Example: Charge transfer integrals with FDE: water dimer¶
Download ElectronTransfer_FDE_H2O.run
#!/bin/sh
# == Expert Option ==
# The electron transfer calculation of a water dimer radical cation in this
# example is aimed at:
# - calculate site energies and couplings of FDE-derived charge-localized states
# - calculate the charge-transfer excitation energy from a two-state model that
# includes the two charge-localized states involved in the calculation
# - the output also includes a rough evaluation of the error introduced by the
# density fitting on the site energies and coupling
# First the isolated neutral fragments are obtained. Symmetry NOSYM is used.
# Next in the first FDE calculation the localized state D+A is calculated, which
# means that the first water molecule has charge +1, and the second water
# molecule is neutral. The resulting adf.rkf files must be renamed to fragA1.t21
# and fragA2.t21. In the second FDE calculation the localized state DA+ is
# calculated, now the second water molecule has charge +1, and the first water
# molecule is neutral. The resulting adf.rkf files must be renamed to fragB1.t21
# and fragB2.t21. The FDE freeze and thaw cycle is done manually, and a spin-
# unrestricted calculation is performed.
# The electron transfer calculation is next. The files fragA1.t21, fragA2.t21,
# fragB1.t21, and fragB2.t21 must exist and must have these names. The program
# must be execute in serial mode. Hybrids are not supported. NumericalQuality
# good is needed for accuracy.
# == The output of this example is discussed here ==
# ============ Electron Transfer RESULTS ===================
# Electronic Coupling = 0.000000 eV
# Electronic Coupling = -0.000006 cm-1
# H11-H22 = -1.396836 eV
# Excitation Energy = 1.396836 eV
# Overlap = 0.000000
# H11 H22 H12 = -152.443044906236 -152.391712133030 -151.743951196449 Eh
# S11 S22 S12 = 0.981761438554 0.980941502465 -0.000000000038
# =========== END Electron Transfer RESULTS ================
# Due to symmetry, the overlap is almost diagonal (Overlap = 0.00), thus the
# transition density is evaluated with one less electron as explained in Ref.
# [JCP 138 (2013) 054101, https://doi.org/10.1063/1.4789418].
# The electronic coupling between the state with a positive charge localized on
# one water molecule and another with the charge localized on the other water
# molecule is given by 'Electronic Coupling' and is reported in eV and cm^-1.
# 'H11-H22' is the difference of the site energies in eV. Values of the site
# energies are given by the first two values of 'H11 H22 H12' in atomic units.
# 'Excitation Energy' reports the value of the transfer excitation energy as
# calculated by diagonalization of the 2X2 generalized eigenvalue problem in
# the basis of the charge-localized states, see Refs.
# [JCP 135 (2011) 234103, https://doi.org/10.1063/1.3666005] and
# [JCP 138 (2013) 054101, https://doi.org/10.1063/1.4789418].
# 'S11 S22 S12' are the values of the non-normalized overlaps.
# ==================================================
# OBTAIN ISOLATED FRAGMENTS
# ==================================================
AMS_JOBNAME=Iso1 $AMSBIN/ams <<eor
System
atoms
O 0.0000000000 0.0000000000 0.0000000000
H -0.9358409558 .2646136961 0.0000000000
H -0.0304663436 -0.9828924420 0.0000000000
end
end
Task SinglePoint
Engine ADF
eprint
sfo NOEIG NOOVL NOORBPOP
end
basis
core None
type TZP
end
noprint BAS FUNCTIONS
Relativity Level=None
numericalquality good
scf
iterations 90
end
symmetry NOSYM
title Isolated water molecule 1
xc
gga PW91
end
EndEngine
eor
mv Iso1.results/adf.rkf t21.iso.rho1
AMS_JOBNAME=Iso2 $AMSBIN/ams <<eor
System
atoms
O 0.0000000000 -2.9053396088 0.0000000000
H -0.4092227596 -3.3374838250 -0.7701260000
H -0.4092227596 -3.3374838250 0.7701260000
end
end
Task SinglePoint
Engine ADF
eprint
sfo NOEIG NOOVL NOORBPOP
end
basis
core None
type TZP
end
noprint BAS FUNCTIONS
Relativity Level=None
numericalquality good
scf
iterations 90
end
symmetry NOSYM
title isolated water molecule 2
xc
gga PW91
end
EndEngine
eor
mv ams.results prev.results
mv Iso2.results/adf.rkf t21.iso.rho2
# ==================================================
# FIRST FDE CALCULATION: STATE D+A
# note: the freeze and thaw is done manually
# as we have open-shell fragments
# ==================================================
AMS_JOBNAME=Emb1 $AMSBIN/ams <<eor
System
atoms
O 0.0000000000 0.0000000000 0.0000000000 adf.f=rho1
H -0.9358409558 .2646136961 0.0000000000 adf.f=rho1
H -0.0304663436 -0.9828924420 0.0000000000 adf.f=rho1
O 0.0000000000 -2.9053396088 0.0000000000 adf.f=rho2
H -0.4092227596 -3.3374838250 -0.7701260000 adf.f=rho2
H -0.4092227596 -3.3374838250 0.7701260000 adf.f=rho2
end
charge 1
end
Task SinglePoint
Engine ADF
allow PARTIALSUPERFRAGS
eprint
sfo NOEIG NOOVL NOORBPOP
end
fde
ggapotcfd pw91c
ggapotxfd pw91x
pw91k
end
fragments
rho1 t21.iso.rho1
rho2 t21.iso.rho2
end
fdefragments
rho2 type=fde
end
noprint BAS FUNCTIONS
Relativity Level=None
numericalquality good
scf
iterations 90
end
spinpolarization 1
symmetry NOSYM
title MODCO: Fragment no. 1; (polarized)
unrestricted
xc
gga PW91
end
EndEngine
eor
mv Emb1.results/adf.rkf t21.emb.rho1
AMS_JOBNAME=Emb2 $AMSBIN/ams <<eor
System
atoms
O 0.0000000000 0.0000000000 0.0000000000 adf.f=rho1
H -0.9358409558 .2646136961 0.0000000000 adf.f=rho1
H -0.0304663436 -0.9828924420 0.0000000000 adf.f=rho1
O 0.0000000000 -2.9053396088 0.0000000000 adf.f=rho2
H -0.4092227596 -3.3374838250 -0.7701260000 adf.f=rho2
H -0.4092227596 -3.3374838250 0.7701260000 adf.f=rho2
end
end
Task SinglePoint
Engine ADF
allow PARTIALSUPERFRAGS
eprint
sfo NOEIG NOOVL NOORBPOP
end
fde
ggapotcfd pw91c
ggapotxfd pw91x
pw91k
end
fragments
rho1 t21.emb.rho1
rho2 t21.iso.rho2
end
fdefragments
rho1 subfrag=active type=fde
end
noprint BAS FUNCTIONS
Relativity Level=None
numericalquality good
scf
iterations 90
end
symmetry NOSYM
title MODCO: Fragment no. 2; (polarized)
xc
gga PW91
end
EndEngine
eor
mv Emb2.results/adf.rkf t21.emb.rho2
AMS_JOBNAME=Emb1r $AMSBIN/ams <<eor
System
atoms
O 0.0000000000 0.0000000000 0.0000000000 adf.f=rho1
H -0.9358409558 .2646136961 0.0000000000 adf.f=rho1
H -0.0304663436 -0.9828924420 0.0000000000 adf.f=rho1
O 0.0000000000 -2.9053396088 0.0000000000 adf.f=rho2
H -0.4092227596 -3.3374838250 -0.7701260000 adf.f=rho2
H -0.4092227596 -3.3374838250 0.7701260000 adf.f=rho2
end
charge 1
end
Task SinglePoint
EngineRestart t21.emb.rho1
Engine ADF
allow PARTIALSUPERFRAGS
eprint
sfo NOEIG NOOVL NOORBPOP
end
fde
ggapotcfd pw91c
ggapotxfd pw91x
pw91k
end
fragments
rho1 t21.iso.rho1
rho2 t21.emb.rho2
end
fdefragments
rho2 subfrag=active type=fde
end
noprint BAS FUNCTIONS
Relativity Level=None
numericalquality good
scf
iterations 90
end
spinpolarization 1
symmetry NOSYM
title MODCO: Fragment no. 1; relaxed
unrestricted
xc
gga PW91
end
EndEngine
eor
mv Emb1r.results/adf.rkf t21.emb.rho1
AMS_JOBNAME=Emb2r $AMSBIN/ams <<eor
System
atoms
O 0.0000000000 0.0000000000 0.0000000000 adf.f=rho1
H -0.9358409558 .2646136961 0.0000000000 adf.f=rho1
H -0.0304663436 -0.9828924420 0.0000000000 adf.f=rho1
O 0.0000000000 -2.9053396088 0.0000000000 adf.f=rho2
H -0.4092227596 -3.3374838250 -0.7701260000 adf.f=rho2
H -0.4092227596 -3.3374838250 0.7701260000 adf.f=rho2
end
end
Task SinglePoint
Engine ADF
allow PARTIALSUPERFRAGS
eprint
sfo NOEIG NOOVL NOORBPOP
end
fde
ggapotcfd pw91c
ggapotxfd pw91x
pw91k
end
fragments
rho1 t21.emb.rho1
rho2 t21.emb.rho2
end
fdefragments
rho1 subfrag=active type=fde
rho2 subfrag=active
end
noprint BAS FUNCTIONS
Relativity Level=None
numericalquality good
scf
iterations 90
end
symmetry NOSYM
title MODCO: Fragment no. 2; relaxed
xc
gga PW91
end
EndEngine
eor
mv Emb2.results/adf.rkf t21.emb.rho2
mv t21.emb.rho1 fragA1.t21
mv t21.emb.rho2 fragA2.t21
# ==================================================
# SECOND FDE CALCULATION: STATE DA+
# note: the freeze and thaw is done manually
# as we have open-shell fragments
# note: now rho1 is the second fragment
# as rho2 is the cation
# ==================================================
AMS_JOBNAME=Emb2p $AMSBIN/ams <<eor
System
atoms
O 0.0000000000 0.0000000000 0.0000000000 adf.f=rho1
H -0.9358409558 .2646136961 0.0000000000 adf.f=rho1
H -0.0304663436 -0.9828924420 0.0000000000 adf.f=rho1
O 0.0000000000 -2.9053396088 0.0000000000 adf.f=rho2
H -0.4092227596 -3.3374838250 -0.7701260000 adf.f=rho2
H -0.4092227596 -3.3374838250 0.7701260000 adf.f=rho2
end
charge 1
end
Task SinglePoint
Engine ADF
allow PARTIALSUPERFRAGS
eprint
sfo NOEIG NOOVL NOORBPOP
end
fde
ggapotcfd pw91c
ggapotxfd pw91x
pw91k
end
fragments
rho1 t21.iso.rho1
rho2 t21.iso.rho2
end
fdefragments
rho1 type=fde
end
noprint BAS FUNCTIONS
Relativity Level=None
numericalquality good
scf
iterations 90
end
spinpolarization 1
symmetry NOSYM
title MODCO: Fragment no. 2; (polarized)
unrestricted
xc
gga PW91
end
EndEngine
eor
mv Emb2p.results/adf.rkf t21.emb.rho2
AMS_JOBNAME=Emb1p $AMSBIN/ams <<eor
System
atoms
O 0.0000000000 0.0000000000 0.0000000000 adf.f=rho1
H -0.9358409558 .2646136961 0.0000000000 adf.f=rho1
H -0.0304663436 -0.9828924420 0.0000000000 adf.f=rho1
O 0.0000000000 -2.9053396088 0.0000000000 adf.f=rho2
H -0.4092227596 -3.3374838250 -0.7701260000 adf.f=rho2
H -0.4092227596 -3.3374838250 0.7701260000 adf.f=rho2
end
end
Task SinglePoint
Engine ADF
allow PARTIALSUPERFRAGS
eprint
sfo NOEIG NOOVL NOORBPOP
end
fde
ggapotcfd pw91c
ggapotxfd pw91x
pw91k
end
fragments
rho1 t21.iso.rho1
rho2 t21.emb.rho2
end
fdefragments
rho2 subfrag=active type=fde
end
noprint BAS FUNCTIONS
Relativity Level=None
numericalquality good
scf
iterations 90
end
symmetry NOSYM
title MODCO: Fragment no. 1; (polarized)
xc
gga PW91
end
EndEngine
eor
mv Emb1p.results/adf.rkf t21.emb.rho1
AMS_JOBNAME=Emb2pr $AMSBIN/ams <<eor
System
atoms
O 0.0000000000 0.0000000000 0.0000000000 adf.f=rho1
H -0.9358409558 .2646136961 0.0000000000 adf.f=rho1
H -0.0304663436 -0.9828924420 0.0000000000 adf.f=rho1
O 0.0000000000 -2.9053396088 0.0000000000 adf.f=rho2
H -0.4092227596 -3.3374838250 -0.7701260000 adf.f=rho2
H -0.4092227596 -3.3374838250 0.7701260000 adf.f=rho2
end
charge 1
end
Task SinglePoint
EngineRestart t21.emb.rho2
Engine ADF
allow PARTIALSUPERFRAGS
eprint
sfo NOEIG NOOVL NOORBPOP
end
fde
ggapotcfd pw91c
ggapotxfd pw91x
pw91k
end
fragments
rho1 t21.emb.rho1
rho2 t21.iso.rho2
end
fdefragments
rho1 subfrag=active type=fde
end
noprint BAS FUNCTIONS
Relativity Level=None
numericalquality good
scf
iterations 90
end
spinpolarization 1
symmetry NOSYM
title MODCO: Fragment no. 2; relaxed
unrestricted
xc
gga PW91
end
EndEngine
eor
mv Emb2pr.results/adf.rkf t21.emb.rho2
AMS_JOBNAME=Embp1r $AMSBIN/ams <<eor
System
atoms
O 0.0000000000 0.0000000000 0.0000000000 adf.f=rho1
H -0.9358409558 .2646136961 0.0000000000 adf.f=rho1
H -0.0304663436 -0.9828924420 0.0000000000 adf.f=rho1
O 0.0000000000 -2.9053396088 0.0000000000 adf.f=rho2
H -0.4092227596 -3.3374838250 -0.7701260000 adf.f=rho2
H -0.4092227596 -3.3374838250 0.7701260000 adf.f=rho2
end
end
Task SinglePoint
Engine ADF
allow PARTIALSUPERFRAGS
eprint
sfo NOEIG NOOVL NOORBPOP
end
fde
ggapotcfd pw91c
ggapotxfd pw91x
pw91k
end
fragments
rho1 t21.emb.rho1
rho2 t21.emb.rho2
end
fdefragments
rho1 subfrag=active
rho2 subfrag=active type=fde
end
noprint BAS FUNCTIONS
Relativity Level=None
numericalquality good
scf
iterations 90
end
symmetry NOSYM
title MODCO: Fragment no. 1; relaxed
xc
gga PW91
end
EndEngine
eor
mv Embp1r.results/adf.rkf t21.emb.rho1
# ======================================
# NOW THE adf.rkf FILES MUST BE RENAMED
#
# TO: fragA1.t21, fragA2.t21
# .... up to a max of fragA999.t21
# AND: fragB1.t21, fragB2.t21
# .... up to a max of fragB999.t21
# ======================================
mv t21.emb.rho1 fragB1.t21
mv t21.emb.rho2 fragB2.t21
# ======================================
# Electron Transfer calculation is next
#
# 1) note the ELECTRONTRANSFER block keyword
# 2) the program must be execute in
# serial mode (parallel mode not
# supported)
# 3) hybrids not supported
# 4) NumericalQuality good is
# needed for accuracy
# ======================================
AMS_JOBNAME=ET $AMSBIN/ams <<eor
System
atoms
O 0.0000000000 0.0000000000 0.0000000000 adf.f=rho1
H -0.9358409558 .2646136961 0.0000000000 adf.f=rho1
H -0.0304663436 -0.9828924420 0.0000000000 adf.f=rho1
O 0.0000000000 -2.9053396088 0.0000000000 adf.f=rho2
H -0.4092227596 -3.3374838250 -0.7701260000 adf.f=rho2
H -0.4092227596 -3.3374838250 0.7701260000 adf.f=rho2
end
charge 1
end
Task SinglePoint
Engine ADF
electrontransfer
numfrag 2
end
eprint
scf NOPOP
sfo NOEIG NOOVL NOORBPOP
end
fragments
rho1 t21.iso.rho1
rho2 t21.iso.rho2
end
noprint BAS FUNCTIONS
Relativity Level=None
numericalquality good
scf
iterations 0
end
spinpolarization 1
symmetry nosym
title ElectronTransfer calculation
unrestricted
xc
gga PW91
end
EndEngine
eor