Example: Fragments: PtCl4H2 2-¶
The (scalar) ZORA relativistic option formalism) is used because of the presence of the heavy Pt atom. The complex is built from fragments H2 and PtCl4 2- .
The calculations of the molecule and larger fragments are performed with GGA’s.
Fragments H2 and PtCl4 2-
The two fragments H2 and PtCl4 2- are first calculated, from which we are going to build the final complex.
$ADFBIN/adf <<eor Title H2 R=1.68a.u. NoPrint sfo,frag,functions Units length bohr End Atoms H 0.0 0.0 0.84 H 0.0 0.0 -0.84 End Basis Type DZP End XC GGA becke perdew End Relativistic Scalar ZORA End Input eor mv TAPE21 t21H2
The result file TAPE21 is renamed and saved to serve as fragment file.
$adf <<eor title PtCl4 (2-) noprint sfo,frag,functions units length bohr end ATOMS Pt 0 0 0 Cl 4.361580 0.000000 0 Cl 0.000000 4.361580 0 Cl -4.361580 0.000000 0 Cl 0.000000 -4.361580 0 end Basis Type DZP Pt DZ/Pt.4d End xc GGA becke perdew end relativistic scalar ZORA charge -2 end input eor mv TAPE21 t21PtCl4
The key charge is used to specify the net total charge. The default for the net total charge is the sum-of-fragment-charges. The fragments (Pt and Cl atoms) have been computed neutrally, but we want to calculate the PtCl4 complex as a 2- ion.
Finally we compute PtCl4 H2 2- from the fragments PtCl4 2- and H2 .
$ADFBIN/adf <<eor title PtCl4 H2 units length bohr end EPRINT SFO eig ovl END xc GGA becke perdew end relativistic scalar ZORA ATOMS Pt 0 0 0 f=PtCl4 Cl 0.000000 -4.361580 0.00000000 f=PtCl4 Cl 0.000000 4.361580 0.00000000 f=PtCl4 Cl -4.361580 0.000000 0.00000000 f=PtCl4 Cl 4.361580 0.000000 0.00000000 f=PtCl4 H 0.0 0.0 5.58 f=H2 H 0.0 0.0 7.26 f=H2 end fragments PtCl4 PtCl4.t21 H2 H2.t21 end end input eor
Note that, although the key charge is not supplied, the molecule is not neutral: the default charge (that is, omitting the keys charge, occupations) is the sum-of-fragments: the fragments here are H2 and PtCl4 2- , yielding a net charge for the molecule of minus two.
Note the f= fragment specification in the Atoms block. No fragment-numbering suffix (/n) is required because there is only one fragment of each fragment type.