Example: Electron Pair bonding in NaCl: open shell fragments¶

#! /bin/sh


# This example illustrates advanced usage of the bond energy decomposition
# scheme used in ADF.

# This example shows the energy decomposition analysis of NaCl with
# neutral fragments: Na and Cl, both open shell atoms
# See also the example with ionic fragments: Na+ and Cl-.

# 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 Na-Cl single bond between two
# open shell atoms. Two methods are described here.
# The first method uses spin-restricted fragments but simulates unrestricted fragments
# with the use of the FRAGOCCUPATIONS key.
# The second method uses real unrestricted atoms.

# Unrestricted fragments with fragoccuaptions
# -------------------------------------------

# The proper spins in this method are specified in the calculation of the overall
# molecule using the FragOccupations key. Note that this implies a slight
# approximation because the bond energy computed in this way refers to the
# energy difference between closed-shell NaCl and two open shell atoms 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 NaCl and the two
# open shell atoms 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 Na and Cl atom using the spin
# restricted atoms as a fragment.

# Real unrestricted fragments
# ---------------------------

# The unrestricted calculated Na and Cl atom are used as fragments.

# Prepared for bonding
# --------------------

# Note that the Cl atom that is used as fragment is given an electron
# configuration that is so called 'prepared for bonding' in order to minimize
# the Pauli repulsion in the electron pair bond.
# In this case it means that there is a hole in the valence Cl p_z orbital,
# that will later form an electron pair bond with the valence s orbital of Na.

# Pair bonding
# ------------

# 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 the bond energy analysis is performed in
# the absence of (almost) all virtual fragment orbitals, using the key REMOVEALLFRAGVIRTUALS.
# Note that in the calculation there is a slight orbital relaxation term in addition to the 
# pure orbital interaction, because not only the bonding combination of the singly occupied
# orbitals of the fragments are included, but also the anti-bonding combination.

AMS_JOBNAME=Na_r $AMSBIN/ams <<eor
System
  atoms
     Na 0.0 0.0 0.0
  end
end

Task SinglePoint

Engine ADF
  basis
    core None
    type TZ2P
    CreateOutput Yes
  end
  numericalquality Good
  relativity
    level scalar
    formalism ZORA
  end
  xc
    gga BECKE PERDEW
  end
EndEngine
eor


AMS_JOBNAME=Cl_r $AMSBIN/ams <<eor
System
  atoms
     Cl  0.0 0.0 0.0
  end
end

Task SinglePoint

Engine ADF
  irrepoccupations
     SIGMA.g 6
     SIGMA.u 2 1
     PI.u    8
  end
  basis
    core None
    type TZ2P
    CreateOutput Yes
  end
  numericalquality Good
  relativity
    level scalar
    formalism ZORA
  end
  symmetry D(LIN)
  xc
    gga BECKE PERDEW
  end
EndEngine
eor


AMS_JOBNAME=Na_u $AMSBIN/ams <<eor
System
  atoms
     Na 0.0 0.0 0.0 adf.f=Na
  end
end

Task SinglePoint

Engine ADF
  fragments
     Na  Na_r.results/adf.rkf
  end
  fragoccupations
     Na
     S 3 // 2
     P 3 // 3
     SubEnd
  end
  irrepoccupations
     S 3 // 2
     P 3 // 3
  end
  numericalquality Good
  relativity
    level scalar
    formalism ZORA
  end
  spinpolarization 1
  title unrestricted Na
  unrestricted
  xc
    gga BECKE PERDEW
  end
EndEngine
eor


AMS_JOBNAME=Cl_u $AMSBIN/ams <<eor
System
  atoms
     Cl  0.0 0.0 0.0 adf.f=Cl
  end
end

Task SinglePoint

Engine ADF
  fragments
     Cl   Cl_r.results/adf.rkf
  end
  fragoccupations
     Cl
     SIGMA.g 3 // 3
     SIGMA.u 1 // 2
     PI.u    4 // 4
     SubEnd
  end
  irrepoccupations
     SIGMA.g 3 // 3
     SIGMA.u 1 // 2
     PI.u    4 // 4
  end
  numericalquality Good
  relativity
    level scalar
    formalism ZORA
  end
  spinpolarization -1
  symmetry D(LIN)
  title unrestricted Cl
  unrestricted
  xc
    gga BECKE PERDEW
  end
EndEngine
eor


AMS_JOBNAME=NaCl_pb $AMSBIN/ams <<eor
System
  atoms
     Na 0.0 0.0 0.0   adf.f=Na
     Cl 0.0 0.0 2.361 adf.f=Cl
  end
end

Task SinglePoint

Engine ADF
  eprint
    orbpop 20  20
    end
    sfo eig ovl
  end
  fragments
     Na  Na_r.results/adf.rkf
     Cl  Cl_r.results/adf.rkf
  end
  fragoccupations
     Na
     S 3 // 2
     P 3 // 3
     SubEnd
     Cl
     SIGMA.g 3 // 3
     SIGMA.u 1 // 2
     PI.u    4 // 4
     SubEnd
  end
  numericalquality Good
  relativity
    level scalar
    formalism ZORA
  end
  removeallfragvirtuals
  title fragoccupations pair bonding
  xc
    gga BECKE PERDEW
  end
EndEngine
eor


AMS_JOBNAME=NaCl $AMSBIN/ams <<eor
System
  atoms
     Na 0.0 0.0 0.0   adf.f=Na
     Cl 0.0 0.0 2.361 adf.f=Cl
  end
end

Task SinglePoint

Engine ADF
  eprint
    orbpop 20  20
    end
    sfo eig ovl
  end
  fragments
     Na  Na_r.results/adf.rkf
     Cl  Cl_r.results/adf.rkf
  end
  fragoccupations
     Na
     S 3 // 2
     P 3 // 3
     SubEnd
     Cl
     SIGMA.g 3 // 3
     SIGMA.u 1 // 2
     PI.u    4 // 4
     SubEnd
  end
  numericalquality Good
  relativity
    level scalar
    formalism ZORA
  end
  title fragoccupations
  xc
    gga BECKE PERDEW
  end
EndEngine
eor


AMS_JOBNAME=NaCl_unrfrag_pb $AMSBIN/ams <<eor
System
  atoms
     Na 0.0 0.0 0.0   adf.f=Na
     Cl 0.0 0.0 2.361 adf.f=Cl
  end
end

Task SinglePoint

Engine ADF
  eprint
    orbpop 20  20
    end
    sfo eig ovl
  end
  fragments
     Na  Na_u.results/adf.rkf
     Cl  Cl_u.results/adf.rkf
  end
  numericalquality Good
  relativity
    level scalar
    formalism ZORA
  end
  removeallfragvirtuals
  spinpolarization 0
  title unrestricted fragments pair bonding
  unrestricted
  unrestrictedfragments
  xc
    gga BECKE PERDEW
  end
EndEngine
eor


AMS_JOBNAME=NaCl_unrfrag $AMSBIN/ams <<eor
System
  atoms
     Na 0.0 0.0 0.0   adf.f=Na
     Cl 0.0 0.0 2.361 adf.f=Cl
  end
end

Task SinglePoint

Engine ADF
  eprint
    orbpop 20  20
    end
    sfo eig ovl
  end
  fragments
     Na  Na_u.results/adf.rkf
     Cl  Cl_u.results/adf.rkf
  end
  numericalquality Good
  relativity
    level scalar
    formalism ZORA
  end
  spinpolarization 0
  title unrestricted fragments
  unrestricted
  unrestrictedfragments
  xc
    gga BECKE PERDEW
  end
EndEngine
eor