visualize_charge_density

The script plotdensity.py can make 3D and 2D plots of the electron density from a closed-shell SCF calculation. For 2D plots, it is more efficient than generating .cube files since the density is computed only on the required 2D grid.

Thanks to Numba, it's multithreaded and fast!

You must supply:

1. a .json file describing the geometry of the molecule and the basis set used
2. A .npy file containing a density matrix

The script psi4getdensity.py can generate these for you if you have Psi4. A few examples are provided in the exampledata folder. Unless otherwise specified, these examples use the cc-pVDZ basis set with cartesian GTOs.

Dependencies

plotdensity.py has the following dependencies:

• NumPy
• Numba
• SciPy
• matplotlib, if you want to make 2D contour plots
• PyVista, if you want to make interactive 3D plots

If you have pipenv, just type pipenv install to obtain these.

Getting started

For usage information, run ./plotdensity.py --help.

By default, the script will produce 2D contour plots of the density on the x-y plane:

./plotdensity.py exampledata/benzene.json exampledata/benzene.npy

Output:

Number of atoms:                           12
Number of shells:                          54
Number of basis functions:                120
Number of primitives:                     288
Primitive pairs:                        41328
Unique primitive pair centers:           2490

Try out 3D interactive mode with the -i flag:

./plotdensity.py exampledata/benzene.json exampledata/benzene.npy -i

If all you want to do is evaluate the electron density on a 2D grid, then you can use the script dumpdensity.py:

./dumpdensity.py exampledata/benzene.json exampledata/benzene.npy -o density_on_2d_grid.npz

By default, the density is evaluated on the plane {z=0}. You can choose another plane via the options --plane_origin, --plane_x, and --plane_y. For instance, the following command will sample on the plane {y=0.5}.

./dumpdensity.py exampledata/benzene.json exampledata/benzene.npy \
-o density_on_2d_grid.npz \
--plane_origin 0.5 0.5 0.5 \
--plane_x 1 0 0 \
--plane_y 0 0 1

You can use these options for plotting too.