Example: Mode Tracking¶

#! /bin/sh

# This example demonstrates the usage of the AMS vibrational analysis tools
# on the cyclohexanone molecule.


# 1. Optimization with DFT
# ------------------------

AMS_JOBNAME=DFT $AMSBIN/ams << EOF

   System
      Atoms
        C         0.000000    0.000000    0.000000
        C         0.978606    1.950589   -1.251328
        C         0.978606    1.950589    1.251328
        C         0.812569    2.806732    0.000000
        C        -0.039622    0.802151    1.272926
        C        -0.039622    0.802151   -1.272926
        O         0.062619   -1.251283    0.000000
        H         0.123306    0.119861    2.122758
        H        -1.060012    1.229063    1.372200
        H         0.871524    2.560541    2.167037
        H         2.001065    1.521810    1.263746
        H        -0.196785    3.268312    0.000000
        H         1.549313    3.631809    0.000000
        H         0.871524    2.560541   -2.167037
        H         2.001065    1.521810   -1.263746
        H         0.123306    0.119861   -2.122758
        H        -1.060012    1.229063   -1.372200
      End
   End

   Task GeometryOptimization

   GeometryOptimization
      Convergence Gradients=1.0e-4
   End

   Engine BAND
   EndEngine

EOF


# 2. Obtain DFTB hessian and modes as preconditioner and guess
# ------------------------------------------------------------

AMS_JOBNAME=DFTB $AMSBIN/ams << EOF

   LoadSystem
      File DFT.results/ams.rkf
   End

   Task GeometryOptimization

   GeometryOptimization
      Convergence Gradients=1.0e-4
   End

   Properties
      NormalModes Yes
   End

   Engine DFTB
      Model DFTB3
      ResourcesDir DFTB.org/3ob-freq-1-2
   EndEngine

EOF


# 3. ModeScanning of DFTB C=O stretch mode with DFT
# -------------------------------------------------

AMS_JOBNAME=ModeScanning $AMSBIN/ams << EOF

   LoadSystem
      File DFTB.results/ams.rkf
   End
   LoadEngine DFT.results/band.rkf

   Task VibrationalAnalysis

   VibrationalAnalysis
      Type ModeScanning
      NormalModes
         ModeFile DFTB.results/dftb.rkf
         ModeSelect
            HighIR 1 # This should select the C=O stretch
         End
      End
   End

EOF


# 4. Mode tracking with DFT starting from DFTB C=O stretch mode
# -------------------------------------------------------------

AMS_JOBNAME=ModeTracking $AMSBIN/ams << EOF

   LoadSystem
      File DFT.results/ams.rkf
   End
   LoadEngine DFT.results/band.rkf

   Task VibrationalAnalysis

   VibrationalAnalysis
      Type ModeTracking
      ModeTracking
         HessianGuess File
         HessianPath DFTB.results
      End
      NormalModes
         ModeInputFormat File      
         ModeFile DFTB.results/dftb.rkf
         ModeSelect
            HighIR 1 # This should select the C=O stretch
         End
      End
   End

EOF


# 5. Mode tracking with DFT starting from a pure C=O stretch
# ----------------------------------------------------------

AMS_JOBNAME=ModeTracking_COStretch $AMSBIN/ams << EOF

   LoadSystem
      File DFT.results/ams.rkf
   End
   LoadEngine DFT.results/band.rkf

   Task VibrationalAnalysis

   VibrationalAnalysis
      Type ModeTracking
      NormalModes
         ModeInputFormat Inline
         ModeInline
            0.0  0.0  0.7071 # This is the C attached to the O
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0 -0.7071 # This is the O
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0  0.0
            0.0  0.0  0.0
         End
         ModeSelect
            HighIR 1 # This should select the C=O stretch
         End
      End
      ModeTracking
         HessianGuess File
         HessianPath DFTB.results
         TrackingMethod OverlapPrevious
                      #     ^-- Probably better than the default.
                      #         Our initial mode is not particularly close yet ...         
      End
   End

EOF