#! /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