{
"cells": [
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"Examples input for the Cantera interface\n",
"****************************************\n",
"\n",
"Imports\n",
"=======\n",
"\n",
"Import the mumpce interface and the interface to Cantera. "
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:40:38.332211Z",
"start_time": "2018-09-20T20:40:37.905543Z"
}
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/opt/anaconda3/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88\n",
" return f(*args, **kwds)\n"
]
}
],
"source": [
"import mumpce as mumpce\n",
"import mumpce.cantera_utils as mpct"
]
},
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"Import Numerical Python and Pandas"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:40:38.336634Z",
"start_time": "2018-09-20T20:40:38.334158Z"
}
},
"outputs": [],
"source": [
"import numpy as np\n",
"import pandas as pd"
]
},
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"Creating the Measurements\n",
"=========================\n",
"\n",
"Reading the experimental data file\n",
"----------------------------------"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:40:38.514871Z",
"start_time": "2018-09-20T20:40:38.338248Z"
}
},
"outputs": [],
"source": [
"filename = 'Example_measurements.xlsx'\n",
"df_dict = pd.read_excel(filename,sheet_name=None)"
]
},
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"This creates a dictionary of Pandas DataFrame objects, keyed by the sheet name in Excel. We will use these to create the measurement lists.\n",
"\n",
"Initializing the experimental measurement list\n",
"----------------------------------------------\n",
"\n",
"Use each DataFrame in the data dictionary to initialize a measurement list."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:41:56.854787Z",
"start_time": "2018-09-20T20:40:38.517394Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Flame speeds\n",
"Ignition delay\n",
"Single-pulse shock tube\n",
"Reactions\n"
]
}
],
"source": [
"measurements = dict()\n",
"\n",
"for key in df_dict:\n",
" print(key)\n",
" df = df_dict[key]\n",
" measurements[key] = mpct.measurement_initialize_pd(df)"
]
},
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"Write out comma-separated versions of the DataFrames for use in other parts of the documentation."
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:41:56.940673Z",
"start_time": "2018-09-20T20:41:56.857802Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Flame speeds.csv\n",
"Ignition delay.csv\n",
"Single-pulse shock tube.csv\n",
"Reactions.csv\n"
]
}
],
"source": [
"for key in df_dict:\n",
" csv_file = key + '.csv'\n",
" csv_example_file = key + ' example.csv'\n",
" print(csv_file)\n",
" df = df_dict[key].drop('Comment',axis=1)\n",
" df.to_csv(csv_file,index=False)\n",
" df[0:4].to_csv(csv_example_file,index=False)"
]
},
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"Including activation energies as active parameters\n",
"--------------------------------------------------"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:42:41.782066Z",
"start_time": "2018-09-20T20:41:56.942856Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Single-pulse shock tube\n",
"Reactions\n"
]
}
],
"source": [
"keys_include_E = ['Single-pulse shock tube','Reactions']\n",
"for key in keys_include_E:\n",
" print(key)\n",
" df = df_dict[key]\n",
" measurements[key] = mpct.measurement_initialize_pd(df,no_energy=False)"
]
},
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"Parameter uncertainties\n",
"-----------------------\n",
"\n",
"Read the parameter uncertainties, which we will use when we conduct a full MUM-PCE analysis later"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:42:43.038345Z",
"start_time": "2018-09-20T20:42:41.784029Z"
}
},
"outputs": [],
"source": [
"from read_uncertainties import read_uncertainties\n",
"\n",
"mpct_model = measurements['Single-pulse shock tube'][0].model\n",
"parameter_uncertainties = read_uncertainties(uncertainty_file='uncert.txt',mumpce_cantera_model=mpct_model)"
]
},
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"Creating the Projects\n",
"=====================\n",
"\n",
"Projects from a single list\n",
"---------------------------\n",
"\n",
"Each measurement list can be used to create an independent project."
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:42:43.042602Z",
"start_time": "2018-09-20T20:42:43.039842Z"
}
},
"outputs": [],
"source": [
"projects = dict()\n",
"for key in df_dict:\n",
" projects[key] = mumpce.Project(measurement_list=measurements[key],name=key)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:42:43.170795Z",
"start_time": "2018-09-20T20:42:43.043896Z"
},
"scrolled": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Single-pulse shock tube\n",
"15 measurements\n",
"pro_Aa1 (Active): Specified mole frac: 850 K, 211.63 kPa, C4H10:0.010711755,C6H5CH3:0.040294685,tBPO:3.32e-05,O2:0,AR:0.9489603600000001, mole fraction of C2H4 at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pro_Aa2 (Active): Specified mole frac: 950 K, 295.51 kPa, C4H10:0.010711755,C6H5CH3:0.040294685,tBPO:3.32e-05,O2:0,AR:0.9489603600000001, mole fraction of C2H4 at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pro_Aa3 (Active): Specified mole frac: 1050 K, 363.41 kPa, C4H10:0.010711755,C6H5CH3:0.040294685,tBPO:3.32e-05,O2:0,AR:0.9489603600000001, mole fraction of C2H4 at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pro_Ab1 (Active): Specified mole frac: 850 K, 211.63 kPa, C4H10:0.010711755,C6H5CH3:0.040294685,tBPO:3.32e-05,O2:0,AR:0.9489603600000001, mole fraction of C3H6 at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pro_Ab2 (Active): Specified mole frac: 950 K, 295.51 kPa, C4H10:0.010711755,C6H5CH3:0.040294685,tBPO:3.32e-05,O2:0,AR:0.9489603600000001, mole fraction of C3H6 at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pro_Ab3 (Active): Specified mole frac: 1050 K, 363.41 kPa, C4H10:0.010711755,C6H5CH3:0.040294685,tBPO:3.32e-05,O2:0,AR:0.9489603600000001, mole fraction of C3H6 at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Ac1 (Active): Concentration ratio: 850 K, 211.63 kPa, C4H10:0.010711755,C6H5CH3:0.040294685,tBPO:3.32e-05,O2:0,AR:0.9489603600000001, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Ac2 (Active): Concentration ratio: 950 K, 295.51 kPa, C4H10:0.010711755,C6H5CH3:0.040294685,tBPO:3.32e-05,O2:0,AR:0.9489603600000001, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Ac3 (Active): Concentration ratio: 1050 K, 363.41 kPa, C4H10:0.010711755,C6H5CH3:0.040294685,tBPO:3.32e-05,O2:0,AR:0.9489603600000001, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Cc1 (Active): Concentration ratio: 900 K, 137.66 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Cc2 (Active): Concentration ratio: 950 K, 157.68 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Cc3 (Active): Concentration ratio: 1000 K, 175.70 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Cc4 (Active): Concentration ratio: 1050 K, 192.00 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Cc5 (Active): Concentration ratio: 1100 K, 206.82 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Cc6 (Active): Concentration ratio: 1150 K, 220.34 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"\n"
]
}
],
"source": [
"project = projects['Single-pulse shock tube']\n",
"print(project)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:42:43.244257Z",
"start_time": "2018-09-20T20:42:43.173149Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Reactions\n",
"9 measurements\n",
"rxn_632_297 (Active): Reaction C4H10 + H <=> H2 + pC4H9:E: 297 K, 303.98 kPa\n",
" K.R. Jennings, R.J. Cvetanovic, J. Chem. Phys. 35 (1961), 1233-1240.\n",
"rxn_632_329 (Active): Reaction C4H10 + H <=> H2 + pC4H9:E: 329 K, 303.98 kPa\n",
" K. Yang, J. Phys. Chem. 67 (1963), 562-566.\n",
"rxn_632_513 (Active): Reaction C4H10 + H <=> H2 + pC4H9:E: 513 K, 303.98 kPa\n",
" K. Yang, J. Phys. Chem. 67 (1963), 562-566.\n",
"rxn_63r_318 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 318 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"rxn_63r_325 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 325 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"rxn_63r_350 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 350 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"rxn_63r_375 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 375 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"rxn_63r_400 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 400 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"rxn_63r_413 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 413 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"\n"
]
}
],
"source": [
"project = projects['Reactions']\n",
"print(project)"
]
},
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"Projects from a combined list\n",
"-----------------------------\n",
"\n",
"Measurements from different lists can be split and combined to create a custom measurement list for a bigger project. In this case, we want to create a study of H-atom abstraction from butane by H atoms, a subset of the study by `Manion, Sheen, & Awan <http://dx.doi.org/10.1021/acs.jpca.5b01004>`_. We start by building the project's application list, which is going to be all of the single-pulse shock tube measurements where H-atom attack is the primary process. These measurements have names of the form 'pul_Cxx'."
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:42:43.324871Z",
"start_time": "2018-09-20T20:42:43.247113Z"
}
},
"outputs": [],
"source": [
"applist = [item for item in measurements['Single-pulse shock tube'] if '_C' in item.name]"
]
},
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"Then we create the reaction list by pulling the experimental rate ratios from the list. We don't include the low-temperature rate constant measurements because we already know from `Manion, Sheen, & Awan <http://dx.doi.org/10.1021/acs.jpca.5b01004>`_ that JetSurF is inconsistent with those measurements. The rate ratio measurements have names of the form 'rxn_63r_xxx'."
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:42:43.401346Z",
"start_time": "2018-09-20T20:42:43.327869Z"
}
},
"outputs": [],
"source": [
"rxnlist = [item for item in measurements['Reactions'] if 'r_' in item.name]"
]
},
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"Then we create the measurement list by using python's :py:func:`list.pop` method, which lets us pull the 1 and 5 elements from the applist. We create the measurement list as a new list with these items, and then attach the reaction rate ratio measurements."
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:42:43.479198Z",
"start_time": "2018-09-20T20:42:43.404183Z"
}
},
"outputs": [],
"source": [
"mlist = [applist.pop(5),applist.pop(1)] + rxnlist"
]
},
{
"cell_type": "raw",
"metadata": {
"raw_mimetype": "text/restructuredtext"
},
"source": [
"Now with the measurement and application lists created, we initialize a new :py:class:`Project` with these lists. Notice that the application list has all of the 'pul_Cxx' except for those we added to the measurement list."
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T20:42:43.547387Z",
"start_time": "2018-09-20T20:42:43.482510Z"
},
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"H_abstraction_from_butane_by_H\n",
"12 measurements\n",
"pul_Cc6 (Active): Concentration ratio: 1150 K, 220.34 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Cc2 (Active): Concentration ratio: 950 K, 157.68 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"rxn_63r_318 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 318 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"rxn_63r_325 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 325 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"rxn_63r_350 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 350 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"rxn_63r_375 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 375 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"rxn_63r_400 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 400 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"rxn_63r_413 (Active): Rate ratio k_[C4H10 + H <=> H2 + sC4H9:E]/k_[C4H10 + H <=> H2 + pC4H9:E]: 413 K, 303.98 kPa\n",
" J.M. Campbell, O.P. Strausz, H.E. Gunning, Can. J. Chem. 47 (1969), 3759-3762\n",
"pul_Cc1 (Application): Concentration ratio: 900 K, 137.66 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Cc3 (Application): Concentration ratio: 1000 K, 175.70 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Cc4 (Application): Concentration ratio: 1050 K, 192.00 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"pul_Cc5 (Application): Concentration ratio: 1100 K, 206.82 kPa, C4H10:0.001020921,HME:5.73e-05,O2:0,AR:0.998921779, [C2H4]/[C3H6] at 0.5 ms\n",
" J. A. Manion, D. A. Sheen, I. A. Awan, J. Phys. Chem. A 119 (2015), 7637-7658.\n",
"\n"
]
}
],
"source": [
"project_Habs = mumpce.Project(measurement_list=mlist,application_list=applist,\n",
" name='H_abstraction_from_butane_by_H',\n",
" parameter_uncertainties=parameter_uncertainties\n",
" )\n",
"print(project_Habs)"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T21:10:57.613561Z",
"start_time": "2018-09-20T20:42:43.550331Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"pul_Cc6\n"
]
},
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},
"metadata": {},
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},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"pul_Cc2\n"
]
},
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},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"rxn_63r_318\n",
"rxn_63r_325\n",
"rxn_63r_350\n",
"rxn_63r_375\n",
"rxn_63r_400\n",
"rxn_63r_413\n",
"pul_Cc1\n"
]
},
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},
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},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"pul_Cc3\n"
]
},
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},
"metadata": {},
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},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"pul_Cc4\n"
]
},
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},
"metadata": {},
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},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"pul_Cc5\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\n"
]
}
],
"source": [
"project_Habs.find_sensitivity()"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T21:10:57.627165Z",
"start_time": "2018-09-20T21:10:57.618818Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"pul_Cc6\n",
"pul_Cc2\n",
"rxn_63r_318\n",
"rxn_63r_325\n",
"rxn_63r_350\n",
"rxn_63r_375\n",
"rxn_63r_400\n",
"rxn_63r_413\n"
]
}
],
"source": [
"project_Habs.find_active_parameters(0.02)"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T21:10:57.816047Z",
"start_time": "2018-09-20T21:10:57.631706Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[ 377 540 541 877 878 879 880 881 898 914 915 942 968 988\n",
" 989 990 991 992 1009 1312]\n"
]
}
],
"source": [
"sensitivity_cutoff = 0.02\n",
"\n",
"project_Habs.active_parameters = np.array([],dtype=int)\n",
"for meas in project_Habs:\n",
" all_parameters = np.arange(meas.model.number_parameters,dtype=int)\n",
" \n",
" uncertainties_this = project_Habs.parameter_uncertainties[:meas.model.number_parameters]\n",
" \n",
" impact_factor_list = meas.sensitivity_list * np.log(uncertainties_this)\n",
" max_sens = abs(impact_factor_list).max()*sensitivity_cutoff\n",
" active_parameters_this = all_parameters[abs(impact_factor_list) > max_sens]\n",
" \n",
" project_Habs.active_parameters = np.union1d(project_Habs.active_parameters,active_parameters_this)\n",
"project_Habs.active_parameter_uncertainties = project_Habs.parameter_uncertainties[project_Habs.active_parameters]\n",
"\n",
"print(project_Habs.active_parameters)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T21:10:57.892233Z",
"start_time": "2018-09-20T21:10:57.818024Z"
}
},
"outputs": [],
"source": [
"project_Habs.set_active_parameters()"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"ExecuteTime": {
"end_time": "2018-09-20T21:23:20.872497Z",
"start_time": "2018-09-20T21:10:57.894895Z"
},
"scrolled": false
},
"outputs": [
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"text": [
"(20,)\n",
"Both actual and predicted relative reductions in the sum of squares\n",
" are at most 0.000000\n"
]
}
],
"source": [
"m = project_Habs.run_optimization()"
]
},
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"execution_count": 21,
"metadata": {
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"text": [
"\n",
"Parameter name Value Uncert FactVal FactUnc NewVal Uncert \n",
"C2H4 + H (+M) <=> C2H5 (+M):HpA : 1.4e+06 3.00 0.63 0.79 2.7e+06 2.38\n",
"C3H6 + H <=> C2H4 + CH3:A : 8e+18 2.00 -0.10 0.99 7.5e+18 1.99\n",
"C3H6 + H <=> C2H4 + CH3:E : 4.7e+07 1.12 0.09 0.99 4.7e+07 1.12\n",
"C4H81 + H (+M) <=> sC4H9 (+M):HpA : 1.3e+10 3.00 -0.05 0.98 1.3e+10 2.93\n",
"C4H81 + H <=> C2H4 + C2H5:A : 1.6e+19 3.00 -0.08 1.00 1.5e+19 2.99\n",
"C4H81 + H <=> C2H4 + C2H5:E : 4.7e+07 1.20 0.06 1.00 4.7e+07 1.19\n",
"C4H81 + H <=> C3H6 + CH3:A : 3.2e+19 5.00 0.22 0.97 4.6e+19 4.77\n",
"C4H81 + H <=> C3H6 + CH3:E : 4.7e+07 1.20 -0.12 0.99 4.6e+07 1.20\n",
"C4H82 + H (+M) <=> sC4H9 (+M):HpA : 1.3e+10 3.00 0.06 0.98 1.4e+10 2.93\n",
"H + iC4H8 <=> C3H6 + CH3:A : 8e+18 3.00 0.15 0.99 9.4e+18 2.96\n",
"H + iC4H8 <=> C3H6 + CH3:E : 4.7e+07 1.20 -0.11 0.99 4.6e+07 1.19\n",
"C3H6 + CH3 (+M) <=> sC4H9 (+M):HpA : 1.7e+08 2.00 0.19 0.95 1.9e+08 1.93\n",
"tC4H9 (+M) <=> H + iC4H8 (+M):HpA : 8.3e+13 2.00 -0.09 1.00 7.8e+13 1.99\n",
"2 C2H5 (+M) <=> C4H10 (+M):HpA : 1.9e+11 2.00 0.25 0.97 2.2e+11 1.96\n",
"C4H10 + H <=> H2 + pC4H9:A : 9.2e+02 3.00 -0.09 0.73 8.3e+02 2.24\n",
"C4H10 + H <=> H2 + pC4H9:E : 2.8e+07 1.20 0.06 0.54 2.9e+07 1.10\n",
"C4H10 + H <=> H2 + sC4H9:A : 2.4e+03 3.00 -0.03 0.71 2.3e+03 2.19\n",
"C4H10 + H <=> H2 + sC4H9:E : 1.9e+07 1.20 0.21 0.83 1.9e+07 1.16\n",
"C4H10 + CH3 <=> CH4 + pC4H9:A : 0.0009 3.00 -0.00 1.00 0.0009 3.00\n",
"HME <=> 2 tC4H9:E : 2.9e+08 1.02 0.11 0.99 2.9e+08 1.02\n"
]
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},
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"text": [
"(20,)\n",
"Both actual and predicted relative reductions in the sum of squares\n",
" are at most 0.000000\n",
"No inconsistent measurements\n"
]
}
],
"source": [
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"execution_count": 23,
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"text": [
"\n",
"Name Value Unc OptVal OptUnc MdlVal MdlUnc\n",
"pul_Cc6 : 0.20 0.05 0.24 0.06 0.30 0.75 \n",
"pul_Cc2 : -0.14 0.05 -0.18 0.07 -0.24 0.86 \n",
"rxn_63r_318 : 3.61 0.13 3.65 0.07 3.77 1.50 \n",
"rxn_63r_325 : 3.55 0.13 3.58 0.06 3.69 1.48 \n",
"rxn_63r_350 : 3.32 0.13 3.33 0.05 3.42 1.40 \n",
"rxn_63r_375 : 3.13 0.13 3.11 0.05 3.20 1.34 \n",
"rxn_63r_400 : 2.97 0.13 2.92 0.05 2.99 1.28 \n",
"rxn_63r_413 : 2.88 0.13 2.83 0.05 2.90 1.26 \n",
"pul_Cc1 : -0.25 0.05 2.80 3.55 -0.47 10.77 \n",
"pul_Cc3 : -0.04 0.05 -0.07 0.19 -0.09 0.96 \n",
"pul_Cc4 : 0.05 0.05 0.00 0.07 0.03 0.82 \n",
"pul_Cc5 : 0.13 0.05 0.12 0.06 0.16 0.80 \n"
]
}
],
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]
},
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"Parameter name Value Uncert FactVal FactUnc NewVal Uncert \n",
"C2H4 + H (+M) <=> C2H5 (+M):HpA : 1.4e+06 3.00 0.63 0.79 2.7e+06 2.38\n",
"C3H6 + H <=> C2H4 + CH3:A : 8e+18 2.00 -0.10 0.99 7.5e+18 1.99\n",
"C3H6 + H <=> C2H4 + CH3:E : 4.7e+07 1.12 0.09 0.99 4.7e+07 1.12\n",
"C4H81 + H (+M) <=> sC4H9 (+M):HpA : 1.3e+10 3.00 -0.05 0.98 1.3e+10 2.93\n",
"C4H81 + H <=> C2H4 + C2H5:A : 1.6e+19 3.00 -0.08 1.00 1.5e+19 2.99\n",
"C4H81 + H <=> C2H4 + C2H5:E : 4.7e+07 1.20 0.06 1.00 4.7e+07 1.19\n",
"C4H81 + H <=> C3H6 + CH3:A : 3.2e+19 5.00 0.22 0.97 4.6e+19 4.77\n",
"C4H81 + H <=> C3H6 + CH3:E : 4.7e+07 1.20 -0.12 0.99 4.6e+07 1.20\n",
"C4H82 + H (+M) <=> sC4H9 (+M):HpA : 1.3e+10 3.00 0.06 0.98 1.4e+10 2.93\n",
"H + iC4H8 <=> C3H6 + CH3:A : 8e+18 3.00 0.15 0.99 9.4e+18 2.96\n",
"H + iC4H8 <=> C3H6 + CH3:E : 4.7e+07 1.20 -0.11 0.99 4.6e+07 1.19\n",
"C3H6 + CH3 (+M) <=> sC4H9 (+M):HpA : 1.7e+08 2.00 0.19 0.95 1.9e+08 1.93\n",
"tC4H9 (+M) <=> H + iC4H8 (+M):HpA : 8.3e+13 2.00 -0.09 1.00 7.8e+13 1.99\n",
"2 C2H5 (+M) <=> C4H10 (+M):HpA : 1.9e+11 2.00 0.25 0.97 2.2e+11 1.96\n",
"C4H10 + H <=> H2 + pC4H9:A : 9.2e+02 3.00 -0.09 0.73 8.3e+02 2.24\n",
"C4H10 + H <=> H2 + pC4H9:E : 2.8e+07 1.20 0.06 0.54 2.9e+07 1.10\n",
"C4H10 + H <=> H2 + sC4H9:A : 2.4e+03 3.00 -0.03 0.71 2.3e+03 2.19\n",
"C4H10 + H <=> H2 + sC4H9:E : 1.9e+07 1.20 0.21 0.83 1.9e+07 1.16\n",
"C4H10 + CH3 <=> CH4 + pC4H9:A : 0.0009 3.00 -0.00 1.00 0.0009 3.00\n",
"HME <=> 2 tC4H9:E : 2.9e+08 1.02 0.11 0.99 2.9e+08 1.02\n"
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