SCM: Examples

PtCl₄H₂²: Fragments again

Sample directory: adf/e_Frags_PtCl4H2

The (scalar) relativistic option (Pauli formalism) is used because of the presence of the relativistic Pt atom. The complex is built from fragments H₂ and PtCl₄^2�.

Dirac: relativistic core potentials

The program dirac is applied to generate the corepotentials file for all involved atom types, including Hydrogen. The latter has no frozen core, let alone a relativistic one, but the corepotentials file also contains the total (relativistic) atomic potential. The (relativistic) atomic total potential is used in some types of relativistic options only, but it is a good idea to simply always run DIRAC for all the atoms whenever you do a relativistic calculation.

$ADFBIN/dirac <$adfresources/Dirac/Cl.2p
$ADFBIN/dirac <$adfresources/Dirac/Pt.4d
$ADFBIN/dirac <$adfresources/Dirac/H

mv TAPE12 t12.rel

The script above generates one TAPE12 file. The second and third dirac runs recognize the presence of the TAPE12 file (with the standard name 'TAPE12') that resulted from the earlier ones and they write their resulting data to the tail of it.

Basic atoms, non-default settings

$ADFBIN/adf <<eor
Create H file=$ADFRESOURCES/DZP/H
XC
  LDA  vwn
  GGA  becke perdew
End

Relativistic Scalar
CorePotentials  t12.rel &
  H   3
End
End Input
eor

mv TAPE21 t21H

The final calculations of the molecule and larger fragments are performed with gga ('NonLocal') xc corrections. Although it is not necessary to use the same settings in the Create runs, applying them looks 'nicer' and gives a better approximation of the bond energy of the molecule with respect to the basic atoms. Here it serves to show that also in a Create run various options can be used.

$ADFBIN/adf <<eor
create Cl file=$ADFRESOURCES/DZP/Cl.2p
xc
  lda vwn
  GGA  becke perdew
end

relativistic scalar
corepotentials  t12.rel  &
  Cl     1
end

end input
eor

mv TAPE21 t21Cl


$ADFBIN/adf <<eor
Create Pt file=$ADFRESOURCES/DZ/Pt.4d
XC
  lda vwn
  GGA  becke perdew
End

Relativistic scalar
CorePotentials  t12.rel  &
  Pt     2
End

End Input
eor

mv TAPE21 t21Pt

It is important to use the relativistic option in the creation of the fragments if the final molecule will use it as well. The corepotentials file is attached and the input indicates that the section on that file for Cl is #1, while the Pt data are in section #2.

Fragments H₂ and PtCl₄^2-

Now, all basic atoms have been generated. We go on to generate the two larger fragments H₂ and PtCl₄^2- 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

Fragments
H         t21H
End

XC
  lda vwn
  GGA  becke perdew
End

Relativistic Scalar
CorePotentials  t12.rel &
  H  3
End

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

fragments
Pt     t21Pt
Cl     t21Cl
end

xc
lda vwn
  GGA  becke perdew
end

relativistic scalar
corepotentials  t12.rel  &
Cl    1
Pt    2
end

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 PtCl₄H₂^2- from the fragments PtCl₄^2- and H₂.

$ADFBIN/adf <<eor
title   PtCl4 H2

units
length bohr
end

integration 4.0

xc
lda vwn
  GGA  becke perdew
end

relativistic scalar
corepotentials  t12.rel  &
H     3
Cl    1
Pt    2
end

ATOMS
Pt   0             0             0             f=PtCl4
Cl   4.361580      0.000000      0.00000000    f=PtCl4
Cl   0.000000      4.361580      0.00000000    f=PtCl4
Cl  -4.361580      0.000000      0.00000000    f=PtCl4
Cl   0.000000     -4.361580      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     t21PtCl4
H2        t21H2
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.