Select the 'Save' command from the 'File' menu. Enter the name 'TlH_SO' in the 'File name' field. Click 'OK'.
Now you have saved your current options and molecule information. Since we have set up a fragment calculation, also the .adf and .run files for the fragment have been saved. Just to be sure what the fragment will look like, lets check it in ADFinput:
Open the 'Task: FragmentAnalysis' panel (click on the "..." to the right of 'Fragment Analysis' in the Main panel) Click on the 'Open' button
A new ADFinput window will also appear with the name 'TlH_SO.TlH_SR.adf. This is the name of the fragment. You can check that the fragment has the 'Scalar' relativistic option selected. This is required for a molecule that will be used as a fragment. You can change the calculation options for the fragment here. However, in this case we do not need to change the options for the fragment file, so close this ADFinput window:
Select the ADFinput window with the name 'TlH_SO.TlH_SR.adf. Select File → Quit
Now we want to actually perform the calculation, both for the fragment and the whole molecule.
Select the ADFinput window with the name 'TlH_SO.adf. Select File → Run Click 'Yes' when asked to run on the default machine.
Now two calculations will run: first the building fragment (the scalar version), and next the version including spin-orbit coupling. You will see the two matching logfiles. Wait until both calculations have finished:
Wait until ADFtail shows 'Job ... has finished' as last line Select File → Quit Repeat for the second ADFtail
