Scripting Examples
******************


Example: COSMO result files
===========================

"Download COSMO_files.run"

   #! /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 2> job.err
   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 2> job3.err
   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 2> job2.err
   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"


Example: COSMO-RS parameters and analysis
=========================================

"Download Parameters_and_Analysis.run"

   #! /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"


Example: COSMO-RS properties
============================

"Download Properties.run"

   #! /bin/sh

   # This example tries to do the same as COSMO-RS GUI Tutorial: Properties, using scripts.

   echo "Results"

   # This example starts with copying 4 coskf files to the current directory,
   # and modifying the benzene.coskf file such that the number of ring atoms is 6,
   # like in the previous example.

   rm -f job.sh
   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 .
   cp $AMSHOME/examples/COSMO-RS/Properties/2-hexanone.coskf .
   cp $AMSHOME/examples/COSMO-RS/Properties/acetic_acid.coskf .

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

   # Step 2: Vapor pressure
   # ----------------------

   # In step 2 of the example the vapor pressure of methanol is calculated at the
   # default temperature of 298.15 K (result file step2a.crskf),
   # and next for a series of temperatures ranging from 273.15 K to 373.15 K
   # in 10 steps (result file step2b.crskf).


   touch job.sh
   chmod +x job.sh
   "$AMSBIN/crsprep" -t PUREVAPORPRESSURE -j step2a \
                     -c methanol.coskf > job.sh
   "$AMSBIN/crsprep" -t PUREVAPORPRESSURE -temperature 273.15 -temperature 373.15 -j step2b \
                     -c methanol.coskf >> job.sh
   ./job.sh
   echo "Step 2a"
   "$AMSBIN/amsreport" step2a.crskf temperature
   "$AMSBIN/amsreport" step2a.crskf pressure
   "$AMSBIN/amsreport" step2a.crskf enthalpy-vaporization
   echo "Step 2b"
   "$AMSBIN/amsreport" step2b.crskf temperature
   "$AMSBIN/amsreport" step2b.crskf pressure
   "$AMSBIN/amsreport" step2b.crskf enthalpy-vaporization


   # Step 3: Boiling point
   # ---------------------

   # In step 3 of the example the boiling point of a mixture of methanol and ethanol
   # is calculated, for a series of pressures ranging from 0.101325 to 1.01325 bar
   # in 10 steps (result file step3.crskf).
   # This mixture consist of 50% mole fraction methanol and 50% mole fraction ethanol.

   "$AMSBIN/crsprep" -t BOILINGPOINT -pressure 0.101325 -pressure 1.01325 -j step3 \
                     -c methanol.coskf -frac1 0.5 \
                     -c ethanol.coskf -frac1 0.5 > job.sh
   ./job.sh
   echo "Step 3"
   "$AMSBIN/amsreport" step3.crskf temperature
   "$AMSBIN/amsreport" step3.crskf pressure


   # Step 4: Flash point
   # -------------------

   # In step 4 of the example the flash point of a mixture of ethanol and water
   # is calculated (result file step4.crskf).
   # This mixture consist of 44.2% mass fraction methanol and 55.8% mass fraction ethanol.
   # For a flash point calculation the pure compound flash points are needed as input,
   # since COSMO-RS does not predict pure compound flash points.
   # For pure ethanol a flash point of 286 K is saved in the file ethanol.coskf.


   "$AMSBIN/crsprep" -c ethanol.coskf -flashpoint 286 -savecompound

   "$AMSBIN/crsprep" -t FLASHPOINT -massfraction -j step4 \
                     -c ethanol.coskf -frac1 0.442 \
                     -c water.coskf -frac1 0.558 > job.sh
   ./job.sh
   echo "Step 4 flash point"
   $AMSBIN/amsreport step4.crskf temperature

   # Step 5: Activity coefficients, Henry coefficients, Solvation free energies
   # --------------------------------------------------------------------------

   # In step 5 of the example the infinite diluted solutes benzene, methanol,and
   # ethanol are calculated in the solvent water (result file step5.crskf).
   # Activity coefficients, Henry coefficients and solvation free energies
   # will be calculated.
   # One one should include -s flag for water, since it is the solvent,
   # and considered here to be a special compound.


   "$AMSBIN/crsprep" -t ACTIVITYCOEF -j step5 \
                     -s water.coskf \
                     -c benzene.coskf -c ethanol.coskf -c methanol.coskf > job.sh
   ./job.sh
   echo "Step 5 Activity coefficients, Henry's law constants, Solvation energy"
   "$AMSBIN/amsreport" step5.crskf Activity-Coefficient
   "$AMSBIN/amsreport" step5.crskf Henry
   "$AMSBIN/amsreport" step5.crskf Gibbs-energy-solvation

   # Step 6: Partition coefficients (log P)
   # --------------------------------------

   # In step 6 of the example the partition coefficients of infinitely diluted
   # solutes in a mixture of two immiscible solvents are calculated.
   # In step 6a the default Octanol/Water partition coefficients are calculated
   # (default -preset 2) (result file step6a.crskf).
   # In step 6b a user defined (-preset 0) Benzene/Water partition coefficients
   # are calculated (result file step6b.crskf).
   # In this case one should include -s flag for benzene and water, since these
   # are the two immiscible solvents, and considered here to be the special compounds.
   # The order of the compounds benzene and water is important, because the
   # molar volume of phase 1 (benzene) divided by the the molar volume of phase 2
   # (water) is given with the flag -volumequotient.


   "$AMSBIN/crsprep" -t LOGP -j step6a \
                     -c benzene.coskf -c ethanol.coskf -c methanol.coskf > job.sh
   "$AMSBIN/crsprep" -t LOGP -preset 0 -volumequotient 4.93 -j step6b \
                     -s benzene.coskf -s water.coskf \
                     -c ethanol.coskf -c methanol.coskf >> job.sh
   ./job.sh
   echo "Step 6a octanol/water"
   "$AMSBIN/amsreport" step6a.crskf logp
   echo "Step 6b benzene/water"
   "$AMSBIN/amsreport" step6b.crskf logp

   # Step 7: Solubility
   # ------------------

   # In step 7 of the example the solubility of a compound is calculated.
   # The solute can either be a liquid, solid, or gas.
   # First some pure compound properties for benzene are set: the melting point,
   # enthalpy of fusion, and the boiling point (file benzene.coskf).


   "$AMSBIN/crsprep" -c benzene.coskf -meltingpoint 278.7 -hfusion 2.37 -savecompound
   "$AMSBIN/crsprep" -c benzene.coskf -tvap 353.3 -pvap 1.01325 -savecompound

   # In step 7a the solubility of benzene in water is calculated for a range of
   # temperatures ranging from 273.15 K to 373.15 K in 10 steps (result file step7a.crskf).
   # If the template PURESOLUBILITY is used, the special compound is the solute,
   # benzene in this case.
   # Below 278.7 K, benzene is a solid. This will be taken into account, since the
   # melting point and enthalpy of fusion are present on the file benzene.coskf.
   # At higher temperatures benzene is assumed to be a liquid.
   # Note that tn this calcuation above the normal boiling point of benzene
   # the vapor pressure of benzene will be higher than 1.01325 bar.

   "$AMSBIN/crsprep" -t PURESOLUBILITY -temperature 273.15 -temperature 373.15 -j step7a \
                     -s benzene.coskf \
                     -c water.coskf > job.sh

   # In step 7b again the solubility of benzene in water is calculated for a (different)
   # range of temperatures (result file step7b.crs) using the template SOLUBILITY.
   # If the template SOLUBILITY is used, the special compound is the solvent,
   # water in this case.
   # For the density of the solvent water 1.0 kg/L is used.
   # Below 278.7 K benzene is a solid. This will be taken into account, since the melting
   # point and enthalpy of fusion are present on the file benzene.coskf.
   # At higher temperatures benzene is assumed to be a liquid.

   "$AMSBIN/crsprep" -t SOLUBILITY -temperature 273.15 -temperature 283.15 \
                      -densitysolvent 1.0 -j step7b \
                     -s water.coskf \
                     -c benzene.coskf >> job.sh
   # In step 7c again the solubility of benzene in water is calculated for a range
   # of temperatures above the boiling point of benzene (result file step7c.crs)
   # using the template SOLUBILITY.
   # If the template SOLUBILITY is used, the special compound is the solvent,
   # water in this case.
   # For the density of water 1.0 kg/L is used.
   # For the vapor pressure of benzene 1.01325 bar is used.

   "$AMSBIN/crsprep" -t SOLUBILITY -temperature 353.3 -temperature 373.15 \
                     -densitysolvent 1.0 -solphase Gas -pressure 1.01325 -j step7c \
                     -s water.coskf \
                     -c benzene.coskf >> job.sh

   # The solubility of a gas in a solvent can also be calculated using Henry's law,
   # which is valid for ideal dilute solutions.
   # Henry coefficients can be calculated with the template ACTIVITYCOEF.
   # In step 7d of the example the infinite diluted solutes benzene is calculated
   # in the solvent water (result file step7d.crskf)
   # at a temperature of 363.15 K.
   # If the template ACTIVITYCOEF is used, the special compound is the solvent,
   # water in this case.
   # For the density of water 1.0 kg/L is used.

   "$AMSBIN/crsprep" -t ACTIVITYCOEF -temperature 363.15 -densitysolvent 1.0 -j step7d \
                     -s water.coskf \
                     -c benzene.coskf >> job.sh

   # Next the job.sh is run which will produce the crskf files,
   # and a report is made for all calculations in step 7.

   ./job.sh
   echo "Step 7a"
   "$AMSBIN/amsreport" step7a.crskf solubility-x
   echo "Step 7b"
   "$AMSBIN/amsreport" step7b.crskf solubility-g
   echo "Step 7c"
   "$AMSBIN/amsreport" step7c.crskf solubility-m
   echo "Step 7d"
   "$AMSBIN/amsreport" step7d.crskf henry


   # Step 8: Binary mixtures VLE/LLE
   # -------------------------------

   # In step 8 phase diagrams of a mixture of two components are be calculated
   # with the template BINMIXCOEF.
   # Exactly two compound should be given.
   # In step 8a of the example a binary mixture of water and methanol
   # is calculated at 298.14 K (result file step8a.crskf).

   "$AMSBIN/crsprep" -t BINMIXCOEF -temperature 298.14 -j step8a \
                     -s water.coskf \
                     -s methanol.coskf > job.sh

   # In step 8b of the example a binary mixture of water and ethanol is calculated
   # at 322.45 K (result file step8b.crskf).
   # Pure compound vapor pressures are given with -tvap (temperature in K)
   # and -pvap (vapor pressure in bar).
   # Preferably both -tvap and -pvap should be included for both compounds.
   # If only one -tvap and one -pvap is given, it is assumed to be for the first compound.
   # Note that these pure compound values are not saved to water.coskf or
   # ethanol.coskf in this case.


   "$AMSBIN/crsprep" -t BINMIXCOEF -temperature 322.45 -j step8b \
                     -s water.coskf -tvap 322.45 -pvap 0.123416 \
                     -s ethanol.coskf -tvap 322.45 -pvap 0.294896 >> job.sh

   # In step 8c of the example a binary mixture of water and benzene
   # is calculated at 323.15 K (result file step8c.crskf).
   # Water and benzene do not mix very well. In this case a
   # liquid-liquid equilibrium (LLE) will be calculated.
   # The number of mixtures for which the binary mixture is calculated should be not too small,
   # otherwise the properties of the 2 immiscible liquid phases will not be so accurate.
   # In this case for the number of mixtures 100 is chosen.
   # The actual number of mixtures is 5 more, thus 105 in this case.

   "$AMSBIN/crsprep" -t BINMIXCOEF -temperature 323.15 -n 100 -j step8c \
                     -s water.coskf \
                     -s benzene.coskf >> job.sh

   # In step 8d of the example a binary mixture of methanol and ethanol is calculated
   # at a constant total vapor pressure (-iso isobar) of 1.01325 bar (result file step8d.crskf).
   # Pure compound vapor pressures are given with -tvap (temperature in K)
   # and -pvap (vapor pressure in bar).
   # Preferably both -tvap and -pvap should be included for both compounds.
   # If only one -tvap and one -pvap is given, it is assumed to be for the first compound.
   # Note that these pure compound values are not saved to methanol.coskf
   # or ethanol.coskf in this case.

   "$AMSBIN/crsprep" -t BINMIXCOEF -iso isobar -pressure 1.01325 -j step8d \
                     -s methanol.coskf -tvap 338 -pvap 1.01325 \
                     -s ethanol.coskf -tvap 351 -pvap 1.01325 >> job.sh

   # Next the job.sh is run which will produce the crskf files,
   # and a report is made for all calculations in step 8.

   ./job.sh
   echo "Step 8a"
   "$AMSBIN/amsreport" step8a.crskf molar-fraction
   "$AMSBIN/amsreport" step8a.crskf excess-g
   "$AMSBIN/amsreport" step8a.crskf excess-h
   echo "Step 8b"
   "$AMSBIN/amsreport" step8b.crskf vapor-pressure
   echo "Step 8c"
   "$AMSBIN/amsreport" step8c.crskf miscibility-gap
   "$AMSBIN/amsreport" step8c.crskf miscibility-gap-x
   "$AMSBIN/amsreport" step8c.crskf miscibility-gap-a
   echo "Step 8d"
   "$AMSBIN/amsreport" step8d.crskf temperature


   # Step 9: Ternary mixtures VLE/LLE
   # --------------------------------
   # 
   # In step 9 phase diagrams of a mixture of three components are be calculated
   # with the template TERNARYMIX.
   # Exactly three compound should be given.
   # For convenience first some pure compound properties (normal boiling points)
   # are saved to the .coskf files.


   "$AMSBIN/crsprep" -c water.coskf    -tvap 373.15 -pvap 1.01325 -savecompound
   "$AMSBIN/crsprep" -c methanol.coskf -tvap 338    -pvap 1.01325 -savecompound
   "$AMSBIN/crsprep" -c ethanol.coskf  -tvap 351    -pvap 1.01325 -savecompound
   "$AMSBIN/crsprep" -c benzene.coskf  -tvap 353.3  -pvap 1.01325 -savecompound

   # In step 9a of the example a ternary mixture of methanol, ethanol, and benzene
   # is calculated at 343.15 K (result file step9a.crskf).
   # In step 9b of the example a ternary mixture of water, ethanol, and benzene is calculated
   # at a constant total vapor pressure (-iso isobar) of 1.01325 bar (result file step9b.crskf).
   # In step 9b a miscibility gap of the ternary mixture will be calculated.
   # In this case, within the miscibility gap there are two immiscible phases of
   # the liquid in equilibrium.
   # The composition of the two phases, which are in equilibrium,
   # can be found at the end points of the tie lines, that are calculated.

   "$AMSBIN/crsprep" -t TERNARYMIX -temperature 343.15 -j step9a \
                     -s methanol.coskf -s ethanol.coskf -s benzene.coskf  > job.sh
   "$AMSBIN/crsprep" -t TERNARYMIX -iso isobar -pressure 1.01325 -j step9b \
                     -s water.coskf -s ethanol.coskf -s benzene.coskf >> job.sh
   ./job.sh
   echo "Step 9a"
   "$AMSBIN/amsreport" step9a.crskf molar-fraction
   "$AMSBIN/amsreport" step9a.crskf pressure
   "$AMSBIN/amsreport" step9a.crskf miscibility-gap
   echo "Step 9b"
   "$AMSBIN/amsreport" step9b.crskf miscibility-gap
   echo "First 4 tie-lines"
   "$AMSBIN/amsreport" step9b.crskf -r "TERNARYMIX%xll#1:24#12.4f##6"
   "$AMSBIN/amsreport" step9b.crskf temperature

   # Note that for printing all tie-lines that are calculated in step9b one can simply use
   # "$AMSBIN/amsreport" step9b.crskf tie-lines-x
   # instead of the more complicated
   # "$AMSBIN/amsreport" step9b.crskf -r "TERNARYMIX%xll#1:24#12.4f##6"
   # which also only reports the first 4 tie-lines

   # Step 10: A composition line between solvents s1 and s2
   # ------------------------------------------------------

   # In step 10 a phase diagram of a mixture of two solvents, which both are mixtures,
   # is calculated with the template COMPOSITIONLINE.
   # In this step one of the tie lines of the ternary mixture of water, ethanol, and benzene
   # of step 9b will be investigated in more detail.
   # Note that here the .coskf files are used in which the normal boiling points were saved to (in step 9).
   # The mixture will be calculated for a list of molar (or mass) fractions of the solvents
   # between zero and one, and the compositions of solvent 1 and solvent 2 are linearly interpolated.
   # In this case solvent 1 consists of 0.3 molar fraction ethanol and 0.7 molar fraction benzene, and
   # solvent 2 consists of 0.9 molar fraction water and 0.1 molar fraction ethanol.
   # In step 10a of the example this mixture is calculated at a constant total vapor pressure (-iso isobar)
   # of 1.01325 bar (result file step10a.crskf).
   # In step 10b of the example this mixture is calculated at 341.05 K (result file step10b.crskf).
   # Why this temperature was chosen can be found in step 10 of COSMO-RS GUI Tutorial: Properties.

   "$AMSBIN/crsprep" -t COMPOSITIONLINE -iso isobar -pressure 1.01325 -n 100 -j step10a \
                     -s water.coskf   -frac1 0.0 -frac2 0.9 \
                     -s ethanol.coskf -frac1 0.3 -frac2 0.1 \
                     -s benzene.coskf -frac1 0.7 -frac2 0.0 > job.sh
   "$AMSBIN/crsprep" -t COMPOSITIONLINE -temperature 341.05 -n 100 -j step10b \
                     -s water.coskf   -frac1 0.0 -frac2 0.9 \
                     -s ethanol.coskf -frac1 0.3 -frac2 0.1 \
                     -s benzene.coskf -frac1 0.7 -frac2 0.0 >> job.sh
   ./job.sh
   echo "Step 10a"
   $AMSBIN/amsreport step10a.crskf ncomp
   $AMSBIN/amsreport step10a.crskf frac1
   $AMSBIN/amsreport step10a.crskf frac2
   $AMSBIN/amsreport step10a.crskf solvent-fraction
   $AMSBIN/amsreport step10a.crskf molar-fraction
   $AMSBIN/amsreport step10a.crskf activity-coefficient

   echo "Step 10b"
   $AMSBIN/amsreport step10b.crskf Gibbs-energy-mixing

   # Step 11: Phase Stability Test and LLE
   # -------------------------------------

   "$AMSBIN/crsprep" -t STABILITY -temperature 298.15 -j step11a \
                     -s water.coskf -frac1 0.4 -s ethanol.coskf -frac1 0.4 -s benzene.coskf -frac1 0.2 > job.sh
   "$AMSBIN/crsprep" -t LLE -temperature 298.15 -j step11b \
                     -s water.coskf -frac1 0.4 -s ethanol.coskf -frac1 0.4 -s benzene.coskf -frac1 0.2 >> job.sh

   ./job.sh
   echo "Step 11a"
   $AMSBIN/amsreport step11a.crskf ncomp
   $AMSBIN/amsreport step11a.crskf UNSTABLE

   echo "Step 11b"
   $AMSBIN/amsreport step11b.crskf ncomp
   $AMSBIN/amsreport step11b.crskf UNSTABLE
   $AMSBIN/amsreport step11b.crskf MOLAR-FRACTION-PHASE-I
   $AMSBIN/amsreport step11b.crskf MOLAR-FRACTION-PHASE-II
   $AMSBIN/amsreport step11b.crskf ACTIVITY-COEFFICIENT-PHASE-I
   $AMSBIN/amsreport step11b.crskf ACTIVITY-COEFFICIENT-PHASE-II


   # Step 12: Pure Compound Properties
   # ---------------------------------

   # In step 11 a QSPR (Quantitative Structure-Property Relationship) method is used
   # to estimate some pure compound properties. 
   # This QSPR method needs a SMILES string as input.

   echo "Step 12"
   "$AMSBIN"/prop_prediction --smiles "c1ccccc1" --boilingpoint -d

   # Step 13: Solvent Optimizations: Optimize Solubility
   # ---------------------------------------------------

   # In this step a solvent is optimized in order to maximize or minimize
   # the mole fraction solubility of a solid solute in the liquid mixture.

   echo "Step 13"
   "$AMSBIN"/solvent_opt -t SOLUBILITY -method COSMO-RS -temperature 273.15 -max \
                         -c "benzene.coskf" -solute -meltingpoint 278.7 -hfusion 2.37 \
                         -c "ethanol.coskf" -c "methanol.coskf" -c "water.coskf" -d > max_solubility
   grep benzene.coskf max_solubility
   grep " ethanol.coskf" max_solubility
   "$AMSBIN"/solvent_opt -t SOLUBILITY -method COSMO-RS -temperature 273.15 -min \
                         -c "benzene.coskf" -solute -meltingpoint 278.7 -hfusion 2.37 \
                         -c "ethanol.coskf" -c "methanol.coskf" -c "water.coskf" -d > min_solubility
   grep benzene.coskf min_solubility
   grep water.coskf min_solubility

   # Step 14: Solvent Optimizations: Optimize Liquid-Liquid Extraction
   # -----------------------------------------------------------------

   # In this step a mixture of immiscible solvents is optimized in order to maximize or minimize
   # the distribution ratio (D) of two solutes between the two liquid phases. 

   "$AMSBIN"/solvent_opt -t LLEXTRACTION -method COSMO-RS -multistart 10 -temperature 298.15 -max \
                         -c "water.coskf" -solute  -c "acetic_acid.coskf" -solute \
                         -c "benzene.coskf" -c "water.coskf" -c "2-hexanone.coskf" -c "ethanol.coskf" -d > max_lle

   echo "Step 14"
   "$AMSBIN/amsreport" CRSKF -r "OPT_LLEXTRACTION%obj#8.3f"

   echo "Ready"


Example: The COSMO-RS compound database
=======================================

"Download Database.run"

   #! /bin/sh

   # This example tries to do the same as in the COSMO-RS GUI Tutorial: The COSMO-RS compound database,
   # using scripts.
   # In many of the next examples fewer compounds are included than in the COSMO-RS GUI Tutorial.


   # First some .coskf files are copied to the location where the scripts are running.
   # These .coskf files are a sample of the full database.

   echo "Results"

   cp $AMSHOME/examples/COSMO-RS/Database/*coskf .

   rm -f job.sh
   touch job.sh
   chmod +x job.sh

   # 4.2 Octanol-Water partition coefficients (log P_OW)
   # ---------------------------------------------------

   "$AMSBIN/crsprep" -t LOGP -j t4.2 \
                     -c Methanol.coskf > job.sh
   ./job.sh
   echo "4.2"
   "$AMSBIN/amsreport" t4.2.crskf compounds-name
   "$AMSBIN/amsreport" t4.2.crskf logp



   # 4.3: Henry's law constants
   # --------------------------

   "$AMSBIN/crsprep" -t ACTIVITYCOEF -temperature 293.15 -densitysolvent 0.998 -j t4.3a \
                     -s Water.coskf \
                     -c Acetone.coskf -c Benzene.coskf -c Ethanol.coskf -c Methanol.coskf > job.sh
   ./job.sh
   echo "4.3a"
   "$AMSBIN/amsreport" t4.3a.crskf compounds-name
   "$AMSBIN/amsreport" t4.3a.crskf henry

   "$AMSBIN/crsprep" -s Acetone.coskf  -pvap 0.246 -tvap 293.15 -savecompound
   "$AMSBIN/crsprep" -s Benzene.coskf  -pvap 0.100 -tvap 293.15 -savecompound
   "$AMSBIN/crsprep" -s Ethanol.coskf  -pvap 0.059 -tvap 293.15 -savecompound
   "$AMSBIN/crsprep" -s Methanol.coskf -pvap 0.129 -tvap 293.15 -savecompound
   "$AMSBIN/crsprep" -s Water.coskf    -pvap 0.02536 -tvap 293.15 -savecompound

   "$AMSBIN/crsprep" -t ACTIVITYCOEF -temperature 293.15 -densitysolvent 0.998 -j t4.3b \
                     -s Water.coskf \
                     -c Benzene.coskf -c Ethanol.coskf -c Methanol.coskf > job.sh
   ./job.sh
   echo "4.3b"
   "$AMSBIN/amsreport" t4.3b.crskf henry


   # 4.4: Solubility of Vanillin in organic solvents
   # -----------------------------------------------

   "$AMSBIN/crsprep" -s Vanillin.coskf -meltingpoint 355 -hfusion 5.35 -savecompound
   "$AMSBIN/crsprep" -t PURESOLUBILITY -j t4.4 \
                     -s Vanillin.coskf \
                     -c Ethanol.coskf -c Methanol.coskf -c Water.coskf > job.sh
   ./job.sh
   echo "4.4"
   "$AMSBIN/amsreport" t4.4.crskf compounds-name
   "$AMSBIN/amsreport" t4.4.crskf solubility-x
   "$AMSBIN/amsreport" t4.4.crskf solubility-m

   # 4.5: Binary mixture of Methanol and Hexane
   # ------------------------------------------

   "$AMSBIN/crsprep" -s Methanol.coskf -pvap 0.845 -tvap 333.15 -savecompound
   "$AMSBIN/crsprep" -s Hexane.coskf   -pvap 0.77  -tvap 333.15 -savecompound
   "$AMSBIN/crsprep" -t BINMIXCOEF -temperature 333.15 -n 100 -j t4.5a \
                     -s Methanol.coskf \
                     -s Hexane.coskf > job.sh
   ./job.sh
   echo "4.5a"
   "$AMSBIN/amsreport" t4.5a.crskf compounds-name
   "$AMSBIN/amsreport" t4.5a.crskf molar-fraction
   "$AMSBIN/amsreport" t4.5a.crskf pressure
   "$AMSBIN/amsreport" t4.5a.crskf miscibility-gap
   "$AMSBIN/amsreport" t4.5a.crskf miscibility-gap-x
   "$AMSBIN/amsreport" t4.5a.crskf miscibility-gap-a

   "$AMSBIN/crsprep" -s Methanol.coskf -pvap 1.01325 -tvap 337.8 -savecompound
   "$AMSBIN/crsprep" -s Hexane.coskf   -pvap 1.01325 -tvap 342   -savecompound
   "$AMSBIN/crsprep" -t BINMIXCOEF -pressure 1.01325 -iso isobar -n 100 -j t4.5b \
                     -s Methanol.coskf \
                     -s Hexane.coskf > job.sh
   ./job.sh
   echo "4.5b"
   "$AMSBIN/amsreport" t4.5b.crskf molar-fraction
   "$AMSBIN/amsreport" t4.5b.crskf temperature
   "$AMSBIN/amsreport" t4.5b.crskf miscibility-gap
   "$AMSBIN/amsreport" t4.5b.crskf miscibility-gap-x
   "$AMSBIN/amsreport" t4.5b.crskf miscibility-gap-a

   # 4.6: Large infinite dilution activity coefficients in Water
   # -----------------------------------------------------------

   "$AMSBIN/crsprep" -t ACTIVITYCOEF -temperature 298.15 -j t4.6 \
                     -s Water.coskf \
                     -c Benzene.coskf > job.sh
   ./job.sh
   echo "4.6"
   "$AMSBIN/amsreport" t4.6.crskf compounds-name
   "$AMSBIN/amsreport" t4.6.crskf activity-coefficient


   # 4.7: Parametrization of ADF COSMO-RS: solvation energies,
   # vapor pressures, partition coefficients
   # ---------------------------------------------------------

   cat << eor > small.compoundlist
   Hexane.coskf
   Methanol.coskf
   Ethanol.coskf
   Acetone.coskf
   Benzene.coskf
   Water.coskf
   eor

   "$AMSBIN/crsprep" -t ACTIVITYCOEF -temperature 298.15 -densitysolvent 0.997 -j t4.7a \
                     -inputpurevap 0 \
                     -s Water.coskf \
                     -c small.compoundlist > job.sh
   ./job.sh
   echo "4.7a"
   "$AMSBIN/amsreport" t4.7a.crskf compounds-name
   "$AMSBIN/amsreport" t4.7a.crskf gibbs-energy-solvation

   "$AMSBIN/crsprep" -t PUREVAPORPRESSURE -temperature 298.15 -j t4.7b \
                     -c small.compoundlist -inputpurevap 0 > job.sh
   ./job.sh
   echo "4.7b"
   "$AMSBIN/amsreport" t4.7b.crskf compounds-name
   "$AMSBIN/amsreport" t4.7b.crskf vapor-pressure

   "$AMSBIN/crsprep" -t LOGP -j t4.7c -c small.compoundlist > job.sh
   ./job.sh
   echo "4.7c Octanol/Water"
   "$AMSBIN/amsreport" t4.7c.crskf compounds-name
   "$AMSBIN/amsreport" t4.7c.crskf logp

   "$AMSBIN/crsprep" -t LOGP -preset 5 -j t4.7d -c small.compoundlist > job.sh
   ./job.sh
   echo "4.7d Hexane/Water"
   "$AMSBIN/amsreport" t4.7d.crskf logp

   "$AMSBIN/crsprep" -t LOGP -preset 3 -j t4.7e -c small.compoundlist > job.sh
   ./job.sh
   echo "4.7e Benzene/Water"
   "$AMSBIN/amsreport" t4.7e.crskf logp

   "$AMSBIN/crsprep" -t LOGP -preset 4 -j t4.7f -c small.compoundlist > job.sh
   ./job.sh
   echo "4.7f Ether/Water"
   "$AMSBIN/amsreport" t4.7f.crskf logp


   # 4.8: COSMO-SAC 2013-ADF
   # -----------------------

   "$AMSBIN/crsprep" -t PURESIGMAPROFILE -method COSMOSAC2013 -c Water.coskf \
                     -c Ethanol.coskf -j t4.8a > job.sh
   ./job.sh
   echo "4.8a"
   "$AMSBIN/amsreport" t4.8a.crskf sigma
   "$AMSBIN/amsreport" t4.8a.crskf sigma-profile
   "$AMSBIN/amsreport" t4.8a.crskf sigma-profile-hb

   "$AMSBIN/crsprep" -s Methanol.coskf -density 0.7918  -savecompound
   "$AMSBIN/crsprep" -s Ethanol.coskf  -density 0.789  -savecompound
   "$AMSBIN/crsprep" -s Acetone.coskf  -density 0.791  -savecompound

   "$AMSBIN/crsprep" -t LOGP -method COSMOSAC2013 -j t4.8b \
                     -c Methanol.coskf -c Ethanol.coskf -c Acetone.coskf > job.sh
   ./job.sh
   echo "4.8b Octanol/Water"
   "$AMSBIN/amsreport" t4.8b.crskf compounds-name
   "$AMSBIN/amsreport" t4.8b.crskf logp

   "$AMSBIN/crsprep" -t LOGP -method COSMOSAC2013 -preset 5 -j t4.8c \
                     -c Methanol.coskf -c Ethanol.coskf -c Acetone.coskf > job.sh
   ./job.sh
   echo "4.8c Hexane/Water"
   "$AMSBIN/amsreport" t4.8c.crskf logp

   "$AMSBIN/crsprep" -t LOGP -method COSMOSAC2013 -preset 3 -j t4.8d \
                     -c Methanol.coskf -c Ethanol.coskf -c Acetone.coskf > job.sh
   ./job.sh
   echo "4.8d Benzene/Water"
   "$AMSBIN/amsreport" t4.8d.crskf logp

   "$AMSBIN/crsprep" -t LOGP -method COSMOSAC2013 -preset 4 -j t4.8e \
                     -c Methanol.coskf -c Ethanol.coskf -c Acetone.coskf > job.sh
   ./job.sh
   echo "4.8e Ether/Water"
   "$AMSBIN/amsreport" t4.8e.crskf logp

   "$AMSBIN/crsprep" -s Acetone.coskf -density 0.791 -pvap 3.7     -tvap 373.15 -savecompound
   "$AMSBIN/crsprep" -s Water.coskf   -density 0.997 -pvap 1.01325 -tvap 373.15 -savecompound

   "$AMSBIN/crsprep" -t BINMIXCOEF -method COSMOSAC2013 -temperature 373.15 -n 20 -j t4.8f \
                     -s Acetone.coskf \
                     -s Water.coskf > job.sh
   ./job.sh
   echo "4.8f"
   "$AMSBIN/amsreport" t4.8f.crskf molar-fraction
   "$AMSBIN/amsreport" t4.8f.crskf vapor-pressure
   "$AMSBIN/amsreport" t4.8f.crskf pressure

   echo "Ready"


Example: pKa values
===================

"Download pKa.run"

   #! /bin/sh

   # This example tries to do the same as in the COSMO-RS GUI Tutorial: pKa values,
   # using scripts
   # First some .coskf files are copied to the location where the scripts are running,
   # next the jobs are prepared and the reports are made.
   # Check the COSMO-RS GUI Tutorial: pKa values to see what to do with the results.

   echo "Results"

   rm -f job.sh
   cp $AMSHOME/examples/COSMO-RS/pKa/*.coskf .
   cp $AMSHOME/examples/COSMO-RS/pKa/*compoundlist .

   touch job.sh
   chmod +x job.sh

   echo "Acids"
   "$AMSBIN/crsprep" -t ACTIVITYCOEF -j t5.1a \
                     -c tutoral5.1_acid.compoundlist -no_pdh > job.sh
   ./job.sh
   "$AMSBIN/amsreport" t5.1a.crskf compounds-name
   "$AMSBIN/amsreport" t5.1a.crskf Activity-Coefficient
   "$AMSBIN/amsreport" t5.1a.crskf Gibbs-energy-solvation
   "$AMSBIN/amsreport" t5.1a.crskf Gibbs-energy-solute

   "$AMSBIN/crsprep" -t ACTIVITYCOEF -j t5.1b \
                     -c tutoral5.1_base.compoundlist -no_pdh > job.sh
   ./job.sh
   "$AMSBIN/amsreport" t5.1b.crskf compounds-name
   "$AMSBIN/amsreport" t5.1b.crskf Activity-Coefficient
   "$AMSBIN/amsreport" t5.1b.crskf Gibbs-energy-solvation
   "$AMSBIN/amsreport" t5.1b.crskf Gibbs-energy-solute

   echo "Ready"


Example: Polymers
=================

"Download Polymers.run"

   #! /bin/sh

   # This example tries to do the same as in the COSMO-RS GUI Tutorial: Polymers,
   # using scripts.

   # First some .coskf files are copied to the location where the scripts are running.
   # Some of the .coskf files are a sample of the full polymer database ADFCRS-POLYMERS-2019.
   # In the first part of the example crsprep is used to set pure compound parameters.
   # Pure compound densities are required for every species in a calculation involving any polymers.
   # For some pure compounds the VPM1 vapor pressure equation is set including vapor pressure coefficients.

   echo "Results"

   cp $AMSHOME/examples/COSMO-RS/Database/*coskf .
   cp $AMSHOME/examples/COSMO-RS/Polymers/*coskf .

   "$AMSBIN/crsprep" -c Benzene.coskf -density 0.876 -savecompound
   "$AMSBIN/crsprep" -c Water.coskf -density 1.0 -savecompound
   "$AMSBIN/crsprep" -c Methanol.coskf -density 0.792 -savecompound \
                     -vp_equation VPM1 -vp_params "-7057.597287 -9.936895562 0.00608530790 77.10002032 0"
   "$AMSBIN/crsprep" -c Hexane.coskf -density 0.655 -savecompound \
                     -vp_equation VPM1 -vp_params "-5575.417318 -6.612402250 0.00437376138 53.36969532 0"

   rm -f job.sh
   touch job.sh
   chmod +x job.sh

   "$AMSBIN/crsprep" -t ACTIVITYCOEF -j Polymers.1 \
                     -s "Poly(ethylene).coskf" -frac1 0.5 -s Benzene.coskf -frac1 0.5 \
                     -massfraction > job.sh
   ./job.sh
   echo "Polymers.1"
   "$AMSBIN/amsreport" Polymers.1.crskf compounds-name Flory-Huggins WF-activity-coefficient

   "$AMSBIN/crsprep" -t VAPORPRESSURE -temperature 298.15 -temperature 398.15 -n 10 -j Polymers.2 \
                     -s "Poly(dimethylsiloxane).coskf" -frac1 0.5 -s Methanol.coskf -frac1 0.25 \
                     -s Hexane.coskf -frac1 0.25 \
                     -massfraction > job.sh
   ./job.sh
   echo "Polymers.2"
   "$AMSBIN/amsreport" Polymers.2.crskf compounds-name temperature pressure

   "$AMSBIN/crsprep" -t LOGP -preset 0 -j Polymers.3 \
                     -s "Poly(ethylene).coskf" -s Water.coskf \
                     -c Methanol.coskf > job.sh
   ./job.sh
   echo "Polymers.3"
   "$AMSBIN/amsreport" Polymers.3.crskf logp

   "$AMSBIN/crsprep" -t PURESOLUBILITY -temperature 398.15 -temperature 498.15 -n 10 -j Polymers.4 \
                     -s Hexane.coskf -solphase Gas -pressure 1.01325 \
                     -c "Poly(styrene).coskf" > job.sh
   ./job.sh
   echo "Polymers.4"
   "$AMSBIN/amsreport" Polymers.4.crskf solubility-g

   "$AMSBIN/crsprep" -t BINMIXCOEF -method COSMOSAC2013 -j Polymers.5 \
                     -s "Poly(ethyl_ethylene).coskf" -s Benzene.coskf \
                     -massfraction > job.sh
   ./job.sh
   echo "Polymers.5"
   "$AMSBIN/amsreport" Polymers.5.crskf polymer-fraction Flory-Huggins

   echo "Ready"
