VMOdes for Windows VMOdes for Windows Virtual Molecular Orbital description Program
(Current version available is A 7.2)
The most popular modern quantum-chemical packages like Gaussian, HyperChem, Spartan, GAMESS, and ADF generate numerical description of molecular orbitals in output files. However, the main question for chemists is the contribution of different shell(s), atom(s), and fragment(s) to the molecular orbital of interest. So, how to do this? Your may spend a lot of time to calculate such a contributions using calculator or develop your own program which will give information on which you is looking for. VMOdes is an alternative way. It is easy to use it. It is freeware. It will be extended in a future. So, why not try it today? Just read a short manual and download the program!
Part 1. Program capabilities and limitations.
Part 2. Examples of using VMOdes.
Part 3. List of files distributed with VMOdes program and installation notes.
Program capabilities and limitations.
VMOdes (Virtual Molecular Orbital description Program) is a small program for the calculation of the percentage from selected atomic orbital(s) contribution to molecular orbital(s). Selected atomic orbital(s) can represent atomic shell(s) (for instance metal d-fold, dz2 orbital, px orbital, etc.), atom(s), or group(s) of atoms or shell(s). As a result, VMOdes is produces publication quality tables with the molecular orbital(s) analysis.
We developed this program in order to analyze the chemical interactions between atom(s) or fragment(s) in molecular systems for the molecular orbital(s) of interest. We are interested in this program because in general, the most of the quantum-chemical software packages are not capable for atomic orbital conribution analysis into molecular orbital.
The current version of VMOdes processes output files from the following quantum-chemical programs:
Output files from restricted, restricted-open, and unrestricted calculations at semi-empirical, ab initio , and DFT levels are process by VMOdes.
In the current version of VMOdes only the most popular for the molecular orbital description c^2 population analysis is available (P. Ros and G. C. A. Schuit, Theoret. Chim.Acta (Berl.) 1966, 4, 1-12).
Operating System: Windows Me, 2000, or XP (I stop to support Windows 95, 98, & NT OS)
System Requirements: Pentium processor with 32MB RAM is minimum, but the more the better. For some of output files with about 200Mb size you will need ~2Gb of RAM.
Gaussian 03 and 03W output files processes with VMOdes.
Windows XP (Home & Professional) included to the lists of the VMOdes supported OS.
GAMESS ( USA ) output files processes with VMOdes;
For unrestricted wavefunctions now it is possible to analyse Alpha and Beta orbital sets separately.
Maximum number of orbitals: 1500
Maximum number of groups in subunit: 15
Maximum number of subunits: 7
Description:
VMOdes is not works well with UNIX/LINUX Gaussian 98 and GAMESS (USA) output files.
Solution:
Delete all the UNIX/LINUX generated path lines before line “Entering Link 1 =…” (for Gaussian) or “****…” (for GAMESS (USA)) output files.
Description:
Some times VMOdes is not responds when it runs under Windows 95.
Solution:
Close VMOdes using Task Manager. VMOdes output file is already generated.
The ADF and Spartan output files will process with VMOdes.
The number of subunits will be increased to 10.
Citation of the VMOdes is the part of the license agreement.
Cite this program as: VMOdes Program, Revision A 7.2
V. N. Nemykin, P. Basu; University of Minnesota Duluth and Duquesne University; 2001, 2003, 2005.
Examples of using VMOdes.
Before you start, make sure that:
- Your output file contains all the necessary information on the molecular orbitals;
- Your “data.txt” file contains all the necessary information on the shell(s), atom(s), or group(s) of interest.
To make sure that your output file contains all the necessary information on the molecular orbitals use the following settings:
Software Settings
Gaussian Pop=Full
GAMESS no specific settings
HyperChem QuantumPrintLevel = 1 (or higher, I am typically using QuantumPrintLevel = 9)
All information on subunits of interest should be located in “data.txt” file. This is an ASCII file which can be edited by using any ASCII file editors (Notepad, WordPad, FAR manager, etc.). The format of the “data.txt” file for VMOdes should be the following:
Line 1: Number of subunits (any integer number between 1 and 7)
Line 2: Subunit specification: i) number of shell(s), atom(s), or group(s) in subunit, ii) name of subunit following coma, iii) first and the last basis function values for each shell(s), atom(s), or group(s) in subunit.
Line 3: Specification of next subunit (if necessary).
The “data.txt” file listed below is respects to MoOS(SH)2(NH3)2 calculation using Gaussian 98:
7
1 Molybdenum, 1 37
1 Molybdenum d-orbitals, 16 37
1 Oxygen atom, 38 44
1 Sulfur atom (Mo=S), 45 51
2 SH ligands, 52 62 74 76
2 NH3 ligand, 63 73 77 80
1 Total, 1 80
In total 7 subunits are considered.
The first one is all AOs o Molybdenum (basis functions from 1 to 37).
Second subunit is d-metal fold of Molybdenum (basis functions from 16 to 37).
Third subunit is Oxygen atom (basis functions from 38 to 44).
Fourth subunit is Sulfur atom (basis functions from 45 to 51).
Fifth subunit are two SH groups consists of two subgroups. The first one, is two Sulfur atoms (basis functions from 52 to 62) while the second one is Hydrogen atoms (basis functions from 74 to 76).
Sixth subunit is NH3 ligands consists of one Nitrogen atom (basis functions from 63 to 73) and three Hydrogens (basis functions from 77 to 80).
Seventh subunit is total. If you have less that 7 subunits considered, it is recommended to use “total” subunit in order to be sure that the sum of all basis functions will give you 100% of the MOs contribution (VMOdes is a freeware and still may contains a bugs!). For more detailed discussion on “data.txt” file, see full examples below.
As soon as you will have unziped VMOdes.zip file, start VMOdes*.exe. As soon, as you will start it, the message box (I hope so :-) ) will appear. Click OK. Now you should to get the main window of VMOdes peogram:
.
Click on File Open button or use File/Open menu. Select and open file like as usual in Windows interface:
.
Choose Run/Ci Square Method from menu:
.
The new window will appear:
.
Next, choose output file type ( Gaussian 98, Gaussian 03, GAMESS ( USA ), or HyperChem ) from the upper menu. Choose the orbital(s) of interest. You may choose between “All orbitals” (all orbitals will be considered), “5x5” (only 5 highest occupied and 5 lowest unoccupied orbitals will be considered), “10x10” (only 10 highest occupied and 10 lowest unoccupied orbitals will be considered), “20x20” (only 20ighest occupied and 20owest unoccupied orbitals will be considered), or individual orbital (from 1 up to 1500):
.
Next, choose orbital set (alpha or beta). This option is only active for unrestricted calculations. You are all set.
Press “Start” button (or Alt+S) and type VMOdes output file name in the box which will appear:
.
As soon as all calculations will be done, you will see “Status: Calculation Complete” message and output information (only for small files!) in the output window:
.
Now you may terminate VMOdes program or click on “Cancel/Back” button and load the next output file. Below you will find a few examples, which you may test by VMOdes program (please rename data-*-example.txt files to data.txt).
FULL EXAMPLE 1 shows the Gaussian output file for methane molecule calculated at B3LYP level using 6-31G(d) basis set.
The part of the Gaussian output file looks like:
1 2 3 4 5
(A1)--O (A1)--O (T2)--O (T2)--O (T2)--O
EIGENVALUES -- -11.20980 -0.94056 -0.54367 -0.54367 -0.54367
1 1 C 1S 0.99565 -0.19375 0.00000 0.00000 0.00000
2 2S 0.02830 0.35807 0.00000 0.00000 0.00000
3 2PX 0.00000 0.00000 0.00000 0.00000 0.43425
4 2PY 0.00000 0.00000 0.43425 0.00000 0.00000
5 2PZ 0.00000 0.00000 0.00000 0.43425 0.00000
6 3S -0.01314 0.36696 0.00000 0.00000 0.00000
7 3PX 0.00000 0.00000 0.00000 0.00000 0.23009
8 3PY 0.00000 0.00000 0.23009 0.00000 0.00000
9 3PZ 0.00000 0.00000 0.00000 0.23009 0.00000
10 4XX -0.00204 0.01013 0.00000 0.00000 0.00000
11 4YY -0.00204 0.01013 0.00000 0.00000 0.00000
12 4ZZ -0.00204 0.01013 0.00000 0.00000 0.00000
13 4XY 0.00000 0.00000 0.00000 0.03600 0.00000
14 4XZ 0.00000 0.00000 0.03600 0.00000 0.00000
15 4YZ 0.00000 0.00000 0.00000 0.00000 0.03600
16 2 H 1S 0.00004 0.13373 0.16821 0.16821 0.16821
17 2S 0.00243 0.03807 0.14014 0.14014 0.14014
18 3 H 1S 0.00004 0.13373 -0.16821 0.16821 -0.16821
19 2S 0.00243 0.03807 -0.14014 0.14014 -0.14014
20 4 H 1S 0.00004 0.13373 0.16821 -0.16821 -0.16821
21 2S 0.00243 0.03807 0.14014 -0.14014 -0.14014
22 5 H 1S 0.00004 0.13373 -0.16821 -0.16821 0.16821
23 2S 0.00243 0.03807 -0.14014 -0.14014 0.14014
Let say, we would like to calculate carbon, carbon s-orbitals, and hydrogen atoms contributions to each MO. In this case, “data.txt” file may looks like following:
4
1 Carbon, 1 15
2 Carbon s orbitals, 1 2 6 6
1 Hydrogen atoms, 16 23
1 Total, 1 23
A VMOdes output file will looks like:
Input Gaussian file:
C:\All Users\Calculations\Qbasic\MyPrograms\SDI-1\e2_02.out
Output VMOdes file: test.out
Full point group is: TD
Number of Basis Functions = 23
5 Alpha electrons 5 Beta electrons
Group 1 is: Carbon
This group consist of 1 subunits. The Basis Functions range is:
1 15
Group 2 is: Carbon s orbitals
This group consist of 2 subunits. The Basis Functions range is:
1 2
6 6
Group 3 is: Hydrogen atoms
This group consist of 1 subunits. The Basis Functions range is:
16 23
Group 4 is: Total
This group consist of 1 subunits. The Basis Functions range is:
1 23
All MO's will be printed.
Molecular Orbitals Indexes, Energies, and Group Contributions
Orbital Group Number
_________________________ ____________________________________
Number Index Energy,eV 1 2 3 4
1 (A1)--O -305.037 100.0 100.0 0.0 100.0
2 (A1)--O -25.594 79.5 79.5 20.5 100.0
3 (T2)--O -14.794 55.9 0.0 44.1 100.0
4 (T2)--O -14.794 55.9 0.0 44.1 100.0
5 (T2)--O -14.794 55.9 0.0 44.1 100.0
6 (A1)--V 6.941 64.2 64.2 35.8 100.0
7 (T2)--V 8.846 30.4 0.0 69.6 100.0
8 (T2)--V 8.846 30.4 0.0 69.6 100.0
9 (T2)--V 8.846 30.4 0.0 69.6 100.0
10 (T2)--V 19.912 85.7 0.0 14.3 100.0
11 (T2)--V 19.912 85.7 0.0 14.3 100.0
12 (T2)--V 19.912 85.7 0.0 14.3 100.0
13 (T2)--V 31.988 34.8 0.0 65.2 100.0
14 (T2)--V 31.988 34.8 0.0 65.2 100.0
15 (T2)--V 31.988 34.8 0.0 65.2 100.0
16 (A1)--V 33.628 60.0 59.8 40.0 100.0
17 (A1)--V 35.683 88.3 88.2 11.7 100.0
18 (E)--V 52.860 100.0 0.0 0.0 100.0
19 (E)--V 52.860 100.0 0.0 0.0 100.0
20 (T2)--V 70.137 60.7 0.0 39.3 100.0
21 (T2)--V 70.137 60.7 0.0 39.3 100.0
22 (T2)--V 70.137 60.7 0.0 39.3 100.0
23 (A1)--V 125.281 96.2 56.0 3.8 100.0
FULL EXAMPLE 2 shows the Pc GAMESS (USA) output file for methylene (1A1 singlet state) molecule calculated at RHF level using STO-3G basis set.
The part of the Pc GAMESS (USA) output file looks like:
1 2 3 4 5
-11.0013 -0.8395 -0.5271 -0.3016 0.2280
A1 A1 B1 A1 B2
1 C 1 S 0.993035 -0.216249 0.000000 0.133125 0.000000
2 C 1 S 0.030638 0.657554 0.000000 -0.610829 0.000000
3 C 1 X 0.000000 0.000000 0.528825 0.000000 0.000000
4 C 1 Y 0.000000 0.000000 0.000000 0.000000 1.000000
5 C 1 Z 0.006480 0.169457 0.000000 0.782815 0.000000
6 H 2 S -0.007445 0.273533 -0.458157 0.213567 0.000000
7 H 3 S -0.007445 0.273533 0.458157 0.213567 0.000000
Let say, we would like to calculate carbon, and hydrogen atoms contributions to each MO. In this case, “data.txt” file may looks like following:
3
1 Carbon, 1 5
1 Hydrogen atoms, 6 7
1 Total, 1 7
A VMOdes output file will looks like:
Input GAMESS (USA) file:
C:\All Users\Calculations\Qbasic\MyPrograms\SDI-1\Symm-rhf.out
Output VMOdes file: test.out
Full point group is: CNV
The order of the principal axis is: 2
Number of Basis Functions = 7
Number of Electrons = 8
Number of Alpha Electrons = 4
Number of Beta Electrons = 4
Group 1 is: Carbon
This group consist of 1 subunits. The Basis Functions range is:
1 5
Group 2 is: Hydrogen atoms
This group consist of 1 subunits. The Basis Functions range is:
6 7
Group 3 is: Total
This group consist of 1 subunits. The Basis Functions range is:
1 7
All MO's will be printed.
Molecular Orbitals Indexes, Energies, and Group Contributions
Orbital Group Number
_________________________ ___________________________
Number Index Energy,eV 1 2 3
1 A1 -299.363 100.0 0.0 100.0
2 A1 -22.844 77.2 22.8 100.0
3 B1 -14.343 40.0 60.0 100.0
4 A1 -8.207 91.7 8.3 100.0
-----Unoccupied orbitals-----
5 B2 6.204 100.0 0.0 100.0
6 A1 18.741 53.5 46.5 100.0
7 B1 19.805 46.8 53.2 100.0
FULL EXAMPLE 3 shows the HyperChem 6.02 output file for ammonia molecule calculated at PM3 level.
The part of the HyperChem 6.02 output file looks like:
Mol. Orbital 1 2 3 4 5 6
Symmetry: 1 A1 1 E 1 E 2 A1 3 A1 2 E
Eigenvalue -27.61762 -14.76440 -14.76440 -9.67861 2.79812 4.95296
S N 1 0.76519 0.00000 0.00000 0.37169 -0.52567 -0.00000
Px N 1 0.04791 0.65326 -0.07465 -0.30355 -0.14490 -0.08318
Py N 1 0.02818 0.02742 0.68444 -0.17854 -0.08523 0.69972
Pz N 1 0.12959 -0.24746 -0.12123 -0.82110 -0.39195 -0.12140
S H 2 0.36268 0.49547 -0.30880 -0.14562 0.42496 0.30685
S H 3 0.36268 -0.51516 -0.27469 -0.14562 0.42496 0.26340
S H 4 0.36268 0.01969 0.58349 -0.14562 0.42496 -0.57026
Let say, we would like to calculate nitrogen, nitrogen p-orbitals, and hydrogen atoms contributions to each MO. In this case, “data.txt” file may looks like following:
4
1 Nitrogen, 1 4
1 Nitrogen p orbitals, 2 4
1 Hydrogen atoms, 5 7
1 Total, 1 7
A VMOdes output file looks like:
Input HyperChem file:
C:\All Users\Calculations\Qbasic\MyPrograms\SDI-1\chem-NH3-rhf.log
Output VMOdes file: test.out
Number of electrons = 8
Number of alpha electrons: 4
Number of beta electrons: 4
Number of basis functions = 7
Group 1 is: Nitrogen
This group consist of 1 subunits. The Basis Functions range is:
1 4
Group 2 is: Nitrogen p orbitals
This group consist of 1 subunits. The Basis Functions range is:
2 4
Group 3 is: Hydrogen atoms
This group consist of 1 subunits. The Basis Functions range is:
5 7
Group 4 is: Total
This group consist of 1 subunits. The Basis Functions range is:
1 7
All MO's will be printed.
Molecular Orbitals Indexes, Energies, and Group Contributions
Orbital Group Number
_________________________ ____________________________________
Number Index Energy,eV 1 2 3 4
1 1 A1 -27.618 60.5 2.0 39.5 100.0
2 1 E -14.764 48.9 48.9 51.1 100.0
3 1 E -14.764 48.9 48.9 51.1 100.0
4 2 A1 -9.679 93.6 79.8 6.4 100.0
-----Unoccupied orbitals-----
5 3 A1 2.798 45.8 18.2 54.2 100.0
6 2 E 4.953 51.1 51.1 48.9 100.0
7 2 E 4.953 51.1 51.1 48.9 100.0
Full point group is: C3V
List of files distributed with VMOdes program
VMOdes*.exe – current version of VMOdes program
License.dat – license file (should be updated by request)
Help.txt – help file
data-Gaussian-example.txt – example of “data.txt” file for Gaussian job
data-GAMESS-example.txt - example of “data.txt” file for GAMESS (USA) job
data-HyperChem-example.txt - example of “data.txt” file for HyperChem job
Gaussian-example.out – example of Gaussian output file
GAMESS-example.out – example of GAMESS (USA) output file
HyperChem-example.log – example of HyperChem output file
Installation of VMOdes for Windows:
Just simply send an e-mail to: vnemykin@d.umn.edu and include the following information:
a) Your name and (if you are student) name of your supevisor
b) Name of the University or company you are working for
c) Contact address & e-mail.
I will use this information only for the VMOdes users/updates database.
Once information received, you will get a “secret” code, which is necessary for unzipping of VMOdes. Good luck!
© 2004-2005 Victor Nemykin, All Rights Reserved
Comments: vnemykin@d.umn.edu
Last Updated May 19, 2005