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Merge pull request #1735 from ReactionMechanismGenerator/ipython
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Update IPython notebooks
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@amarkpayne
amarkpayne authored Oct 26, 2019
2 parents 7147277 + 8a057a4 commit f70d761
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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
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Original file line number Diff line number Diff line change
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
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