Example: Fragments: PtCl4H2 2-¶

#! /bin/sh

# 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
# PtCl_4^2- .

# The calculations of the molecule and larger fragments are performed with
# GGA's.


# == fragments H2 and PtCl_4^2- ==

# The two fragments H2 and PtCl_4^2- are first calculated, from which we are
# going to build the final complex.


AMS_JOBNAME=H2 $AMSBIN/ams <<eor
System
  atoms [Bohr]
     H       0.0             0.0             0.84
     H       0.0             0.0            -0.84
  end
end

Task SinglePoint

Engine ADF
  title H2
  basis
    type DZP
    CreateOutput Yes
  end
  noprint sfo,frag,functions
  relativity
    level scalar
    formalism ZORA
  end
  xc
    gga becke perdew
  end
EndEngine
eor

AMS_JOBNAME=PtCl4 $AMSBIN/ams <<eor
System
  atoms [Bohr]
     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
  charge -2
end

Task SinglePoint

Engine ADF
  title PtCl4 (2-)
  basis
    PerAtomType Symbol=Pt File=ZORA/DZ/Pt.4d
    type DZP
    CreateOutput Yes
  end
  noprint sfo,frag,functions
  relativity
    level scalar
    formalism ZORA
  end
  xc
    gga becke perdew
  end
EndEngine
eor


# 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 PtCl_4^2- and H2/


AMS_JOBNAME=PtCl4H2 $AMSBIN/ams <<eor
System
  atoms [Bohr]
     Pt   0             0             0             adf.f=PtCl4
     Cl   0.000000     -4.361580      0.00000000    adf.f=PtCl4
     Cl   0.000000      4.361580      0.00000000    adf.f=PtCl4
     Cl  -4.361580      0.000000      0.00000000    adf.f=PtCl4
     Cl   4.361580      0.000000      0.00000000    adf.f=PtCl4
     H    0.0           0.0           5.58          adf.f=H2
     H    0.0           0.0           7.26          adf.f=H2
  end
  charge -2
end

Task SinglePoint

Engine ADF
  title PtCl4 H2
  eprint
    sfo eig ovl
  end
  fragments
     PtCl4     PtCl4.results/adf.rkf
     H2        H2.results/adf.rkf
  end
  relativity
    level scalar
    formalism ZORA
  end
  xc
    gga becke perdew
  end
EndEngine
eor

# Note the adf.f=fragment specification in the Atoms block. No fragment-numbering
# suffix (|n) is required because there is only one fragment of each fragment
# type.