 0.0602 0.0361Br 0.0701 0.1850Rb 0.0420 0.0402I 0.0469 0.1735
Cs 0.0307 0.0374
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Summary
• STOs are really, really nasty to work with
• GTOs fit to STOs by reproducing the Coulomb self-repulsion integrals yield excellent approximations
• Use in QEq and QTPIE result in very little error (< 0.00001e)
• There is very little basis to the claim that STOs can be used “for extra accuracy”
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Sparse matrices in QTPIE
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!
"1.0 0.4 0.00.4 1.0 0.00.0 0.0 1.0
#
$do i = 1, N do j = 1, N u(i) = M(i, j) * v(j) end doend do
1.0 0.4 0.0 0.4 1.0 0.0 0.0 0.0 1.0
In (linear) memory, matrix data structure looks like this:
Matrix-vector multiplication in computer memory
M(:)
k = 0do i = 1, N do j = 1, N k = k + 1 u(i) = M(k) * v(j) end doend do
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1 2 1 2 31.0 0.4 0.4 1.0 1.0
1 3 5 6
columndata
row start
!
"1.0 0.4 0.00.4 1.0 0.00.0 0.0 1.0
#
$
k = 0do i = 1, N do j = 1, N k = k + 1 u(i) = M(k) * v(j) end doend do
do i = 1, N do k=M%r(i),M%r(i+1)-1 j = M%c(k) u(i) = M%d(k) * v(j) end doend do
Fewer operations and lower memory latency, so faster!
1.0 0.4 0.0 0.4 1.0 0.0 0.0 0.0 1.0
Compressed sparse row (CSR) data structure
Conventional matrix data structure
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• In QTPIE, minimize
• The linear coefficients are given by
• The main costs are matrix-vector multiplication and memory latency
Calculating the linear coefficients in QTPIE
vi =!
j(!i ! !j)Sij!j! Sij!
E(q1, . . . , qN ;R) =!
i
qivi(R) +12
!
ij
qiqjJij(R)
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Using conjugate gradients for
constrained problems
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• In matrix notation,
• Solving QTPIE with a Lagrange multiplier,
• J is positive definite but this constrained problem is not (the constraint introduces a negative eigenvalue). Conjugate gradients can (and does) fail by going uphill, thinking it’s going downhill.
QTPIE is a saddle-point problem
!J 11T 0
" !qµ
"=
!!v0
"
minq: q·1=0
!qT v +
12qT Jq
"
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However...
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Solving the saddle-point problem
• There exists a block inversion formula1 for 2 x 2 structured matrices
• The analytic solution is given by
!J 11T 0
"!1
=!
J!1 + J!11S1T J!1 !J!11S!S1T J!1 S
"
1. e.g. P.-O. Löwdin, Linear algebra for quantum mechanics
!qµ
"=
!J 11T 0
"!1 !!v0
"=
!!J!1 (v ! µ1)#
1T J!1v$S
"
S = ! 11T J!11
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Solving the saddle-point problem with CG
• Analytic solution can be solved numerically with two symmetric, positive definite problems (CG is guaranteed to work)
S = ! 11T J!11
!qµ
"=
!!J!1 (v ! µ1)#
1T J!1v$S
"
µ = !w · v
w · 1
Jw = 1
Jy = !v
q = y ! µw
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II. Fixing the translational invariance of dipole moments and
polarizabilities
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Dipoles and polarizabilities in QEq• The regular story: the charge model is
solved by
• The energy is therefore minimized by
• Want to calculate dipole moments and polarizabilities
q = !J!1v
E = !12vT J!1v
d! =!
i
!E
!Ri!!!" =
!
j
"d!
"Rj"
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How to calculate dipoles and polarizabilities
• Dipole coupling prescription
• The external field shifts the voltages on each atom by an external potential
• Now calculate dipole moments and polarizabilities
E(q1, . . . , qN ;R,!") =!
i
qivi(R) +12
!
ij
qiqjJij(R)!!
i
qi!Ri · !"
E(q1, . . . , qN ;R,!") =!
i
qi
"vi(R)! !Ri · !"
#+
12
!
ij
qiqjJij(R)
d! =!E
!"!!!" =
"2E
"#!"#"
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Physically, the universe is translationally invariant.Therefore, electrostatic properties (mostly) don’t
depend on the choice of origin.
!x !" !x + !"
!d !" !d + !"Q!!!" !" !!"
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The solution in the literature is to fix an origin arbitrarily, even though nobody has a good physical
reason why that should be the “correct” origin
This is not the case in QEq!
!d !" !d + !"!1T J!1v
"
!!" !" !!" # 1T J!1 · ("!R" + R!"")# "!""1T J!11
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As it turns out, QEq and other fluctuating charge models do obey the correct translational
properties, as long as one works with the correct solution of the constrained minimization
q != "J!1v
q = !J!1 (v ! µ1) = !J!1v ! J!111T J!11
The second term actually generates counterterms under translation that kill all the pathological terms.
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!µ! = ! (Rµ)T J!1R! !!1T J!1Rµ
" !1T J!1R!
"
1T J!11
dµ = ! (Rµ)T J!1v !!1T J!1v + Q
" 1T J!1Rµ
1T J!11
The analytic solutions for the dipole moment and polarizability in QTPIE
are given by
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dµ !" # (Rµ + !µ1)T J!1v
#!1T J!1v + Q
" 1T J!1
1T J!11(Rµ + !µ1)
= # (Rµ)T J!1v +!1T J!1v + Q
" 1T J!1Rµ
1T J!11
#!µ1T J!1v + !µ!1T J!1v + Q
" 1T J!111T J!11
= dµ # !µ1T J!1v + !µ!1T J!1v + Q
"
= dµ + !µQ
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!µ! !" # (Rµ + "µ1)T J!1 (R! + "!1)
#!1T J!1 (Rµ + "µ1)
" !1T J!1 (R! + "!1)
"
1T J!11= # (Rµ)T J!1R! # "µ"!1T J!11
#"µ1T J!1R! # "! (Rµ)T J!11
#!1T J!1Rµ
" !1T J!1R!
"
1T J!11
#"µ"!
!1T J!11
" !1T J!11
"
1T J!11
#"µ
!1T J!11
" !1T J!1R!
"
1T J!11
#"!
!1T J!1Rµ
" !1T J!11
"
1T J!11= !µ!
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III. Fixing the size extensivity of dipole
moments and polarizabilities
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Not size extensive!
= 24
Why?
limn!"
!"#$n
2n! "# $
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Work it out analytically for N identical, noninteracting subsystems...
Rµ =
!
"""#
R̄µ
R̄µ + !µ1...
R̄µ + (N ! 1) !µ1
$
%%%&=
!
"""#
R̄µ
R̄µ
...R̄µ
$
%%%&+ !µ
!
"""#
01...
(N ! 1)1
$
%%%&
J =
!
""""#
J̄ 0 · · · 0
0 J̄. . .
......
. . . . . ....
0 · · · · · · J̄
$
%%%%&v =
!
"""#
v̄v̄...v̄
$
%%%&
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dµ = ! (Rµ)T J!1
!v ! 1
1T J!11"1T J!1v + Q
#$
= !
%
&&&'
R̄µ
R̄µ + !µ1...
R̄µ + (N ! 1) !µ1
(
)))*·
%
&&&'
%
&&&'
J̄!1v̄J̄!1v̄
...J̄!1v̄
(
)))*! N1T J̄!1v̄ + Q
N1T J̄!11
%
&&&'
J̄!11J̄!11
...J̄!11
(
)))*
(
)))*
= !N
!"R̄µ
#T J̄!1v̄ ! 1T J!1v̄ + Q/N
1T J!11"R̄µ
#T J̄!11$
!!µN!1+
n=0
n
!1T J̄!1v̄ ! 1T J!1v̄ + Q/N
1T J!111T J̄!11
$
= Nd̄µ ! (N ! 1) (N ! 2)2
!µ"1T J̄!1v̄ ! 1T J!1v̄ !Q/N
#
= Nd̄µ ! (N ! 1) (N ! 2) Q
2N!µ
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!µ! = ! (Rµ)T J!1R! +!1T J!1Rµ
" !1T J!1R!
"
1T J!11
= !
#
$$$%
R̄µ
R̄µ + !µ1...
R̄µ + (N ! 1) !µ1
&
'''(
T#
$$$$%
J̄!1 0 · · · 0
0 J̄!1 . . ....
.... . . . . .
...0 · · · · · · J̄!1
&
''''(
#
$$$%
R̄!
R̄! + !!1...
R̄! + (N ! 1) !!1
&
'''(
+
#
$$$%
1T J̄!1R̄µ
1T J̄!1!R̄µ + !µ1
"
...1T J̄!1
!R̄µ + (N ! 1) !µ1
"
&
'''(
#
$$$%
1T J̄!1R̄!
1T J̄!1!R̄! + !!1
"
...1T J̄!1
!R̄! + (N ! 1) !!1
"
&
'''(
N1T J̄!11
= !N!1)
n=0
*!R̄µ
"T J̄!1R̄! + n!!!R̄µ
"T J̄!11 + n!µ1J̄!1R̄! + n2!µ!!1T J̄!11+
+
*,N!1n=0
!R̄µ
"T J̄!11 + n!µ1T J̄!11+ *,N!1
n!=0
!R̄!
"T J̄!11 + n"!!1T J̄!11+
N1T J̄!11
= !N!R̄µ
"T J̄!1R̄! ! (N ! 1) (N ! 2)2
!!!R̄µ
"T J̄!11
! (N ! 1) (N ! 2)2
!µ1J̄!1R̄! ! (N ! 1) (N ! 2) (2N ! 3)6
!µ!!1T J̄!11
+N
*!R̄µ
"T J̄!11+ *!
R̄!"T J̄!11
+
1T J̄!11+
(N ! 1)2 (N ! 2)2
N!µ!!
!1T J̄!11
"
+(N ! 1) (N ! 2)
2
*!R̄µ
"T J̄!11!! +!R̄!
"T J̄!11!µ+
= N !̄µ! !(N ! 1) (N ! 2)
6N
!N2 ! 3N ! 6
"!µ!!1T J̄!11
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Dipole moments have the correct translational properties because the terms and counterterms
cancel perfectly.
The terms in the polarizabilities cancel only to second order; the cubic terms do not cancel
perfectly, giving rise to anomalous cubic scaling.
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Modified dipole couplingIn QEq, the external field shifts the electronegativities on
each atom by an external potential
vi(R) = !i !" !i # "Ri · "#
E(q1, . . . , qN ;R) =!
i
qivi(R) +12
!
ij
qiqjJij(R)
E(q1, . . . , qN ;R,!") =!
i
qi
"vi(R)! !Ri · !"
#+
12
!
ij
qiqjJij(R)
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Modified dipole couplingWe propose to apply the same coupling in QTPIE, which
shifts the atomic voltages in a less trivial manner
E(q1, . . . , qN ;R) =!
i
qivi(R) +12
!
ij
qiqjJij(R)
!i !" !i # "Ri · "#
vi =!
j(!i ! !j)Sij!j! Sij!
vi(R) !" vi(R,!") =!
j (#i # #j)Sij!j! Sij!
# !" ·
!j
"!Ri # !Rj
#Sij
!j! Sij!
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With this coupling, the dipole moments and polarizabilities become
dµ =!
i
"k Sik (Rµ
i !Rµk )"
l Sil
#J!1v
$i
!
#1T J!1v
$%
"i!
#1T J!1
$i!
Pk! S
i!k!
“Rµ
i!!Rµ
k!
”
Pl! S
i!l!
&
1T J!11
!µ! = !!
ij
"k Sik (Rµ
i !Rµk )
#J!1
$ij
"l Sjl
#R!
j !R!l
$"
k! Sik!"
l! Sjl!
+
%"i
#1T J!1
$i
Pk Sik(Rµ
i !Rµk)P
l Sil
& %"i!
#1T J!1
$i!
Pk! Si!k!(R!
i!!R!k!)P
l! Si!l!
&
1T J!11
![Page 40: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/40.jpg)
More importantly, these expressions are still translationally invariant, but are now size-extensive
!J!1
"ij
#
l
Sjl
!R!
j !R!l
"=
$
%%%%&
J̄!1 0 · · · 0
0 J̄!1 . . ....
.... . . . . .
...0 · · · · · · J̄!1
'
(((()
ij
#
l
$
%%%%&
S̄ 0 · · · 0
0 S̄. . .
......
. . . . . ....
0 · · · · · · S̄
'
(((()
jl
"
$
%%%&
$
%%%&
R̄!
R̄! + !!1...
R̄! + (N ! 1) !!1
'
((()
j
!
$
%%%&
R̄!
R̄! + !!1...
R̄! + (N ! 1) !!1
'
((()
l
'
((()
=!J̄!1
"ij
#
l
S̄jl
!R̄!
j ! R̄!l
"
The key difference is that the overlap matrix attenuates any contributions across subsystems to terms of this form
! = N !̄
! !" !dµ !" dµ
dµ = N !dµ
![Page 41: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/41.jpg)
-2.5e+10
-2e+10
-1.5e+10
-1e+10
-5e+09
0
5e+09
0 500 1000 1500 2000 2500 3000
Pola
rizab
ility
(boh
r^3)
Number of atoms
Planar water chains with z-spacing 10.00 Angstroms
zz-polarizabilitylinear fit (gradient = -5773165.409344, intercept = 1434581215.053739)
-900
-800
-700
-600
-500
-400
-300
-200
-100
0
0 500 1000 1500 2000 2500 3000
Pola
rizab
ility
(boh
r^3)
Number of atoms
Planar water chains with z-spacing 10.00 Angstroms
zz-polarizabilitylinear fit (gradient = -0.325919, intercept = 0.007088)
![Page 42: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/42.jpg)
IV. Parameters for water
![Page 43: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/43.jpg)
Strategy
• Aim: reproduce ab initio data (LCCSD(T)/aug-cc-pVTZ) with three-site water model
• First determine QTPIE parameters (4) by fitting to dipole moments
• Then fit other parameters (10) to energies (up to constant)
21
3
4
5
6
E = EOHB (R12) + EOH
B (R13) + EOHB (R45) + EOH
B (R46)+EHOH
A (R12, R13, R23) + EHOHA (R45, R46, R56)
+EOOvdW (R14)
+EOHvdW (R15) + EOH
vdW (R16) + EOHvdW (R42) + EOH
vdW (R43)+EHH
vdW (R25) + EHHvdW (R26) + EHH
vdW (R35) + EHHvdW (R36)
+EQTPIE (R)
EOHB (r) = kOH
!r ! rOH
0
"2
EHOHA (!) = "OH
!! ! !HOH
0
"2
EABvdW (r) = !AB
!""AB
r
#12!
""AB
r
#6$
![Page 44: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/44.jpg)
Geometries• 1,230 water monomer
geometries generated by directly varying internal coordinates
• 890 water dimer geometries generated by classical MD sampling (TINKER, flexible SPC water model, 1000K)
• O-O distance constrained by varying vdW radius of O
• 10 ps equilibration then 10 geometries at 1ps intervals
![Page 45: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/45.jpg)
Fitting method
• Weighted least-squares fitting with Boltzmann weight (β = 100)
• Fitting done with Neader-Mead downhill simplex algorithm in scipy
import scipy.optimizez0 = (8.741, 13.364, 4.528, 13.890)zopt = scipy.optimize.fmin(f, z0)print "Optimal parameters = ", zopt
f(!) =!
i
e!!Ei!
""{x,y,z}
(dab initioi" ! dQTPIE
i" (!))2
![Page 46: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/46.jpg)
Best-fit parameters
Par./eV QEq New
χ(H) 4.5280 5.6841
η(H) 13.8904 12.4166
χ(O) 8.741 7.9173
η(O) 13.364 13.1643
![Page 47: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/47.jpg)
Dipoles correlation
ab initio
QTPIE
![Page 48: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/48.jpg)
Dipole moment per water / D
Number of water molecules
![Page 49: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/49.jpg)
yy-polarizability per water / ų
Number of water molecules
![Page 50: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/50.jpg)
zz-polarizability per water / ų
Number of water molecules
![Page 51: QTPIE and water (Part 2)](https://reader034.vdocument.in/reader034/viewer/2022042623/54c6b6454a7959aa228b45cb/html5/thumbnails/51.jpg)
That’s all, folks!