Having described Route-1, the adjustments to the isy file to obtain a script performing a Route-2 type of calculation are quite easy. Only a few points should be taken into account.
The first step is to run an HF or DFT Gaussian calculation, which could be a single point energy or a geometry optimization calculation, saving the check point file.
Transform the check point file in a formatted file.
Run MOMO check_point.fchk, writing an isy file.
As an example, let us consider the borazine molecule and the following Gaussian input file, for a geometry optimization at the B3LYP/6-31G(d) level.
1 %chk=borazine.chk 2 # opt freq b3lyp/6-31g(d) 10f 6d 3 4 borazine geo opt at b3lyp/6-31g(d) 5 6 0 1 7 X1 8 X2 X1 1.0 9 N1 X2 NX X1 90.0 10 X3 X2 1.0 N1 90.0 X1 180.0 11 N2 X2 NX X1 90.0 N1 120.0 12 N3 X2 NX X1 90.0 N1 -120.0 13 B1 X2 BX X1 90.0 N1 180.0 14 B2 X2 BX X1 90.0 B1 120.0 15 B3 X2 BX X1 90.0 B1 -120.0 16 H1 X2 HN X1 90.0 N1 0.0 17 H2 X2 HN X1 90.0 N2 0.0 18 H3 X2 HN X1 90.0 N3 0.0 19 H4 X2 HB X1 90.0 B1 0.0 20 H5 X2 HB X1 90.0 B2 0.0 21 H6 X2 HB X1 90.0 B3 0.0 22 Variables: 23 NX 1.407110 24 HN 2.409672 25 BX 1.447738 26 HB 2.643086 27
When the Gaussian calculation has finished, type the commands
prompt> formchk borazine prompt> MOMO borazine.fchk
and, whitin the MOMO run, type
yxz spg D3d write borazine.isy y q
Then, the borazine.isy file should read:
1 #!/bin/bash 2 mo230xl << next 3 BORAZINE GEO OPT AT B3LYP/6-31G(D) 4 5 D3H 6 N1 2.66600150E+00 0.00000000E+00 0.00000000E+00 7 S 6 8 4.17351146E+03 1.83477216E-03 9 6.27457911E+02 1.39946270E-02 10 1.42902093E+02 6.85865518E-02 11 4.02343293E+01 2.32240873E-01 12 1.28202129E+01 4.69069948E-01 13 4.39043701E+00 3.60455199E-01 14 S 3 15 1.16263619E+01 -1.14961182E-01 16 2.71627981E+00 -1.69117479E-01 17 7.72218397E-01 1.14585195E+00 18 P 3 19 1.16263619E+01 6.75797439E-02 20 2.71627981E+00 3.23907296E-01 21 7.72218397E-01 7.40895140E-01 22 S 1 23 2.12031498E-01 1.00000000E+00 24 P 1 25 2.12031498E-01 1.00000000E+00 26 D 1 27 8.00000000E-01 1.00000000E+00 28 N2 N1 -1.33300075E+00 2.30882502E+00 -6.07049125E-17 29 N2 N1 -1.33300075E+00 -2.30882502E+00 6.07049125E-17 30 B1 -2.74211085E+00 0.00000000E+00 0.00000000E+00 31 S 6 32 2.06888225E+03 1.86627459E-03 33 3.10649570E+02 1.42514817E-02 34 7.06830330E+01 6.95516185E-02 35 1.98610803E+01 2.32572933E-01 36 6.29930484E+00 4.67078712E-01 37 2.12702697E+00 3.63431440E-01 38 S 3 39 4.72797107E+00 -1.30393797E-01 40 1.19033774E+00 -1.30788951E-01 41 3.59411683E-01 1.13094448E+00 42 P 3 43 4.72797107E+00 7.45975799E-02 44 1.19033774E+00 3.07846677E-01 45 3.59411683E-01 7.43456834E-01 46 S 1 47 1.26751247E-01 1.00000000E+00 48 P 1 49 1.26751247E-01 1.00000000E+00 50 D 1 51 6.00000000E-01 1.00000000E+00 52 B2 B1 1.37105543E+00 -2.37473766E+00 6.87768824E-17 53 B2 B1 1.37105543E+00 2.37473766E+00 -6.87768824E-17 54 H1 4.57733472E+00 0.00000000E+00 8.75811540E-47 55 S 3 56 1.87311370E+01 3.34946043E-02 57 2.82539436E+00 2.34726953E-01 58 6.40121692E-01 8.13757326E-01 59 S 1 69 1.61277759E-01 1.00000000E+00 61 H2 H1 -2.28866736E+00 3.96408815E+00 -4.13715765E-17 62 H2 H1 -2.28866736E+00 -3.96408815E+00 4.13715765E-17 63 H2 H1 -5.00445550E+00 0.00000000E+00 -8.75811540E-47 64 H2 H1 2.50222775E+00 -4.33398559E+00 8.66709485E-17 65 H2 H1 2.50222775E+00 4.33398559E+00 -8.66709485E-17 66 67 next 68 if [ $? == 0 ]; then 69 mo400xl << next 70 BORAZINE GEO OPT AT B3LYP/6-31G(D) 71 SODILI 1E-6 EOSCISTOP 50 72 gaumos borazine.fchk yxz 73 74 21 75 next 76 if [ $? == 0 ]; then 77 mo600xl << next 78 BORAZINE GEO OPT AT B3LYP/6-31G(D) 79 80 momento-di-dipolo salva 81 momento-lineare salva 82 momento-angolare salva 83 84 next 85 if [ $? == 0 ]; then 86 mo690xl << next 87 BORAZINE GEO OPT AT B3LYP/6-31G(D) 88 HFEXCHANGE x.xx 89 90 91 next 92 if [ $? == 0 ]; then 93 mo710xl << next 94 BORAZINE GEO OPT AT B3LYP/6-31G(D) 95 HFEXCHANGE 0.20 96 97 98 next 99 if [ $? == 0 ]; then 100 rm -f fort.4 fort.20 101 tar -a -cf borazine.tgz fort.* 102 rm -f fort.* 103 fi 104 fi 105 fi 106 fi 107 fi 108 exit
In this case also, to perform a magnetic perturbed calculation only, lines 85-91 must be deleted, as well as line 103. Now the script is ready and can be submitted to perform the B3LYP/6-31G(d) calculation of the magnetic perturbation using the command
prompt> ./borazine.isy >& borazine.osy &
SYSMO program output files are collected in the borazine.osy file and borazine.tgz contains the FORTRAN files for the subsequent current density calculations.
Some concluding remarks for this section are as follows.
Geometry and basis set are taken from the fchk file, this is the only way.
Always using Cartesian Gaussian functions by means of the 6d and 10f options on the Gaussian route card.
The MOMO program recognizes only a few functionals and their HF exchange fractions. Therefore, always check line 95 of the isy file to see whether the correct HFEXCHANGE value has been inserted.
Pure functionals require HFEXCHANGE 0 and the calculation of two-electron integrals can be skipped by inserting the string MAXREC 0 in line 4 followed by a new blank line. In this case the calculation is very fast.
If the Gaussian calculation is at HF level, remove line 95.