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 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 subfrag=active type=fde
rho2 t21.iso.rho2
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 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 subfrag=active type=fde
rho2 t21.emb.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 type=fde
rho2 t21.iso.rho2
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 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 subfrag=active type=fde
rho2 t21.iso.rho2
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 subfrag=active
rho2 t21.emb.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