## page was renamed from AJMGrpOnly/orient/dispersion-models/pyr2-disp-orient ## page was renamed from ajm/orient/dispersion-models/pyr2-disp-orient #acl +All:read apw185:read,write,delete Known:read All: <> Back to [[ajm/orient/dispersion-models|Orient dispersion main page]]. = 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. [[attachment: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 Finish }}} There are three files that are **included** by this command file: 1. pyr.mom : contains the molecular geometry and multipole moments. 1. pyr2-disp.pot : Contains the dispersion coefficients. 1. pyr2.geom : Contains a set of dimer geometries. Here is what the multipole moment file should contain: [[attachment: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 }}} Save this into file //pyr.mom//. Include all blank lines. The format of this file has been described on the main [[ajm/orient/energy-calculations|Orient Energy Calculations]] page. The dispersion coefficients for this calculation have been provided on a [[ajm/orient/dispersion-models/pyridine-c12iso|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 [[ajm/orient/dispersion-models|main dispersion page]]. == Check!!! == Have you got the following files? 1. pyr.mom 1. pyr2-disp.pot 1. pyr2.ornt