Example: Fragments: PtCl4H2 2-¶

Download Frags_PtCl4H2.run

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.

Main calculation

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.