Orbitals and Densities

Orbitals are exported in three forms:

• Molden format, which can be directly read by a number of visualization programs

• As a compact script for the Jmol program

• Cube files of densities created by ORBKIT

Using the Jmol script

After running analyze_tden.py (analyze_sden.py) the file nto_jmol.spt (ndo_jmol.spt) is created. This is an input file for jmol, which can be directly executed as

jmol -n nto_jmol.spt

For more flexibility, the following semi-interactive procedure can be applied:

1. Open Jmol

2. Run the first few lines of the script to preview the settings (simply copy them into the Jmol console)

3. Adjust the perspective

4. Run the remaining lines of the script (by copying into the Jmol console)

5. Open the file nto.html (ndo.html) to view the result (Example).

Density plotting (ORBKIT)

Cube files of densities can be directly created with ORBKIT. The interface is controlled via theoinp.

The cube files can be loaded into VMD and visualized using VMD network files provided by ORBKIT or by using the vmd_plots.py facility of TheoDORE. For the latter, just run:

vmd_plots.py *.cb

ORBKIT is somewhat sensitive in terms of the molden file with orbital information. To achieve the best result, it is advisable to create this file within Molden rather than through TheoDORE.

Density plotting (Molden)

The weighted sum over the NTOs gives the hole / particle densities, while the NDOs yield the attachment / detachment densities.

The following procedure is suggested:

• Create Molden format files of the NTOs / NDOs using analyze_tden.py / analyze_sden.py

• To extract the separate hole / particle contributions use the extract_molden.py script

Run, e.g.:

extract_molden.py nto_1-1-a.mld

This will create a new directory nto_1-1-a.mld.dir containing the files nto_1-1-a.mld_elec.mld and
nto_1-1-a.mld_hole.mld with the separate contributions.

• Open nto_1-1-a.mld_elec.mld in Molden (or preferably gmolden)
  • Go to "density mode"
  • Select "Plot Function" - "Density"
  • Use "Plot Mode" - "Space"
  • The result is the particle density as defined in this Ref.