Example: Grimme Molecular Mechanics dispersion-corrected functionals (DFT-D3-BJ)¶
#! /bin/sh
# In this example a structure with 2 benzene molecules and a hydrogen molecule
# is optimized with the Grimme dispersion corrected PBE, in this case the (so
# far) latest variant the DFT-D family, which is DFT-D3-BJ. Needed is the subkey
# DISPERSION in the key XC, and the arguments Grime3 and BJDAMP. If one starts
# with atomic fragments the part of the bond energy that is due to the Grimme
# dispersion corrected functional is both inter-molecular as well as intra-
# molecular.
AMS_JOBNAME=Grimme_dispersion $AMSBIN/ams <<eor
System
atoms
C 0.0 1.39730802 -3.09
H 0.0 2.48914064 -3.09
C 1.21010424 0.69865401 -3.09
H 2.15565903 1.24457032 -3.09
C 1.21010424 -0.69865401 -3.09
H 2.15565903 -1.24457032 -3.09
C 0.0 -1.39730802 -3.09
H 0.0 -2.48914064 -3.09
C -1.21010424 -0.69865401 -3.09
H -2.15565903 -1.24457032 -3.09
C -1.21010424 0.69865401 -3.09
H -2.15565903 1.24457032 -3.09
C -1.21010424 -0.69865401 3.09
H -2.15565903 -1.24457032 3.09
C 0.0 -1.39730802 3.09
H 0.0 -2.48914064 3.09
C 1.21010424 -0.69865401 3.09
H 2.15565903 -1.24457032 3.09
C 1.21010424 0.69865401 3.09
H 2.15565903 1.24457032 3.09
C 0.0 1.39730802 3.09
H 0.0 2.48914064 3.09
C -1.21010424 0.69865401 3.09
H -2.15565903 1.24457032 3.09
H 0.0 0.0 -0.37
H 0.0 0.0 0.37
end
end
Task GeometryOptimization
GeometryOptimization
Convergence
Gradients 1E-4
End
End
Engine ADF
title Geometry optimization with Grimme3-BJ dispersion correction for GGA
basis
type TZP
core small
end
noprint sfo
xc
dispersion Grimme3 BJDAMP
gga PBE
end
EndEngine
eor
# The next calculations in this example demonstrate dispersion corrections when
# using non-atomic fragments. First three molecules (2 benzene molecules and a
# hydrogen molecule) are calculated . Needed again is the subkey DISPERSION in
# the key XC.
AMS_JOBNAME=benzene1 $AMSBIN/ams <<eor
System
atoms
C 0.000000 1.398973 -3.054539
H 0.000000 2.490908 -3.049828
C 1.211546 0.699486 -3.054539
H 2.157190 1.245454 -3.049828
C 1.211546 -0.699486 -3.054539
H 2.157190 -1.245454 -3.049828
C 0.000000 -1.398973 -3.054539
H 0.000000 -2.490908 -3.049828
C -1.211546 -0.699486 -3.054539
H -2.157190 -1.245454 -3.049828
C -1.211546 0.699486 -3.054539
H -2.157190 1.245454 -3.049828
end
end
Task SinglePoint
Engine ADF
title Grimme3-BJ dispersion-corrected GGA
basis
core small
type TZP
end
noprint sfo
scf
converge 1.0E-06 1.0E-6
iterations 60
end
xc
dispersion Grimme3 BJDAMP
gga PBE
end
EndEngine
eor
AMS_JOBNAME=benzene2 $AMSBIN/ams <<eor
System
atoms
C -1.211546 -0.699486 3.054539
H -2.157190 -1.245454 3.049828
C 0.000000 -1.398973 3.054539
H 0.000000 -2.490908 3.049828
C 1.211546 -0.699486 3.054539
H 2.157190 -1.245454 3.049828
C 1.211546 0.699486 3.054539
H 2.157190 1.245454 3.049828
C 0.000000 1.398973 3.054539
H 0.000000 2.490908 3.049828
C -1.211546 0.699486 3.054539
H -2.157190 1.245454 3.049828
end
end
Task SinglePoint
Engine ADF
title Grimme3-BJ dispersion-corrected GGA
basis
core small
type TZP
end
noprint sfo
xc
dispersion Grimme3 BJDAMP
gga PBE
end
EndEngine
eor
AMS_JOBNAME=h2 $AMSBIN/ams <<eor
System
atoms
H 0.000000 0.000000 -0.377906
H 0.000000 0.000000 0.377906
end
end
Task SinglePoint
Engine ADF
title Grimme3-BJ dispersion-corrected GGA
basis
core small
type TZP
end
noprint sfo
xc
dispersion Grimme3 BJDAMP
gga PBE
end
EndEngine
eor
AMS_JOBNAME=fragments $AMSBIN/ams <<eor
System
atoms
C 0.000000 1.398973 -3.054539 adf.f=b1
H 0.000000 2.490908 -3.049828 adf.f=b1
C 1.211546 0.699486 -3.054539 adf.f=b1
H 2.157190 1.245454 -3.049828 adf.f=b1
C 1.211546 -0.699486 -3.054539 adf.f=b1
H 2.157190 -1.245454 -3.049828 adf.f=b1
C 0.000000 -1.398973 -3.054539 adf.f=b1
H 0.000000 -2.490908 -3.049828 adf.f=b1
C -1.211546 -0.699486 -3.054539 adf.f=b1
H -2.157190 -1.245454 -3.049828 adf.f=b1
C -1.211546 0.699486 -3.054539 adf.f=b1
H -2.157190 1.245454 -3.049828 adf.f=b1
C -1.211546 -0.699486 3.054539 adf.f=b2
H -2.157190 -1.245454 3.049828 adf.f=b2
C 0.000000 -1.398973 3.054539 adf.f=b2
H 0.000000 -2.490908 3.049828 adf.f=b2
C 1.211546 -0.699486 3.054539 adf.f=b2
H 2.157190 -1.245454 3.049828 adf.f=b2
C 1.211546 0.699486 3.054539 adf.f=b2
H 2.157190 1.245454 3.049828 adf.f=b2
C 0.000000 1.398973 3.054539 adf.f=b2
H 0.000000 2.490908 3.049828 adf.f=b2
C -1.211546 0.699486 3.054539 adf.f=b2
H -2.157190 1.245454 3.049828 adf.f=b2
H 0.000000 0.000000 -0.377906 adf.f=h2
H 0.000000 0.000000 0.377906 adf.f=h2
end
end
Task SinglePoint
Engine ADF
title Grimme3-BJ dispersion-corrected GGA
fragments
b1 benzene1.results/adf.rkf
b2 benzene2.results/adf.rkf
h2 h2.results/adf.rkf
end
noprint sfo
xc
dispersion Grimme3 BJDAMP
gga PBE
end
EndEngine
eor