def running_full_shock_tube(self,processor=None,
experiment_dictonary:dict={},
kineticSens = 1,
physicalSens = 1,
dk = .01,
exp_number=1):
shock_tube = st.shockTube(pressure = experiment_dictonary['pressure'],
temperature = experiment_dictonary['temperature'],
observables = experiment_dictonary['observables'],
kineticSens = kineticSens,
physicalSens = physicalSens,
conditions = experiment_dictonary['conditions'],
initialTime = experiment_dictonary['initialTime'],
finalTime = experiment_dictonary['finalTime'],
thermalBoundary = experiment_dictonary['thermalBoundary'],
mechanicalBoundary = experiment_dictonary['mechanicalBoundary'],
processor = processor,
save_timeHistories = 1,
save_physSensHistories = 1,
moleFractionObservables = experiment_dictonary['moleFractionObservables'],
concentrationObservables = experiment_dictonary['concentrationObservables'],
fullParsedYamlFile = experiment_dictonary)
csv_paths = [x for x in experiment_dictonary['moleFractionCsvFiles'] + experiment_dictonary['concentrationCsvFiles'] if x is not None]
exp_data = shock_tube.importExperimentalData(csv_paths)
shock_tube.run()
########################################################################
#check this tomorrow
################################################################################
int_ksens_exp_mapped= shock_tube.map_and_interp_ksens()#ksens is wiped on rerun so int it before
shock_tube.sensitivity_adjustment(temp_del = dk)
shock_tube.sensitivity_adjustment(pres_del = dk)
shock_tube.species_adjustment(dk)
############################################### check to make sure these aren't effected
int_tp_psen_against_experimental = shock_tube.interpolate_experimental([shock_tube.interpolate_physical_sensitivities(index=1),
shock_tube.interpolate_physical_sensitivities(index=2)])
int_spec_psen_against_experimental = shock_tube.interpolate_experimental(pre_interpolated=shock_tube.interpolate_species_sensitivities())
###############saving the shock tube experimental interpolated time history
single_data = shock_tube.interpolate_experimental(single=shock_tube.timeHistories[0])
shock_tube.savingInterpTimeHistoryAgainstExp(single_data)
#tab starting here tomorrow
shock_tube.interpolatePressureandTempToExperiment(shock_tube,exp_data)
############### ###############
experiment = self.build_single_exp_dict(exp_number,
shock_tube,
int_ksens_exp_mapped,
int_tp_psen_against_experimental,
int_spec_psen_against_experimental,
experimental_data = exp_data)
#write test case and check if we can get as far as just returnign the experiment
return experiment
) #get rid of this at some point with central test script or when package is built
os.chdir('../../')
import MSI.simulations.instruments.shock_tube as st
import MSI.cti_core.cti_processor as pr
import cantera as ct
test_p = pr.Processor('MSI/data/test_data/FFCM1.cti')
test_tube = st.shockTube(pressure=1.74,
temperature=1880,
observables=['OH', 'H2O'],
kineticSens=1,
physicalSens=0,
conditions={
'H2O': .013,
'O2': .0099,
'H': .0000007,
'Ar': 0.9770993
},
initialTime=0,
finalTime=0.1,
thermalBoundary='Adiabatic',
mechanicalBoundary='constant pressure',
processor=test_p,
save_timeHistories=1)
test_tube.run()
test_tube.sensitivity_adjustment(temp_del=.01)
test_tube.species_adjustment(spec_del=.01)
print(test_tube.timeHistories)
test_tube.write_time_histories()
for ii,specie in enumerate(species_list):
if specie !=0.0:
conditions_dict[species_string[ii]] = specie
if species_string[ii] != 'Ar':
temp_uncertainty.append(uncertainty_string[ii])
temp_uncertainty_species.append(species_string[ii])
print(conditions_dict)
test_tube = st.shockTube(pressure=Press,
temperature=Temp,
observables=['OH'],
kineticSens=0,
physicalSens=0,
conditions=conditions_dict,
initialTime=0,
finalTime=0.02,
thermalBoundary='Adiabatic',
mechanicalBoundary='constant volume',
processor=test_p,
save_timeHistories=1,
save_physSensHistories=1)
test_tube.run()
time_History = test_tube.timeHistory
fall_off = time_History['H'][0]/time_History['H']
temp=None
for j,value in enumerate(fall_off):
if value>5:
temp = j-1
# processor=test_p,
# save_timeHistories=1,
# save_physSensHistories=1)
test_p = pr.Processor('MSI/data/test_data/FFCM1.cti')
test_tube = st.shockTube(pressure=0.986923,
temperature=295,
observables=['CH3', 'OH', 'HO2'],
kineticSens=1,
physicalSens=0,
conditions={
'CH3': 1.2094157562676408e-06,
'HO2': 7.614839946870331e-07,
'OH': 3.041863871824672e-06,
'H2O2': 0.0001531112203220986,
'CH4': 0.0007737003154574132,
'H2O': 0.9990681757005978
},
initialTime=0,
finalTime=0.003,
thermalBoundary='Adiabatic',
mechanicalBoundary='constant volume',
processor=test_p,
save_timeHistories=1,
save_physSensHistories=1)
test_tube.run()
k_sens = test_tube.kineticSensitivities
reactions = test_tube.processor.solution.reaction_equations()
def run_shocktube(self, ksens_marker: int = 1, psens_marker: int = 1):
'''
Function calls and runs a shock tube simulation with the appropriate
ksens_marker and psens_marker depending on the situation.
Parameters
----------
ksens_marker : int, optional
If 1 kinetic sensitivity on, if 0 off.
The default is 1.
psens_marker : TYPE, optional
If 1 physical sensitivity on, if 0 off.
The default is 1.
Returns
-------
shock_tube : shock_tube_object
Shock tube simulation and all variables, functions and
object it contains.
'''
if ksens_marker == 0 and psens_marker == 0:
shock_tube = st.shockTube(
pressure=self.pressure,
temperature=self.temperature,
observables=self.observables,
kineticSens=0,
physicalSens=0,
conditions=self.conditions,
initialTime=self.initialTime,
finalTime=self.finalTime,
thermalBoundary=self.thermalBoundary,
mechanicalBoundary=self.mechanicalBoundary,
processor=self.processor,
save_timeHistories=1,
save_physSensHistories=0,
moleFractionObservables=self.moleFractionObservables,
concentrationObservables=self.concentrationObservables,
fullParsedYamlFile=self.fullParsedYamlFile,
time_shift_value=self.timeshift)
shock_tube.run()
return shock_tube
elif ksens_marker == 1 and psens_marker == 0:
shock_tube = st.shockTube(
pressure=self.pressure,
temperature=self.temperature,
observables=self.observables,
kineticSens=1,
physicalSens=0,
conditions=self.conditions,
initialTime=self.initialTime,
finalTime=self.finalTime,
thermalBoundary=self.thermalBoundary,
mechanicalBoundary=self.mechanicalBoundary,
processor=self.processor,
save_timeHistories=1,
save_physSensHistories=0,
moleFractionObservables=self.moleFractionObservables,
concentrationObservables=self.concentrationObservables,
fullParsedYamlFile=self.fullParsedYamlFile,
time_shift_value=self.timeshift)
shock_tube.run()
return shock_tube
elif ksens_marker == 0 and psens_marker == 1:
shock_tube = st.shockTube(
pressure=self.pressure,
temperature=self.temperature,
observables=self.observables,
kineticSens=0,
physicalSens=1,
conditions=self.conditions,
initialTime=self.initialTime,
finalTime=self.finalTime,
thermalBoundary=self.thermalBoundary,
mechanicalBoundary=self.mechanicalBoundary,
processor=self.processor,
save_timeHistories=1,
save_physSensHistories=0,
moleFractionObservables=self.moleFractionObservables,
concentrationObservables=self.concentrationObservables,
fullParsedYamlFile=self.fullParsedYamlFile,
time_shift_value=self.timeshift)
shock_tube.run()
return shock_tube
elif ksens_marker == 1 and psens_marker == 1:
shock_tube = st.shockTube(
pressure=self.pressure,
temperature=self.temperature,
observables=self.observables,
kineticSens=1,
physicalSens=1,
conditions=self.conditions,
initialTime=self.initialTime,
finalTime=self.finalTime,
thermalBoundary=self.thermalBoundary,
mechanicalBoundary=self.mechanicalBoundary,
processor=self.processor,
save_timeHistories=1,
save_physSensHistories=0,
moleFractionObservables=self.moleFractionObservables,
concentrationObservables=self.concentrationObservables,
fullParsedYamlFile=self.fullParsedYamlFile,
time_shift_value=self.timeshift)
shock_tube.run()
return shock_tube
# test_tube.run()
# #test_tube.printVars()
# time_History = test_tube.timeHistory
test_p = pr.Processor(
'/Users/carlylagrotta/Dropbox/Columbia/MSI/data/branching_reaction_study/FFCM1_custom_cheb_extra_zeros_new_extra_reactions_precursor.cti'
)
test_tube = st.shockTube(pressure=0.6008089141308347,
temperature=1925,
observables=['OH'],
kineticSens=0,
physicalSens=0,
conditions={
'CH3OH': 0.000023898,
'Ar': 0.999976102
},
initialTime=0,
finalTime=.002,
thermalBoundary='Adiabatic',
mechanicalBoundary='constant volume',
processor=test_p,
save_timeHistories=1,
save_physSensHistories=1)
test_tube.run()
#test_tube.printVars()
time_History = test_tube.timeHistory
# plt.plot(time_History['time'],time_History['pressure']/100000)
# plt.ylim(0,140)
# plt.figure()
# plt.plot(time_History['time'],time_History['temperature'])
def running_shock_tube_absorption_only(self,processor=None,
experiment_dictonary:dict={},
absorbance_yaml_file_path = '',
kineticSens = 1,
physicalSens = 1,
dk = .01,
exp_number=1):
shock_tube = st.shockTube(pressure = experiment_dictonary['pressure'],
temperature = experiment_dictonary['temperature'],
observables = experiment_dictonary['observables'],
kineticSens = kineticSens,
physicalSens = physicalSens,
conditions = experiment_dictonary['conditions'],
initialTime = experiment_dictonary['initialTime'],
finalTime = experiment_dictonary['finalTime'],
thermalBoundary = experiment_dictonary['thermalBoundary'],
mechanicalBoundary = experiment_dictonary['mechanicalBoundary'],
processor = processor,
save_timeHistories = 1,
save_physSensHistories = 1,
moleFractionObservables = experiment_dictonary['moleFractionObservables'],
absorbanceObservables = experiment_dictonary['absorbanceObservables'],
concentrationObservables = experiment_dictonary['concentrationObservables'],
fullParsedYamlFile = experiment_dictonary)
shock_tube.run()
abs_instance = csp.Absorb()
parser = yp.Parser()
abs_loaded = parser.load_to_obj(absorbance_yaml_file_path)
abs_data = abs_instance.superimpose_shock_tube(shock_tube,abs_loaded,experiment_dictonary['pathLength'],
kinetic_sens=kineticSens)
#print(abs_data)
perturbed_coef = abs_instance.perturb_abs_coef(dk,
shock_tube,
abs_loaded,
experiment_dictonary['pathLength'],
summed_data = abs_data[0])
shock_tube.sensitivity_adjustment(temp_del = dk)
shock_tube.sensitivity_adjustment(pres_del = dk)
shock_tube.species_adjustment(dk)
abs_phys_sens = abs_instance.absorb_phys_sensitivities(shock_tube,abs_data[0],abs_loaded,
experiment_dictonary['pathLength'],
dk = dk)
#int_ksens_exp_mapped= shock_tube.map_and_interp_ksens()
loaded_experimental_data_absorbance = abs_instance.import_experimental_data(experiment_dictonary['absorbanceCsvFiles'])
interp_abs_exp= abs_instance.interpolate_experimental(shock_tube,loaded_experimental_data_absorbance,
original_summed_absorption=abs_data[0],
abs_kinetic_sens = abs_data[1],
abs_phys_sens = abs_phys_sens,
abs_coef_sens = perturbed_coef)
time_history_interp_against_experiment_dict = abs_instance.interpolate_experimental(shock_tube,
loaded_experimental_data_absorbance,
time_history = shock_tube.timeHistories[0])
experiment = self.build_single_exp_dict(exp_number,
shock_tube,
None,
None,
None,
interpolated_absorbance=interp_abs_exp,
absorbance_experimental_data = loaded_experimental_data_absorbance,
time_history_interpolated_against_absorbance_experiment = time_history_interp_against_experiment_dict)
return experiment
def running_full_shock_tube_absorption(self,processor=None,
experiment_dictonary:dict={},
absorbance_yaml_file_path = '',
kineticSens = 1,
physicalSens = 1,
dk = .01,
exp_number=1):
shock_tube = st.shockTube(pressure = experiment_dictonary['pressure'],
temperature = experiment_dictonary['temperature'],
observables = experiment_dictonary['observables'],
kineticSens = kineticSens,
physicalSens = physicalSens,
conditions = experiment_dictonary['conditions'],
initialTime = experiment_dictonary['initialTime'],
finalTime = experiment_dictonary['finalTime'],
thermalBoundary = experiment_dictonary['thermalBoundary'],
mechanicalBoundary = experiment_dictonary['mechanicalBoundary'],
processor = processor,
save_timeHistories = 1,
save_physSensHistories = 1,
moleFractionObservables = experiment_dictonary['moleFractionObservables'],
absorbanceObservables = experiment_dictonary['absorbanceObservables'],
concentrationObservables = experiment_dictonary['concentrationObservables'],
fullParsedYamlFile = experiment_dictonary)
csv_paths = [x for x in experiment_dictonary['moleFractionCsvFiles'] + experiment_dictonary['concentrationCsvFiles'] if x is not None]
exp_data = shock_tube.importExperimentalData(csv_paths)
shock_tube.run()
#this might be in the wrong spot
int_ksens_exp_mapped= shock_tube.map_and_interp_ksens()
abs_instance = csp.Absorb()
parser = yp.Parser()
abs_loaded = parser.load_to_obj(absorbance_yaml_file_path)
abs_data = abs_instance.superimpose_shock_tube(shock_tube,abs_loaded,experiment_dictonary['pathLength'],
kinetic_sens=kineticSens)
perturbed_coef = abs_instance.perturb_abs_coef(dk,
shock_tube,
abs_loaded,
experiment_dictonary['pathLength'],
summed_data = abs_data[0])
shock_tube.sensitivity_adjustment(temp_del = dk)
shock_tube.sensitivity_adjustment(pres_del = dk)
shock_tube.species_adjustment(dk)
int_tp_psen_against_experimental = shock_tube.interpolate_experimental([shock_tube.interpolate_physical_sensitivities(index=1),
shock_tube.interpolate_physical_sensitivities(index=2)])
int_spec_psen_against_experimental = shock_tube.interpolate_experimental(pre_interpolated=shock_tube.interpolate_species_sensitivities())
abs_phys_sens = abs_instance.absorb_phys_sensitivities(shock_tube,abs_data[0],abs_loaded,
experiment_dictonary['pathLength'],
dk = dk)
loaded_experimental_data_absorbance = abs_instance.import_experimental_data(experiment_dictonary['absorbanceCsvFiles'])
interp_abs_exp= abs_instance.interpolate_experimental(shock_tube,loaded_experimental_data_absorbance,
original_summed_absorption=abs_data[0],
abs_kinetic_sens = abs_data[1],
abs_phys_sens = abs_phys_sens,
abs_coef_sens = perturbed_coef)
time_history_interp_against_experiment_dict = abs_instance.interpolate_experimental(shock_tube,
loaded_experimental_data_absorbance,
time_history = shock_tube.timeHistories[0])
#################################################################################
single_data = shock_tube.interpolate_experimental(single=shock_tube.timeHistories[0])
shock_tube.savingInterpTimeHistoryAgainstExp(single_data)
shock_tube.interpolatePressureandTempToExperiment(shock_tube,exp_data)
####################################################################################
experiment = self.build_single_exp_dict(exp_number,
shock_tube,
int_ksens_exp_mapped,
int_tp_psen_against_experimental,
int_spec_psen_against_experimental,
interpolated_absorbance=interp_abs_exp,
experimental_data = exp_data,
absorbance_experimental_data = loaded_experimental_data_absorbance,
time_history_interpolated_against_absorbance_experiment = time_history_interp_against_experiment_dict )
return experiment
import MSI.simulations.instruments.shock_tube as st
import MSI.cti_core.cti_processor as pr
import MSI.simulations.absorbance.curve_superimpose as csp
import MSI.simulations.yaml_parser as yp
import cantera as ct
test_p = pr.Processor('MSI/data/test_data/optimized_burke.cti')
test_tube = st.shockTube(pressure=3.44187,
temperature=1079,
observables=['OH','H2O'],
kineticSens=1,
physicalSens=0,
conditions={'H2O2':0.00195373,'Ar':0.99804627},
initialTime=0,
finalTime=0.0014,
thermalBoundary='Adiabatic',
mechanicalBoundary='constant pressure',
processor=test_p,
save_timeHistories=1,
save_physSensHistories=1)
test_tube.run()
parser = yp.Parser()
abs_instance = csp.Absorb()
exp_loaded = parser.load_to_obj('MSI/data/test_data/Troe_6.yaml')
abs_loaded = parser.load_to_obj('MSI/data/test_data/Troe_6_abs.yaml')
abs_data = abs_instance.superimpose_shock_tube(test_tube,abs_loaded,30,kinetic_sens=0)
print(abs_data)
import pandas as pd
import matplotlib.pyplot as plt
test_p = pr.Processor(
'MSI/data/hong_H2O2_fake_data/Hong_new_full_temperature_dep_new_approach_high_temperature.cti'
)
test_tube = st.shockTube(pressure=1.635,
temperature=1283,
observables=['OH', 'H2O'],
kineticSens=0,
physicalSens=0,
conditions={
'H2O2': 0.003049,
'H2O': 0.001113,
'O2': 0.000556,
'Ar': 0.995212
},
initialTime=0,
finalTime=0.001,
thermalBoundary='Adiabatic',
mechanicalBoundary='constant pressure',
processor=test_p,
save_timeHistories=1,
save_physSensHistories=1)
#test_p2 = pr.Processor('MSI/data/hong_H2O2_fake_data/Hong_new_half_temperature_dep.cti')
#test_tube2 = st.shockTube(pressure=1.676,
# temperature=1182,
# observables=['OH','H2O'],
# kineticSens=0,
# physicalSens=0,
import numpy as np
import MSI.simulations.instruments.shock_tube as st
import MSI.cti_core.cti_processor as pr
import cantera as ct
test_p2 = pr.Processor('MSI/data/chebyshev_data/FFCM1_custom_cheb_test.cti')
test_tube = st.shockTube(pressure=1.909,
temperature=1398,
observables=['OH', 'H2O'],
kineticSens=1,
physicalSens=0,
conditions={
'O2': 0.00062,
'H2O': 0.001234,
'H2O2': 0.00254,
'Ar': 0.9974968858350951
},
initialTime=0,
finalTime=.0002,
thermalBoundary='Adiabatic',
mechanicalBoundary='constant volume',
processor=test_p2,
save_timeHistories=1,
save_physSensHistories=1)
csv_paths = [
'MSI/data/test_data/hong_oh_0_time_dependent.csv',
'MSI/data/test_data/hong_h2o_0_time_dependent.csv'
]
exp_data = test_tube.importExperimentalData(csv_paths)
test_tube.run()
print(temperature2)
print(conditions2)
test_p = pr.Processor(
'MSI/data/klip_optimization_with_raw_data/FFCM1_custom_extra_reaction_updated.cti'
)
#HONG YAML FILES AND CONDITIONS
test_tube = st.shockTube(pressure=pressure,
temperature=temperature,
observables=['OH', 'H2O', 'H2O2'],
kineticSens=0,
physicalSens=0,
conditions=conditions,
initialTime=0,
finalTime=0.0035,
thermalBoundary='Adiabatic',
mechanicalBoundary='constant pressure',
processor=test_p,
save_timeHistories=1,
save_physSensHistories=1)
test_p2 = pr.Processor(
'MSI/data/klip_optimization_comparison/Hong_new_temp_dependent_reactions.cti'
)
#test_p2 = pr.Processor('MSI/data/hong_H2O2_fake_data/Hong_new_original_reactions.cti')
test_tube2 = st.shockTube(pressure=pressure2,
temperature=temperature2,
observables=['OH', 'H2O'],
import pandas as pd
import matplotlib.pyplot as plt
test_p = pr.Processor(
'MSI/data/branching_reaction_study/FFCM1_custom_cheb_extra_zeros_new_extra_reactions_precursor.cti'
)
test_tube = st.shockTube(pressure=0.772,
temperature=2188,
observables=['OH'],
kineticSens=0,
physicalSens=0,
conditions={
'CH3I': 0.000009954,
'CH3OH': 0.000006016,
'Ar': .999984
},
initialTime=0,
finalTime=0.004,
thermalBoundary='Adiabatic',
mechanicalBoundary='constant pressure',
processor=test_p,
save_timeHistories=1,
save_physSensHistories=1)
#test_p2 = pr.Processor('MSI/data/hong_H2O2_fake_data/Hong_new_half_temperature_dep.cti')
#test_tube2 = st.shockTube(pressure=1.676,
# temperature=1182,
# observables=['OH','H2O'],
# kineticSens=0,
# physicalSens=0,
#,
#'N2O':0.0007737003154574132,
#
test_p = pr.Processor('MSI/data/test_data/FFCM1_custom.cti')
test_p = pr.Processor('gri30.cti')
test_tube = st.shockTube(pressure=.98692,
temperature=295,
observables=['HO2','CH3'],
kineticSens=1,
physicalSens=0,
conditions={'CH3': 0.0000012094157562676408,
'HO2': 0.0000007614839946870331,
'OH': 0.000003041863871824672,
'H2O2':0.0001531112203220986,
'CH4':0.0174693387016437,
'H2O':0.014293095301344845,
'N2O':0.0007737003154574132,
'Ar':0.9990681757005978
},
initialTime=0,
finalTime=0.003,
thermalBoundary='Adiabatic',
mechanicalBoundary='constant volume',
processor=test_p,
save_timeHistories=1,
save_physSensHistories=1)
#test_tube = st.shockTube(pressure=1.635,
# temperature=1283,
import MSI.simulations.instruments.shock_tube as st
import MSI.cti_core.cti_processor as pr
import cantera as ct
import matplotlib.pyplot as plt
test_p = pr.Processor('MSI/data/H_O2/one_reaction.cti')
test_tube = st.shockTube(pressure=0.35757249605664937,
temperature=1387,
observables=['OH'],
kineticSens=0,
physicalSens=0,
conditions={
'O2': 0.001238,
'H2O': 0.001263,
'H': 0.0000010570824524312896,
'OH': 0.0000010570824524312896,
'Ar': 0.9974968858350951
},
initialTime=0,
finalTime=0.02,
thermalBoundary='Adiabatic',
mechanicalBoundary='constant volume',
processor=test_p,
save_timeHistories=1,
save_physSensHistories=1)
#test_tube = st.shockTube(pressure=0.35757249605664937,
# temperature=1387,
# observables=['OH'],
# kineticSens=0,
# physicalSens=0,
