In order to define the atoms which comprise a group, a file, gausssum2.0/groups.txt, should be created with a format similar to the following:
atoms Ru 1 bpy1 2-11,14,17,22,27,34-35,42-43,50,57 bpy2 12,16,18-19,25-26,28-30,39-41,44-46,54-56,58,61 bpy3 13,15,20-21,23-24,31-33,36-38,47-49,51-53,59-60
The first line needs to be either "atoms", "orbitals", "allatoms" or "allorbitals". If it is "allatoms" or "allorbitals", then no further input is required and a separate group will be made for each atom or each orbital. Otherwise, as in the example above, you need to describe which atoms or which orbitals are in each group. The numbers correspond to the order of the atoms/orbitals in the output file. An easy way to obtain these for Gaussian calculations is to open the output file in GaussView and turn on the labels. groups.txt needs to obey the following rules:
Every atom in the molecule must be listed
No atom may be listed more than once
A single point calculation should be done with the following keywords: (Gaussian) pop=full iop(3/33=1,3/36=-1), (GAMESS) NPRINT=3. This creates a large log file containing information on the overlap matrix among other things. (Note: the 3/36=-1 option for Gaussian prevents the calculation and printing of the multipole matrices; this is purely to keep the output file size as small as possible. In some cases, for example SCRF calculations, the multipole matrices must be calculated - if so, leave out the 3/36=-1. It will not affect the calculation of the PDOS.)
Using GaussSum open the log file and choose MO.py. Pick the DOS option. See the previous section for information on the options.
Click on the GaussSum logo. GaussSum calculates the percent contributions of each of the groups to each of the molecular orbitals. This may take a few minutes.
Afterwards, the partial density of states spectra (PDOS) are plotted. Note that each one is stacked on top of the previous one, which means that the line at the greatest height is equal to the sum of all of the partial density of states, and hence equal to the total density of states spectrum. Information on the spectra is written to gausssum2.0/DOS_spectrum.txt.
Information on the molecular orbitals and the percent contributions of the groups is written to gausssum2.0/orbital_data.txt. The last few columns of orbital_data.txt contain more accurate values for the percent contributions and is used by UVVis.py. You should not edit this file if you wish to use the information in it to calculate the changes in charge density associated with electronic transitions, as described in Chapter 8, How do I get the UV-Vis or circular dichroism spectrum of a molecule?.
Creation of PDOS spectra is also supported for unrestricted calculations with Gaussian. The spectrum plotted is of the total DOS broken down by the contribution of each of the groups. orbital_data.txt contains information on the breakdown of the alpha and beta electrons by group.