Example: Compound Fragments: Ni(CO)4

Download Frags_NiCO4.run

#! /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).

# The TAPE21 result file is renamed t21.CO.

$ADFBIN/adf -n1 <<eor
  create Ni  $ADFRESOURCES/TZP/Ni.2p
mv TAPE21 t21.Ni
rm logfile

$ADFBIN/adf -n1 <<eor
  title CO (as fragment for NiCO4)
    converge  1e-8
    SFO eig ovl
    length  bohr
    C   0  0  0
    O   0  0  2.15617844
    Type DZ
    Core Small
mv TAPE21 CO.t21
rm logfile

# 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 TAPE21 or any
# other result file.

# The atomic coordinates (atoms) are given in bohr (Units). To supply the
# numerical values use is made of user-defined constants (define): 2.0053211 and
# 3.2501913. This is convenient and it prevents typing errors when several
# coordinate values are identical, in particular when they carry a lot of
# decimal places.

# 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.

$ADFBIN/adf <<eor
  title Ni(CO)4,  from fragments Ni and CO
    No geometry optimization possible, because not all fragments
    are single atoms
    length  bohr
    SFO eig ovl
    1. Ni   0       0        0  
    2. C    2.0053211    2.0053211     2.0053211     f=CO/1
    3. C   -2.0053211   -2.0053211     2.0053211     f=CO/2
    4. C    2.0053211   -2.0053211    -2.0053211     f=CO/3
    5. C   -2.0053211    2.0053211    -2.0053211     f=CO/4
    6. O    3.2501913   3.2501913    3.2501913     f=CO/1
    7. O   -3.2501913  -3.2501913    3.2501913     f=CO/2
    8. O    3.2501913  -3.2501913   -3.2501913     f=CO/3
    9. O   -3.2501913   3.2501913   -3.2501913     f=CO/4
    CO  CO.t21
    Ni  t21.Ni
mv TAPE21 NiCO4.t21
rm logfile