Normal Coordinate in Gaussian

To get the normal coordinates of a given molecule a frequency calculation is needed.

After this is done, the molecule coordinates can be extracted from a block like the following:
Standard orientation:
———————————————————————
Center     Atomic      Atomic             Coordinates (Angstroms)
Number     Number       Type             X           Y           Z
———————————————————————
1         6           0       -0.667189   -0.020089   -0.000000
2         1           0       -1.087827    0.983730   -0.000001
3         1           0       -1.024813   -0.545474   -0.890589
4         1           0       -1.024814   -0.545473    0.890590
5         8           0        0.749274    0.122568    0.000000
6         1           0        1.146396   -0.752798    0.000000
———————————————————————

The extracted coordinates will look like this (don’t forget to convert Atomic Number to appropriate element symbol):

C   -0.667189   -0.020089   -0.000000
H   -1.087827    0.983730   -0.000001
H   -1.024813   -0.545474   -0.890589
H   -1.024814   -0.545473    0.890590
O    0.749274    0.122568    0.000000
H    1.146396   -0.752798    0.000000

The easiest way to determine the wished vibration is by searching it in the graphical user interface of gaussview03

To view vibrations calculated with gaussian09, with gaussview03 the logfile has to be changed for compatibility reasons.
Therefore the lines containing ”  Atom  AN” have to be changed to ”  Atom AN ” (note the single space between Atom and AN).

Search and replace string with vim:
:%s/\(  Atom\)\(  \)\(AN\)/\1 \3 /

Stream edit (sed) command
sed -i ‘s/\(  Atom\)\(  \)\(AN\)/\1 \3 /’ filename

After the conversion the vibrational data can be read and the frequencies / vibrational modes can be browsed under
Results -> Vibrations.

The normal coordinates of the given frequency can are found in a block similar to the following:

A         A
Frequencies —  3114.2233 3825.0951
Reduced masses —     1.0986    1.0666
Force constants —     6.2777    9.1948
IR Intensities —    28.7103   46.0322
Coord Atom Element:
1     1     6          0.02003  -0.00037
2     1     6         -0.08863  -0.00235
3     1     6          0.00001  -0.00000
1     2     1         -0.35807  -0.00501
2     2     1          0.88663   0.01477
3     2     1          0.00000   0.00000
1     3     1          0.06061  -0.00347
2     3     1          0.07937   0.00022
3     3     1          0.16899   0.00069
1     4     1          0.06064  -0.00347
2     4     1          0.07943   0.00021
3     4     1         -0.16908  -0.00067
1     5     8         -0.00006   0.02765
2     5     8          0.00173  -0.05616
3     5     8         -0.00000   0.00000
1     6     1         -0.00076  -0.42238
2     6     1         -0.01756   0.90410
3     6     1         -0.00000   0.00000

In this example the coordinates of the OH-Stretch-vibration (frequency 3825.0951) are searched. The coordinates have to be split in their respective x, y and z paths. An easy way to do this is by using a “hidden feature” of the unix paste command:

paste – – – < inputfile > outputfile

After that there should be two files extracted of the log file.
One containing atom type and coordinates and one containing the normal coordinates. Pasting these should yield:

C   -0.667189   -0.020089   -0.000000    -0.00037    -0.00235    -0.00000
H   -1.087827    0.983730   -0.000001    -0.00501     0.01477     0.00000
H   -1.024813   -0.545474   -0.890589    -0.00347     0.00022     0.00069
H   -1.024814   -0.545473    0.890590    -0.00347     0.00021    -0.00067
O    0.749274    0.122568    0.000000     0.02765    -0.05616     0.00000
H    1.146396   -0.752798    0.000000    -0.42238     0.90410     0.00000

Now it is easy to generate a scan by just using:

dq = stepwidth
paste coords normalcoords | awk ‘{printf “%s    % lf    % lf    % lf\n”, $1, $2 + ‘dq’*$5, $3 + ‘dq’*$6, $4 + ‘dq’*$7}’

 

# copy paste from mjs

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s