How to plot orbitals from fragment orbitals?

[jjgoings]

Curious how to plot the fragment + bath orbitals from a DMET decomposition, like y'all do for the H10 example in the DMET notebook? It would be helpful for selecting frozen core and ensuring the active orbitals are what I expect.

[alexfleury-sb]

Hi Joshua! For plotting the DMET orbitals, we use the coefficients embedded in the dmet_solver.orbitals.localized_mo and bath_orb variables (dmet_solver is a DMETProblemDecomposition object). Then, we loop through those to get the cube files:

from pyscf import tools
for i in range(dmet_solver.orbitals.localized_mo.shape[1]):
    tools.cubegen.orbital(dmet_solver.orbitals.mol_full, f"M{i+1}.cube", dmet_solver.orbitals.localized_mo[:,i])

Note: to get the bath orbitals, we can switch dmet_solver.orbitals.localized_mo to bath_orb. At this moment, the bath orbitals are not saved in the dmet_solver object (so a little hack is necessary).

If you want specific MOs, the minimum and maximum MO indices for each fragment are listed in the dmet_solver.orb_list2 attribute.

For the visualization step, I personally use VMD. Here is a useful link (in section 2) for the basic steps.