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