Example: Bond Energy analysis open-shell fragments: PCCP¶
Download PCCP_Unr_BondEnergy.run
#! /bin/sh
# This example illustrates advanced usage of the bond energy decomposition
# scheme used in ADF.
# Remark: this calculation simulates unrestricted fragments using the FRAGOCCUPATIONS
# key. Real unrestricted fragments can also be used in ADF.
# A proper decomposition of an electron-pair bond energy requires specifying
# opposite spins for the unpaired electrons of the respective radical fragments,
# which can be done with the input key FragOccupations. The specified alpha- and
# beta-spin configurations of the radical fragments are shown in the output
# section B U I L D.
# Please note that if one neglects explicitly specifying opposite spins for the
# unpaired electrons of the fragments, each of them is treated as being half an
# alpha and half a beta electron and consequently, they enter into a spurious
# Pauli repulsive interaction. This results, among others, into the Pauli
# repulsion term being too repulsive and the orbital interaction term being too
# much stabilizing.
# The example consists of an analysis of the C-C single bond between two CP
# radicals in the four-atomic molecule PCCP. The CP fragment calculations used
# to provide the adf.rkf for the overall PCCP calculation are done here in
# the restricted mode ('cp_fpccp_asr'). The proper spins
# are then specified in the calculation of the overall molecule using the
# FragOccupations key ('pccp_fa1_as'). Note that this implies a slight
# approximation because the bond energy computed in this way refers to the
# energy difference between closed-shell PCCP and two CP radicals that are
# described by orbitals from a spin-restricted SCF calculation, which have been
# given an unrestricted occupation. In other words, the set of alpha- and beta-
# spin orbitals are identical and the effect of spin polarization is missing. In
# practice, this leads to minor energy differences with respect to the correct
# bond energy, that is, the energy difference between closed-shell PCCP and two
# CP radicals treated in the unrestricted mode, i.e., for which the set of
# alpha- and beta-spin orbitals are allowed to relax toward different solutions
# in the SCF procedure. This correction term can be computed directly by
# carrying out an unrestricted computation of the CP radical ('cp_fpccp_asu') using the
# restricted CP radical ('cp_fpccp_asr') as a fragment.
# The pure orbital interaction effect of forming the electron bonding combination
# of the two radicals can be isolated from the full orbital interaction by carrying out a
# separate calculation. In this calculation (pccp_fa1_pb) the bond energy analysis is performed in
# the absence of any virtual CP fragment orbitals, using the key REMOVEFRAGORBITALS.
AMS_JOBNAME=CP $AMSBIN/ams <<eor
System
atoms
C .0000 .0000 .6681
P .0000 .0000 2.2555
end
end
Task SinglePoint
Engine ADF
title cp_fpccp_asr
eprint
sfo eig ovl
end
basis
core Large
type TZ2P
end
numericalquality Good
xc
gga BECKE PERDEW
end
EndEngine
eor
AMS_JOBNAME=CP_Unrestricted $AMSBIN/ams <<eor
System
atoms
C .0000 .0000 .6681 adf.f=CP
P .0000 .0000 2.2555 adf.f=CP
end
end
Task SinglePoint
Engine ADF
title cp_fpccp_asu
eprint
sfo eig ovl
end
fragments
CP CP.results/adf.rkf
end
fragoccupations
CP
SIGMA 3//2
PI 2//2
SUBEND
end
numericalquality Good
spinpolarization 1
unrestricted
xc
gga BECKE PERDEW
end
EndEngine
eor
AMS_JOBNAME=PCCP_pb $AMSBIN/ams <<eor
System
atoms
P .0000 .0000 2.2555 adf.f=CP_A
C .0000 .0000 .6681 adf.f=CP_A
C .0000 .0000 -.6681 adf.f=CP_B
P .0000 .0000 -2.2555 adf.f=CP_B
end
end
Task SinglePoint
Engine ADF
title pccp_fa1_pb
eprint
orbpop 20 20
end
sfo eig ovl
end
fragments
CP_A CP.results/adf.rkf
CP_B CP.results/adf.rkf
end
fragoccupations
CP_A
SIGMA 3//2
PI 2//2
SUBEND
CP_B
SIGMA 2//3
PI 2//2
SUBEND
end
numericalquality Good
removeallfragvirtuals
symmetry C(LIN)
xc
gga BECKE PERDEW
end
print VDDanalysis
EndEngine
eor
AMS_JOBNAME=PCCP $AMSBIN/ams <<eor
System
atoms
P .0000 .0000 2.2555 adf.f=CP_A
C .0000 .0000 .6681 adf.f=CP_A
C .0000 .0000 -.6681 adf.f=CP_B
P .0000 .0000 -2.2555 adf.f=CP_B
end
end
Task SinglePoint
Engine ADF
title pccp_fa1_as
eprint
orbpop 20 20
end
sfo eig ovl
end
fragments
CP_A CP.results/adf.rkf
CP_B CP.results/adf.rkf
end
fragoccupations
CP_A
SIGMA 3//2
PI 2//2
SUBEND
CP_B
SIGMA 2//3
PI 2//2
SUBEND
end
numericalquality Good
symmetry C(LIN)
xc
gga BECKE PERDEW
end
print VDDanalysis
EndEngine
eor
AMS_JOBNAME=CP_B3LYP $AMSBIN/ams <<eor
System
atoms
C .0000 .0000 .6681
P .0000 .0000 2.2555
end
end
Task SinglePoint
Engine ADF
title B3LYP restricted
basis
core None
type TZ2P
end
numericalquality Good
xc
hybrid B3LYP
end
EndEngine
eor
AMS_JOBNAME=CP_B3LYP_Unrestricted $AMSBIN/ams <<eor
System
atoms
C .0000 .0000 .6681 adf.f=CP
P .0000 .0000 2.2555 adf.f=CP
end
end
Task SinglePoint
Engine ADF
title B3LYP unrestricted
fragments
CP CP_B3LYP.results/adf.rkf
end
fragoccupations
CP
SIGMA 7//6
PI 4//4
Subend
end
numericalquality Good
spinpolarization 1
unrestricted
xc
hybrid B3LYP
end
EndEngine
eor
AMS_JOBNAME=PCCP_B3LYP_pb $AMSBIN/ams <<eor
System
atoms
P .0000 .0000 2.2555 adf.f=CP_A
C .0000 .0000 .6681 adf.f=CP_A
C .0000 .0000 -.6681 adf.f=CP_B
P .0000 .0000 -2.2555 adf.f=CP_B
end
end
Task SinglePoint
Engine ADF
title PCCP B3LYP PAIRBONDING
fragments
CP_A CP_B3LYP.results/adf.rkf
CP_B CP_B3LYP.results/adf.rkf
end
fragoccupations
CP_A
SIGMA 7//6
PI 4//4
Subend
CP_B
SIGMA 6//7
PI 4//4
Subend
end
numericalquality Good
removeallfragvirtuals
xc
hybrid B3LYP
end
print VDDanalysis
EndEngine
eor
AMS_JOBNAME=PCCP_B3LYP $AMSBIN/ams <<eor
System
atoms
P .0000 .0000 2.2555 adf.f=CP_A
C .0000 .0000 .6681 adf.f=CP_A
C .0000 .0000 -.6681 adf.f=CP_B
P .0000 .0000 -2.2555 adf.f=CP_B
end
end
Task SinglePoint
Engine ADF
title PCCP B3LYP
fragments
CP_A CP_B3LYP.results/adf.rkf
CP_B CP_B3LYP.results/adf.rkf
end
fragoccupations
CP_A
SIGMA 7//6
PI 4//4
Subend
CP_B
SIGMA 6//7
PI 4//4
Subend
end
numericalquality Good
xc
hybrid B3LYP
end
print VDDanalysis
EndEngine
eor