Example: 3D fields on a grid, QTAIM¶
#! /bin/sh
# just to make sure that the properties are non zero at the first integration point
extend="-4.0"
export AMS_JOBNAME=Methane
$AMSBIN/ams << eor
Task SinglePoint
System
Atoms
C 0.000000000000 0.000000000000 0.000000000000
H 0.863426938600 0.544775641100 0.352297349600
H -0.335313871500 0.422758012300 -0.935542767900
H 0.264056533600 -1.036774276000 -0.147557605600
H -0.792169600700 0.069240623010 0.730803023900
End
End
Engine DFTB
ResourcesDir Demo
Model DFTB0
EndEngine
eor
# cd Methane.results
$AMSBIN/nao << eor
Filename $AMS_JOBNAME.results/dftb.rkf
Grid
Type Coarse
ExtendX $extend
ExtendY $extend
ExtendZ $extend
end
Fields
rho
rho(deformation)
tau(valence)
rho(deformation/fit)
v(coulomb/atoms)
v(coulomb/deformation)
v(coulomb)
End
eor
echo ""
echo "Begin TOC of tape41 (Methane/props)"
$AMSBIN/pkf TAPE41
echo "End TOC of tape41 (Methane/props)"
rm TAPE41
# orbital plotting
$AMSBIN/nao << eor
Filename $AMS_JOBNAME.results/dftb.rkf
Grid
Type Coarse
ExtendX $extend
ExtendY $extend
ExtendZ $extend
end
Fields
Orbitals 1
End
eor
echo ""
echo "Begin TOC of tape41 (Methane/orbitals)"
$AMSBIN/pkf TAPE41
echo "End TOC of tape41 (Methane/orbitals)"
rm TAPE41
# export to cube format
$AMSBIN/nao << eor
Filename $AMS_JOBNAME.results/dftb.rkf
ResultFilename CUBE
Grid
Type Coarse
ExtendX $extend
ExtendY $extend
ExtendZ $extend
end
Fields
rho
rho(deformation)
tau(valence)
rho(deformation/fit)
v(coulomb/atoms)
v(coulomb/deformation)
v(coulomb)
End
eor
echo ""
echo "Begin of cube file v(coulomb)"
head -n 12 v\(coulomb\).cube
echo "End of cube file v(coulomb)"
rm *.cube
# export single field on a .cube file
$AMSBIN/nao << eor
Filename $AMS_JOBNAME.results/dftb.rkf
ResultFilename CUBE
Grid
Type Coarse
ExtendX $extend
ExtendY $extend
ExtendZ $extend
end
Fields
rho
End
eor
echo ""
echo "Begin of cube file"
head -n 12 rho.cube
echo "End of cube file"
rm rho.cube
# the order appears to be random
export NSCM=1
$AMSBIN/nao << eor
Filename $AMS_JOBNAME.results/dftb.rkf
Grid
Type Coarse
end
AIMCriticalPoints
gridSpacing 0.2
End
eor
echo "kf file with QTAIM"
$AMSBIN/pkf $AMS_JOBNAME.results/dftb.rkf
# cd ..
echo "same test on periodic chain"
export AMS_JOBNAME=MethaneChain
$AMSBIN/ams << eor
Task SinglePoint
System
Atoms [Angstrom]
C 0.0 0.0 0.0
H 1.079999998 0 0
H -0.35604780 0 1.019622459440336
H -0.35604780 0.8830189521445 -0.50981122972017
H -0.35604780 -0.8830189521445 -0.50981122972017
End
Lattice
2.5 0.0 0.0
End
End
Engine DFTB
ResourcesDir Demo
Model DFTB0
UseSymmetry yes
KSpace
Type Symmetric
Symmetric KInteg=3
End
Periodic
BandStructure enabled=yes automatic=yes
End
EndEngine
eor
# cd MethaneChain.results
$AMSBIN/nao << eor
Filename $AMS_JOBNAME.results/dftb.rkf
Grid
Type Coarse
ExtendX $extend
ExtendY $extend
ExtendZ $extend
end
Fields
rho
rho(deformation)
tau(valence)
rho(deformation/fit)
v(coulomb/atoms)
v(coulomb/deformation)
v(coulomb)
End
eor
echo "Begin TOC of tape41 (MethaneChain/props)"
$AMSBIN/pkf TAPE41
echo "End TOC of tape41 (MethaneChain/props)"
rm TAPE41
$AMSBIN/nao << eor
Filename $AMS_JOBNAME.results/dftb.rkf
Grid
Type Coarse
ExtendX $extend
ExtendY $extend
ExtendZ $extend
end
Fields
Orbital band=1 kun=3
End
eor
echo "Begin TOC of tape41 (MethaneChain/orbitals)"
$AMSBIN/pkf TAPE41
echo "End TOC of tape41 (MethaneChain/orbitals)"
rm TAPE41
# the order appears to be random
export NSCM=1
$AMSBIN/nao << eor
Filename $AMS_JOBNAME.results/dftb.rkf
Grid
Type Coarse
end
AIMCriticalPoints
End
eor
echo "kf file with periodic QTAIM"
$AMSBIN/pkf $AMS_JOBNAME.results/dftb.rkf
cat << eor > coords.txt
1.0 0.0 0.0
0.2 0.4 0.0
eor
$AMSBIN/nao << eor
Filename $AMS_JOBNAME.results/dftb.rkf
ResultFilename result.txt
Grid
Filename coords.txt
end
Fields
v(coulomb)
End
eor
echo "Begin of result"
cat result.txt
echo "End of result"
echo "test on periodic chain with the gamma only method"
export AMS_JOBNAME=MethaneChainGamma
$AMSBIN/ams << eor
Task SinglePoint
System
Atoms [Angstrom]
C 0.0 0.0 0.0
H 1.079999998 0 0
H -0.35604780 0 1.019622459440336
H -0.35604780 0.8830189521445 -0.50981122972017
H -0.35604780 -0.8830189521445 -0.50981122972017
End
Lattice
2.5 0.0 0.0
End
End
Engine DFTB
ResourcesDir Demo
Model DFTB0
KSpace Quality=GammaOnly
EndEngine
eor
# cd MethaneChainGamma.results
$AMSBIN/nao << eor
Filename $AMS_JOBNAME.results/dftb.rkf
Grid
Type Coarse
ExtendX $extend
ExtendY $extend
ExtendZ $extend
end
Fields
rho
rho(deformation)
tau(valence)
rho(deformation/fit)
v(coulomb/atoms)
v(coulomb/deformation)
v(coulomb)
End
eor
echo ""
echo "Begin TOC of tape41 (MethaneChainGamma/props)"
$AMSBIN/pkf TAPE41
echo "End TOC of tape41 (MethaneChainGamma/props)"
rm TAPE41
# ------------- test with absolute path for AIM, which writes to the file ------------------------
export AMS_JOBNAME=Methane.again
$AMSBIN/ams << eor
Task SinglePoint
System
Atoms
C 0.000000000000 0.000000000000 0.000000000000
H 0.863426938600 0.544775641100 0.352297349600
H -0.335313871500 0.422758012300 -0.935542767900
H 0.264056533600 -1.036774276000 -0.147557605600
H -0.792169600700 0.069240623010 0.730803023900
End
End
Engine DFTB
ResourcesDir Demo
Model DFTB0
EndEngine
eor
# the order appears to be random
export NSCM=1
base=$PWD
if test "$OS" = "Windows_NT"; then
# ignore Windows line endings
base=`pwd -W`
fi
$AMSBIN/nao << eor
Filename $base/$AMS_JOBNAME.results/dftb.rkf
Grid
Type Coarse
end
AIMCriticalPoints
gridSpacing 0.2
End
eor
echo "kf file with QTAIM"
$AMSBIN/pkf $AMS_JOBNAME.results/dftb.rkf