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

$ADFBIN/adf -n 1 <<eor
create O file=$ADFRESOURCES/DZP/O
eor
mv TAPE21 t21.O.DZP
rm logfile

$ADFBIN/adf -n 1 <<eor
create H file=$ADFRESOURCES/DZP/H
eor
mv TAPE21 t21.H.DZP
rm logfile

$ADFBIN/adf -n 1 <<eor
create C file=$ADFRESOURCES/DZP/C
eor
mv TAPE21 t21.C.DZP
rm logfile

$ADFBIN/adf -n 1 <<eor
create N file=$ADFRESOURCES/DZP/N
eor
mv TAPE21 t21.N.DZP
rm logfile

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

$ADFBIN/adf <<eor
Title Input generated by PyADF and later modified

 ATOMS
      O       -1.46800        2.60500        1.37700
      H       -0.95200        3.29800        0.96500
      H       -1.16100        1.79900        0.96100
 END

 SYMMETRY NOSYM tol=1e-2

 FRAGMENTS
   H        t21.H.DZP
   O        t21.O.DZP
 END

 XC
   LDA
 END

 SCF
   iterations  100
   converge 1.0e-06 1.0e-06
 END

 EPRINT
   SFO NOEIG NOOVL NOORBPOP
   SCF NOPOP
 END

 NOPRINT BAS FUNCTIONS
 NUMERICALQUALITY GOOD

eor

mv TAPE21 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
######################################

$ADFBIN/adf <<eor
Title Input generated by PyADF and later modified

 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    f=frag1/1
      H       -0.95200        3.29800        0.96500    f=frag1/1
      H       -1.16100        1.79900        0.96100    f=frag1/1
      O        2.40400       -2.51000       -0.36200    f=frag2/1
      H        2.70000       -3.41900       -0.40900    f=frag2/1
      H        1.77500       -2.50000        0.35900    f=frag2/1
      O       -3.22800       -1.61500        1.18500    f=frag3/1
      H       -3.33300       -2.55300        1.03000    f=frag3/1
      H       -3.14200       -1.23600        0.31000    f=frag3/1
      O        0.84000       -2.61200        2.89000    f=frag3/2
      H        0.58800       -3.43700        3.30500    f=frag3/2
      H        0.02500       -2.11500        2.82900    f=frag3/2
      O        2.95400       -0.85100        2.99700    f=frag3/3
      H        2.12000       -1.22400        2.71200    f=frag3/3
      H        2.71800       -0.24100        3.69600    f=frag3/3
      O        3.62200       -0.74000       -2.19300    f=frag3/4
      H        3.05100       -1.25200       -1.62100    f=frag3/4
      H        4.08100       -0.14200       -1.60200    f=frag3/4
      O       -3.80000       -1.13100       -1.71100    f=frag3/5
      H       -3.02600       -0.80900       -2.17400    f=frag3/5
      H       -4.31600       -0.34500       -1.53300    f=frag3/5
      O       -1.77100       -3.79600       -2.15500    f=frag3/6
      H       -2.71500       -3.79000       -2.31700    f=frag3/6
      H       -1.65100       -3.19400       -1.42100    f=frag3/6
      O        1.60000       -0.17800       -3.98800    f=frag3/7
      H        2.40800       -0.18200       -3.47500    f=frag3/7
      H        1.13900       -0.97100       -3.71300    f=frag3/7
      O       -1.63900       -1.73400        3.28100    f=frag3/8
      H       -1.97000       -1.69700        4.17900    f=frag3/8
      H       -2.38200       -2.04200        2.76400    f=frag3/8
      O        1.57900        2.85500        2.45800    f=frag3/9
      H        0.92600        2.71500        3.14400    f=frag3/9
      H        1.85200        3.76600        2.57000    f=frag3/9
      O       -3.44400        2.36700        3.13700    f=frag3/10
      H       -2.70200        2.29200        2.53700    f=frag3/10
      H       -3.47300        3.29500        3.36800    f=frag3/10
 END

 SYMMETRY tol=1e-2

 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

 XC
   GGA BP86
 END

 SCF
   iterations  100
   converge 1.0e-07 1.0e-07
 END
 
 NUMERICALQUALITY GOOD

 SAVE TAPE10

 EPRINT
   SFO NOEIG NOOVL NOORBPOP
   SCF NOPOP
 END

 NOPRINT BAS FUNCTIONS

 FDE
   PW91k
 END

eor


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


$ADFBIN/nmr <<eor
 NMR
  out tens iso
  nuc 3 
 END
eor

rm TAPE10 TAPE21
rm t21.h2o