Visualize the LUMO state of a water molecule¶
In this tutorial you will learn how to visualize a molecular orbital. As an example, you will visualize the LUMO state of water molecule. Specifically, you will:
- Build the molecule.
- Compute a single point calculation at the DFT level.
- Obtain the molecular eigenenergy spectrum and visualize the LUMO state.
Building the molecule¶
Open VNL and create a new project by clicking Create New. Give the project a Title (here: “Water_LUMO”), select the folder where data will be stored, then click OK and Open to start the project.
Go to the Stash, click. A hydrogen atom appears in the Stash and in the preview window of the Builder.
Go to. Tick the Copy option, increase Z to 1 Å, and click the Apply button twice to add two more hydrogen atoms.
Select all atoms using the left mouse button while holding down the
Ctrlbutton of your keyboard. Go to and set the distances and angles as shown in the picture below (H-O distance 0.972278 Å and H-O-H angle 102.75 degrees).
You have now built the water molecule completely from scratch!
Calculating the LUMO state¶
Select both the Eigenstate and MolecularConfiguration objects stored in the NetCDF file (use a left mouse click while holding down
Ctrl), and drag and drop both objects onto the Viewer, which will then pop up.
Click OK, and click OK again in the next window.
In the Viewer, click on Properties.
To obtain the same image as below, do as follows:
- Go to and uncheck “Compass enabled”.
- Go to and set the Isovalue to 0.087.
- Go to and set the Rendering style to Lines.
- Go to and set the atoms and bonds radious to 0.25 and 0.05, respectively.
Please note the use of the “\(\pm\)isovalue” option. When checked, it divides the full range of available isovalues into two equally large ranges, and plots the two ranges in complimentary colors.