Refactor Frhodo to be a Python package #7
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- Removed duplicate numba channel - Relaxed version for ipopt - Added a newline at the end of the file
- Running by `python src/main.py` is now deprecated. We can have importing as a module or running as a script, both is annoying - Added a `frhodo` command to launch the GUI - Had to change a lot of imports to make it happen - Moved the version to a special file
tsikes
added a commit
that referenced
this pull request
Nov 13, 2023
* Heat Release Rate
Added heat release rate as both an observable and in the sim explorer
* Example Directory Changed and FirstTimeUse.docx made.
* removing opt mech files
* Made CheKiPEUQ_from_Frhodo helper module and also put code into fit_fcn
Right now, these codes are not working. It is just the beginning.
* get_varying_rate_vals_and_bnds
* get_varying_rate_vals_and_bnds
* pars_uncertainty_distribution code
* minor changes
* Update CheKiPEUQ_from_Frhodo.py
* Update CheKiPEUQ_from_Frhodo.py
* Adjusting observed_data and responses shapes for CheKiPEUQ
* got the weightings multiplication to work after transposing and transposing back
* typo correction
* working on get_log_posterior_density and getting varying_rate_vals
* forcing 'final' after minimization to be 'residual'
* Separating Bayesian into 5 steps to simplify things for Travis
* Update CheKiPEUQ_integration_notes.txt
* Update CheKiPEUQ_integration_notes.txt
* Update CiteSoft call for CheKiPEUQ
* Disabling CiteSoft exportations for now
* Update CheKiPEUQ_integration_notes.txt
* Update CheKiPEUQ_from_Frhodo from the CheKiPEUQ_Integration branch
* CheKiPEUQ_integration
Merging from Ashi's branch
Modified GUI to include variables needed for Bayesian optimization
* Merge CheKiPEUQ local (#5)
changing variable names in fit_fcn and separating the bayesian case into an if statement.
Making single return for verbose versus normal case.
Made CheKiPEUQ_from_Frhodo helper module and also put code into fit_fcn
- Right now, these codes are not working. It is just the beginning.
Create ExampleConfig.ini
add comments to fit_fcn.py about what is fed in by "args_list"
renaming obs to obs_sim in fit_fcn
* Update fit_fcn.py
* get_varying_rate_vals_and_bnds
* get_varying_rate_vals_and_bnds
* pars_uncertainty_distribution code
* newOptimization field for creating PE_object.
* Added "Force Bayesian"
* minor changes
* Update CheKiPEUQ_from_Frhodo.py
* Update CheKiPEUQ_from_Frhodo.py
* Adjusting observed_data and responses shapes for CheKiPEUQ
* got the weightings multiplication to work after transposing and transposing back
* typo correction
* update get_last_obs_sim_interp
* moved CheKiPEUQ_PE_object creation into time_adjust_func
* Update fit_fcn.py
* working on get_log_posterior_density and getting varying_rate_vals
* Update fit_fcn.py
* forcing 'final' after minimization to be 'residual'
* switch to negative log P for objective_function_value
* Trying to allow Bayesian way to get past the "QQ" error by feeding residual metrics.
* trying 10**neg_logP in lieu of loss_scalar.
* adding Bayesian_dict to make code easier to follow
* Separating Bayesian into 5 steps to simplify things for Travis
* Update fit_fcn.py
* Update CheKiPEUQ_integration_notes.txt
* Update fit_fcn.py
* Update CheKiPEUQ_integration_notes.txt
* Create CiteSoftLocal.py
* Update CiteSoft call for CheKiPEUQ
* Disabling CiteSoft exportations for now
* Update CheKiPEUQ_integration_notes.txt
* adding CheKiPEUQ local
* CheKiPEUQ_local
* removing things not needed from CheKiPEUQ
* try moving CheKiPEUQ_local
* parmaeter_estimation class still not being found for CheKiPEUQ_local
Specifically from inside CheKiPEUQ_from_Frhodo.py
* Update CheKiPEUQ_from_Frhodo.py
* Trying to use only CheKiPEUQ_local
* Merge Fix
Co-authored-by: Aditya Savara <39929571+AdityaSavara@users.noreply.github.com>
* Bayesian Changes
Changes to Optimization tab GUI
Reverting some changes in fit_fcn now that CheKiPEUQ will be called after simulations.
Prior naming was more correct
* Minor Changes
* making get_consolidated_parameters_arrays
* Bayesian_dict parsing of initial guesses and bounds added
* for params, deepcopy was needed, and added print lines.
* Adding new opt settings
Also spent a long time fixing the scientific spinbox
* Fixing the ligical error for lower bound.
I fixed the logical error, but line 212 is now printing this:
line 212 [True, True, True] [0, 2.4424906541753446e-16, -1.7976931348623155e+288] -1.7976931348623155e+288
That means that the comparison is not working correctly for min_neg_system value. In the next commit, I'm going to use the 1E99 way of doing things.
* cleanup & working towards inclusion of pars_bnds_exist
* rate_constants_parameters_bnds seem to be parsed and passed correctly to CheKiPEUQ
* Adding in unbounded_indices and return_unbounded_indices code
* minor syntax fixes
* Added remove_unbounded_values calls to code to truncate arrays etc.
* Moved more of the Bayesian_Dict fields population to init
* Cleaning up print statements
* Fixing rate_constants_parameters_bnds_exist for multiple rate constants
* Update CheKiPEUQ_integration_notes.txt
* Cleaning up
Boxes in uncertainty function now functional
Also have further modified scientificspinbox
* ChekiPEUQ: First attempt to implement variance per response for too long
* Linear scaling working now, but some 'iterations' of Frhodo are freezing during CheKiPEUQ's PE_object init.
I am trying to track down the reason. It is somewhere in the responses_observed_uncertainties manipulation during CheKiPEUQ's init.
* Reduced the slowdown to the extent of not freezing
I found that the slowdown was (surprisingly) caused in the loop that tried to convert non-zero weightings into tiny finite weightings. Changing the code to use machine epsilon in one of the steps rather than minValue/1E6 made that loop faster (completely sure why).
The shape of the weightings looks odd. In the next commit I will try to print out some array shapes.
* Fixed shape of weighting arrray passed to CheKiPEUQ
Now need to do cleanup of print statements in next commit.
* Removing excess print statements and cleaning up.
* Improving heuristic slightly
* Updating version number and fixing minor error from the recent edits.
* Che ki peuq integration v3 (#8)
* making get_consolidated_parameters_arrays
* Bayesian_dict parsing of initial guesses and bounds added
* for params, deepcopy was needed, and added print lines.
* Fixing the ligical error for lower bound.
I fixed the logical error, but line 212 is now printing this:
line 212 [True, True, True] [0, 2.4424906541753446e-16, -1.7976931348623155e+288] -1.7976931348623155e+288
That means that the comparison is not working correctly for min_neg_system value. In the next commit, I'm going to use the 1E99 way of doing things.
* Changed to -1E99 and +1E99 check
SOMEWHAT SURPRISINGLY, THE COMPARISON IS STILL FAILING. -1E288 > -1E99 is returning True.
* fixing comparisons: There was actually an "abs" I had not noticed.
* extra space deleted
* cleanup & working towards inclusion of pars_bnds_exist
* rate_constants_parameters_bnds seem to be parsed and passed correctly to CheKiPEUQ
* Adding in unbounded_indices and return_unbounded_indices code
* minor syntax fixes
* Added remove_unbounded_values calls to code to truncate arrays etc.
* Moved more of the Bayesian_Dict fields population to init
* Cleaning up print statements
* Fixing rate_constants_parameters_bnds_exist for multiple rate constants
* Update CheKiPEUQ_integration_notes.txt
Co-authored-by: Travis Sikes <50559900+tsikes@users.noreply.github.com>
* Remoing print statement from CheKiPUEQ_local
* Style Changes
* CheKiPEUQ changes
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
Refactoring to clean up fit_fcn
Also changing imports slightly
* Implemented Uncertainty in Observable Data
Implemented GUI elements and linked to CheKiPEUQ.
Uncertainty is %.
Need to handle uncertainties better in opt. Log bayesian is broken
* Added Shaded Unc
Shading has a gradient, will likely remove for speed
* Modifications to absolute uncertainty
Added uncertainty type choice to saved variables
Refactored OoM to convert_units
* Implementing rate coef/bnds on Plogs and falloff eqns
* Troe Optimization
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 7c78008561899297477be22b2d6789d8d9be2619
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Jan 17 14:51:38 2022 -0600
Update main.py
commit 9aee5641e96c5c94c7cf3398e1c8f6c6c113c738
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Nov 8 13:02:15 2021 -0600
Version check bug fix
commit 703d2253328b5f1e59a85e04cb57552a1d0a8c53
Merge: 0634337 7b12b8e
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Nov 8 12:55:21 2021 -0600
Merge branch 'Troe_opt' of https://github.com/tsikes/Frhodo into Troe_opt
commit 063433798bdf084fd79bb37c79b8783ace8375d3
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Nov 8 12:55:18 2021 -0600
Moving Loss Partition Function TCK
commit 7b12b8eceaa5f742e3453bd75d8caa3e69b8c703
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 681051d2afc94aeba90101e686bab51d199d5d32
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Nov 4 16:20:59 2021 -0500
Bug Fix
Fixed CheKiPEUQ interface issues
commit 56645923f1229a17d3f6ac50b4cdce3ebbb91580
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Nov 4 11:01:42 2021 -0500
Bug Fix
Fixed bugs with secondary y axis in sim explorer.
commit 78215871dec25a997e24ab2f4055356f78d6a3f7
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Nov 3 19:46:04 2021 -0500
Update fit_fcn.py
commit f9d11e87d980b7a428c61a5863ae02d5e84d98d9
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
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 7bd4d647cb0e54afa40e3703bd490162f866e189
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Nov 2 15:52:28 2021 -0500
Minor changes
Consolidated bisymlog scaling factor
Added new % abs density gradient to options
commit cf6328b0e9038f68a3a34f51a2d628d95dcd2912
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 15b2acb593cdd15b91c80744ee109665499b5c7f
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
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 943ad8e2950b9c0267a5af2176ce846a243b8aca
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 0eb48ce2e16c69cf8387aadeb94f5a0af17bcc68
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
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 5268062afa75b854fe0eb5e3e25cebd0e46b6b58
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 3df584d3ea1d0896d96aa4bcda3dc8072f4fd1c0
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Aug 31 22:15:05 2021 -0500
Update fit_fcn.py
commit a507f938afdf23a5210739eab9eccd3a33b02dee
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 bc66027fd2576fbfc3c403be1b6b3cd404d3d842
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Aug 31 16:58:18 2021 -0500
Fixed usage of C in loss function/GUI
commit 42d82ff555bb864bb430a756691a41597473fe9a
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 d0d43dc453e170d8f7e6b6d57ff63877f17aa27f
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Aug 29 16:57:00 2021 -0500
Tinkering with generalized loss func
commit 4702ef3d70e4aacedae1ce39b738bc88c9756acb
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 60e782f43ddc6f473a3b7773167bdb46aaa950e2
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 23 23:54:22 2021 -0500
Update loss_integral.py
commit d093dda5fe90a34d197a9842dcf2a63c8e8b7433
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 23 22:45:04 2021 -0500
loss integral fitting
commit 774f70d4ae07539a1153fda94e827beb2e8b1199
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 23 17:41:35 2021 -0500
loss function changes
commit cba7b9e5638efa58970aa93506218514e170c410
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 016ea7ca63c4af2155d1964c1d01d982dfc308bb
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Fri Aug 20 16:31:40 2021 -0500
Create fit_coeffs_pygmo.py
commit b95d5a69e6c8784f2182f9d041dd55dd7aa24786
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Fri Aug 20 16:29:08 2021 -0500
Rollback
Rolling back to working CRS2 Troe opt
commit 3c577e96ed87fb79a47555acf06d3ebdb65ab541
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Aug 19 14:59:26 2021 -0500
Testing Troe Opt
commit 553887b648b4f9e6ff910abdbeea81ddfe44cfbb
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Aug 19 01:36:54 2021 -0500
Update fit_coeffs.py
commit cbfaa20b587b940dc3620f599a3facb7dd1990f7
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Aug 18 16:28:28 2021 -0500
Working on implementing Augmented Lagrangian
commit 520f822e5f61808140d047a8b9f5049ae9e667cc
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 ab97a6def6af9a57731dcf88c5fefc88d175d1ce
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 16 22:52:25 2021 -0500
Moving ipopt and bonmin
commit 3accc3b72cc0e69b5944dda58695470e87013277
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 16 22:41:46 2021 -0500
Including bonmin and ipopt for rbfopt
commit 3289e0ddd4a18f60d3c5dc7be21879e0cd206fc5
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 16 21:12:21 2021 -0500
Working on Pygmo and RBFOpt
commit dc91f303cffb52aacf36acf123bfcaee4e0ddd15
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 91cbd0f243c0d31751ce37c868cc2d93d7ce9e8a
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Aug 15 01:08:16 2021 -0500
Implementing genetic algorithms
commit 30ad17b43445e0b0d2f4dd6d616eb7a53487370b
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Aug 12 08:56:46 2021 -0500
Minimally working Troe
commit 82ee3a198fd4d153f7877887aa710af4b7617714
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Aug 8 23:57:46 2021 -0500
Update fit_coeffs.py
Minor bug catch
commit 0d89b688dad5c8289de4e803c9664dc358f6eccb
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Aug 8 23:26:30 2021 -0500
Maybe working?
commit 5e69b6974732ce2ed7262436da72ee026dfb8c7f
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 c3a5098c2c405c8a62a291302014116ceb595e83
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Fri Aug 6 09:54:08 2021 -0500
Tinkering with ranges and bounds
commit 44d7ddb38b1706c54f68cd829866e9f83df8173c
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Aug 3 14:55:30 2021 -0500
Troe opt changes
Troe opt changes.
fixed bug from updating dependencies
commit 3735e38c33333e09b81d9950e5ccb452dfec82db
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 64070580655a1df81ee7c6cd7f1d38aa7d0a49ff
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Jul 29 10:20:16 2021 -0500
Troe Fitting - Nonfunctional
Redoing Troe Fitting to be similar to PLOG -> Troe.
commit d5731fc23e48ad7f74b468ae9637c68abb71b725
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Jul 6 15:28:43 2021 -0500
Resample Nonuniform Data
Resamples nonuniform data for uncertainty shading smoothing
commit 4e113be44a96730586f92ee1b5b3f17ad3cae9f0
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Jul 5 18:52:25 2021 -0500
Update options_panel_widgets.py
Enable/Disable wavelet levels input box accordingly
commit cf67025f6228c6b8e5945401028aac9db2d6ee39
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Jul 5 18:42:40 2021 -0500
Implemented unc shading over data
commit 2fa08582d44fbc97fd01e2657664cd0eeddcdc1a
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Fri Jul 2 13:59:59 2021 -0500
Minor update
Added error checking for 0D reactors to prevent crashing
commit 5abded10b0b27beac16f61728fa375fe792e0ce8
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Jun 30 20:25:17 2021 -0500
Bug Fix
Fixed some convergence issues related to outlier determination
commit 9e268a8ac9594a7d8dae86a089365f8ee5453618
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Jun 29 21:29:42 2021 -0500
Working Troe Optimization
Refactored Troe fitting into more legible classes.
Enabled multiprocessing
Beginning Testing
commit 951efd3b251ea1d40abc1dc3aecc542620b977e8
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sat Jun 26 23:03:43 2021 -0500
Working
Basic optimization is working
commit e672ca027fd5303045f8efeda6858d81207803a7
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sat Jun 26 00:12:41 2021 -0500
Sort of working
Have nlopt working for fcent
commit 2dbb375cb1a3ac4c5ec989635400fbf2fc8afa96
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Jun 24 17:19:18 2021 -0500
Update fit_coeffs.py
Added constraints, but not fitting well with nlopt
commit d9302247552b820f03303a0632ad7bbb1f2ae5a4
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 afdcdbc5955798bf68f900ffe432fe2825c8e131
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Jun 22 15:26:13 2021 -0500
Reproducing Troe Ok
commit 9d080529713b8ac53c519379b79804c0e8bb3ba6
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Jun 21 22:49:49 2021 -0500
Update fit_coeffs.py
commit 50265c672547ef8d611abca3654020efc08b048d
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Jun 21 14:27:55 2021 -0500
Tinkering
commit ee6501edf5675db221420e98b15f0aa3242e1dd2
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Jun 20 21:05:57 2021 -0500
New Plog Fit Method
commit 3f5619e669e0485c5b06861fb82797bb754aaf82
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Jun 17 13:39:16 2021 -0500
Nothing works
commit 568ea11ecd5be87afa3c573305fecae487c4b3af
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Jun 8 17:27:22 2021 -0500
PLOG working?
commit e9d957f823be4b4129c56ccbc11db135a0b20a85
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon May 3 22:26:22 2021 -0500
Works for PLOG but badly fitting
commit 9fb5d64a3e22beec5b54e5f8b42a2bacad288b1f
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon May 3 22:06:08 2021 -0500
PLOG Residual Working
commit 292d68fb38e29211b22716a567025f7e7a9657c0
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Apr 11 22:13:03 2021 -0500
Troe Progress
commit 6867bf67882ed4a45ce652debc49910536d4122d
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Apr 7 18:22:37 2021 -0500
Update fit_coeffs.py
commit 36b155d038fddf8bb32da3fefc35e8840134810a
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Apr 7 15:07:54 2021 -0500
More Progress
commit e5dec8fae959c28662a911902f301c206f8e6366
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Apr 6 22:12:52 2021 -0500
Making Progress
commit 0c5052034219462ab6b8bb83a5217dc3332bacdb
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Apr 6 15:01:09 2021 -0500
Tinkering
commit 47bc21dcbc99288242ca3b2ffdddd541e668024a
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Apr 5 18:34:20 2021 -0500
Working
commit add6d9dd5681a0c390958a2b85e2b49b11d39570
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 70cab313f211c86434cb79b710f90003b63b51a2
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 f6822d93a11368ced34ea47543ccf43f74fb6422
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Mar 31 13:34:46 2021 -0500
Update misc_fcns.py
commit cef069ba46c9575a21dd39506aa9540a40bc3892
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Mar 29 14:49:16 2021 -0500
Update shock_fcns.py
commit b3e91ea58b024aa40807cc08d024f33415f10f2f
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Mar 29 00:00:18 2021 -0500
Update shock_fcns.py
commit b8744a1ad214bb90bb619a08a289e9f4cc833e10
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Mar 28 23:43:34 2021 -0500
Update shock_fcns.py
Updated shock solver to match paper
commit 198eabf72084b04569be942e3d4d88521eba6c21
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 31fb75facfc140adbeaa2fe8ddcbdfaa2dc4e48e
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Mar 11 16:29:19 2021 -0600
Bug Fixes
commit 9bbdb0689855d38af559d625258782d2a1cff4e1
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 4a6efa520b4048d2fc22ca6733d6da97ee279de1
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Mar 10 23:16:01 2021 -0600
Update mech_optimize.py
Automatically set minimum time between plots when optimizing
commit c177ed6e58ff468a0bc2e75cd532ce8e8d245601
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 397457dbf477f76da4c967f2fa5b9f23a2cc7a61
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Mar 9 00:16:23 2021 -0600
Calculated Troe Derivatives
commit 43a47e944335b0b9316afa63f6f208dd044a4611
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sat Mar 6 13:47:07 2021 -0600
Bug Fixes
commit f0899df6ca3b020e073b843a3eff498f700a6a4e
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Feb 28 20:27:18 2021 -0600
Fixed Branch Errors
commit 687737fe016dd65faacf9d96bbc26df80bfc5121
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Feb 28 18:28:40 2021 -0600
Troe Tinkering
* Bug Fixing
Fixing issues with optimization
* Squashed commit of the following:
commit 7c78008561899297477be22b2d6789d8d9be2619
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Jan 17 14:51:38 2022 -0600
Update main.py
commit 9aee5641e96c5c94c7cf3398e1c8f6c6c113c738
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Nov 8 13:02:15 2021 -0600
Version check bug fix
commit 703d2253328b5f1e59a85e04cb57552a1d0a8c53
Merge: 0634337 7b12b8e
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Nov 8 12:55:21 2021 -0600
Merge branch 'Troe_opt' of https://github.com/tsikes/Frhodo into Troe_opt
commit 063433798bdf084fd79bb37c79b8783ace8375d3
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Nov 8 12:55:18 2021 -0600
Moving Loss Partition Function TCK
commit 7b12b8eceaa5f742e3453bd75d8caa3e69b8c703
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 681051d2afc94aeba90101e686bab51d199d5d32
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Nov 4 16:20:59 2021 -0500
Bug Fix
Fixed CheKiPEUQ interface issues
commit 56645923f1229a17d3f6ac50b4cdce3ebbb91580
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Nov 4 11:01:42 2021 -0500
Bug Fix
Fixed bugs with secondary y axis in sim explorer.
commit 78215871dec25a997e24ab2f4055356f78d6a3f7
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Nov 3 19:46:04 2021 -0500
Update fit_fcn.py
commit f9d11e87d980b7a428c61a5863ae02d5e84d98d9
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
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 7bd4d647cb0e54afa40e3703bd490162f866e189
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Nov 2 15:52:28 2021 -0500
Minor changes
Consolidated bisymlog scaling factor
Added new % abs density gradient to options
commit cf6328b0e9038f68a3a34f51a2d628d95dcd2912
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 15b2acb593cdd15b91c80744ee109665499b5c7f
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
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 943ad8e2950b9c0267a5af2176ce846a243b8aca
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 0eb48ce2e16c69cf8387aadeb94f5a0af17bcc68
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
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 5268062afa75b854fe0eb5e3e25cebd0e46b6b58
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 3df584d3ea1d0896d96aa4bcda3dc8072f4fd1c0
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Aug 31 22:15:05 2021 -0500
Update fit_fcn.py
commit a507f938afdf23a5210739eab9eccd3a33b02dee
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 bc66027fd2576fbfc3c403be1b6b3cd404d3d842
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Aug 31 16:58:18 2021 -0500
Fixed usage of C in loss function/GUI
commit 42d82ff555bb864bb430a756691a41597473fe9a
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 d0d43dc453e170d8f7e6b6d57ff63877f17aa27f
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Aug 29 16:57:00 2021 -0500
Tinkering with generalized loss func
commit 4702ef3d70e4aacedae1ce39b738bc88c9756acb
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 60e782f43ddc6f473a3b7773167bdb46aaa950e2
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 23 23:54:22 2021 -0500
Update loss_integral.py
commit d093dda5fe90a34d197a9842dcf2a63c8e8b7433
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 23 22:45:04 2021 -0500
loss integral fitting
commit 774f70d4ae07539a1153fda94e827beb2e8b1199
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 23 17:41:35 2021 -0500
loss function changes
commit cba7b9e5638efa58970aa93506218514e170c410
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 016ea7ca63c4af2155d1964c1d01d982dfc308bb
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Fri Aug 20 16:31:40 2021 -0500
Create fit_coeffs_pygmo.py
commit b95d5a69e6c8784f2182f9d041dd55dd7aa24786
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Fri Aug 20 16:29:08 2021 -0500
Rollback
Rolling back to working CRS2 Troe opt
commit 3c577e96ed87fb79a47555acf06d3ebdb65ab541
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Aug 19 14:59:26 2021 -0500
Testing Troe Opt
commit 553887b648b4f9e6ff910abdbeea81ddfe44cfbb
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Aug 19 01:36:54 2021 -0500
Update fit_coeffs.py
commit cbfaa20b587b940dc3620f599a3facb7dd1990f7
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Aug 18 16:28:28 2021 -0500
Working on implementing Augmented Lagrangian
commit 520f822e5f61808140d047a8b9f5049ae9e667cc
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 ab97a6def6af9a57731dcf88c5fefc88d175d1ce
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 16 22:52:25 2021 -0500
Moving ipopt and bonmin
commit 3accc3b72cc0e69b5944dda58695470e87013277
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 16 22:41:46 2021 -0500
Including bonmin and ipopt for rbfopt
commit 3289e0ddd4a18f60d3c5dc7be21879e0cd206fc5
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Aug 16 21:12:21 2021 -0500
Working on Pygmo and RBFOpt
commit dc91f303cffb52aacf36acf123bfcaee4e0ddd15
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 91cbd0f243c0d31751ce37c868cc2d93d7ce9e8a
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Aug 15 01:08:16 2021 -0500
Implementing genetic algorithms
commit 30ad17b43445e0b0d2f4dd6d616eb7a53487370b
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Aug 12 08:56:46 2021 -0500
Minimally working Troe
commit 82ee3a198fd4d153f7877887aa710af4b7617714
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Aug 8 23:57:46 2021 -0500
Update fit_coeffs.py
Minor bug catch
commit 0d89b688dad5c8289de4e803c9664dc358f6eccb
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Aug 8 23:26:30 2021 -0500
Maybe working?
commit 5e69b6974732ce2ed7262436da72ee026dfb8c7f
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 c3a5098c2c405c8a62a291302014116ceb595e83
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Fri Aug 6 09:54:08 2021 -0500
Tinkering with ranges and bounds
commit 44d7ddb38b1706c54f68cd829866e9f83df8173c
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Aug 3 14:55:30 2021 -0500
Troe opt changes
Troe opt changes.
fixed bug from updating dependencies
commit 3735e38c33333e09b81d9950e5ccb452dfec82db
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 64070580655a1df81ee7c6cd7f1d38aa7d0a49ff
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Jul 29 10:20:16 2021 -0500
Troe Fitting - Nonfunctional
Redoing Troe Fitting to be similar to PLOG -> Troe.
commit d5731fc23e48ad7f74b468ae9637c68abb71b725
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Jul 6 15:28:43 2021 -0500
Resample Nonuniform Data
Resamples nonuniform data for uncertainty shading smoothing
commit 4e113be44a96730586f92ee1b5b3f17ad3cae9f0
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Jul 5 18:52:25 2021 -0500
Update options_panel_widgets.py
Enable/Disable wavelet levels input box accordingly
commit cf67025f6228c6b8e5945401028aac9db2d6ee39
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Jul 5 18:42:40 2021 -0500
Implemented unc shading over data
commit 2fa08582d44fbc97fd01e2657664cd0eeddcdc1a
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Fri Jul 2 13:59:59 2021 -0500
Minor update
Added error checking for 0D reactors to prevent crashing
commit 5abded10b0b27beac16f61728fa375fe792e0ce8
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Jun 30 20:25:17 2021 -0500
Bug Fix
Fixed some convergence issues related to outlier determination
commit 9e268a8ac9594a7d8dae86a089365f8ee5453618
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Jun 29 21:29:42 2021 -0500
Working Troe Optimization
Refactored Troe fitting into more legible classes.
Enabled multiprocessing
Beginning Testing
commit 951efd3b251ea1d40abc1dc3aecc542620b977e8
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sat Jun 26 23:03:43 2021 -0500
Working
Basic optimization is working
commit e672ca027fd5303045f8efeda6858d81207803a7
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sat Jun 26 00:12:41 2021 -0500
Sort of working
Have nlopt working for fcent
commit 2dbb375cb1a3ac4c5ec989635400fbf2fc8afa96
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Jun 24 17:19:18 2021 -0500
Update fit_coeffs.py
Added constraints, but not fitting well with nlopt
commit d9302247552b820f03303a0632ad7bbb1f2ae5a4
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 afdcdbc5955798bf68f900ffe432fe2825c8e131
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Jun 22 15:26:13 2021 -0500
Reproducing Troe Ok
commit 9d080529713b8ac53c519379b79804c0e8bb3ba6
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Jun 21 22:49:49 2021 -0500
Update fit_coeffs.py
commit 50265c672547ef8d611abca3654020efc08b048d
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Jun 21 14:27:55 2021 -0500
Tinkering
commit ee6501edf5675db221420e98b15f0aa3242e1dd2
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Jun 20 21:05:57 2021 -0500
New Plog Fit Method
commit 3f5619e669e0485c5b06861fb82797bb754aaf82
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Jun 17 13:39:16 2021 -0500
Nothing works
commit 568ea11ecd5be87afa3c573305fecae487c4b3af
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Jun 8 17:27:22 2021 -0500
PLOG working?
commit e9d957f823be4b4129c56ccbc11db135a0b20a85
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon May 3 22:26:22 2021 -0500
Works for PLOG but badly fitting
commit 9fb5d64a3e22beec5b54e5f8b42a2bacad288b1f
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon May 3 22:06:08 2021 -0500
PLOG Residual Working
commit 292d68fb38e29211b22716a567025f7e7a9657c0
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Apr 11 22:13:03 2021 -0500
Troe Progress
commit 6867bf67882ed4a45ce652debc49910536d4122d
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Apr 7 18:22:37 2021 -0500
Update fit_coeffs.py
commit 36b155d038fddf8bb32da3fefc35e8840134810a
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Apr 7 15:07:54 2021 -0500
More Progress
commit e5dec8fae959c28662a911902f301c206f8e6366
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Apr 6 22:12:52 2021 -0500
Making Progress
commit 0c5052034219462ab6b8bb83a5217dc3332bacdb
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Apr 6 15:01:09 2021 -0500
Tinkering
commit 47bc21dcbc99288242ca3b2ffdddd541e668024a
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Apr 5 18:34:20 2021 -0500
Working
commit add6d9dd5681a0c390958a2b85e2b49b11d39570
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 70cab313f211c86434cb79b710f90003b63b51a2
Author: TSikes <50559900+tsikes@users.noreply.github.com>
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 f6822d93a11368ced34ea47543ccf43f74fb6422
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Mar 31 13:34:46 2021 -0500
Update misc_fcns.py
commit cef069ba46c9575a21dd39506aa9540a40bc3892
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Mar 29 14:49:16 2021 -0500
Update shock_fcns.py
commit b3e91ea58b024aa40807cc08d024f33415f10f2f
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Mar 29 00:00:18 2021 -0500
Update shock_fcns.py
commit b8744a1ad214bb90bb619a08a289e9f4cc833e10
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Mar 28 23:43:34 2021 -0500
Update shock_fcns.py
Updated shock solver to match paper
commit 198eabf72084b04569be942e3d4d88521eba6c21
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 31fb75facfc140adbeaa2fe8ddcbdfaa2dc4e48e
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Mar 11 16:29:19 2021 -0600
Bug Fixes
commit 9bbdb0689855d38af559d625258782d2a1cff4e1
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 4a6efa520b4048d2fc22ca6733d6da97ee279de1
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Mar 10 23:16:01 2021 -0600
Update mech_optimize.py
Automatically set minimum time between plots when optimizing
commit c177ed6e58ff468a0bc2e75cd532ce8e8d245601
Author: tsikes <50559900+tsikes@users.noreply.github.com>
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 397457dbf477f76da4c967f2fa5b9f23a2cc7a61
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Mar 9 00:16:23 2021 -0600
Calculated Troe Derivatives
commit 43a47e944335b0b9316afa63f6f208dd044a4611
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sat Mar 6 13:47:07 2021 -0600
Bug Fixes
commit f0899df6ca3b020e073b843a3eff498f700a6a4e
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Feb 28 20:27:18 2021 -0600
Fixed Branch Errors
commit 687737fe016dd65faacf9d96bbc26df80bfc5121
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Feb 28 18:28:40 2021 -0600
Troe Tinkering
commit de2f6d6c72afa2825a718dde98794ee93c3c61c8
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Feb 24 21:06:09 2021 -0600
SRI progress
commit 55c92eaabb86acc4efad28c89e7f8872e6946413
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Feb 24 17:07:25 2021 -0600
Update base_plot.py
commit a99ae6949523491a828c091c95b7a6d43381a4c0
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Feb 24 12:11:30 2021 -0600
Update base_plot.py
commit edbc062de10439f61bb82980e5a21e6963811feb
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Feb 23 17:24:00 2021 -0600
Not going well
commit 738a410f596821b8539a911c963ff33bc3312750
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Feb 22 22:08:43 2021 -0600
New SRI fit
Fitting a,b then all
commit e45563872533d08db378c581b2d5bf58b87bd285
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Feb 21 21:02:36 2021 -0600
SRI - not much progress
commit 5889aec780ca4e1cbce370d6943874f6277d9e69
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Feb 21 01:05:46 2021 -0600
More SRI fun
commit fb0380db74bcc20d98712b15386c9675a55848ee
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Feb 21 00:27:41 2021 -0600
Working on SRI
commit 665ac25ef0fd65db042893e82585c8086014fbb3
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Feb 18 18:07:54 2021 -0600
Working on nlopt SRI
commit a2593ea4e7e2fe31f0c56c24e223c72182d59cef
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Feb 17 17:49:32 2021 -0600
More SRI Fitting
commit f901332049c809c0b2415ca9023d6e31d88c9789
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Feb 16 22:36:23 2021 -0600
SRI fitting
commit f3d33a6f4cde8c68c1b3292fdf79363b35e4bc79
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Feb 16 17:45:57 2021 -0600
SRI fitting progress
commit 3b46b21395a556b2965233961ac080aab8189ae8
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Feb 16 10:00:37 2021 -0600
Working on Falloff Fits
commit 5dab2bff3623e5bedd115384ee0e9c7ec61ff76c
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Feb 15 22:38:09 2021 -0600
Working on falloff
Need to change mech to SRI
Need to save mech as yaml for reverting back to later
commit b67d2b1dd4cfe59943680522e005d8c1579060ab
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Feb 14 22:11:16 2021 -0600
Working on SRI Fit
commit 0aac366aada55b2f552192605e285802bcc6b805
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Feb 14 15:47:26 2021 -0600
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
commit e40d5860ca5495f677aeb4c64117b52a49355508
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Sat Feb 13 00:33:33 2021 -0600
Troe kind of working
commit bbbed46a06bf6770a7cf73e8abe2880a8f731647
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Thu Feb 11 16:12:14 2021 -0600
Arrhenius Optimization working again
Arrhenius working
Work to be done with Falloff
commit 308b5b37bbe290275fe6334411131090d1f8a96d
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Wed Feb 10 17:03:38 2021 -0600
Backend mech work
Changing arrhenius coeffs/coef_bnds to be an item in a list to better match plog and falloff rates
commit f1b2a0c0b3d70546bd361982e0af7bd41bf1274f
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Feb 9 22:05:26 2021 -0600
More back end work on falloff/plogs
commit c1c41c3b8698f6bbc1e0237765e3db84e341f465
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Feb 9 17:20:14 2021 -0600
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.
commit 3b89e99654216a6dcb5eaac8a62d284c7fbe406f
Author: TSikes <50559900+tsikes@users.noreply.github.com>
Date: Tue Feb 9 16:29:06 2021 -0600
Backend mech structures created
Arrhenius optimization functioning again
commit a9c0af4e5e5a064af03a9a08461b090c88ec7db5
Author: tsikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Feb 8 21:18:39 2021 -0600
Nothing Changing
* Updating Frhodo to be compatible with Cantera 3.0.
Adding updated adaptive_weights
Changing to Cantera chemkin output
* Arrhenius mostly fixed
* pressure dependent opt fix
* minor bugfix: selecting experimental dir
* Environment update
* widget fix and drhodz_per_rxn fix
* Mech reading update
* Chebyshev bug fix
* Squashed commit of the following:
commit 5e39ec2191bfbed08ce7d2877f2fb7f1d7da24bd
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Oct 16 16:28:13 2022 -0500
Update package dependencies
commit b4854765ecc4afdd3486599b8c57565f6cd23ada
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Sun Oct 16 16:20:02 2022 -0500
Update options_panel_widgets.py
Minor bug fix. Newer Qt expects int here
commit 2cfe699b7c8defff89ba872dc2d9c87fa4f647ff
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Mar 21 01:05:26 2022 -0500
Version Bump
commit 97d59d0d67aeba280763fea7d282e306a2fa6751
Author: Travis Sikes <50559900+tsikes@users.noreply.github.com>
Date: Mon Mar 21 01:04:05 2022 -0500
Bug Fix
* Soln2ck Fix
Fixed bug in writing thermo if no note exists (like writing from a 'gri30.cti')
* Heat Release Rate
Added heat release rate as both an observable and in the sim explorer
* Example Directory Changed and FirstTimeUse.docx made.
* Update FirstTimeUse.docx
* removing opt mech files
* Update fit_fcn.py
Replace all for following:
change calculate_residuals to calculate_objective_function
change calc_resid_output to calc_objective_function_output
* Update fit_fcn.py
* Update fit_fcn.py
changing variable names in fit_fcn and separating the bayesian case into an if statement.
* Update fit_fcn.py
* Update fit_fcn.py
* Update fit_fcn.py
Making single return for verbose versus normal case.
* Made CheKiPEUQ_from_Frhodo helper module and also put code into fit_fcn
Right now, these codes are not working. It is just the beginning.
* Update fit_fcn.py
* Create ExampleConfig.ini
* add comments to fit_fcn.py about what is fed in by "args_list"
* Update fit_fcn.py
* renaming obs to obs_sim in fit_fcn
* Update fit_fcn.py
* get_varying_rate_vals_and_bnds
* get_varying_rate_vals_and_bnds
* pars_uncertainty_distribution code
* newOptimization field for creating PE_object.
* Added "Force Bayesian"
* minor changes
* Update CheKiPEUQ_from_Frhodo.py
* Update CheKiPEUQ_from_Frhodo.py
* Adjusting observed_data and responses shapes for CheKiPEUQ
* got the weightings multiplication to work after transposing and transposing back
* typo correction
* update get_last_obs_sim_interp
* moved CheKiPEUQ_PE_object creation into time_adjust_func
* Update fit_fcn.py
* working on get_log_posterior_density and getting varying_rate_vals
* Update fit_fcn.py
* forcing 'final' after minimization to be 'residual'
* switch to negative log P for objective_function_value
* Trying to allow Bayesian way to get past the "QQ" error by feeding residual metrics.
* trying 10**neg_logP in lieu of loss_scalar.
* Setting forceBayesian
* adding Bayesian_dict to make code easier to follow
* Separating Bayesian into 5 steps to simplify things for Travis
* Update fit_fcn.py
* Update CheKiPEUQ_integration_notes.txt
* Update fit_fcn.py
* Update CheKiPEUQ_integration_notes.txt
* Create CiteSoftLocal.py
* Update CiteSoft call for CheKiPEUQ
* Disabling CiteSoft exportations for now
* Update CheKiPEUQ_integration_notes.txt
* Variable name changes (#2)
* Variable name changes
Moved image assets and added a GUI screenshot
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.
Co-authored-by: Aditya Savara <39929571+AdityaSavara@users.noreply.github.com>
* CheKiPEUQ_integration
Merging from Ashi's branch
Modified GUI to include variables needed for Bayesian optimization
* Merge CheKiPEUQ local (#5)
changing variable names in fit_fcn and separating the bayesian case into an if statement.
Making single return for verbose versus normal case.
Made CheKiPEUQ_from_Frhodo helper module and also put code into fit_fcn
- Right now, these codes are not working. It is just the beginning.
Create ExampleConfig.ini
add comments to fit_fcn.py about what is fed in by "args_list"
renaming obs to obs_sim in fit_fcn
* Update fit_fcn.py
* get_varying_rate_vals_and_bnds
* get_varying_rate_vals_and_bnds
* pars_uncertainty_distribution code
* newOptimization field for creating PE_object.
* Added "Force Bayesian"
* minor changes
* Update CheKiPEUQ_from_Frhodo.py
* Update CheKiPEUQ_from_Frhodo.py
* Adjusting observed_data and responses shapes for CheKiPEUQ
* got the weightings multiplication to work after transposing and transposing back
* typo correction
* update get_last_obs_sim_interp
* moved CheKiPEUQ_PE_object creation into time_adjust_func
* Update fit_fcn.py
* working on get_log_posterior_density and getting varying_rate_vals
* Update fit_fcn.py
* forcing 'final' after minimization to be 'residual'
* switch to negative log P for objective_function_value
* Trying to allow Bayesian way to get past the "QQ" error by feeding residual metrics.
* trying 10**neg_logP in lieu of loss_scalar.
* adding Bayesian_dict to make code easier to follow
* Separating Bayesian into 5 steps to simplify things for Travis
* Update fit_fcn.py
* Update CheKiPEUQ_integration_notes.txt
* Update fit_fcn.py
* Update CheKiPEUQ_integration_notes.txt
* Create CiteSoftLocal.py
* Update CiteSoft call for CheKiPEUQ
* Disabling CiteSoft exportations for now
* Update CheKiPEUQ_integration_notes.txt
* adding CheKiPEUQ local
* CheKiPEUQ_local
* removing things not needed from CheKiPEUQ
* try moving CheKiPEUQ_local
* parmaeter_estimation class still not being found for CheKiPEUQ_local
Specifically from inside CheKiPEUQ_from_Frhodo.py
* Update CheKiPEUQ_from_Frhodo.py
* Trying to use only CheKiPEUQ_local
* Merge Fix
Co-authored-by: Aditya Savara <39929571+AdityaSavara@users.noreply.github.com>
* Another Merge Fix
* Forced Bayesian Removed
Distribution type and how many sigma the unc represents is now reachable in var
* update comment in fit_fcn.py
* manually updating fit_fcn.py from Travis's CheKiPEUQ_integration branch
Github was not allowing the merge properly, so doing this change manually before merging.
* Update CheKiPEUQ_from_Frhodo from the CheKiPEUQ_Integration branch
* GUI Update
Bayesian tab now hidden when residuals are checked.
Uncertainty/Weights table shows depending upon selection of Residual/Bayesian
* Bayesian Changes
Changes to Optimization tab GUI
Reverting some changes in fit_fcn now that CheKiPEUQ will be called after simulations.
Prior naming was more correct
* Created CheKiPEUQ Dictionary
* Minor Changes
* Update fit_fcn.py
* Update fit_fcn.py
* creating get_last_obs_sim_interp and also working on Bayesian_dict
* Update fit_fcn.py
* Update fit_fcn.py
* Adding in more Bayesian_dict arguments. (#6)
* Update README.rst
Moved image assets and added a GUI screenshot
* Update README.rst
* Moved to Assets Branch
* Update fit_fcn.py
Replace all for following:
change calculate_residuals to calculate_objective_function
change calc_resid_output to calc_objective_function_output
* Update fit_fcn.py
* Update fit_fcn.py
changing variable names in fit_fcn and separating the bayesian case into an if statement.
* Update fit_fcn.py
* Update fit_fcn.py
* Update fit_fcn.py
Making single return for verbose versus normal case.
* Made CheKiPEUQ_from_Frhodo helper module and also put code into fit_fcn
Right now, these codes are not working. It is just the beginning.
* Update fit_fcn.py
* Create ExampleConfig.ini
* add comments to fit_fcn.py about what is fed in by "args_list"
* Update fit_fcn.py
* renaming obs to obs_sim in fit_fcn
* Update fit_fcn.py
* get_varying_rate_vals_and_bnds
* get_varying_rate_vals_and_bnds
* pars_uncertainty_distribution code
* newOptimization field for creating PE_object.
* Added "Force Bayesian"
* minor changes
* Update CheKiPEUQ_from_Frhodo.py
* Update CheKiPEUQ_from_Frhodo.py
* Adjusting observed_data and responses shapes for CheKiPEUQ
* got the weightings multiplication to work after transposing and transposing back
* typo correction
* update get_last_obs_sim_interp
* moved CheKiPEUQ_PE_object creation into time_adjust_func
* Update fit_fcn.py
* working on get_log_posterior_density and getting varying_rate_vals
* Update fit_fcn.py
* forcing 'final' after minimization to be 'residual'
* switch to negative log P for objective_function_value
* Trying to allow Bayesian way to get past the "QQ" error by feeding residual metrics.
* trying 10**neg_logP in lieu of loss_scalar.
* adding Bayesian_dict to make code easier to follow
* Separating Bayesian into 5 steps to simplify things for Travis
* Update fit_fcn.py
* Update CheKiPEUQ_integration_notes.txt
* Update fit_fcn.py
* Update CheKiPEUQ_integration_notes.txt
* Create CiteSoftLocal.py
* Update CiteSoft call for CheKiPEUQ
* Disabling CiteSoft exportations for now
* Update CheKiPEUQ_integration_notes.txt
* update comment in fit_fcn.py
* manually updating fit_fcn.py from Travis's CheKiPEUQ_integration branch
Github was not allowing the merge properly, so doing this change manually before merging.
* Update CheKiPEUQ_from_Frhodo from the CheKiPEUQ_Integration branch
* Update fit_fcn.py
* Update fit_fcn.py
* creating get_last_obs_sim_interp and also working on Bayesian_dict
* Update fit_fcn.py
* Update fit_fcn.py
Co-authored-by: Travis Sikes <50559900+tsikes@users.noreply.github.com>
* Update fit_fcn.py
* Save coefficient x0 and bnds in optimization
Also added Automatic as an option for uncertainty distribution
* Added a couple of missed values
* Update fit_fcn.py
Manually making them match
* making get_consolidated_parameters_arrays
* Bayesian_dict parsing of initial guesses and bounds added
* for params, deepcopy was needed, and added print lines.
* Adding new opt settings
Also spent a long time fixing the scientific spinbox
* Hall of Fame Added
* Che ki peuq integration v3 (#7)
* making get_consolidated_parameters_arrays
* Bayesian_dict parsing of initial guesses and bounds added
* for params, deepcopy was needed, and added print lines.
Co-authored-by: Travis Sikes <50559900+tsikes@users.noreply.github.com>
* Fixed bounds provided to CheKiPEUQ
* CheKiPEUQ Fixes
* Fixing the ligical error for lower bound.
I fixed the logical error, but line 212 is now printing this:
line 212 [True, True, True] [0, 2.4424906541753446e-16, -1.7976931348623155e+288] -1.7976931348623155e+288
That means that the comparison is not working correctly for min_neg_system value. In the next commit, I'm going to use the 1E99 way of doing things.
* Changed to -1E99 and +1E99 check
SOMEWHAT SURPRISINGLY, THE COMPARISON IS STILL FAILING. -1E288 > -1E99 is returning True.
* fixing comparisons: There was actually an "abs" I had not noticed.
* extra space deleted
* Cleaning up
Boxes in uncertainty function now functional
Also have further modified scientificspinbox
* cleanup & working towards inclusion of pars_bnds_exist
* rate_constants_parameters_bnds seem to be parsed and passed correctly to CheKiPEUQ
* Adding in unbounded_indices and return_unbounded_indices code
* minor syntax fixes
* Added remove_unbounded_values calls to code to truncate arrays etc.
* Moved more of the Bayesian_Dict fields population to init
* Cleaning up print statements
* Fixing rate_constants_parameters_bnds_exist for multiple rate constants
* Update CheKiPEUQ_integration_notes.txt
* Che ki peuq integration v3 (#8)
* making get_consolidated_parameters_arrays
* Bayesian_dict parsing of initial guesses and bounds added
* for params, deepcopy was needed, and added print lines.
* Fixing the ligical error for lower bound.
I fixed the logical error, but line 212 is now printing this:
line 212 [True, True, True] [0, 2.4424906541753446e-16, -1.7976931348623155e+288] -1.7976931348623155e+288
That means that the comparison is not working correctly for min_neg…
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Makes it easier to use it as an API.
You now launch Frhodo using the command line argument
frhodoIs there a preferred documentation to edit?