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 
# attept 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