Example: 2D PES scan¶
#!/bin/sh
echo "=============="
echo "Ethane torsion"
echo "=============="
echo
AMS_JOBNAME=ethane_torsion $AMSBIN/ams << EOF
Task PESScan
System
Atoms
C 0.0 0.0 0.76576
C 0.0 0.0 -0.76576
H -0.88668938 0.51193036 1.16677
H 0.88668938 0.51193036 1.16677
H 0.0 -1.02386071 1.16677
H 0.0 1.02386071 -1.16677
H -0.88668938 -0.51193036 -1.16677
H 0.88668938 -0.51193036 -1.16677
End
End
PESScan
# First scan coordinate: C--C bond distance
ScanCoordinate
nPoints 5
Distance 1 2 1.3 1.7
End
# Second scan coordinate: One of the H--C--C--H dihedral angles (others will follow naturally)
ScanCoordinate
nPoints 21
Dihedral 3 1 2 6 60.0 0.0
End
End
GeometryOptimization
Convergence Step=1.0e-3
End
Engine DFTB
Model DFTB3
ResourcesDir DFTB.org/3ob-3-1
DispersionCorrection D3-BJ
EndEngine
EOF
echo "=============="
echo "Ethene torsion"
echo "=============="
echo
AMS_JOBNAME=ethene_torsion $AMSBIN/ams << EOF
Task PESScan
System
Atoms
C 0.0 0.0 0.66687
C 0.0 0.0 -0.66687
H 0.0 0.92974 -1.23912
H 0.0 0.92974 1.23912
H 0.0 -0.92974 1.23912
H 0.0 -0.92974 -1.23912
End
End
PESScan
# First scan coordinate: C--C bond distance
ScanCoordinate
nPoints 5
Distance 1 2 1.1 1.8
End
# Second scan coordinate: Two of the H--C--C--H dihedrals
ScanCoordinate
nPoints 21
Dihedral 4 1 2 3 0.0 60.0
Dihedral 5 1 2 6 0.0 60.0
End
End
GeometryOptimization
Convergence Step=1.0e-3
End
Engine DFTB
Model DFTB3
ResourcesDir DFTB.org/3ob-3-1
DispersionCorrection D3-BJ
EndEngine
EOF
# Below are more technical examples, demonstrating the PES scan gap filling.
# The QUASINANO2015 parameter set shows some discontinuities in the PES,
# which leads to problems with convergence. The first job leaves the
# non-converged steps as is while the second job instructs AMS to
# attempt a second optimization for non-converged point starting from
# a different initial geometry.
echo "============================="
echo "Ethane gap filling test (1/2)"
echo "============================="
echo
AMS_JOBNAME=ethane_nofillgaps $AMSBIN/ams << EOF
Task PESScan
System
Atoms
C -2.333834610464788 -2.268837915270455 -0.2417723425321957
C -0.8081611038872945 -2.334371994724881 -0.04271045326758349
H -0.2505615773096904 -1.473443563856088 -0.38077110593546
H -0.3249814761083244 -3.235478579439597 -0.3904810245975267
H -0.583247370537557 -2.349691649662279 1.013499336841977
H -2.817014238243758 -1.367731330555738 0.1059982287977475
H -2.891434137042391 -3.129766346139247 0.09628831013568076
H -2.558748343814525 -2.253518260333056 -1.297982132641757
End
End
GeometryOptimization
CoordinateType Cartesian
Convergence Step=1.0e-3
End
PESScan
FillUnconvergedGaps False
CalcPropertiesAtPESPoints True
ScanCoordinate
nPoints 10
Distance 1 2 1.4 1.7
End
ScanCoordinate
nPoints 10
Distance 7 1 1.0 1.2
Dihedral 7 1 2 3 60.0 180.0
End
End
Engine DFTB
Model SCC-DFTB
ResourcesDir QUASINANO2015
EndEngine
EOF
echo "============================="
echo "Ethane gap filling test (2/2)"
echo "============================="
echo
AMS_JOBNAME=ethane_fillgaps $AMSBIN/ams << EOF
Task PESScan
System
Atoms
C -2.333834610464788 -2.268837915270455 -0.2417723425321957
C -0.8081611038872945 -2.334371994724881 -0.04271045326758349
H -0.2505615773096904 -1.473443563856088 -0.38077110593546
H -0.3249814761083244 -3.235478579439597 -0.3904810245975267
H -0.583247370537557 -2.349691649662279 1.013499336841977
H -2.817014238243758 -1.367731330555738 0.1059982287977475
H -2.891434137042391 -3.129766346139247 0.09628831013568076
H -2.558748343814525 -2.253518260333056 -1.297982132641757
End
End
GeometryOptimization
CoordinateType Cartesian
Convergence Step=1.0e-3
End
PESScan
FillUnconvergedGaps True
CalcPropertiesAtPESPoints True
ScanCoordinate
nPoints 10
Distance 1 2 1.4 1.7
End
ScanCoordinate
nPoints 10
Distance 7 1 1.0 1.2
Dihedral 7 1 2 3 60.0 180.0
End
End
Engine DFTB
Model SCC-DFTB
ResourcesDir QUASINANO2015
EndEngine
EOF