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Pyridine dimer : Dispersion energy
The Orient command file will look like this. Save this in file //pyr2.ornt//. Here, the //.ornt// ending signifies that this is an Orient command file.
Orient command file for pyridine dimer
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
! The molecular geometries are defined in pyr.mom. This file also contains
! the multipole moments for this system.
Molecule pyr1 at 0.0 0.0 0.0 rotated by 0.0 about 0.0 0.0 1.0
#include ./pyr.mom
End
Molecule pyr2 at Rx Ry Rz ROTATED BY alpha ABOUT Nx Ny Nz
#include ./pyr.mom
End
! Here is where the dispersion model will be defined
Pairs
! We will use a damping model based on the Tang--Toennies incomplete Gamma function
! with damping parameter \beta = 1.67 a.u.
Dispersion damping factor 1.67
! And we will include the dispersion model that should be in file pyr2-disp.pot
#include ./pyr2-disp.pot
End
Units Bohr kJ/mol
! The energies will be evaluated at a set of pyridine dimer geometries that
! will be defined in file pyr2.geom
Comment "Energy calculation"
Energy Table Format e15.7 Print disp
Variables
Index Rx Ry Rz alpha Nx Ny Nz
#include ./pyr2.geom
End
FinishThere are three files that are **included** by this command file:
- pyr.mom : contains the molecular geometry and multipole moments.
- pyr2-disp.pot : Contains the dispersion coefficients.
- pyr2.geom : Contains a set of dimer geometries.
Here is what the multipole moment file should contain:
! 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 0.726285Save this into file //pyr.mom//. Include all blank lines. The format of this file has been described on the main Orient Energy Calculations page.
The dispersion coefficients for this calculation have been provided on a separate page. Copy the dispersion model provided there into a file called //pyr2-disp.pot//. The //.pot// ending signifies that this is a potential file.
The dimer geometry file //pyr2.geom// will be provided on the main dispersion page.
Check!!!
Have you got the following files?
- pyr.mom
- pyr2-disp.pot
- pyr2.ornt