Huckel-Molecular-Orbital-Calculation (HMO)

A program to perform Huckel molecular orbital caluclations on molecules.

HMO is a light-weighted program to perform Huckel molecular orbital calculations on molecules. It is very easy to use and can generate Graphviz input files for the visualization of results.

Compiling HMO

To compile HMO, you need boost and Lapack. You can set the path of the Lapack library in Makefile and then simply type

make

Everything should go well.

Executables

If you do not want to compile HMO, you can go to my website to get the executables.

HMO on my website

Example

An example input file is given in bin/styrene.inp:

1.8 0
 C                 -3.33505854   -4.05509747    0.03172776
 C                 -1.93989854   -4.05509747    0.03172776
 C                 -1.24236054   -2.84734647    0.03172776
 C                 -1.94001454   -1.63883747    0.03052876
 C                 -3.33483954   -1.63891547    0.03004976
 C                 -4.03244054   -2.84712147    0.03104576
 C                 -1.16951047   -0.30544951    0.03044614
 C                 -1.84201131    0.87111682    0.02928423
 C                 -1.06360352    2.19990338    0.03203690
 C                 -1.75320092    3.41233984    0.03084857
 C                  0.33149892    2.19089168    0.03626174
 C                 -1.04780409    4.61603387    0.03357108
 C                  1.03679478    3.39425768    0.03850471
 C                  0.34687625    4.60719876    0.03679910

In the first line,

• 1.8 is a threshold, meaning that two atoms are considered as bonded when their distance is less than 1.8 Angstrom.
• 0 is the charge of the molecule, which can be 0, +1, -2, etc.

The following lines are the coordinates of carbon atoms. Do NOT write coordinates of other atoms.

With this file, run the calculation:

hmo styrene.inp > styrene.out

In styrene.out, you can find orbital energies and coefficients, atomic densities, bond orders, and pi free valence:

  MO Indices:               1               2               3 
  Occupation:               2               2               2 
 Eigenvalues:      3.21050865      3.06407743      2.50466736 
    Energies:      a+2.21051b      a+2.06408b      a+1.50467b 
           1       0.18305145     -0.25721905      0.36874498 
           2       0.20231841     -0.26546002      0.27741927 
           3       0.26417514     -0.29071098      0.04867874 
           4       0.38164303     -0.33458996     -0.20417396 
...
Bond orders:
           #           Bond order
         1-1           1.00000000
         1-2           0.65658339
         1-3           0.00000000
         1-4          -0.29424047
         1-5           0.00000000
         1-6           0.65658339
...
Atomic Properties:
           #     Electron Density           Pi Valence
           1           1.00000000           1.31316679
           2           1.00000000           1.33775485
           3           1.00000000           1.28257491
           4           1.00000000           1.63390015
           5           1.00000000           1.28257491

You can also find a file called styrene.dot, this is an input file for Graphviz, which can visualize our results. Actually, at the end of styrene.out, there is a suggested command to generate the pdf file (Assume Graphviz has been installed. If not, see here):

We suggest to use the following Graphivz command to render styrene.dot:

   >>>>>>  sfdp styrene.dot -Tpdf -o styrene.pdf

You can change pdf to svg or any formats that Graphviz supports. The rendered graph is given below: