3D Visualization of Quantum Dynamics
PyFREC has a module for 3D visualization of populations of excited
states of quantum dynamics trajectory. The PyFREC visualization module
takes CUBE files31 with densities of localized
excited states of separate fragments and the density matrix obtained
from the quantum dynamics simulation and generates JMOL script
for visualization.32 First JMOL loads the PDB
file with coordinates of the molecular complex. Then, CUBE files for all
excited states are loaded and the transparency of the excited state
surface is based on populations of the excited state (unpopulated states
are entirely transparent, completely populated states are totally
opaque). Transparency of orbitals changes as populations of the excited
states evolve during the dynamics simulations (See supporting
information for a sample visualization.)