Plotting MOs#
Forte includes a set of utilities for plotting molecular orbitals saved in the cube file format directly from a Jupyter notebook. A good place to start is this: Tutorial_02.00_plotting_mos.ipynb.
Generating cube files#
The forte.utils.psi4_cubeprop function offers a convenient way to generate cube files
from the information stored in a psi4 Wavefunction object:
import forte.utils
forte.utils.psi4_cubeprop(wfn,path='cubes',nocc=4,nvir=4)
By default this function plots the HOMO-2 to the LUMO+2 orbitals, but in this example we specifically indicate that we want
4 occupied and 4 virtual orbitals.
This function can also take a list of the orbitals to plot via the orbs option and it can return a set of CubeFile objects:
cubes = forte.utils.psi4_cubeprop(wfn, path = '.', orbs = [3,4,5,6], load = True)
Reading, manipulating, and saving cube files#
Cube files can be read from disk via the CubeFile class. To read a cube file instantiate a CubeFile object
by passing the file name:
cube = forte.CubeFile('cubes/Psi_a_15_15-A.cube')
From this object, we can plot the cube file or extract useful information:
# number of atoms
print(f'cube.natoms() -> {cube.natoms()}')
# number of grid points along each direction
print(f'cube.num() -> {cube.num()}')
The CubeFile class supports three type of operations:
scale(double factor): scale all the values on the grid byfactor\(\phi(\mathbf{r}_i) \leftarrow \mathtt{factor} * \phi(\mathbf{r}_i)\)
add(CubeFile cube): add to this cube file the grid values stored in cube\(\phi(\mathbf{r}_i) \leftarrow \phi(\mathbf{r}_i) + \psi(\mathbf{r}_i)\)
pointwise_product(CubeFile cube): multiply each point of this cube file with the values stored in cube\(\phi(\mathbf{r}_i) \leftarrow \phi(\mathbf{r}_i) * \psi(\mathbf{r}_i)\)
For example, we can compute the density of an orbital by taking the pointwise product with itself:
cube = forte.CubeFile('cubes/Psi_a_15_15-A.cube')
dens = forte.CubeFile(cube)
dens.pointwise_product(dens)
To write a CubeFile object to disk for later use just call the save function:
dens.save('cubes/dens.cube')
Plotting cube files#
Forte includes a low-level 3D renderer based on pythreejs and a simple interface to this renderer, the CubeViewer class.
We can tell the CubeViewer class to look for cube files in a specific path (via the path option):
cv = forte.utils.CubeViewer(path='cubes')
Alternatively, we can pass a list of cube files to load (via the cubes options). Here we specify two files and we also change the color scheme:
cv2 = forte.utils.CubeViewer(cubes=['cubes/Psi_a_13_13-A.cube','cubes/Psi_a_16_16-A.cube'],colorscheme='electron')
Generating cube files#
The forte.utils.psi4_cubeprop function offers a convenient way to generate cube files
from the information stored in a psi4 Wavefunction object: