Scripting Examples¶
COSMO result files¶
Sample directory: $ADFHOME/examples/crs/Tutorial1
This example tries to do the same as in the COSMO-RS GUI Tutorial: COSMO result files, using scripts.
In the first part of the example you will find how to use adfprep to construct an ADF COSMO results file. The template ADFCRS will perform a gas phase geometry optimization (for water, in this case), and next a COSMO calculation at the gas phase optimized geometry. The result file adfwater.coskf, which is an ADF COSMO result file, can be used as input for a COSMO-RS calculation.
cat << eor > water.xyz
3
H 0.00000000 0.77121000 0.18071000
O 0.00000000 -0.00000000 -0.36142000
H 0.00000000 -0.77121000 0.18071000
eor
"$ADFBIN/adfprep" -t ADFCRS -m water.xyz -j adfwater >job.sh
chmod +x job.sh
./job.sh
"$ADFBIN/adfreport" adfwater.t21 geometry-a*
"$ADFBIN/adfreport" adfwater.coskf energies
In the second part of the example a MOPAC COSMO result file is 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. The result file mopacwaterresults/mopac.coskf is a MOPAC COSMO result file, which can be used as input for a COSMO-RS calculation.
"$ADFBIN/adfprep" -t MOPAC-GO -m water.xyz -g "mopac.solvation.enabled 1" -g "mopac.solvation.solvent.name CRS" -j mopacwater >job2.sh
chmod +x job2.sh
./job2.sh
"$ADFBIN/adfreport" mopacwater.results geometry-a*
"$ADFBIN/adfreport" mopacwater.results/mopac.coskf energies
COSMO-RS parameters and analysis¶
Sample directory: $ADFHOME/examples/crs/Tutorial2
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 $ADFHOME/examples/crs/Tutorial2/benzene.coskf .
cp $ADFHOME/examples/crs/Tutorial2/ethanol.coskf .
cp $ADFHOME/examples/crs/Tutorial2/methanol.coskf .
cp $ADFHOME/examples/crs/Tutorial2/water.coskf .
Set pure compound parameters¶
In the first part of the example you will find how to use crsprep to set pure compound parameters, in this case to set the number of ring atoms for the benzene molecule, which has 6 ring atoms. The file benzene.coskf is changed, such that it contains the value “6” for the number of ring compounds.
"$ADFBIN/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.
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 (\(\sigma\)-potential) of the four pure compounds (result file step7.crskf). With adfreport one can get the calculated sigma profile or sigma potential from the .crskf file on standard output.
"$ADFBIN/crsprep" -t PURESIGMAPROFILE -c tutorial2.compoundlist -j step6 > job.sh
"$ADFBIN/crsprep" -t PURESIGMAPOTENTIAL -c tutorial2.compoundlist -j step7 >> job.sh
chmod +x job.sh
./job.sh
echo "Results"
"$ADFBIN/adfreport" step6.crskf sigma
"$ADFBIN/adfreport" step6.crskf sigma-profile
"$ADFBIN/adfreport" step6.crskf sigma-profile-hb
"$ADFBIN/adfreport" step7.crskf sigma-potential
echo "Ready"
COSMO-RS properties¶
Sample directory: $ADFHOME/examples/crs/Tutorial3
This example tries to do the same as COSMO-RS GUI Tutorial: properties, using scripts.
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.
cp $ADFHOME/examples/crs/Tutorial2/benzene.coskf .
cp $ADFHOME/examples/crs/Tutorial2/ethanol.coskf .
cp $ADFHOME/examples/crs/Tutorial2/methanol.coskf .
cp $ADFHOME/examples/crs/Tutorial2/water.coskf .
"$ADFBIN/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).
"$ADFBIN/crsprep" -t PUREVAPORPRESSURE -j step2a \
-c methanol.coskf > job.sh
"$ADFBIN/crsprep" -t PUREVAPORPRESSURE -temperature 273.15 -temperature 373.15 \
-j step2b \
-c methanol.coskf >> job.sh
./job.sh
echo "Step 2a"
"$ADFBIN/adfreport" step2a.crskf temperature
"$ADFBIN/adfreport" step2a.crskf pressure
"$ADFBIN/adfreport" step2a.crskf enthalpy-vaporization
echo "Step 2b"
"$ADFBIN/adfreport" step2b.crskf temperature
"$ADFBIN/adfreport" step2b.crskf pressure
"$ADFBIN/adfreport" 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.
"$ADFBIN/crsprep" -t BOILINGPOINT -pressure 0.101325 -pressure 1.01325 -j step3 \
-c methanol.coskf -frac1 0.5 \
-c ethanol.coskf -frac1 0.5 > job.sh
./job.sh
echo "Step 3"
"$ADFBIN/adfreport" step3.crskf temperature
"$ADFBIN/adfreport" step3.crskf pressure
Step 4: Flash point¶
In step 4 of the example the flash point of a mixture of ethanol and water is calculated (result file step4.crskf). This mixture consist of 44.2% mass fraction methanol and 55.8% mass fraction ethanol. For a flash point calculation the pure compound flash points are needed as input, since COSMO-RS does not predict pure compound flash points. For pure ethanol a flash point of 286 K is saved in the file ethanol.coskf.
"$ADFBIN/crsprep" -c ethanol.coskf -flashpoint 286 -savecompound
"$ADFBIN/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"
$ADFBIN/adfreport step4.crskf temperature
Step 5: Activity coefficients, Henry coefficients, Solvation free energies¶
In step 5 of the example the infinite diluted solutes benzene, methanol, and ethanol are calculated in the solvent water (result file step5.crskf). Activity coefficients, Henry coefficients and solvation free energies will be calculated. One one should include -s flag for water, since it is the solvent, and considered here to be a special compound.
"$ADFBIN/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"
"$ADFBIN/adfreport" step5.crskf Activity-Coefficient
"$ADFBIN/adfreport" step5.crskf Henry
"$ADFBIN/adfreport" step5.crskf Gibbs-energy-solvation
Step 6: Partition coefficients (log P)¶
In step 6 of the example the partition coefficients of infinitely diluted solutes in a mixture of two immiscible solvents are calculated. In step 6a the default Octanol/Water partition coefficients are calculated (default -preset 2) (result file step6a.crskf). In step 6b a user defined (-preset 0) Benzene/Water partition coefficients are calculated (result file step6b.crskf). In this case one should include -s flag for benzene and water, since these are the two immiscible solvents, and considered here to be the special compounds. The order of the compounds benzene and water is important, because the molar volume of phase 1 (benzene) divided by the the molar volume of phase 2 (water) is given with the flag -volumequotient.
"$ADFBIN/crsprep" -t LOGP -j step6a \
-c benzene.coskf -c ethanol.coskf -c methanol.coskf > job.sh
"$ADFBIN/crsprep" -t LOGP -preset 0 -volumequotient 4.93 -j step6b \
-s benzene.coskf -s water.coskf \
-c ethanol.coskf -c methanol.coskf >> job.sh
./job.sh
echo "Step 6a octanol/water"
"$ADFBIN/adfreport" step6a.crskf logp
echo "Step 6b benzene/water"
"$ADFBIN/adfreport" step6b.crskf logp
Step 7: Solubility¶
In step 7 of the example the solubility of a compound is calculated. The solute can either be a liquid, solid, or gas. First some pure compound properties for benzene are set: the melting point, enthalpy of fusion, and the boiling point (file benzene.coskf).
"$ADFBIN/crsprep" -c benzene.coskf -meltingpoint 278.7 -hfusion 2.37 -savecompound
"$ADFBIN/crsprep" -c benzene.coskf -tvap 353.3 -pvap 1.01325 -savecompound
In step 7a the solubility of benzene in water is calculated for a range of temperatures ranging from 273.15 K to 373.15 K in 10 steps (result file step7a.crskf). If the template PURESOLUBILITY is used, the special compound is the solute, benzene in this case. Below 278.7 K, benzene is a solid. This will be taken into account, since the melting point and enthalpy of fusion are present on the file benzene.coskf. At higher temperatures benzene is assumed to be a liquid. Note that tn this calcuation above the normal boiling point of benzene the vapor pressure of benzene will be higher than 1.01325 bar.
"$ADFBIN/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.
"$ADFBIN/crsprep" -t SOLUBILITY -temperature 273.15 -temperature 283.15 \
-densitysolvent 1.0 -j step7b \
-s water.coskf \
-c benzene.coskf >> job.sh
In step 7c again the solubility of benzene in water is calculated for a range of temperatures above the boiling point of benzene (result file step7c.crs) using the template SOLUBILITY. If the template SOLUBILITY is used, the special compound is the solvent, water in this case. For the density of water 1.0 kg/L is used. For the vapor pressure of benzene 1.01325 bar is used.
"$ADFBIN/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.
"$ADFBIN/crsprep" -t ACTIVITYCOEF -temperature 363.15 -densitysolvent 1.0 -j step7d \
-s water.coskf \
-c benzene.coskf >> job.sh
Next the job.sh is run which will produce the crskf files, and a report is made for all calculations in step 7.
./job.sh
echo "Step 7a"
"$ADFBIN/adfreport" step7a.crskf solubility-x
echo "Step 7b"
"$ADFBIN/adfreport" step7b.crskf solubility-g
echo "Step 7c"
"$ADFBIN/adfreport" step7c.crskf solubility-m
echo "Step 7d"
"$ADFBIN/adfreport" step7d.crskf henry
Step 8: Binary mixtures VLE/LLE¶
In step 8 phase diagrams of a mixture of two components are be calculated with the template BINMIXCOEF. Exactly two compound should be given. In step 8a of the example a binary mixture of water and methanol is calculated at 298.14 K (result file step8a.crskf).
"$ADFBIN/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.
"$ADFBIN/crsprep" -t BINMIXCOEF -temperature 322.45 -j step8b \
-s water.coskf -tvap 322.45 -pvap 0.123416 \
-s ethanol.coskf -tvap 322.45 -pvap 0.294896 >> job.sh
In step 8c of the example a binary mixture of water and benzene is calculated at 323.15 K (result file step8c.crskf). Water and benzene do not mix very well. In this case a a liquid-liquid equilibrium (LLE) will be calculated. The number of mixtures for which the binary mixture is calculated should be not too small, otherwise the properties of the 2 immiscible liquid phases will not be so accurate. In this case for the number of mixtures 100 is chosen. The actual number of mixtures is 5 more, thus 105 in this case.
"$ADFBIN/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.
"$ADFBIN/crsprep" -t BINMIXCOEF -iso isobar -pressure 1.01325 -j step8d \
-s methanol.coskf -tvap 338 -pvap 1.01325 \
-s ethanol.coskf -tvap 351 -pvap 1.01325 >> job.sh
Next the job.sh is run which will produce the crskf files, and a report is made for all calculations in step 8.
./job.sh
echo "Step 8a"
"$ADFBIN/adfreport" step8a.crskf molar-fraction
"$ADFBIN/adfreport" step8a.crskf excess-g
"$ADFBIN/adfreport" step8a.crskf excess-h
echo "Step 8b"
"$ADFBIN/adfreport" step8b.crskf vapor-pressure
echo "Step 8c"
"$ADFBIN/adfreport" step8c.crskf miscibility-gap
"$ADFBIN/adfreport" step8c.crskf miscibility-gap-x
"$ADFBIN/adfreport" step8c.crskf miscibility-gap-a
echo "Step 8d"
"$ADFBIN/adfreport" step8d.crskf temperature
Step 9: Ternary mixtures VLE/LLE¶
In step 9 phase diagrams of a mixture of three components are be calculated with the template TERNARYMIX. Exactly three compound should be given. For convenience first some pure compound properties (normal boiling points) are saved to the .coskf files.
"$ADFBIN/crsprep" -c water.coskf -tvap 373.15 -pvap 1.01325 -savecompound
"$ADFBIN/crsprep" -c methanol.coskf -tvap 338 -pvap 1.01325 -savecompound
"$ADFBIN/crsprep" -c ethanol.coskf -tvap 351 -pvap 1.01325 -savecompound
"$ADFBIN/crsprep" -c benzene.coskf -tvap 353.3 -pvap 1.01325 -savecompound
In step 9a of the example a ternary mixture of methanol, ethanol, and benzene is calculated at 343.15 K (result file step9a.crskf). In step 9b of the example a ternary mixture of water, ethanol, and benzene is calculated at a constant total vapor pressure (-iso isobar) of 1.01325 bar (result file step9b.crskf). In step 9b a miscibility gap of the ternary mixture will be calculated. In this case, within the miscibility gap there are two immiscible phases of the liquid in equilibrium. The composition of the two phases, which are in equilibrium, can be found at the end points of the tie lines, that are calculated.
"$ADFBIN/crsprep" -t TERNARYMIX -temperature 343.15 -j step9a \
-s methanol.coskf -s ethanol.coskf -s benzene.coskf > job.sh
"$ADFBIN/crsprep" -t TERNARYMIX -iso isobar -pressure 1.01325 -j step9b \
-s water.coskf -s ethanol.coskf -s benzene.coskf >> job.sh
./job.sh
echo "Step 9a"
"$ADFBIN/adfreport" step9a.crskf molar-fraction
"$ADFBIN/adfreport" step9a.crskf pressure
"$ADFBIN/adfreport" step9a.crskf miscibility-gap
echo "Step 9b"
"$ADFBIN/adfreport" step9b.crskf miscibility-gap
"$ADFBIN/adfreport" step9b.crskf tie-lines-x
"$ADFBIN/adfreport" step9b.crskf temperature
Step 10: A composition line between solvents s1 and s2¶
In step 10 a phase diagram of a mixture of two solvents, which both are mixtures, is calculated with the template COMPOSITIONLINE. In this step one of the tie lines of the ternary mixture of water, ethanol, and benzene of step 9b will be investigated in more detail. Note that here the .coskf files are used in which the normal boiling points were saved to (in step 9). The mixture will be calculated for a list of molar (or mass) fractions of the solvents between zero and one, and the compositions of solvent 1 and solvent 2 are linearly interpolated. In this case solvent 1 consists of 0.3 molar fraction ethanol and 0.7 molar fraction benzene, and solvent 2 consists of 0.9 molar fraction water and 0.1 molar fraction ethanol. In step 10a of the example this mixture is calculated at a constant total vapor pressure (-iso isobar) of 1.01325 bar (result file step10a.crskf). In step 10b of the example this mixture is calculated at 341.05 K (result file step10b.crskf). Why this temperature was chosen can be found in step 10 of COSMO-RS GUI Tutorial: properties,
"$ADFBIN/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
"$ADFBIN/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"
$ADFBIN/adfreport step10a.crskf ncomp
$ADFBIN/adfreport step10a.crskf frac1
$ADFBIN/adfreport step10a.crskf frac2
$ADFBIN/adfreport step10a.crskf solvent-fraction
$ADFBIN/adfreport step10a.crskf molar-fraction
$ADFBIN/adfreport step10a.crskf activity-coefficient
echo "Step 10b"
$ADFBIN/adfreport step10b.crskf Gibbs-energy-mixing
The COSMO-RS compound database¶
Sample directory: $ADFHOME/examples/crs/Tutorial4
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.
cp $ADFHOME/examples/crs/Tutorial4/*coskf .
4.2 Octanol-Water partition coefficients (log POW )¶
"$ADFBIN/crsprep" -t LOGP -j t4.2 \
-c Methanol.coskf > job.sh
./job.sh
echo "4.2"
"$ADFBIN/adfreport" t4.2.crskf compounds-name
"$ADFBIN/adfreport" t4.2.crskf logp
4.3: Henry’s law constants¶
"$ADFBIN/crsprep" -t ACTIVITYCOEF -temperature 293.15 -densitysolvent 0.998 -j t4.3a \
-s Water.coskf \
-c Acetone.coskf -c Benzene.coskf -c Ethanol.coskf \
-c Methanol.coskf > job.sh
./job.sh
echo "4.3a"
"$ADFBIN/adfreport" t4.3a.crskf compounds-name
"$ADFBIN/adfreport" t4.3a.crskf henry
"$ADFBIN/crsprep" -s Acetone.coskf -pvap 0.246 -tvap 293.15 -savecompound
"$ADFBIN/crsprep" -s Benzene.coskf -pvap 0.100 -tvap 293.15 -savecompound
"$ADFBIN/crsprep" -s Ethanol.coskf -pvap 0.059 -tvap 293.15 -savecompound
"$ADFBIN/crsprep" -s Methanol.coskf -pvap 0.129 -tvap 293.15 -savecompound
"$ADFBIN/crsprep" -s Water.coskf -pvap 0.02536 -tvap 293.15 -savecompound
"$ADFBIN/crsprep" -t ACTIVITYCOEF -temperature 293.15 -densitysolvent 0.998 -j t4.3b \
-s Water.coskf \
-c Benzene.coskf -c Ethanol.coskf -c Methanol.coskf > job.sh
./job.sh
echo "4.3b"
"$ADFBIN/adfreport" t4.3b.crskf henry
4.4: Solubility of Vanillin in organic solvents¶
"$ADFBIN/crsprep" -s Vanillin.coskf -meltingpoint 355 -hfusion 5.35 -savecompound
"$ADFBIN/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"
"$ADFBIN/adfreport" t4.4.crskf compounds-name
"$ADFBIN/adfreport" t4.4.crskf solubility-x
"$ADFBIN/adfreport" t4.4.crskf solubility-m
4.5: Binary mixture of Methanol and Hexane¶
"$ADFBIN/crsprep" -s Methanol.coskf -pvap 0.845 -tvap 333.15 -savecompound
"$ADFBIN/crsprep" -s Hexane.coskf -pvap 0.77 -tvap 333.15 -savecompound
"$ADFBIN/crsprep" -t BINMIXCOEF -temperature 333.15 -n 100 -j t4.5a \
-s Methanol.coskf \
-s Hexane.coskf > job.sh
./job.sh
echo "4.5a"
"$ADFBIN/adfreport" t4.5a.crskf compounds-name
"$ADFBIN/adfreport" t4.5a.crskf molar-fraction
"$ADFBIN/adfreport" t4.5a.crskf pressure
"$ADFBIN/adfreport" t4.5a.crskf miscibility-gap
"$ADFBIN/adfreport" t4.5a.crskf miscibility-gap-x
"$ADFBIN/adfreport" t4.5a.crskf miscibility-gap-a
"$ADFBIN/crsprep" -s Methanol.coskf -pvap 1.01325 -tvap 337.8 -savecompound
"$ADFBIN/crsprep" -s Hexane.coskf -pvap 1.01325 -tvap 342 -savecompound
"$ADFBIN/crsprep" -t BINMIXCOEF -pressure 1.01325 -iso isobar -n 100 -j t4.5b \
-s Methanol.coskf \
-s Hexane.coskf > job.sh
./job.sh
echo "4.5b"
"$ADFBIN/adfreport" t4.5b.crskf molar-fraction
"$ADFBIN/adfreport" t4.5b.crskf temperature
"$ADFBIN/adfreport" t4.5b.crskf miscibility-gap
"$ADFBIN/adfreport" t4.5b.crskf miscibility-gap-x
"$ADFBIN/adfreport" t4.5b.crskf miscibility-gap-a
4.6: Large infinite dilution activity coefficients in Water¶
"$ADFBIN/crsprep" -t ACTIVITYCOEF -temperature 298.15 -j t4.6 \
-s Water.coskf \
-c Benzene.coskf > job.sh
./job.sh
echo "4.6"
"$ADFBIN/adfreport" t4.6.crskf compounds-name
"$ADFBIN/adfreport" t4.6.crskf activity-coefficient
4.7: Parametrization of ADF COSMO-RS: solvation energies, vapor pressures, partition coefficients¶
cat << eor > small.compoundlist
Hexane.coskf
Methanol.coskf
Ethanol.coskf
Acetone.coskf
Benzene.coskf
Water.coskf
eor
"$ADFBIN/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"
"$ADFBIN/adfreport" t4.7a.crskf compounds-name
"$ADFBIN/adfreport" t4.7a.crskf gibbs-energy-solvation
"$ADFBIN/crsprep" -t PUREVAPORPRESSURE -temperature 298.15 -j t4.7b \
-c small.compoundlist -inputpurevap 0 > job.sh
./job.sh
echo "4.7b"
"$ADFBIN/adfreport" t4.7b.crskf compounds-name
"$ADFBIN/adfreport" t4.7b.crskf vapor-pressure
"$ADFBIN/crsprep" -t LOGP -j t4.7c -c small.compoundlist > job.sh
./job.sh
echo "4.7c Octanol/Water"
"$ADFBIN/adfreport" t4.7c.crskf compounds-name
"$ADFBIN/adfreport" t4.7c.crskf logp
"$ADFBIN/crsprep" -t LOGP -preset 5 -j t4.7d -c small.compoundlist > job.sh
./job.sh
echo "4.7d Hexane/Water"
"$ADFBIN/adfreport" t4.7d.crskf logp
"$ADFBIN/crsprep" -t LOGP -preset 3 -j t4.7e -c small.compoundlist > job.sh
./job.sh
echo "4.7e Benzene/Water"
"$ADFBIN/adfreport" t4.7e.crskf logp
"$ADFBIN/crsprep" -t LOGP -preset 4 -j t4.7f -c small.compoundlist > job.sh
./job.sh
echo "4.7f Ether/Water"
"$ADFBIN/adfreport" t4.7f.crskf logp
4.8: COSMO-SAC 2013-ADF¶
"$ADFBIN/crsprep" -t PURESIGMAPROFILE -m COSMOSAC2013 -c Water.coskf \
-c Ethanol.coskf -j t4.8a > job.sh
./job.sh
echo "4.8a"
"$ADFBIN/adfreport" t4.8a.crskf sigma
"$ADFBIN/adfreport" t4.8a.crskf sigma-profile
"$ADFBIN/adfreport" t4.8a.crskf sigma-profile-hb
"$ADFBIN/crsprep" -s Methanol.coskf -density 0.7918 -savecompound
"$ADFBIN/crsprep" -s Ethanol.coskf -density 0.789 -savecompound
"$ADFBIN/crsprep" -s Acetone.coskf -density 0.791 -savecompound
"$ADFBIN/crsprep" -t LOGP -m COSMOSAC2013 -j t4.8b -c Methanol.coskf \
-c Ethanol.coskf -c Acetone.coskf > job.sh
./job.sh
echo "4.8b Octanol/Water"
"$ADFBIN/adfreport" t4.8b.crskf compounds-name
"$ADFBIN/adfreport" t4.8b.crskf logp
"$ADFBIN/crsprep" -t LOGP -m COSMOSAC2013 -preset 5 -j t4.8c -c Methanol.coskf \
-c Ethanol.coskf -c Acetone.coskf > job.sh
./job.sh
echo "4.8c Hexane/Water"
"$ADFBIN/adfreport" t4.8c.crskf logp
"$ADFBIN/crsprep" -t LOGP -m COSMOSAC2013 -preset 3 -j t4.8d -c Methanol.coskf \
-c Ethanol.coskf -c Acetone.coskf > job.sh
./job.sh
echo "4.8d Benzene/Water"
"$ADFBIN/adfreport" t4.8d.crskf logp
"$ADFBIN/crsprep" -t LOGP -m COSMOSAC2013 -preset 4 -j t4.8e -c Methanol.coskf \
-c Ethanol.coskf -c Acetone.coskf > job.sh
./job.sh
echo "4.8e Ether/Water"
"$ADFBIN/adfreport" t4.8e.crskf logp
"$ADFBIN/crsprep" -s Acetone.coskf -density 0.791 \
-pvap 3.7 -tvap 373.15 -savecompound
"$ADFBIN/crsprep" -s Water.coskf -density 0.997 \
-pvap 1.01325 -tvap 373.15 -savecompound
"$ADFBIN/crsprep" -t BINMIXCOEF -m COSMOSAC2013 -temperature 373.15 -n 20 -j t4.8f \
-s Acetone.coskf \
-s Water.coskf > job.sh
./job.sh
echo "4.8f"
"$ADFBIN/adfreport" t4.8f.crskf molar-fraction
"$ADFBIN/adfreport" t4.8f.crskf vapor-pressure
"$ADFBIN/adfreport" t4.8f.crskf pressure
pKa values¶
Sample directory: $ADFHOME/examples/crs/Tutorial5
This example tries to do the same as in the COSMO-RS GUI Tutorial: pKa values, 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 what to do with the results.
cp $ADFHOME/examples/crs/Tutorial5/*.coskf .
cp $ADFHOME/examples/crs/Tutorial5/*compoundlist .
echo "Acids"
"$ADFBIN/crsprep" -t ACTIVITYCOEF -j t5.1a \
-c tutoral5.1_acid.compoundlist > job.sh
./job.sh
"$ADFBIN/adfreport" t5.1a.crskf compounds-name
"$ADFBIN/adfreport" t5.1a.crskf Activity-Coefficient
"$ADFBIN/adfreport" t5.1a.crskf Gibbs-energy-solvation
"$ADFBIN/adfreport" t5.1a.crskf Gibbs-energy-solute
echo "Bases"
"$ADFBIN/crsprep" -t ACTIVITYCOEF -j t5.1b \
-c tutoral5.1_base.compoundlist > job.sh
./job.sh
"$ADFBIN/adfreport" t5.1b.crskf compounds-name
"$ADFBIN/adfreport" t5.1b.crskf Activity-Coefficient
"$ADFBIN/adfreport" t5.1b.crskf Gibbs-energy-solvation
"$ADFBIN/adfreport" t5.1b.crskf Gibbs-energy-solute
echo "Ready"
Polymers¶
Sample directory: $ADFHOME/examples/crs/Polymers
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.
cp $ADFHOME/examples/crs/Tutorial4/*coskf .
cp $ADFHOME/examples/crs/Polymers/*coskf .
"$ADFBIN/crsprep" -c Benzene.coskf -density 0.876 -savecompound
"$ADFBIN/crsprep" -c Water.coskf -density 1.0 -savecompound
"$ADFBIN/crsprep" -c Methanol.coskf -density 0.792 -savecompound \
-vp_equation VPM1 \
-vp_params "-7057.597287 -9.936895562 0.00608530790 77.10002032 0"
"$ADFBIN/crsprep" -c Hexane.coskf -density 0.655 -savecompound \
-vp_equation VPM1 \
-vp_params "-5575.417318 -6.612402250 0.00437376138 53.36969532 0"
rm -f job.sh
touch job.sh
chmod +x job.sh
"$ADFBIN/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"
"$ADFBIN/adfreport" Polymers.1.crskf compounds-name Flory-Huggins WF-activity-coefficient
"$ADFBIN/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"
"$ADFBIN/adfreport" Polymers.2.crskf compounds-name temperature pressure
"$ADFBIN/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"
"$ADFBIN/adfreport" Polymers.3.crskf logp
"$ADFBIN/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"
"$ADFBIN/adfreport" Polymers.4.crskf solubility-g
"$ADFBIN/crsprep" -t BINMIXCOEF -method COSMOSAC2013 -j Polymers.5 \
-s "Poly(ethyl_ethylene).coskf" -s Benzene.coskf \
-massfraction > job.sh
./job.sh
echo "Polymers.5"
"$ADFBIN/adfreport" Polymers.5.crskf polymer-fraction Flory-Huggins
echo "Ready"