Example: PES scan and transition state search for H2 on graphene¶

#! /bin/sh

# First we do a 2D PES scan varying the z-coordinate of the two hydrogen atoms
# In this example we will keep the graphene slab fixed. From a physical/chemical
# standpoint this is not a good approximation. The graphene slab is
# intentionally not perfectly symmetric.

AMS_JOBNAME=PESScan $AMSBIN/ams << EOF

   Task PESScan

   System
      Atoms
         H   0.0      1.53633037    1.1
         H   0.0     -0.11341359    1.1
         C   0.001    1.42028166    0.0
         C   1.230    2.13042249    0.0
         C   1.230   -0.71014083    0.0
         C   2.460    0.00000000    0.0
         C   2.460    1.42028167    0.0
         C   0.000    0.00000000    0.0
      End
      Lattice
         3.69   -2.13042249   0.0
         0.00    4.26084499   0.0
      End
   End

   PESScan
      ScanCoordinate
         nPoints 10
         Coordinate 1 Z 1.1 2.0
      End
      ScanCoordinate
         nPoints 10
         Coordinate 2 Z 1.1 2.0
      End
   End

   GeometryOptimization
      Convergence Step=1.0e-3
   End

   Constraints
      # Fix the entire graphene slab.
      Atom 3
      Atom 4
      Atom 5
      Atom 6
      Atom 7
      Atom 8
   End

   Engine DFTB
      Model DFTB
      ResourcesDir DFTB.org/3ob-3-1
      DispersionCorrection D3-BJ
      KSpace
        Type Symmetric
        Symmetric KInteg=3
      End
   EndEngine

EOF


# A human looks at the PES scan and picks a reasonable starting point for the
# TS search. (Normally you would do that in AMSMovie by looking at the PES and
# then exporting the geometry into an xyz file.)

#           _           ____
#        ___))         [  | \
#        ) //o          | | ]
#     _ (_    >         | | ]
#    (O)  \__<          | | ]
#    [/] /   \)        [__|/_
#    [\]|  ( \         __/___\_____
#    [/]|   \ \__  ___|            |
#    [\]|    \___E/%%/|____________|_
#    [/]|=====__   (_________________)

cat << EOF > initial_geometry_for_TS.xyz
8

H    0.4145668856457391      1.72927656037925      1.100000023839768     region=H2
H   -0.05533871972549955    -0.06805093626643093   1.500000013242627     region=H2
C    0.001                   1.42028166            0.0
C    1.230                   2.13042249            0.0
C    1.230                  -0.71014083            0.0
C    2.460                   0.00000000            0.0
C    2.460                   1.42028167            0.0
C    0.000                   0.00000000            0.0
VEC1 3.69 -2.13042249 0.0
VEC2 0.0   4.26084499 0.0
EOF


# Compute the partial initial Hessian to be used in the transition state
# search. (The Hessian will be computed only for the hydrogen atoms.)

AMS_JOBNAME=Hessian $AMSBIN/ams << EOF

   Task SinglePoint

   System
      # Load the geometry we just saved.
      GeometryFile initial_geometry_for_TS.xyz
   End

   Properties
      # Calculate the Hessian (implied when calculating normal modes) ...
      NormalModes True
      # ... but only the part related to the hydrogen atoms.
      SelectedRegionForHessian H2
   End

   Engine DFTB
      Model DFTB
      ResourcesDir DFTB.org/3ob-3-1
      DispersionCorrection D3-BJ
      KSpace
        Type Symmetric
        Symmetric KInteg=3
      End
   EndEngine

EOF

echo "Extract the frequencies from the kf file using amsreport:"
$AMSBIN/amsreport Hessian.results/dftb.rkf -r "Vibrations%Frequencies[cm-1]##1"


# Do a transition state search using the initial Hessian just computed (the
# Graphene slab is constrained). Also compute the final Hessian for the
# hydrogen atoms to validate the TS.

AMS_JOBNAME=TS $AMSBIN/ams << EOF

   Task TransitionStateSearch

   System
      # Load the geometry we just saved.
      GeometryFile initial_geometry_for_TS.xyz
   End

   GeometryOptimization
      Quasi-Newton
         Step TrustRadius=0.05
      End
      Convergence Gradients=1.0e-4
      InitialHessian
          # Load previously calculated Hessian as initial Hessian for a
          # transition state search with the Quasi-Newton optimizer.
          Type FromFile
          File Hessian.results/dftb.rkf
      End
   End

   TransitionStateSearch
       # Follow the mode with the smallest frequency.
       ModeToFollow 1
       # (This is also the default, we wouldn't need to specify this.)
   End

   Constraints
      # Fix the entire graphene slab.
      Atom 3
      Atom 4
      Atom 5
      Atom 6
      Atom 7
      Atom 8
   End

   Properties
      NormalModes Yes
      SelectedRegionForHessian H2
   End

   Engine DFTB
       Model DFTB
       ResourcesDir DFTB.org/3ob-3-1
       DispersionCorrection D3-BJ
      KSpace
        Type Symmetric
        Symmetric KInteg=3
      End
   EndEngine

EOF

echo "Extract energy from the rkf file using amsreport:"
$AMSBIN/amsreport TS.results/dftb.rkf -r "AMSResults%Energy"