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