├── .gitignore ├── Development ├── Ideas.txt ├── Random Testing │ ├── Chemkin Export │ │ ├── ARAMCOMECH20.THERM │ │ ├── AramcoMech2.0.mech │ │ ├── Mech_test.inp │ │ ├── cheb.txt │ │ ├── generated_mech.yaml │ │ ├── mech.ck │ │ ├── soln2ck.py │ │ └── test.py │ ├── TreeView │ │ └── test.py │ ├── Yaml │ │ ├── config_io.py │ │ ├── cti2yaml.py │ │ └── default_config.yaml │ ├── cross_correlation_testing │ │ ├── tShiftTest.py │ │ ├── test.py │ │ └── test2.py │ ├── detachable tab widget │ │ └── DetachTabWidget.py │ ├── large mech │ │ ├── ARAMCOMECH30.THERM │ │ ├── AramcoMech3.0.MECH │ │ └── generated_mech.cti │ ├── loss func integral │ │ ├── loss_integral.py │ │ ├── loss_integral_surface_notes.txt │ │ └── res.csv │ ├── mech test │ │ ├── MFuller.cti │ │ ├── Styrene mech.therm │ │ ├── Styrene v0.3.0 - 120 torr.mech │ │ ├── ck2yaml.py │ │ ├── generated_mech.yaml │ │ ├── mech.ck │ │ ├── nasa9-test-therm.dat │ │ ├── nasa9-test.inp │ │ ├── soln2ck.py │ │ └── test.py │ ├── no_file_cantera_conversion │ │ ├── Styrene.mech │ │ ├── Styrene.therm │ │ ├── ck2yaml-nofile.py │ │ └── out.yaml │ ├── pysidesender │ │ └── sendertest.py │ ├── reaction path analysis │ │ └── test.py │ ├── sk-learn kernel density │ │ └── plot.py │ └── threaded_plot.py └── changelog.txt ├── Doc ├── Manual.pdf ├── SRI deriv.docx └── Troe deriv.docx ├── Example Input Files └── ExampleConfig.ini ├── Example ├── Experiment │ ├── Shock1.exp │ ├── Shock1.rho │ └── Shock1raw1.sig ├── FirstTimeUse.docx ├── Input_Readme.pdf ├── Mechanism │ ├── Cycloheptane.mech │ └── Cycloheptane.therm └── Simulation │ └── README.txt ├── LICENSE.txt ├── README.rst ├── frhodo_environment_pinned.yml ├── frhodo_environment_pinned_all.yml ├── frhodo_environment_unpinned.yml └── src ├── CiteSoftLocal.py ├── UI ├── error_window.ui ├── graphics │ ├── arrowdown.png │ ├── check_icon.png │ ├── main_icon.png │ └── x_icon.png ├── main_window.ui └── save_dialog.ui ├── appdirs.py ├── bonmin ├── bonmin-linux64 │ ├── bonmin │ └── coin-license.txt ├── bonmin-osx │ ├── bonmin │ └── coin-license.txt └── bonmin-win64 │ ├── bonmin.exe │ ├── coin-license.txt │ └── libipoptfort.dll ├── calculate ├── __init__.py ├── convert_units.py ├── integrate.py ├── mech_fcns.py ├── optimize │ ├── CheKiPEUQ_from_Frhodo.py │ ├── CheKiPEUQ_integration_notes.txt │ ├── CheKiPEUQ_local │ │ ├── CombinationGeneratorModule.py │ │ ├── InverseProblem.py │ │ ├── LICENSE.txt │ │ ├── MANUAL.txt │ │ ├── UserInput.py │ │ ├── __init__.py │ │ ├── mumpce_custom_plotting_example.py │ │ ├── nestedObjectsFunctionsLocal.py │ │ ├── parallel_processing.py │ │ ├── plotting_functions.py │ │ └── test_pytest.py │ ├── __init__.py │ ├── adaptive_loss.py │ ├── adaptive_loss_tck.py │ ├── fit_coeffs.py │ ├── fit_coeffs_pygmo.py │ ├── fit_fcn.py │ ├── mech_optimize.py │ ├── misc_fcns.py │ └── optimize_worker.py ├── reactors.py ├── shock_fcns.py └── smooth_data.py ├── colors.py ├── config_io.py ├── error_window.py ├── help_menu.py ├── ipopt ├── ipopt-linux64 │ ├── coin-license.txt │ └── 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