Example: Activation Strain Model Analysis using PyFrag
******************************************************

"Download pyfrag.run"

   #!/bin/bash


   # The trajectory is a concatenated xyz-file:

   cat << eor > coords.xyz
   C        -1.741968   -2.220880    0.000000
   Pd       -2.137509   -0.237843    0.000000
   H        -2.809570   -2.499547    0.000000
   H        -1.265288   -2.629932    0.895677
   H        -1.265288   -2.629932   -0.895677
   H        -0.755099   -0.885698    0.00000

   C        -1.741968   -2.220880    0.000000
   Pd       -2.137509   -0.250000    0.000000
   H        -2.809570   -2.499547    0.000000
   H        -1.265288   -2.629932    0.895677
   H        -1.265288   -2.629932   -0.895677
   H        -0.755099   -0.885698    0.00000
   eor

   # Input options for ADF:

   # One should generally symmetrize the coordinates by setting AMS.System.Symmetrize=Yes 

   cat << eor > adfinputfile
   AMS.Task=SinglePoint
   AMS.System.Charge=0
   AMS.System.Symmetrize=Yes
   ADF.NumericalQuality=VeryGood
   ADF.XC.GGA=OPBE
   ADF.basis.core=None
   ADF.Symmetry=AUTO
   ADF.Relativity.Level=Scalar
   ADF.Relativity.Formalism=ZORA
   ADF.eprint.sfo=eig ovl
   eor

   # Here we call the PyFrag script.

   # PyFrag conducts a total of six single point calculations, one for each fragment and the 
   # whole system for each of the two geometries in the trajectory, respectively. 
   # The intermediate results for each geometry are printed during the calculation. 
   # At the end of its run PyFrag summarizes all results in a table which is also written 
   # to an output file PyFrag<SystemName>.txt

   $AMSBIN/amspython $AMSHOME/scripting/standalone/pyfrag/PyFrag.py  \
   --xyzpath coords.xyz \
   --fragment 2 --fragment 1 3 4 5 6 --strain 0 --strain -554.1 \
   --bondlength 1 6 1.093 \
   --angle 2 1 6 180 \
   --VDD 2 1 6 \
   --hirshfeld frag1 \
   --irrepOI AA \
   --irrepOI AAA \
   --orbitalenergy frag1 HOMO \
   --orbitalenergy frag2 LUMO \
   --orbitalenergy AA frag2 5 \
   --population frag1 HOMO \
   --population AA frag2 5 \
   --overlap frag1 HOMO frag2 LUMO \
   --overlap S frag1 5 AA frag2 4 \
   --adfinput ADF.basis.type=DZP \
   --adfinputfile adfinputfile
