# 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).

$AMSBIN/dirac -n1 <$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 $AMSBIN/ams <<eor System atoms [bohr] C 0 0 0 O 0 0 2.15617844 end end Task SinglePoint Engine ADF title CO (as fragment for NiCO4) eprint sfo eig ovl end basis core Small type DZ end scf converge 1e-8 end EndEngine eor # One needs to include the subkey SFO of the key EPRINT with arguments eig and # ovl in order to get the SFO MO coefficients and SFO overlap matrix printed on # standard output. # == Main calculation == # Apart from the title, the input contains comment. This does not specify # computational parameters but is only echoed in the output header, similar to # the title. Contrary to the title, however, such comments are not preserved, # apart from their echo in output and they are not written to adf.rkf or any # other result file. # The atomic coordinates (atoms) are given in bohr (Units). To supply the # numerical values use is made of user-defined constants (define): 2.0053211 and # 3.2501913. This is convenient and it prevents typing errors when several # coordinate values are identical, in particular when they carry a lot of # decimal places. # The Atoms records contain also a specification of the fragments to which the # respective atoms belong: four different CO fragments. No fragment is specified # for the Ni atom, which implies that it is a fragment on its own. # The numbers at the very left of the records (1 through 9, with (optionally) a # period after them), have no relevance. You can set them for ease of reference # or counting. AMS_JOBNAME=NiCO4$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