Example: Compound Fragments: Ni(CO)4¶

#! /bin/sh


# An illustration of the fragment feature of ADF.

# A transition metal complex is built from a Nickel atom and four CO fragments.
# The outcomes allows for an analysis (of molecular orbitals and the Bonding
# energy) in terms of the fragment properties. It is a Single Point calculation.
# Geometry optimization would not have been possible in this set-up because an
# optimization requires that only single-atom fragments are used.

# The three atoms are created first: C, O, and Ni. For Carbon and Oxygen a type-
# DZ basis set is used (double-zeta) using the Basis key, while Ni gets a type-
# TZP basis (triple-zeta plus polarization).


# == CO ==


# The CO molecule, to serve as a fragment template in Ni(CO)4 , is computed from
# the atomic fragments C and O. The coordinate values (atoms) are in bohr,
# rather than in Angstrom because the unit-of-length is redefined by the key
# units with subkey length.

# The key scf is used to specify a somewhat tighter convergence criterion than
# the default, just to illustrate how to do this (normal settings are quite
# adequate).

$AMSBIN/dirac -n1 < $AMSRESOURCES/Dirac/Ni.2p
mv TAPE12 t12.rel

AMS_JOBNAME=Ni $AMSBIN/ams <<eor > tmp
System
  Atoms
    Ni 0.0 0.0 0.0
  End
End
Task SinglePoint
Engine ADF
  create Ni  $AMSRESOURCES/ADF/ZORA/TZP/Ni.2p
  corepotentials t12.rel
     Ni 1
  end
EndEngine
eor


AMS_JOBNAME=CO $AMSBIN/ams <<eor
System
  atoms [bohr]
     C   0  0  0
     O   0  0  2.15617844
  end
end

Task SinglePoint

Engine ADF
  title CO (as fragment for NiCO4)
  eprint
    sfo eig ovl
  end
  basis
    core Small
    type DZ
  end
  scf
    converge 1e-8
  end
EndEngine
eor


# One needs to include the subkey SFO of the key EPRINT with arguments eig and
# ovl in order to get the SFO MO coefficients and SFO overlap matrix printed on
# standard output.


# == Main calculation ==


# Apart from the title, the input contains comment. This does not specify
# computational parameters but is only echoed in the output header, similar to
# the title. Contrary to the title, however, such comments are not preserved,
# apart from their echo in output and they are not written to adf.rkf or any
# other result file.

# The atomic coordinates (atoms) are given in bohr (Units).

# The Atoms records contain also a specification of the fragments to which the
# respective atoms belong: four different CO fragments. No fragment is specified
# for the Ni atom, which implies that it is a fragment on its own.

# The numbers at the very left of the records (1 through 9, with (optionally) a
# period after them), have no relevance. You can set them for ease of reference
# or counting.


AMS_JOBNAME=NiCO4 $AMSBIN/ams <<eor
System
  atoms [bohr]
     Ni   0.0          0.0           0.0
     C    2.0053211    2.0053211     2.0053211     adf.f=CO|1
     C   -2.0053211   -2.0053211     2.0053211     adf.f=CO|2
     C    2.0053211   -2.0053211    -2.0053211     adf.f=CO|3
     C   -2.0053211    2.0053211    -2.0053211     adf.f=CO|4
     O    3.2501913    3.2501913     3.2501913     adf.f=CO|1
     O   -3.2501913   -3.2501913     3.2501913     adf.f=CO|2
     O    3.2501913   -3.2501913    -3.2501913     adf.f=CO|3
     O   -3.2501913    3.2501913    -3.2501913     adf.f=CO|4
  end
end

Task SinglePoint

Engine ADF
  title Ni(CO)4,  from fragments Ni and CO
  eprint
    sfo eig ovl
  end
  fragments
     CO  CO.results/adf.rkf
     Ni  Ni.results/adf.rkf
  end
EndEngine
eor