Update from tsikes/Frhodo #3
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Fixed bug in writing thermo if no note exists (like writing from a 'gri30.cti')
Added heat release rate as both an observable and in the sim explorer
pulling latest
Replace all for following: change calculate_residuals to calculate_objective_function change calc_resid_output to calc_objective_function_output
changing variable names in fit_fcn and separating the bayesian case into an if statement.
Making single return for verbose versus normal case.
Right now, these codes are not working. It is just the beginning.
Che ki peuq integration v3
Removing some print statements and adding a .flatten() that is needed when analyzing multiple experiments.
Che ki peuq integration v3
CheKiPEUQ was checking bounds after they had already been enforced. Differing ways of checking bounds was causing CheKiPEUQ to throw -inf. CheKiPEUQ no longer checks bounds CheKiPEUQ obj_obj function no longer shows raw -1*log_posterior_density, but is instead the relative change from the initial guess. This should not alter convergence or how it runs, but it does make it easier to see how the value is changing.
Refactoring to clean up fit_fcn Also changing imports slightly
Further abstracting weight function for uncertainty implementation Renamed CheKiPEUQ interface class
Implemented GUI elements and linked to CheKiPEUQ. Uncertainty is %. Need to handle uncertainties better in opt. Log bayesian is broken
Bayesian uncertainty now functioning for log scale
Shading has a gradient, will likely remove for speed
I prefer this version. It's quicker without much loss. Need to consider adding absolute uncertainties
Added uncertainty type choice to saved variables Refactored OoM to convert_units
x and y axes now are animated objects that update with draggable
Che ki peuq integration
Backend mech structures created Arrhenius optimization functioning again Bug fix and mech.reset work Fixed mechanism double loading from setting use_thermo_file_box programmatically mech.reset now includes Plog and Falloff properly. More back end work on falloff/plogs Backend mech work Changing arrhenius coeffs/coef_bnds to be an item in a list to better match plog and falloff rates Arrhenius Optimization working again Arrhenius working Work to be done with Falloff Troe kind of working Troe kinda works Troe kinda works but it's very slow to fit the coefficients. I'm going to switch to SRI and hope for a faster convergence time to fitting the coefficients Working on SRI Fit Working on falloff Need to change mech to SRI Need to save mech as yaml for reverting back to later Working on Falloff Fits SRI fitting progress SRI fitting More SRI Fitting Working on nlopt SRI Working on SRI More SRI fun SRI - not much progress New SRI fit Fitting a,b then all Not going well Update base_plot.py Update base_plot.py SRI progress Troe Optimization and Full Update Updated Environment and bugs popped up Quick fixes to address those Squashed commit of the following: commit 7c78008 Author: Travis Sikes <[email protected]> Date: Mon Jan 17 14:51:38 2022 -0600 Update main.py commit 9aee564 Author: Travis Sikes <[email protected]> Date: Mon Nov 8 13:02:15 2021 -0600 Version check bug fix commit 703d225 Merge: 0634337 7b12b8e Author: Travis Sikes <[email protected]> Date: Mon Nov 8 12:55:21 2021 -0600 Merge branch 'Troe_opt' of https://github.com/tsikes/Frhodo into Troe_opt commit 0634337 Author: Travis Sikes <[email protected]> Date: Mon Nov 8 12:55:18 2021 -0600 Moving Loss Partition Function TCK commit 7b12b8e Author: TSikes <[email protected]> Date: Mon Nov 8 11:47:03 2021 -0600 Working on Bug Fix New bug with RBFopt when using as executable. Working on fixing. (command window is flashing each iteration) commit 681051d Author: Travis Sikes <[email protected]> Date: Thu Nov 4 16:20:59 2021 -0500 Bug Fix Fixed CheKiPEUQ interface issues commit 5664592 Author: TSikes <[email protected]> Date: Thu Nov 4 11:01:42 2021 -0500 Bug Fix Fixed bugs with secondary y axis in sim explorer. commit 7821587 Author: Travis Sikes <[email protected]> Date: Wed Nov 3 19:46:04 2021 -0500 Update fit_fcn.py commit f9d11e8 Author: Travis Sikes <[email protected]> Date: Wed Nov 3 18:09:27 2021 -0500 Optimization Bug Fixing Fixed setting rate parametrization constant uncertainties to zero for residual based method. commit 7bd4d64 Author: TSikes <[email protected]> Date: Tue Nov 2 15:52:28 2021 -0500 Minor changes Consolidated bisymlog scaling factor Added new % abs density gradient to options commit cf6328b Author: TSikes <[email protected]> Date: Mon Nov 1 16:22:59 2021 -0500 Bug Fixing Fixing bugs in explorer widget/base plot with limit setting and widget type not defined commit 15b2acb Author: Travis Sikes <[email protected]> Date: Mon Oct 4 21:56:17 2021 -0500 Minor Update Fixed Torr added bisymlog to opt type Fixed plot error where left limit == right limit commit 943ad8e Author: TSikes <[email protected]> Date: Thu Sep 23 16:36:40 2021 -0500 Update for New Tranter Exp Format New format does not have tOpt/PT spacing but instead gives velocity commit 0eb48ce Author: Travis Sikes <[email protected]> Date: Sun Sep 19 22:55:06 2021 -0500 Opt Update Moved bisymlog out of multiple locations into convert_units Changed calculate residuals log to bisymlog commit 5268062 Author: TSikes <[email protected]> Date: Thu Sep 16 15:35:24 2021 -0500 Changed Fit Function Changed fit function to mean instead of median Changed so that Bayesian doesn't include penalty function at end. Need to check commit 3df584d Author: tsikes <[email protected]> Date: Tue Aug 31 22:15:05 2021 -0500 Update fit_fcn.py commit a507f93 Author: tsikes <[email protected]> Date: Tue Aug 31 19:30:38 2021 -0500 Changed adaptive loss function Adaptive loss function now optimizes inside of rate optimization loop. It's much more efficient. It also means each individual experiment has it's own loss alpha commit bc66027 Author: TSikes <[email protected]> Date: Tue Aug 31 16:58:18 2021 -0500 Fixed usage of C in loss function/GUI commit 42d82ff Author: tsikes <[email protected]> Date: Sun Aug 29 18:26:13 2021 -0500 Modified loss function Removed prior scaling from loss function to bring it back to publication formula commit d0d43dc Author: TSikes <[email protected]> Date: Sun Aug 29 16:57:00 2021 -0500 Tinkering with generalized loss func commit 4702ef3 Author: tsikes <[email protected]> Date: Sun Aug 29 15:51:28 2021 -0500 Changed to adaptive loss function The shape value is now broken into an optimized parameter for inside experiments and between experiments commit 60e782f Author: tsikes <[email protected]> Date: Mon Aug 23 23:54:22 2021 -0500 Update loss_integral.py commit d093dda Author: tsikes <[email protected]> Date: Mon Aug 23 22:45:04 2021 -0500 loss integral fitting commit 774f70d Author: tsikes <[email protected]> Date: Mon Aug 23 17:41:35 2021 -0500 loss function changes commit cba7b9e Author: TSikes <[email protected]> Date: Mon Aug 23 13:30:17 2021 -0500 Experiment import update Updated experimental conditions import to work for old Tranter style experiment files commit 016ea7c Author: tsikes <[email protected]> Date: Fri Aug 20 16:31:40 2021 -0500 Create fit_coeffs_pygmo.py commit b95d5a6 Author: tsikes <[email protected]> Date: Fri Aug 20 16:29:08 2021 -0500 Rollback Rolling back to working CRS2 Troe opt commit 3c577e9 Author: TSikes <[email protected]> Date: Thu Aug 19 14:59:26 2021 -0500 Testing Troe Opt commit 553887b Author: tsikes <[email protected]> Date: Thu Aug 19 01:36:54 2021 -0500 Update fit_coeffs.py commit cbfaa20 Author: tsikes <[email protected]> Date: Wed Aug 18 16:28:28 2021 -0500 Working on implementing Augmented Lagrangian commit 520f822 Author: TSikes <[email protected]> Date: Wed Aug 18 12:44:48 2021 -0500 Small changes bonmin path wasn't working with network path as string reduced min_T_range changing Troe eqn to be continuous for all Fcent values and other cases commit ab97a6d Author: tsikes <[email protected]> Date: Mon Aug 16 22:52:25 2021 -0500 Moving ipopt and bonmin commit 3accc3b Author: tsikes <[email protected]> Date: Mon Aug 16 22:41:46 2021 -0500 Including bonmin and ipopt for rbfopt commit 3289e0d Author: TSikes <[email protected]> Date: Mon Aug 16 21:12:21 2021 -0500 Working on Pygmo and RBFOpt commit dc91f30 Author: tsikes <[email protected]> Date: Sun Aug 15 21:55:11 2021 -0500 Troe updates Implemented genetic algorithms into GUI Sped GA's up through Numba Sped GA's up by only using DIRECT_L instead of CRS2. This is less accurate but much faster commit 91cbd0f Author: tsikes <[email protected]> Date: Sun Aug 15 01:08:16 2021 -0500 Implementing genetic algorithms commit 30ad17b Author: TSikes <[email protected]> Date: Thu Aug 12 08:56:46 2021 -0500 Minimally working Troe commit 82ee3a1 Author: tsikes <[email protected]> Date: Sun Aug 8 23:57:46 2021 -0500 Update fit_coeffs.py Minor bug catch commit 0d89b68 Author: tsikes <[email protected]> Date: Sun Aug 8 23:26:30 2021 -0500 Maybe working? commit 5e69b69 Author: tsikes <[email protected]> Date: Sun Aug 8 21:44:16 2021 -0500 Update fit_coeffs.py Almost ready to test, but switching to optimizing arrhenius parameters instead of lpl, hpl rates commit c3a5098 Author: TSikes <[email protected]> Date: Fri Aug 6 09:54:08 2021 -0500 Tinkering with ranges and bounds commit 44d7ddb Author: TSikes <[email protected]> Date: Tue Aug 3 14:55:30 2021 -0500 Troe opt changes Troe opt changes. fixed bug from updating dependencies commit 3735e38 Author: tsikes <[email protected]> Date: Sun Aug 1 20:44:04 2021 -0500 Redoing Troe Fit Redoing fit. Need to do more work on constraints of fitting LPL, HPL, Fcent commit 6407058 Author: TSikes <[email protected]> Date: Thu Jul 29 10:20:16 2021 -0500 Troe Fitting - Nonfunctional Redoing Troe Fitting to be similar to PLOG -> Troe. commit d5731fc Author: TSikes <[email protected]> Date: Tue Jul 6 15:28:43 2021 -0500 Resample Nonuniform Data Resamples nonuniform data for uncertainty shading smoothing commit 4e113be Author: tsikes <[email protected]> Date: Mon Jul 5 18:52:25 2021 -0500 Update options_panel_widgets.py Enable/Disable wavelet levels input box accordingly commit cf67025 Author: tsikes <[email protected]> Date: Mon Jul 5 18:42:40 2021 -0500 Implemented unc shading over data commit 2fa0858 Author: tsikes <[email protected]> Date: Fri Jul 2 13:59:59 2021 -0500 Minor update Added error checking for 0D reactors to prevent crashing commit 5abded1 Author: tsikes <[email protected]> Date: Wed Jun 30 20:25:17 2021 -0500 Bug Fix Fixed some convergence issues related to outlier determination commit 9e268a8 Author: tsikes <[email protected]> Date: Tue Jun 29 21:29:42 2021 -0500 Working Troe Optimization Refactored Troe fitting into more legible classes. Enabled multiprocessing Beginning Testing commit 951efd3 Author: tsikes <[email protected]> Date: Sat Jun 26 23:03:43 2021 -0500 Working Basic optimization is working commit e672ca0 Author: tsikes <[email protected]> Date: Sat Jun 26 00:12:41 2021 -0500 Sort of working Have nlopt working for fcent commit 2dbb375 Author: TSikes <[email protected]> Date: Thu Jun 24 17:19:18 2021 -0500 Update fit_coeffs.py Added constraints, but not fitting well with nlopt commit d930224 Author: TSikes <[email protected]> Date: Thu Jun 24 10:33:31 2021 -0500 Semi working Troe is working, but need to implement constraints on Fcent fitting. Should be working for Plog -> Troe after implementing those constraints commit afdcdbc Author: TSikes <[email protected]> Date: Tue Jun 22 15:26:13 2021 -0500 Reproducing Troe Ok commit 9d08052 Author: tsikes <[email protected]> Date: Mon Jun 21 22:49:49 2021 -0500 Update fit_coeffs.py commit 50265c6 Author: TSikes <[email protected]> Date: Mon Jun 21 14:27:55 2021 -0500 Tinkering commit ee6501e Author: tsikes <[email protected]> Date: Sun Jun 20 21:05:57 2021 -0500 New Plog Fit Method commit 3f5619e Author: TSikes <[email protected]> Date: Thu Jun 17 13:39:16 2021 -0500 Nothing works commit 568ea11 Author: TSikes <[email protected]> Date: Tue Jun 8 17:27:22 2021 -0500 PLOG working? commit e9d957f Author: tsikes <[email protected]> Date: Mon May 3 22:26:22 2021 -0500 Works for PLOG but badly fitting commit 9fb5d64 Author: tsikes <[email protected]> Date: Mon May 3 22:06:08 2021 -0500 PLOG Residual Working commit 292d68f Author: tsikes <[email protected]> Date: Sun Apr 11 22:13:03 2021 -0500 Troe Progress commit 6867bf6 Author: tsikes <[email protected]> Date: Wed Apr 7 18:22:37 2021 -0500 Update fit_coeffs.py commit 36b155d Author: TSikes <[email protected]> Date: Wed Apr 7 15:07:54 2021 -0500 More Progress commit e5dec8f Author: tsikes <[email protected]> Date: Tue Apr 6 22:12:52 2021 -0500 Making Progress commit 0c50520 Author: TSikes <[email protected]> Date: Tue Apr 6 15:01:09 2021 -0500 Tinkering commit 47bc21d Author: tsikes <[email protected]> Date: Mon Apr 5 18:34:20 2021 -0500 Working commit add6d9d Author: tsikes <[email protected]> Date: Mon Apr 5 13:48:45 2021 -0500 Big Changes Refactored calculation-type functions Set mechanism now generates mechanism programmatically rather than from yaml text in memory. This is necessary to be able to switch reaction types commit 70cab31 Author: TSikes <[email protected]> Date: Wed Mar 31 16:56:05 2021 -0500 set_mechanism changes Working on changing reaction types. Side benefit will be faster initialization during optimization commit f6822d9 Author: TSikes <[email protected]> Date: Wed Mar 31 13:34:46 2021 -0500 Update misc_fcns.py commit cef069b Author: TSikes <[email protected]> Date: Mon Mar 29 14:49:16 2021 -0500 Update shock_fcns.py commit b3e91ea Author: tsikes <[email protected]> Date: Mon Mar 29 00:00:18 2021 -0500 Update shock_fcns.py commit b8744a1 Author: tsikes <[email protected]> Date: Sun Mar 28 23:43:34 2021 -0500 Update shock_fcns.py Updated shock solver to match paper commit 198eabf Author: tsikes <[email protected]> Date: Mon Mar 22 00:03:21 2021 -0500 Troe Falloff functional Fitting the falloff parameters is working. Need to think more about initial parameters and see if I can fit LPL and HPL at the same time(this makes PLOGS work) commit 31fb75f Author: TSikes <[email protected]> Date: Thu Mar 11 16:29:19 2021 -0600 Bug Fixes commit 9bbdb06 Author: tsikes <[email protected]> Date: Wed Mar 10 23:24:09 2021 -0600 Update mech_fcns.py Accidentally removed sleep for mech changing. This must remain until incident shock reactor is rewritten commit 4a6efa5 Author: tsikes <[email protected]> Date: Wed Mar 10 23:16:01 2021 -0600 Update mech_optimize.py Automatically set minimum time between plots when optimizing commit c177ed6 Author: tsikes <[email protected]> Date: Wed Mar 10 22:46:13 2021 -0600 Plotting Improved Set plots to only draw if they are being shown Set minimum time since last draw for optimization End result: Much faster plotting and program does not appear to hang like before commit 397457d Author: tsikes <[email protected]> Date: Tue Mar 9 00:16:23 2021 -0600 Calculated Troe Derivatives commit 43a47e9 Author: tsikes <[email protected]> Date: Sat Mar 6 13:47:07 2021 -0600 Bug Fixes commit f0899df Author: tsikes <[email protected]> Date: Sun Feb 28 20:27:18 2021 -0600 Fixed Branch Errors commit 687737f Author: tsikes <[email protected]> Date: Sun Feb 28 18:28:40 2021 -0600 Troe Tinkering
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Significant changes in backend mech/gui
Troe optimization included (there's room for improvement)
CheKiPEUQ added