Visualize the LUMO state of a water molecule
Follow the steps below to visualize the LUMO eigenstate of a water molecule, computed with DFT. We will build the molecule from scratch to show some very basic functionality in the Builder tool. We will also calculate the molecular energy spectrum. It is however possible to add a pre-build H2O-molecule from the Database.
- Start VNL.
- Open the Builder tool by clicking its icon on the main toolbar.
- Go to Stash, Click Add>New Configuration. A hydrogen atom appears in Stash and in the 3D view.
- Go to Coordinate Tools>Translate. Tick Copy and increase Z to 1Å and click Apply twice to add two more hydrogen atoms.
- Go to the 3D view. Press Ctrl+R to center the view and select the atom in the middle. Use the Periodic Table tool in the toolbar to the left to change it to Oxygen. Now we have the constituents for the water molecule.
- Select all atoms. Go to Coordinate Tools>Z-matrix 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).We have now built the water molecule.
- Click the "Send to" icon in the lower right-hand corner of the window, and select Script Generator.
- Double-click "New Calculator" in the left-hand column.
- Double-click "Analysis" and select "MolecularEnergySpectrum" from the menu that appears.
- Double-click "Analysis" and select "Eigenstate" from the menu that appears.
- Click the "..." button next to "Default output file" and define a suitable location and name (for instance "h2o.nc") of the NetCDF file in which the results will be saved.
- Now double-click the "Eigenstate" block that was inserted in the script, in the right-hand panel. Since water has 8 valence electrons (one for each hydrogen and six for oxygen; the two 1s electrons are part of the pseudocore in ATK), there will be 4 occupied states, each one doubly degenerate since this is a spin-independent calculation. Therefore set the quantum number to 4 for the LUMO state (remember, counting starts from zero in ATK!).
- Save the script (menu File>Save) for later reference.
If you are interested in inspecting the actual Python script, you can now send the scipt, again using the "Send to" icon, to the Editor. Note that this will minimize the Script Generator window.
- To run the script, click the "Send to" icon in the Script Generator, and send the script to the Job Manager. When the Job Manager opens up, click the button "Run Queue" to run the script.
- When the script has finished (it takes a minute or so), go back to the main VNL window, and navigate to the directory where you chose to save the NetCDF file. Select the created NetCDF file, and the upper right panel will display a list of the objects contained in the file.
- Select the Eigenstate, and from the list of actions in the lower right panel click "Show" next to Isosurface. Note how the quantum number is also displayed in the lower panel, which is quite useful in case the file contains several eigenstates.
- Then, drag and drop the "Molecular configuration" also stored in the NetCDF file onto the Viewer window that opened.
- Pressing Ctrl-P or selecting "Plots>Properties" from the menu now allows us to modify the elements of the plot.
- To obtain the same image as below, do as follows:
- Go to Plots>Axes and uncheck “Visible”.
- Go to Plots>Isosurface and set the Isovalue to 0.2, the Grid Sampling to 1 and select Wire frame.
- Go to Plots>Bonds and set the Radius to 0.05.
- To export the image to a PNG file, press Ctrl-E (or use the "Plot" menu).