Example: FDE NMR shielding: Acetonitrile in water

Download FDE_NMR_relax.run

#! /bin/sh


# This examples demonstrates both the calculation of NMR shieldings using FDE,
# and how the approximate environment density can be improved by partial
# relaxation of individual solvent molecules. The test system is a cluster of
# acetonitrile and 12 solvent water molecules, of which for two the densities
# are relaxed, while for the remaining 10 the frozen density of the isolated
# water is used. For details, see Refs. C. R. Jacob, J. Neugebauer, and L.
# Visscher, A flexible implementation of frozendensity embedding for use in
# multilevel simulation, submitted, 2007. R. E. Bulo, Ch. R. Jacob, and L.
# Visscher, NMR Solvent Shifts of Acetonitrile from Frozen-Density Embedding
# Calculation

# First, the isolated solvent water molecule is prepared. Again, because this
# will be rotated and translated afterwards, the option NOSYMFIT has to be
# included.


# create atomic fragment files

AMS_JOBNAME=O $AMSBIN/ams <<eor
System
  Atoms
    O 0.0 0.0 0.0
  End
End
Task SinglePoint
Engine ADF
  create O file=$AMSRESOURCES/ADF/DZP/O
  Relativity Level=None
EndEngine
eor
mv O.results/adf.rkf t21.O.DZP

AMS_JOBNAME=H $AMSBIN/ams <<eor
System
  Atoms
    H 0.0 0.0 0.0
  End
End
Task SinglePoint
Engine ADF
  create H file=$AMSRESOURCES/ADF/DZP/H
  Relativity Level=None
EndEngine
eor
mv H.results/adf.rkf t21.H.DZP

AMS_JOBNAME=C $AMSBIN/ams <<eor
System
  Atoms
    C 0.0 0.0 0.0
  End
End
Task SinglePoint
Engine ADF
  create C file=$AMSRESOURCES/ADF/DZP/C
  Relativity Level=None
EndEngine
eor
mv C.results/adf.rkf t21.C.DZP

AMS_JOBNAME=N $AMSBIN/ams <<eor
System
  Atoms
    N 0.0 0.0 0.0
  End
End
Task SinglePoint
Engine ADF
  create N file=$AMSRESOURCES/ADF/DZP/N
  Relativity Level=None
EndEngine
eor
mv N.results/adf.rkf t21.N.DZP

#############################
# prepare H2O
#############################

AMS_JOBNAME=H2O $AMSBIN/ams <<eor
System
  atoms
     O       -1.46800        2.60500        1.37700
     H       -0.95200        3.29800        0.96500
     H       -1.16100        1.79900        0.96100
  end
end

Task SinglePoint

Engine ADF
  eprint
    scf NOPOP
    sfo NOEIG NOOVL NOORBPOP
  end
  fragments
     H        t21.H.DZP
     O        t21.O.DZP
  end
  noprint BAS FUNCTIONS
  numericalquality GOOD
  scf
    converge 1.0e-06 1.0e-06
    iterations 100
  end
  symmetry NOSYM
  symmetrytolerance 1e-2
  title Input generated by PyADF and later modified
  xc
    lda
  end
  Relativity Level=None
EndEngine
eor

mv H2O.results/adf.rkf t21.h2o


# Afterwards, the FDE calculation is performed. In addition to the nonfrozen
# acetonitrile molecule, three different fragments are used for the solvent
# water molecules. The first two fragments frag1 and frag2 are relaxed (in up to
# two freeze-and-thaw cycles), while the third fragment is used for the
# remaining 10 solvent molecules. Since a calculation of the shielding is
# performed afterwards, the option has to be included.

######################################
# and the embedding calculation
######################################

AMS_JOBNAME=FDE $AMSBIN/ams <<eor
System
  atoms
     C        0.83000        0.66100       -0.44400
     N        0.00000        0.00000        0.00000
     C        1.87800        1.55900       -0.81900
     H        1.78500        2.40300       -0.13500
     H        1.76200        1.94900       -1.83000
     H        2.82900        1.12200       -0.51300
     O       -1.46800        2.60500        1.37700    adf.f=frag1|1
     H       -0.95200        3.29800        0.96500    adf.f=frag1|1
     H       -1.16100        1.79900        0.96100    adf.f=frag1|1
     O        2.40400       -2.51000       -0.36200    adf.f=frag2|1
     H        2.70000       -3.41900       -0.40900    adf.f=frag2|1
     H        1.77500       -2.50000        0.35900    adf.f=frag2|1
     O       -3.22800       -1.61500        1.18500    adf.f=frag3|1
     H       -3.33300       -2.55300        1.03000    adf.f=frag3|1
     H       -3.14200       -1.23600        0.31000    adf.f=frag3|1
     O        0.84000       -2.61200        2.89000    adf.f=frag3|2
     H        0.58800       -3.43700        3.30500    adf.f=frag3|2
     H        0.02500       -2.11500        2.82900    adf.f=frag3|2
     O        2.95400       -0.85100        2.99700    adf.f=frag3|3
     H        2.12000       -1.22400        2.71200    adf.f=frag3|3
     H        2.71800       -0.24100        3.69600    adf.f=frag3|3
     O        3.62200       -0.74000       -2.19300    adf.f=frag3|4
     H        3.05100       -1.25200       -1.62100    adf.f=frag3|4
     H        4.08100       -0.14200       -1.60200    adf.f=frag3|4
     O       -3.80000       -1.13100       -1.71100    adf.f=frag3|5
     H       -3.02600       -0.80900       -2.17400    adf.f=frag3|5
     H       -4.31600       -0.34500       -1.53300    adf.f=frag3|5
     O       -1.77100       -3.79600       -2.15500    adf.f=frag3|6
     H       -2.71500       -3.79000       -2.31700    adf.f=frag3|6
     H       -1.65100       -3.19400       -1.42100    adf.f=frag3|6
     O        1.60000       -0.17800       -3.98800    adf.f=frag3|7
     H        2.40800       -0.18200       -3.47500    adf.f=frag3|7
     H        1.13900       -0.97100       -3.71300    adf.f=frag3|7
     O       -1.63900       -1.73400        3.28100    adf.f=frag3|8
     H       -1.97000       -1.69700        4.17900    adf.f=frag3|8
     H       -2.38200       -2.04200        2.76400    adf.f=frag3|8
     O        1.57900        2.85500        2.45800    adf.f=frag3|9
     H        0.92600        2.71500        3.14400    adf.f=frag3|9
     H        1.85200        3.76600        2.57000    adf.f=frag3|9
     O       -3.44400        2.36700        3.13700    adf.f=frag3|10
     H       -2.70200        2.29200        2.53700    adf.f=frag3|10
     H       -3.47300        3.29500        3.36800    adf.f=frag3|10
  end
end

Task SinglePoint

Engine ADF
  eprint
    scf NOPOP
    sfo NOEIG NOOVL NOORBPOP
  end
  fde
    pw91k
  end
  fragments
     H        t21.H.DZP
     C        t21.C.DZP
     N        t21.N.DZP
     frag1  t21.h2o   type=FDE  &
     fdeoptions RELAX
     RELAXCYCLES 2
     SubEnd
     frag2  t21.h2o   type=FDE  &
     fdeoptions RELAX
     RELAXCYCLES 2
     SubEnd
     frag3  t21.h2o   type=FDE  &
     FDEDENSTYPE SCFexact
     SubEnd
  end
  noprint BAS FUNCTIONS
  numericalquality GOOD
  save TAPE10
  scf
    converge 1.0e-07 1.0e-07
    iterations 100
  end
  symmetrytolerance 1e-2
  title Input generated by PyADF and later modified
  xc
    gga BP86
  end
  Relativity Level=None
EndEngine
eor


# Finally, the calculation of the NMR shielding of the nitrogen atom is
# performed using the NMR program.


$AMSBIN/nmr <<eor
 tape10file FDE.results/TAPE10
 adffile FDE.results/adf.rkf
 NMR
  out tens iso
  nuc 3 
 END
eor