#! /bin/sh

# Frequently when searching for a transition state, one needs an accurate second
# derivatives matrix, a Hessian. An exact Hessian may be obtained analytically
# but this may be very expensive for large molecules. In such cases it may be
# beneficial to calculate Hessian matrix elements only for atoms directly
# involved in the reaction for which a transition state is sought for. The rest
# of the Hessian can then be approximated using a cheaper method.

# In this example, a saddle point of the ethane internal rotation around C-C
# bond is found. In principle, only hydrogen atoms contribute to the normal mode
# we are interested in. Therefore we calculate a partial Hessian matrix
# including hydrogen atoms only. For this purpose, the SelectedRegionForHessian
# key is used.
# In the calculation symmetry will be used.

AMS_JOBNAME=Partial_Hessian $AMSBIN/ams <<eor
System
  Symmetrize
  atoms
     C       0.000000000000       0.000000000000       0.767685465031
     C       0.000000000000       0.000000000000      -0.767685465031
     H       0.964354016767       0.347635559279       1.177128271450 region=hess
     H      -0.181115782790      -1.008972856410       1.177128271450 region=hess
     H      -0.783238233981       0.661337297125       1.177128271450 region=hess
     H      -0.500471876676       0.894626767091      -1.177128271450 region=hess
     H      -0.524533568868      -0.880734742626      -1.177128271450 region=hess
     H       1.025005445540      -0.013892024465      -1.177128271450 region=hess
  end
end

Task SinglePoint

Properties
  NormalModes Yes
  SelectedRegionForHessian hess
End

Engine ADF
  title Ethane transition state search using partial Hessian
  beckegrid
    quality good
  end
  basis
    core Large
    type DZ
    CreateOutput Yes
  end
EndEngine
eor

# After the Hessian is calculated, the resulting TAPE21 file is used for a
# subsequent transition state search:

AMS_JOBNAME=TS $AMSBIN/ams <<eor
LoadSystem
   File Partial_Hessian.results/ams.rkf
End

Task TransitionStateSearch

GeometryOptimization
   InitialHessian
      Type FromFile
      File Partial_Hessian.results/adf.rkf
   End
End

EngineRestart Partial_Hessian.results/adf.rkf

Engine ADF
  title Ethane transition state search using partial Hessian
  beckegrid
    quality good
  end
  basis
    core Large
    type DZ
  end
EndEngine

eor

# Important note: care should be taken to specify correct mode in the
# TransitionState keyword. Because a significant part of the Hessian will not be
# calculated exactly, it is possible that it will have more than one negative
# eigenvalue, in which case the one we are interested in may not be the first
# one. In such a case, one needs to specify the correct mode number in the
# TransitionState keyword.