#! /bin/sh

# This example tries to do the same as in the COSMO-RS GUI Tutorial: COSMO result files,
# using scripts.
#
# In the first part of the example you will find how to use amsprep to construct 
# an ADF COSMO results file.
# The template ADFCRS will perform a gas phase geometry optimization (for water, in this case),
# and next a COSMO calculation at the gas phase optimized geometry.
# The result file adfwater.coskf, which is an ADF COSMO result file, can be used as input for
# a COSMO-RS calculation. amsreport is used to extract data from the resulting .coskf file.

echo "Results"

rm -f water.xyz
rm -f job.sh
cat << eor > water.xyz
3

H       0.00000000       0.77121000       0.18071000
O       0.00000000      -0.00000000      -0.36142000
H       0.00000000      -0.77121000       0.18071000
eor

"$AMSBIN/amsprep" -t GO -runtype "COSMO-RS Compound" -m water.xyz -j adfwater >job.sh
chmod +x job.sh
./job.sh

echo "ADF"
"$AMSBIN/amsreport" adfwater.results geometry-a*
cp adfwater.coskf adffile.coskf
"$AMSBIN/amsreport" adffile.coskf energies

# The template ADFCRS can also be used for generating an "average monomer" COSMO result file.
# The calculation could take up quite some time.

echo "POLYMER"
$AMSBIN/amsprep -t GO -runtype "COSMO-RS Compound" -smiles "C{-}C{n+}(c1ccccc1)" -j adfpolystyrene >job3.sh
grep -i coskfatoms job3.sh |wc -w


# A MOPAC COSMO result file can also be constructed.
# Note that the syntax for MOPAC is not the same as in ADF2018.
# The template MOPAC-GO will perform a COSMO geometry optimization, 
# if -g "mopac.solvation.enabled 1" -g "mopac.solvation.solvent.name CRS" is included.
# If -g "mopac.solvation.nspa 362" is included the maximum number of COSMO surface points
# is 362, which is more than the default 42.
# The result file mopacwaterresults/mopac.coskf is a MOPAC COSMO result file,
# which can be used as input for a COSMO-RS calculation.

"$AMSBIN/amsprep" -t MOPAC-GO -m water.xyz -g "mopac.solvation.enabled 1" \
                  -g "mopac.solvation.solvent.name CRS" -g "mopac.solvation.nspa 362" \
                  -j mopacwater >job2.sh
chmod +x job2.sh
./job2.sh

echo "MOPAC"
"$AMSBIN/amsreport" mopacwater.results geometry-a*
"$AMSBIN/amsreport" mopacwater.results/mopac.coskf energies

# Fast Sigma can provide estimates of COSMO-RS sigma profiles in milliseconds.

echo "FAST SIGMA"
"$AMSBIN/fast_sigma" --smiles "CC(Cc1ccc(cc1)[C@@H](C(=O)O)C)C" -o ibuprofen.compkf
"$AMSBIN/amsreport" ibuprofen.compkf formula
"$AMSBIN/amsreport" ibuprofen.compkf energies

echo "Ready"