Step 2. Define fragments

All atoms within ADFinput are always assigned to a fragment. Initially this means that you have one fragment (with name 'Untitled') that consists of all atoms. You can see this if you click on a single atom. The atom properties are visible below the editing window, and will tell you to what fragment an atom belongs.

With the pop-up menu that you get by click-and-hold on an atom, or by right-click on an atom, you can change to which fragment one (or the selected) atom(s) belong:

• The 'New Fragment...' command allows you to specify a new fragment name.
• the 'Add to ... fragment' allows you to add the selection to an existing fragment.
• 'Another ... fragment' allows you to use multiple copies of one fragment in a molecule.

Repeated fragments are indicated with the fragment name followed by '/n', with n the number of the copy. All copies must match such that one fragment can be positioned exactly over another fragment by rotation and translation. ADF checks for this, currently ADFinput does not. In this particular example all four CO fragments are obviously identical by symmetry.

Using these commands you will now define Ni fragment and the repeated CO fragments:

Select one CO ligand
Use the Atom Popup → New Fragment... command
Define this as a CO fragment (enter CO as name)
In turn, select the other three CO ligands, and use the pop up menu 'Another CO Fragment'
Select the Ni Atom
Use the Atom Popup → New Fragment... command to make this into a Ni-atom fragment

Now the fragments are defined. Next, use the 'Fragment Analysis' preset to set up the fragment analysis calculation:

Select the 'Fragment Analysis' preset
Open the 'Task: FragmentAnalysis' panel

In the Fragment Analysis panel you will see that indeed two fragments are present, without charge. Also, note that the Task has been set to FragmentAnalysis.