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Update IPython notebooks #1735

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merged 9 commits into from Oct 26, 2019
Merged

Update IPython notebooks #1735

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44ab843
Remove Species import from rmgpy.molecule.draw
mliu49 Sep 27, 2019
50ffd9e
Refactor entry sorting in kinetics rules
mliu49 Sep 27, 2019
b31cd43
Adjust reaction template retrieval when parsing reaction comments
mliu49 Sep 28, 2019
e30e430
Fix leftover uses of format in molecule.draw
mliu49 Sep 28, 2019
402e974
Update example model in ipython/data/parse_source
mliu49 Sep 28, 2019
cfb4268
Update IPython notebooks with Python 3 and RMG changes
mliu49 Sep 30, 2019
355ada2
Standardize ipython notebook filenames
mliu49 Sep 30, 2019
216340f
Fix incorrect argument in call to RDKit
mliu49 Oct 10, 2019
8a057a4
Fix get_labeled_reactants_and_products for new families
mliu49 Oct 11, 2019
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72 changes: 36 additions & 36 deletions ipython/canteraSensitivityComparison.ipynb → ipython/cantera_sensitivity_comparison.ipynb
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Expand Up @@ -18,7 +18,7 @@
"outputs": [],
"source": [
"import cantera\n",
"print cantera.__version__ # Check Cantera version"
"print(cantera.__version__) # Check Cantera version"
]
},
{
Expand All @@ -31,10 +31,10 @@
"\n",
"from IPython.display import display, Image\n",
"\n",
"from rmgpy.chemkin import loadChemkinFile\n",
"from rmgpy.chemkin import load_chemkin_file\n",
"from rmgpy.species import Species\n",
"from rmgpy.tools.canteraModel import Cantera, getRMGSpeciesFromUserSpecies\n",
"from rmgpy.tools.plot import SimulationPlot, ReactionSensitivityPlot, parseCSVData\n",
"from rmgpy.tools.canteraModel import Cantera, get_rmg_species_from_user_species\n",
"from rmgpy.tools.plot import SimulationPlot, ReactionSensitivityPlot, parse_csv_data\n",
"from rmgpy.tools.simulate import run_simulation"
]
},
Expand All @@ -51,9 +51,9 @@
"metadata": {},
"outputs": [],
"source": [
"speciesList, reactionList = loadChemkinFile('./data/ethane_model/chem_annotated.inp',\n",
" './data/ethane_model/species_dictionary.txt',\n",
" './data/ethane_model/tran.dat')"
"species_list, reaction_list = load_chemkin_file('./data/ethane_model/chem_annotated.inp',\n",
" './data/ethane_model/species_dictionary.txt',\n",
" './data/ethane_model/tran.dat')"
]
},
{
Expand All @@ -70,19 +70,19 @@
"outputs": [],
"source": [
"# Find the species: ethane and methane\n",
"user_ethane = Species().fromSMILES('CC')\n",
"user_methane = Species().fromSMILES('C')\n",
"speciesDict = getRMGSpeciesFromUserSpecies([user_ethane, user_methane], speciesList)\n",
"ethane = speciesDict[user_ethane]\n",
"methane = speciesDict[user_methane]\n",
"sensitiveSpecies = [ethane, methane]\n",
"user_ethane = Species().from_smiles('CC')\n",
"user_methane = Species().from_smiles('C')\n",
"species_dict = get_rmg_species_from_user_species([user_ethane, user_methane], species_list)\n",
"ethane = species_dict[user_ethane]\n",
"methane = species_dict[user_methane]\n",
"sensitive_species = [ethane, methane]\n",
"\n",
"#reactorTypeList = ['IdealGasReactor']\n",
"reactorTypeList = ['IdealGasConstPressureTemperatureReactor']\n",
"molFracList=[{ethane: 1}]\n",
"#reactor_type_list = ['IdealGasReactor']\n",
"reactor_type_list = ['IdealGasConstPressureTemperatureReactor']\n",
"mol_frac_list = [{ethane: 1}]\n",
"Tlist = ([1300], 'K')\n",
"Plist = ([1], 'bar')\n",
"reactionTimeList = ([0.5], 'ms')"
"reaction_time_list = ([0.5], 'ms')"
]
},
{
Expand All @@ -92,17 +92,17 @@
"outputs": [],
"source": [
"# Create cantera object, loading in the species and reactions\n",
"job = Cantera(speciesList=speciesList, reactionList=reactionList, outputDirectory='temp', sensitiveSpecies=sensitiveSpecies)\n",
"job = Cantera(species_list=species_list, reaction_list=reaction_list, output_directory='temp', sensitive_species=sensitive_species)\n",
"# The cantera file must be created from an associated chemkin file\n",
"\n",
"# We can either load the Model from the initialized set of rmg species and reactions\n",
"job.loadModel()\n",
"job.load_model()\n",
"\n",
"# Or load it from a chemkin file by uncommenting the following line:\n",
"#job.loadChemkinModel('data/minimal_model/chem_annotated.inp',transportFile='data/minimal_model/tran.dat')\n",
"#job.load_chemkin_model('data/ethane_model/chem_annotated.inp',transport_file='data/ethane_model/tran.dat')\n",
"\n",
"# Generate the conditions based on the settings we declared earlier\n",
"job.generateConditions(reactorTypeList, reactionTimeList, molFracList, Tlist, Plist)"
"job.generate_conditions(reactor_type_list, reaction_time_list, mol_frac_list, Tlist, Plist)"
]
},
{
Expand All @@ -117,10 +117,10 @@
"\n",
"# Show the plots in the ipython notebook\n",
"for i, condition in enumerate(job.conditions):\n",
" print 'Cantera Simulation: Condition {0} Species Mole Fractions'.format(i+1)\n",
" print('Cantera Simulation: Condition {0} Species Mole Fractions'.format(i+1))\n",
" display(Image(filename=\"temp/{0}_mole_fractions.png\".format(i+1)))\n",
" \n",
" print 'Cantera Simulation: Condition {0} Ethane Reaction Sensitivity'.format(i+1)\n",
" print('Cantera Simulation: Condition {0} Ethane Reaction Sensitivity'.format(i+1))\n",
" display(Image(filename=\"temp/{0}_ethane(1)_sensitivity.png\".format(i+1)))"
]
},
Expand Down Expand Up @@ -149,10 +149,10 @@
"metadata": {},
"outputs": [],
"source": [
"print 'RMG Native Simulation: Species Mole Fractions'\n",
"print('RMG Native Simulation: Species Mole Fractions')\n",
"display(Image(filename=\"./temp/solver/simulation_1_27.png\"))\n",
"\n",
"print 'RMG Native Simulation: Ethane Reaction Sensitivity'\n",
"print('RMG Native Simulation: Ethane Reaction Sensitivity')\n",
"display(Image(filename=\"./temp/solver/sensitivity_1_SPC_1_reactions.png\"))"
]
},
Expand All @@ -164,14 +164,14 @@
"source": [
"# Let's also compare against the same simulation and sensitivity analysis that was conducted in CHEMKIN\n",
"# and saved as a .csv file\n",
"time, dataList = parseCSVData('./data/ethane_model/chemkin_mole_fractions.csv')\n",
"SimulationPlot(xVar=time, yVar=dataList, numSpecies=10).plot('./temp/chemkin_mole_fractions.png')\n",
"print 'CHEMKIN Simulation: Species Mole Fractions'\n",
"time, data_list = parse_csv_data('./data/ethane_model/chemkin_mole_fractions.csv')\n",
"SimulationPlot(x_var=time, y_var=data_list, num_species=10).plot('./temp/chemkin_mole_fractions.png')\n",
"print('CHEMKIN Simulation: Species Mole Fractions')\n",
"display(Image(filename=\"./temp/chemkin_mole_fractions.png\"))\n",
"\n",
"time, dataList = parseCSVData('./data/ethane_model/chemkin_sensitivity_ethane.csv')\n",
"ReactionSensitivityPlot(xVar=time, yVar=dataList, numReactions=10).barplot('./temp/chemkin_sensitivity_ethane.png')\n",
"print 'CHEMKIN Simulation: Ethane Reaction Sensitivity'\n",
"time, data_list = parse_csv_data('./data/ethane_model/chemkin_sensitivity_ethane.csv')\n",
"ReactionSensitivityPlot(x_var=time, y_var=data_list, num_reactions=10).barplot('./temp/chemkin_sensitivity_ethane.png')\n",
"print('CHEMKIN Simulation: Ethane Reaction Sensitivity')\n",
"display(Image(filename=\"./temp/chemkin_sensitivity_ethane.png\"))"
]
},
Expand All @@ -185,21 +185,21 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"display_name": "Python [conda env:rmg_env]",
"language": "python",
"name": "python2"
"name": "conda-env-rmg_env-py"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.15"
"pygments_lexer": "ipython3",
"version": "3.7.4"
}
},
"nbformat": 4,
Expand Down
94 changes: 47 additions & 47 deletions ipython/canteraSimulation.ipynb → ipython/cantera_simulation.ipynb
View file
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Expand Up @@ -15,8 +15,8 @@
"source": [
"from IPython.display import display, Image\n",
"\n",
"from rmgpy.chemkin import loadChemkinFile\n",
"from rmgpy.tools.canteraModel import Cantera, getRMGSpeciesFromUserSpecies\n",
"from rmgpy.chemkin import load_chemkin_file\n",
"from rmgpy.tools.canteraModel import Cantera, get_rmg_species_from_user_species\n",
"from rmgpy.species import Species"
]
},
Expand All @@ -33,9 +33,9 @@
"metadata": {},
"outputs": [],
"source": [
"speciesList, reactionList = loadChemkinFile('data/ethane_model/chem_annotated.inp',\n",
" 'data/ethane_model/species_dictionary.txt',\n",
" 'data/ethane_model/tran.dat')"
"species_list, reaction_list = load_chemkin_file('data/ethane_model/chem_annotated.inp',\n",
" 'data/ethane_model/species_dictionary.txt',\n",
" 'data/ethane_model/tran.dat')"
]
},
{
Expand All @@ -52,15 +52,15 @@
"outputs": [],
"source": [
"# Find the species: ethane\n",
"user_ethane=Species().fromSMILES('CC')\n",
"speciesDict = getRMGSpeciesFromUserSpecies([user_ethane], speciesList)\n",
"ethane = speciesDict[user_ethane]\n",
"user_ethane=Species().from_smiles('CC')\n",
"species_dict = get_rmg_species_from_user_species([user_ethane], species_list)\n",
"ethane = species_dict[user_ethane]\n",
"\n",
"reactorTypeList = ['IdealGasReactor']\n",
"molFracList=[{ethane: 1}]\n",
"Tlist = ([1300,1500,2000], 'K')\n",
"reactor_type_list = ['IdealGasReactor']\n",
"mol_frac_list=[{ethane: 1}]\n",
"Tlist = ([1300, 1500, 2000], 'K')\n",
"Plist = ([1], 'bar')\n",
"reactionTimeList = ([0.5], 'ms')"
"reaction_time_list = ([0.5], 'ms')"
]
},
{
Expand All @@ -70,17 +70,17 @@
"outputs": [],
"source": [
"# Create cantera object, loading in the species and reactions\n",
"job = Cantera(speciesList=speciesList, reactionList=reactionList, outputDirectory='temp')\n",
"job = Cantera(species_list=species_list, reaction_list=reaction_list, output_directory='temp')\n",
"# The cantera file must be created from an associated chemkin file\n",
"\n",
"# We can either load the Model from the initialized set of rmg species and reactions\n",
"job.loadModel()\n",
"job.load_model()\n",
"\n",
"# Or load it from a chemkin file by uncommenting the following line:\n",
"#job.loadChemkinModel('data/minimal_model/chem_annotated.inp',transportFile='data/minimal_model/tran.dat')\n",
"#job.load_chemkin_model('data/ethane_model/chem_annotated.inp',transport_file='data/ethane_model/tran.dat')\n",
"\n",
"# Generate the conditions based on the settings we declared earlier\n",
"job.generateConditions(reactorTypeList, reactionTimeList, molFracList, Tlist, Plist)"
"job.generate_conditions(reactor_type_list, reaction_time_list, mol_frac_list, Tlist, Plist)"
]
},
{
Expand All @@ -95,7 +95,7 @@
"\n",
"# Show the plots in the ipython notebook\n",
"for i, condition in enumerate(job.conditions):\n",
" print 'Condition {0}'.format(i+1)\n",
" print('Condition {0}'.format(i+1))\n",
" display(Image(filename=\"temp/{0}_mole_fractions.png\".format(i+1)))"
]
},
Expand All @@ -106,15 +106,15 @@
"outputs": [],
"source": [
"# We can get the cantera model Solution's species and reactions\n",
"ctSpecies = job.model.species()\n",
"ctReactions = job.model.reactions()\n",
"ct_species = job.model.species()\n",
"ct_reactions = job.model.reactions()\n",
"\n",
"# We can view a cantera species or reaction object from this\n",
"ct_ethane = ctSpecies[4]\n",
"ct_rxn = ctReactions[0]\n",
"ct_ethane = ct_species[4]\n",
"ct_rxn = ct_reactions[0]\n",
"\n",
"print ct_ethane\n",
"print ct_rxn"
"print(ct_ethane)\n",
"print(ct_rxn)"
]
},
{
Expand All @@ -127,32 +127,32 @@
"# RMG objects first, then using the `modifyReactionKinetics` or `modifySpeciesThermo` functions\n",
"\n",
"# Alter the RMG objects in place, lets pick ethane and the first reaction\n",
"rmg_ethane = speciesDict[user_ethane]\n",
"rmg_ethane.thermo.changeBaseEnthalpy(2*4184) # Change base enthalpy by 2 kcal/mol\n",
"rmg_ethane = species_dict[user_ethane]\n",
"rmg_ethane.thermo.change_base_enthalpy(2*4184) # Change base enthalpy by 2 kcal/mol\n",
"\n",
"rmg_rxn = reactionList[0]\n",
"rmg_rxn.kinetics.changeRate(4) # Change A factor by multiplying by a factor of 4\n",
"rmg_rxn = reaction_list[0]\n",
"rmg_rxn.kinetics.change_rate(4) # Change A factor by multiplying by a factor of 4\n",
"\n",
"# Take a look at the state of the cantera model before and after\n",
"print 'Cantera Model: Before'\n",
"ctSpecies = job.model.species()\n",
"ctReactions = job.model.reactions()\n",
"print 'Ethane Thermo = {} kcal/mol'.format(ctSpecies[4].thermo.h(300)/1000/4184)\n",
"print 'Reaction 1 Kinetics = {}'.format(ctReactions[0].rate)\n",
"print('Cantera Model: Before')\n",
"ct_species = job.model.species()\n",
"ct_reactions = job.model.reactions()\n",
"print('Ethane Thermo = {} kcal/mol'.format(ct_species[4].thermo.h(300)/1000/4184))\n",
"print('Reaction 1 Kinetics = {}'.format(ct_reactions[0].rate))\n",
"\n",
"# Now use the altered RMG objects to modify the kinetics and thermo\n",
"job.modifyReactionKinetics(0, rmg_rxn)\n",
"job.modifySpeciesThermo(4, rmg_ethane, useChemkinIdentifier = True)\n",
"job.modify_reaction_kinetics(0, rmg_rxn)\n",
"job.modify_species_thermo(4, rmg_ethane, use_chemkin_identifier = True)\n",
"\n",
"# If we modify thermo, the cantera model must be refreshed. If only kinetics are modified, this does not need to be done.\n",
"job.refreshModel()\n",
"job.refresh_model()\n",
"\n",
"print ''\n",
"print 'Cantera Model: After'\n",
"ctSpecies = job.model.species()\n",
"ctReactions = job.model.reactions()\n",
"print 'Ethane Thermo = {} kcal/mol'.format(ctSpecies[4].thermo.h(300)/1000/4184)\n",
"print 'Reaction 1 Kinetics = {}'.format(ctReactions[0].rate)"
"print('')\n",
"print('Cantera Model: After')\n",
"ct_species = job.model.species()\n",
"ct_reactions = job.model.reactions()\n",
"print('Ethane Thermo = {} kcal/mol'.format(ct_species[4].thermo.h(300)/1000/4184))\n",
"print('Reaction 1 Kinetics = {}'.format(ct_reactions[0].rate))"
]
},
{
Expand All @@ -167,7 +167,7 @@
"\n",
"# Show the plots in the ipython notebook\n",
"for i, condition in enumerate(job.conditions):\n",
" print 'Condition {0}'.format(i+1)\n",
" print('Condition {0}'.format(i+1))\n",
" display(Image(filename=\"temp/{0}_mole_fractions.png\".format(i+1)))"
]
},
Expand All @@ -181,21 +181,21 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 2",
"display_name": "Python [conda env:rmg_env]",
"language": "python",
"name": "python2"
"name": "conda-env-rmg_env-py"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 2
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython2",
"version": "2.7.15"
"pygments_lexer": "ipython3",
"version": "3.7.4"
}
},
"nbformat": 4,
Expand Down