Defining Fragments in the atomic Section in the Jaguar Input File

You can use the frag keyword in the atomic section to specify that all atoms with the same frag entry be treated in the same fragment. You can then request that all the atoms in one fragment be treated as dummy atoms or counterpoise atoms, or used as the only atoms for which numerical frequencies will be calculated (where Hessian elements for other atoms are zero).

The default frag value for each atom is 0, meaning it is not considered part of any fragment. To assign a group of atoms to the same fragment, in the frag column of the atomic section, enter the same value for each atom.

To treat all atoms in a fragment as counterpoise atoms, set icpfrag=fragno in the gen section of the input file, where fragno is the integer fragment label from the frag column of the atomic section. To treat them all as dummy atoms, make the keyword setting idelfrag=fragno in the gen section. To compute partial frequencies for a particular fragment, make the setting freqfrag=fragno in the gen section of a frequency input file.

One further use of fragments is for antiferromagnetic systems, for which standard transition metal initial guesses do not work. For an antiferromagnetic system containing two metal atoms that are not bonded, you can use a 2spin column to set up the initial guess. When the metals are within bonding distance, or when there are more than two metals, you should assign the metal atoms to separate fragments using the frag column of the atomic section. Finally, add formal and 2spin values in the atomic section.