#! /bin/sh

# This example tries to part of the COSMO-RS GUI Tutorial: parameters and analysis using scripts.
#
# First some .coskf files are copied to the location where the scripts are running.

cp $AMSHOME/examples/COSMO-RS/Parameters_and_Analysis/benzene.coskf .
cp $AMSHOME/examples/COSMO-RS/Parameters_and_Analysis/ethanol.coskf .
cp $AMSHOME/examples/COSMO-RS/Parameters_and_Analysis/methanol.coskf .
cp $AMSHOME/examples/COSMO-RS/Parameters_and_Analysis/water.coskf .

# Set pure compound parameters
# ----------------------------

# In the first part of the example you will find how to use crsprep to set pure compound parameters,
# in this case to set the number of ring atoms for the benzene molecule, which has 6 ring atoms.
# The file benzene.coskf is changed, such that it contains the value "6" for the number of ring compounds.

"$AMSBIN/crsprep" -c benzene.coskf -nring 6 -savecompound

# The sigma profile and the sigma potential
# -----------------------------------------
# 
# Next for convenience a file tutorial2.compoundlist is made that consists of 4 coskf files.


rm -f tutorial2.compoundlist
rm -f job
cat << eor > tutorial2.compoundlist
benzene.coskf
ethanol.coskf
methanol.coskf
water.coskf
eor

# In the second part of the example sigma profiles are calculated for the four compounds
# (result file step6.crskf), and next the sigma potentials of the four pure compounds
# (result file step7.crskf).
# With *amsreport* one can get the calculated sigma profile or sigma potential from
# the .crskf file on standard output.


"$AMSBIN/crsprep" -t PURESIGMAPROFILE -c tutorial2.compoundlist -j step6 > job.sh
"$AMSBIN/crsprep" -t PURESIGMAPOTENTIAL -c tutorial2.compoundlist -j step7 >> job.sh
chmod +x job.sh
./job.sh
echo "Results"
"$AMSBIN/amsreport" step6.crskf sigma
"$AMSBIN/amsreport" step6.crskf sigma-profile
"$AMSBIN/amsreport" step6.crskf sigma-profile-hb
"$AMSBIN/amsreport" step7.crskf sigma-potential
echo "Ready"