Transition State Search with a Partial Hessian¶

Step 1: Create the system¶

We are going to make a one layer Li (001) slab with a 2x2 unit cell, assuming familiarity with the build tools

Start ADFinput and switch to BAND mode.

From the structure tool select ‘Cubic’ and ‘bcc’

Set ‘Element’ to Li

Set the lattice parameter to 3.49

Press ‘OK’

Invoke the Slice tool

Set the Miller indices to 001, select ‘Cartesian’, and enter 1 layer.

Press ‘OK’

Use the Edit → Crystal → Generate Super Cell... command

Select the preset ‘2x2’ and press ‘OK’

Panel bar Model → Coordinates

Your screen should look like this:

Add with the mouse two hydrogen atoms anywhere in the screen

Set in the table the coordinates of the first hydrogen atom to (0, -0.5, 2)

Set the second H atom coordinates to (0, 0.5, 2)

The final geometry looks like this

Step 2: Calculate a partial Hessian¶

Select the ‘BAND Main’ panel

Select the Frequencies preset

Set ‘Basis Set’ to ‘SZ’

Go to the ‘Frequencies’ details panel (click on the ‘...’ button)

Select with the mouse the two tiny Hydrogen atoms (zoom in to make selecting them easier)

Click on the ‘+’ button next to ‘Partial Hessian For:’

File → Run, name the job H2onLi_freq

Say ‘No’ when asked to update the coordinates

Let us examine the eigen-modes that we have found for the Hydrogen molecule

Select the SCM → Spectra menu command

Now you will see that there is an eigen-mode at 465 cm-1 and one at 2428 cm-1. Convince yourself that the 465 mode moves the H2 perpendicular to the service and that the 2428 mode is essentially an H2 stretch mode. The lowest mode looks like a promising start to find the transition state for dissociation over the Li surface.

Step 3: Transition state search with a frozen substrate¶

We have just found the vibrational modes of the Hydrogen molecule, assuming that the Li substrate remains fixed. Let us now find the transition state under the same assumption.

Close the ‘ADFspectra’ window and go back to BANDinput.

Select the ‘BAND Main’ panel and select the ‘Transition State Search’ preset

Panel bar Model → Geometry Constraints

The two hydrogen atoms are still selected, if not select them again

Use the Select → Invert Selection command

Click on the ‘+’ button next to ‘freeze selected atoms’

Panel bar Details → Geometry Convergence

Set the initial Hessian to ‘H2onLi_freq.runkf’

File → Save As..., use name H2onLi_ts

File → Run

After the run has completed:

SCM → Movie

In the movie window: Graph → Energy

View → View Direction → Along x axis

Reorient to get a good look

It should look like