Example: FDE NMR shielding: Acetonitrile in water¶
#! /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