Example: PESScan ethane
***********************

"Download PESScan.run"

   #!/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
