Contents
Pyridine : Model(1)
Summary:
- - L4 ISA-DMA model for electrostatics. No damping. - L1, isotropic damped polarization model
- $C_6$, isotropic damped dispersion model - Isotropic Born-Mayer short-range terms
Units: Atomic Units
Citations
A. J. Misquitta & A. J. Stone, Ab initio atom–atom potentials using CamCASP: Theory
A. J. Misquitta & A. J. Stone, Ab initio atom–atom potentials using CamCASP: Application to pyridine
Geometry and multipoles
Source: BS-ISA, A+DF $\zeta=0.1$ d-aug-cc-pVTZ main basis with aQZ/set2 aux basis. PBE0/AC. CamCASP 5.8.
pyr.mom
! Multipole moments for pyridine
! Based on DF-type : ISA
H1 -3.87454677 2.40829326 0.00000000 Type H1 Rank 4
0.061471
0.000000 -0.050749 0.036166
-0.033021 0.000000 0.000000 -0.046058 0.050787
0.000000 0.192664 -0.108250 0.000000 0.000000
0.000098 0.062916
-0.185895 0.000000 0.000000 0.090360 -0.212359
0.000000 0.000000 -0.009016 0.017231
H2 -4.05745524 -2.27382980 0.00000000 Type H2 Rank 4
0.139293
0.000000 -0.035408 -0.018515
-0.014446 0.000000 0.000000 -0.038619 -0.057252
0.000000 0.206783 0.106450 0.000000 0.000000
-0.013135 -0.058056
-0.213268 0.000000 0.000000 0.120076 0.161027
0.000000 0.000000 -0.001913 0.001330
H3 0.00000000 -4.70080300 0.00000000 Type H3 Rank 4
0.097072
0.000000 0.000000 -0.049607
-0.027536 0.000000 0.000000 0.070457 0.000000
0.000000 -0.000003 0.231686 0.000000 0.000000
-0.000002 0.042166
-0.205392 0.000000 0.000000 -0.227994 0.000001
0.000000 0.000000 0.024111 -0.000007
H4 4.05745524 -2.27382980 0.00000000 Type H2 Rank 4
0.139293
0.000000 0.035413 -0.018518
-0.014447 0.000000 0.000000 -0.038618 0.057251
0.000000 -0.206778 0.106446 0.000000 0.000000
0.013136 -0.058050
-0.213274 0.000000 0.000000 0.120080 -0.161035
0.000000 0.000000 -0.001911 -0.001315
H5 3.87454677 2.40829326 0.00000000 Type H1 Rank 4
0.061469
0.000000 0.050756 0.036171
-0.033021 0.000000 0.000000 -0.046058 -0.050784
0.000000 -0.192662 -0.108244 0.000000 0.000000
-0.000097 0.062914
-0.185896 0.000000 0.000000 0.090361 0.212361
0.000000 0.000000 -0.009015 -0.017239
N 0.00000000 2.61319624 0.00000000 Type N Rank 4
-0.449971
0.000000 0.000001 -0.244265
0.045510 0.000000 0.000000 0.316527 0.000011
0.000000 0.000032 -0.504088 0.000000 0.000000
0.000004 1.475723
-0.382475 0.000000 0.000000 0.396937 0.000017
0.000000 0.000000 -0.831627 -0.000005
C1 -2.14372406 1.30476509 0.00000000 Type C1 Rank 4
0.228761
0.000000 0.130985 0.026047
-0.129155 0.000000 0.000000 0.019084 0.064717
0.000000 0.408435 0.163515 0.000000 0.000000
-0.058246 0.913013
-1.652743 0.000000 0.000000 -0.054676 0.500720
0.000000 0.000000 -0.031698 -0.726274
C2 -2.24974336 -1.31486189 0.00000000 Type C2 Rank 4
-0.268306
0.000000 0.053328 0.000501
-0.145870 0.000000 0.000000 0.043185 0.136925
0.000000 0.173628 0.017677 0.000000 0.000000
-0.180072 -0.354243
-0.910322 0.000000 0.000000 0.042759 -0.104278
0.000000 0.000000 -0.107168 0.564049
C3 0.00000000 -2.65300899 0.00000000 Type C3 Rank 4
0.030478
0.000000 0.000002 0.062223
-0.103883 0.000000 0.000000 -0.037043 -0.000025
0.000000 0.000072 0.289346 0.000000 0.000000
0.000034 0.842877
-1.365969 0.000000 0.000000 0.368386 -0.000090
0.000000 0.000000 1.137529 0.000040
C4 2.24974336 -1.31486189 0.00000000 Type C2 Rank 4
-0.268316
0.000000 -0.053314 0.000497
-0.145815 0.000000 0.000000 0.043213 -0.136935
0.000000 -0.173576 0.017727 0.000000 0.000000
0.180015 -0.354040
-0.910243 0.000000 0.000000 0.042858 0.104270
0.000000 0.000000 -0.107146 -0.564034
C5 2.14372406 1.30476509 0.00000000 Type C1 Rank 4
0.228755
0.000000 -0.130972 0.026056
-0.129109 0.000000 0.000000 0.019114 -0.064710
0.000000 -0.408369 0.163502 0.000000 0.000000
0.058243 0.912796
-1.652630 0.000000 0.000000 -0.054614 -0.500771
0.000000 0.000000 -0.031678 0.726285
Polarizability
Source: WSM L1,iso. Main basis: d-aug-cc-pVTZ; Aux-basis: aug-cc-pVQZ. PBE0/AC with ALDA+CHF kernel. CamCASP 5.8.
pyr.pol H1 H1 0.000 0.0000000 0.0000000 0.0000000 0.000 3.5508628 0.0000000 0.0000000 0.000 0.0000000 3.5508628 0.0000000 0.000 0.0000000 0.0000000 3.5508628 H2 H2 0.000 0.0000000 0.0000000 0.0000000 0.000 2.6784625 0.0000000 0.0000000 0.000 0.0000000 2.6784625 0.0000000 0.000 0.0000000 0.0000000 2.6784625 H3 H3 0.000 0.0000000 0.0000000 0.0000000 0.000 2.2864035 0.0000000 0.0000000 0.000 0.0000000 2.2864035 0.0000000 0.000 0.0000000 0.0000000 2.2864035 H4 H4 0.000 0.0000000 0.0000000 0.0000000 0.000 2.6784625 0.0000000 0.0000000 0.000 0.0000000 2.6784625 0.0000000 0.000 0.0000000 0.0000000 2.6784625 H5 H5 0.000 0.0000000 0.0000000 0.0000000 0.000 3.5508628 0.0000000 0.0000000 0.000 0.0000000 3.5508628 0.0000000 0.000 0.0000000 0.0000000 3.5508628 N N 0.000 0.0000000 0.0000000 0.0000000 0.000 9.1995184 0.0000000 0.0000000 0.000 0.0000000 9.1995184 0.0000000 0.000 0.0000000 0.0000000 9.1995184 C1 C1 0.000 0.0000000 0.0000000 0.0000000 0.000 4.9206625 0.0000000 0.0000000 0.000 0.0000000 4.9206625 0.0000000 0.000 0.0000000 0.0000000 4.9206625 C2 C2 0.000 0.0000000 0.0000000 0.0000000 0.000 8.9845877 0.0000000 0.0000000 0.000 0.0000000 8.9845877 0.0000000 0.000 0.0000000 0.0000000 8.9845877 C3 C3 0.000 0.0000000 0.0000000 0.0000000 0.000 7.6763173 0.0000000 0.0000000 0.000 0.0000000 7.6763173 0.0000000 0.000 0.0000000 0.0000000 7.6763173 C4 C4 0.000 0.0000000 0.0000000 0.0000000 0.000 8.9845877 0.0000000 0.0000000 0.000 0.0000000 8.9845877 0.0000000 0.000 0.0000000 0.0000000 8.9845877 C5 C5 0.000 0.0000000 0.0000000 0.0000000 0.000 4.9206625 0.0000000 0.0000000 0.000 0.0000000 4.9206625 0.0000000 0.000 0.0000000 0.0000000 4.9206625
Potential & Damping
Model(1) : Tang-Toennies damping. Single damping coeff for all sites.
pyr2.pot
! Pair-Potential: Atom-Atom Potential
! Sites:
! H1 H2 H3 N C1 C2 C3
Induction damping factor 1.10
Dispersion damping factor 1.67
H1 H1 rho alpha C6
00 00 0 0.400890E+01 0.179597E+01 0.706913E+01
END
H1 H2 rho alpha C6
00 00 0 0.375216E+01 0.200670E+01 0.559589E+01
END
H1 H3 rho alpha C6
00 00 0 0.383135E+01 0.183361E+01 0.494268E+01
END
H1 N rho alpha C6
00 00 0 0.505845E+01 0.171121E+01 0.187214E+02
END
H1 C1 rho alpha C6
00 00 0 0.462556E+01 0.181972E+01 0.496706E+01
END
H1 C2 rho alpha C6
00 00 0 0.522471E+01 0.150198E+01 0.148082E+02
END
H1 C3 rho alpha C6
00 00 0 0.486455E+01 0.164089E+01 0.114146E+02
END
H2 H2 rho alpha C6
00 00 0 0.367441E+01 0.199738E+01 0.517730E+01
END
H2 H3 rho alpha C6
00 00 0 0.378315E+01 0.195453E+01 0.435117E+01
END
H2 N rho alpha C6
00 00 0 0.506747E+01 0.159039E+01 0.185123E+02
END
H2 C1 rho alpha C6
00 00 0 0.452919E+01 0.193394E+01 0.392763E+01
END
H2 C2 rho alpha C6
00 00 0 0.506970E+01 0.145685E+01 0.988117E+01
END
H2 C3 rho alpha C6
00 00 0 0.483443E+01 0.182153E+01 0.153399E+02
END
H3 H3 rho alpha C6
00 00 0 0.374602E+01 0.195782E+01 0.424110E+01
END
H3 N rho alpha C6
00 00 0 0.507005E+01 0.161814E+01 0.141257E+02
END
H3 C1 rho alpha C6
00 00 0 0.469760E+01 0.180276E+01 0.906494E+01
END
H3 C2 rho alpha C6
00 00 0 0.502963E+01 0.156364E+01 0.497467E+01
END
H3 C3 rho alpha C6
00 00 0 0.482612E+01 0.175929E+01 0.132862E+02
END
N N rho alpha C6
00 00 0 0.597856E+01 0.164810E+01 0.562217E+02
END
N C1 rho alpha C6
00 00 0 0.606134E+01 0.171463E+01 0.420339E+02
END
N C2 rho alpha C6
00 00 0 0.605134E+01 0.186072E+01 0.531670E+02
END
N C3 rho alpha C6
00 00 0 0.589588E+01 0.209308E+01 0.456637E+02
END
C1 C1 rho alpha C6
00 00 0 0.563543E+01 0.181319E+01 0.211990E+02
END
C1 C2 rho alpha C6
00 00 0 0.596767E+01 0.140361E+01 0.322704E+02
END
C1 C3 rho alpha C6
00 00 0 0.580330E+01 0.183439E+01 0.281295E+02
END
C2 C2 rho alpha C6
00 00 0 0.632407E+01 0.166354E+01 0.470196E+02
END
C2 C3 rho alpha C6
00 00 0 0.608952E+01 0.169620E+01 0.439993E+02
END
C3 C3 rho alpha C6
00 00 0 0.593747E+01 0.180197E+01 0.375136E+02
END
Sample Orient command file
You will need the above files present in the directory as they are included into this Orient file.
Orient version: 4.7/4.8
pyridine_model1.ornt
UNITS BOHR
Parameters
Sites 100 polarizable 100
S-functions 50000
Alphas 50000
Parameter-sets 50000
Pairs 100000
Molecules 10
End
Types
H1 Z 1
H2 Z 1
H3 Z 1
H4 Z 1
H5 Z 1
N Z 7
C1 Z 6
C2 Z 6
C3 Z 6
C4 Z 6
C5 Z 6
End
Variables
Rx 10.0 B
Ry 0.0 B
Rz 0.0 B
alpha 0.0 D
Nx 0.0
Ny 0.0
Nz 1.0
Index 0
End
Molecule pyr1 at 0.0 0.0 0.0 rotated by 0.0 about 0.0 0.0 1.0
#include ./pyr.mom
End
Edit pyr1
Limit rank 4 for H1 H2 H3 H4 H5 N C1 C2 C3 C4 C5
End
Polarizabilities for pyr1
! Assumed that the pols are in the local-axes
! So they are read after axes are defined
Read rank 1
#include ./pyr.pol
End
Limit rank 1 for +++
H1 H2 H3 H4 H5 N C1 C2 C3 C4 +++
C5
End
Molecule pyr2 at Rx Ry Rz ROTATED BY alpha ABOUT Nx Ny Nz
#include ./pyr.mom
End
Edit pyr2
Limit rank 4 for H1 H2 H3 H4 H5 N C1 C2 C3 C4 C5
End
Polarizabilities for pyr2
! Assumed that the pols are in the local-axes
! So they are read after axes are defined
Read rank 1
#include ./pyr.pol
End
Limit rank 1 for +++
H1 H2 H3 H4 H5 N C1 C2 C3 C4 +++
C5
End
Pairs
#include ./pyr2.pot
End
Units Bohr kJ/mol
Switch Induce On Iterate On
Options
Induction Iterations 100 Convergence 1e-12
End
Units Bohr kJ/mol
Comment "Energy calculation"
Energy Table Format e15.7 Print es er ind disp total
Variables
Index Rx Ry Rz alpha Nx Ny Nz
! Configs read from file : Min-1-Hb1.geom
! Minimum 12, energy = -16.148904 KJ/MOL
! R-scalings 0.80 0.85 0.90 0.95 1.00 1.05 1.10 1.20 1.40
! UNITS BOHR DEGREE KJ/MOL
1 -4.62746800 7.42808480 -0.00000080 179.99990900 -0.00000100 -0.00000200 -1.00000000
2 -4.91668475 7.89234010 -0.00000085 179.99990900 -0.00000100 -0.00000200 -1.00000000
3 -5.20590150 8.35659540 -0.00000090 179.99990900 -0.00000100 -0.00000200 -1.00000000
4 -5.49511825 8.82085070 -0.00000095 179.99990900 -0.00000100 -0.00000200 -1.00000000
5 -5.78433500 9.28510600 -0.00000100 179.99990900 -0.00000100 -0.00000200 -1.00000000
6 -6.07355175 9.74936130 -0.00000105 179.99990900 -0.00000100 -0.00000200 -1.00000000
7 -6.36276850 10.21361660 -0.00000110 179.99990900 -0.00000100 -0.00000200 -1.00000000
8 -6.94120200 11.14212720 -0.00000120 179.99990900 -0.00000100 -0.00000200 -1.00000000
9 -8.09806900 12.99914840 -0.00000140 179.99990900 -0.00000100 -0.00000200 -1.00000000
End
FinishOutput should end with
end of output
Energy calculation
Rx Ry Rz alpha Nx Ny Nz Index es er ind disp total
1.00000 -4.62747 7.42808 -0.00000 179.99991 -0.00000 -0.00000 -1.00000 -0.9109696E+02 0.5631058E+03 -0.2019916E+02 -0.1015467E+03 0.3502629E+03
2.00000 -4.91668 7.89234 -0.00000 179.99991 -0.00000 -0.00000 -1.00000 -0.4978455E+02 0.2291852E+03 -0.1171792E+02 -0.6318192E+02 0.1045008E+03
3.00000 -5.20590 8.35660 -0.00000 179.99991 -0.00000 -0.00000 -1.00000 -0.3005944E+02 0.9294555E+02 -0.6747423E+01 -0.3941395E+02 0.1672473E+02
4.00000 -5.49512 8.82085 -0.00000 179.99991 -0.00000 -0.00000 -1.00000 -0.1925548E+02 0.3763489E+02 -0.3905840E+01 -0.2484998E+02 -0.1037641E+02
5.00000 -5.78433 9.28511 -0.00000 179.99991 -0.00000 -0.00000 -1.00000 -0.1282351E+02 0.1522736E+02 -0.2293231E+01 -0.1591543E+02 -0.1580481E+02
6.00000 -6.07355 9.74936 -0.00000 179.99991 -0.00000 -0.00000 -1.00000 -0.8783222E+01 0.6157240E+01 -0.1374807E+01 -0.1038649E+02 -0.1438728E+02
7.00000 -6.36277 10.21362 -0.00000 179.99991 -0.00000 -0.00000 -1.00000 -0.6147458E+01 0.2487614E+01 -0.8455804E+00 -0.6918768E+01 -0.1142419E+02
8.00000 -6.94120 11.14213 -0.00000 179.99991 -0.00000 -0.00000 -1.00000 -0.3160826E+01 0.4045267E+00 -0.3487799E+00 -0.3272124E+01 -0.6377203E+01
9.00000 -8.09807 12.99915 -0.00000 179.99991 -0.00000 -0.00000 -1.00000 -0.9375720E+00 0.1049672E-01 -0.8295216E-01 -0.9278066E+00 -0.1937834E+01