Code

Update from tsikes/Frhodo#3

Code

Merged

tsikes merged 147 commits intoArgonne-National-Laboratory:masterArgonne-National-Laboratory/Frhodo:masterfrom tsikes:mastertsikes/Frhodo:masterCopy head branch name to clipboardJan 17, 2022

+561,034-2,781

Commits

Commits on Dec 19, 2020

• Soln2ck Fix

  Show description for 076c508
  tsikes

  committed
  076c508

Commits on Jan 6, 2021

• Heat Release Rate

  Show description for 208904a
  tsikes

  committed
  208904a

Commits on Jan 11, 2021

• Merge pull request #1 from tsikes/master

  Show description for eb593d5
  AdityaSavara

  authored
  eb593d5

Commits on Jan 13, 2021

• Example Directory Changed and FirstTimeUse.docx made.

  AdityaSavara

  committed
  8204997

• Update FirstTimeUse.docx

  AdityaSavara

  committed
  5ab4a40

Commits on Jan 14, 2021

• removing opt mech files

  AdityaSavara

  committed
  51d1d3a

• Update fit_fcn.py

  Show description for 199b462
  AdityaSavara

  committed
  199b462

• Update fit_fcn.py

  AdityaSavara

  committed
  c64cfe5

• Update fit_fcn.py

  Show description for d560094
  AdityaSavara

  committed
  d560094

• Update fit_fcn.py

  AdityaSavara

  committed
  6daf773

• Update fit_fcn.py

  AdityaSavara

  committed
  5b47cd4

• Update fit_fcn.py

  Show description for 765290d
  AdityaSavara

  committed
  765290d

Commits on Jan 15, 2021

• Made CheKiPEUQ_from_Frhodo helper module and also put code into fit_fcn

  Show description for a320c8b
  AdityaSavara

  committed
  a320c8b

Commits on Jan 16, 2021

• Update fit_fcn.py

  AdityaSavara

  committed
  4511a75

• Create ExampleConfig.ini

  AdityaSavara

  committed
  873b3e3

• add comments to fit_fcn.py about what is fed in by "args_list"

  AdityaSavara

  committed
  347972d

• Update fit_fcn.py

  AdityaSavara

  committed
  822e669

• renaming obs to obs_sim in fit_fcn

  AdityaSavara

  committed
  490bd8c

• Update fit_fcn.py

  AdityaSavara

  committed
  620440a

• get_varying_rate_vals_and_bnds

  AdityaSavara

  committed
  99f5458

• get_varying_rate_vals_and_bnds

  AdityaSavara

  committed
  893d490

• pars_uncertainty_distribution code

  AdityaSavara

  committed
  868d45c

• newOptimization field for creating PE_object.

  AdityaSavara

  committed
  00d5876

• Added "Force Bayesian"

  AdityaSavara

  committed
  97fef0e

• minor changes

  AdityaSavara

  committed
  07f4051

• Update CheKiPEUQ_from_Frhodo.py

  AdityaSavara

  committed
  e33d42c

• Update CheKiPEUQ_from_Frhodo.py

  AdityaSavara

  committed
  50ab6f6

• Adjusting observed_data and responses shapes for CheKiPEUQ

  AdityaSavara

  committed
  c5c5c51

• got the weightings multiplication to work after transposing and transposing back

  AdityaSavara

  committed
  029a8c2

• typo correction

  AdityaSavara

  committed
  96d3dfa

• update get_last_obs_sim_interp

  AdityaSavara

  committed
  9a33b23

• moved CheKiPEUQ_PE_object creation into time_adjust_func

  AdityaSavara

  committed
  86a2f8d

• Update fit_fcn.py

  AdityaSavara

  committed
  74faf26

• working on get_log_posterior_density and getting varying_rate_vals

  AdityaSavara

  committed
  03d8651

• Update fit_fcn.py

  AdityaSavara

  committed
  159dd11

• forcing 'final' after minimization to be 'residual'

  AdityaSavara

  committed
  381c645

• switch to negative log P for objective_function_value

  AdityaSavara

  committed
  e00df41

• Trying to allow Bayesian way to get past the "QQ" error by feeding residual metrics.

  AdityaSavara

  committed
  d9c8f71

• trying 10**neg_logP in lieu of loss_scalar.

  AdityaSavara

  committed
  6386700

• Setting forceBayesian

  AdityaSavara

  committed
  e7424af

Commits on Jan 17, 2021

• adding Bayesian_dict to make code easier to follow

  AdityaSavara

  committed
  089da10

• Separating Bayesian into 5 steps to simplify things for Travis

  AdityaSavara

  committed
  02af7f1

• Update fit_fcn.py

  AdityaSavara

  committed
  1cb8cfb

• Update CheKiPEUQ_integration_notes.txt

  AdityaSavara

  committed
  cc02098

• Update fit_fcn.py

  AdityaSavara

  committed
  7dd837e

• Update CheKiPEUQ_integration_notes.txt

  AdityaSavara

  committed
  46cb111

• Create CiteSoftLocal.py

  AdityaSavara

  committed
  dc33fb4

• Update CiteSoft call for CheKiPEUQ

  AdityaSavara

  committed
  5eea030

• Disabling CiteSoft exportations for now

  AdityaSavara

  committed
  f0d76dc

• Update CheKiPEUQ_integration_notes.txt

  AdityaSavara

  committed
  ce9b7a7

Commits on Jan 18, 2021

• Merge pull request #1 from AdityaSavara/documentation_update

  Show description for 90ad23b
  tsikes

  authored
  90ad23b

• Variable name changes (#2)

  Show description for 12442cc
  

  tsikes

  and

  AdityaSavara

  authored
  12442cc

• CheKiPEUQ_integration

  Show description for 996f685
  tsikes

  committed
  996f685

• Merge CheKiPEUQ local (#5)

  Show description for cfd61a9
  

  tsikes

  and

  AdityaSavara

  authored
  cfd61a9

• Another Merge Fix

  tsikes

  committed
  63a3834

• Forced Bayesian Removed

  Show description for ddc294f
  tsikes

  committed
  ddc294f

• Merge pull request #3 from tsikes/CheKiPEUQ_integration

  Show description for 2573717
  AdityaSavara

  authored
  2573717

• update comment in fit_fcn.py

  AdityaSavara

  committed
  7bfb888

• manually updating fit_fcn.py from Travis's CheKiPEUQ_integration branch

  Show description for 7f851b9
  AdityaSavara

  committed
  7f851b9

• Update CheKiPEUQ_from_Frhodo from the CheKiPEUQ_Integration branch

  AdityaSavara

  committed
  839087d

• Merge pull request #4 from AdityaSavara/CheKiPEUQ-integration

  Show description for 80f7aa6
  AdityaSavara

  authored
  80f7aa6

Commits on Jan 19, 2021

• GUI Update

  Show description for 88c85d7
  tsikes

  committed
  88c85d7

• Bayesian Changes

  Show description for 4fd57ca
  tsikes

  committed
  4fd57ca

• Created CheKiPEUQ Dictionary

  tsikes

  committed
  4f2775b

Commits on Jan 20, 2021

• Minor Changes

  tsikes

  committed
  e2cd3c2

• Update fit_fcn.py

  AdityaSavara

  committed
  71a829a

• Merge pull request #7 from AdityaSavara/merging-fit-fcn-manually

  Show description for 80d82e1
  AdityaSavara

  authored
  80d82e1

• Update fit_fcn.py

  AdityaSavara

  committed
  40b8722

• Merge pull request #8 from AdityaSavara/merging-fit-fcn-manually

  Show description for 814cf41
  AdityaSavara

  authored
  814cf41

• Merge pull request #5 from tsikes/CheKiPEUQ_integration

  Show description for 3b768dc
  AdityaSavara

  authored
  3b768dc

• creating get_last_obs_sim_interp and also working on Bayesian_dict

  AdityaSavara

  committed
  ad9729c

• Update fit_fcn.py

  AdityaSavara

  committed
  934d5b6

• Update fit_fcn.py

  AdityaSavara

  committed
  f41db75

• Adding in more Bayesian_dict arguments. (#6)

  Show description for 63997b7
  

  AdityaSavara

  and

  tsikes

  authored
  63997b7

• Update fit_fcn.py

  tsikes

  committed
  29107bc

• Save coefficient x0 and bnds in optimization

  Show description for 4b7ae32
  tsikes

  committed
  4b7ae32

Commits on Jan 21, 2021

• Added a couple of missed values

  tsikes

  committed
  e6a8a2c

• Update fit_fcn.py

  Show description for cb66044
  AdityaSavara

  committed
  cb66044

• Merge pull request #9 from tsikes/CheKiPEUQ_integration_v3

  Show description for 325381d
  AdityaSavara

  authored
  325381d

• making get_consolidated_parameters_arrays

  AdityaSavara

  committed
  a59caf5

• Bayesian_dict parsing of initial guesses and bounds added

  AdityaSavara

  committed
  7adb04a

• for params, deepcopy was needed, and added print lines.

  AdityaSavara

  committed
  75e06fa

• Adding new opt settings

  Show description for 6e8f4e1
  tsikes

  committed
  6e8f4e1

• Hall of Fame Added

  tsikes

  committed
  80d591b

Commits on Jan 22, 2021

• Che ki peuq integration v3 (#7)

  Show description for fb3d241
  

  AdityaSavara

  and

  tsikes

  authored
  fb3d241

• Fixed bounds provided to CheKiPEUQ

  tsikes

  committed
  4d76832

• Merge pull request #10 from tsikes/CheKiPEUQ_integration_v3

  Show description for 007ef52
  AdityaSavara

  authored
  007ef52

Commits on Jan 23, 2021

• CheKiPEUQ Fixes

  tsikes

  committed
  aa86d57

• Merge pull request #11 from tsikes/CheKiPEUQ_integration_v3

  Show description for 5646ddb
  AdityaSavara

  authored
  5646ddb

• Fixing the ligical error for lower bound.

  Show description for 021c463
  AdityaSavara

  committed
  021c463

• Changed to -1E99 and +1E99 check

  Show description for 0143a83
  AdityaSavara

  committed
  0143a83

• fixing comparisons: There was actually an "abs" I had not noticed.

  AdityaSavara

  committed
  88aa845

• extra space deleted

  AdityaSavara

  committed
  d23fb31

• Cleaning up

  Show description for b311b0a
  tsikes

  committed
  b311b0a

• cleanup & working towards inclusion of pars_bnds_exist

  AdityaSavara

  committed
  15b80ec

Commits on Jan 24, 2021

• rate_constants_parameters_bnds seem to be parsed and passed correctly to CheKiPEUQ

  AdityaSavara

  committed
  9ca5549

• Adding in unbounded_indices and return_unbounded_indices code

  AdityaSavara

  committed
  20337d3

• minor syntax fixes

  AdityaSavara

  committed
  aeb14b4

• Added remove_unbounded_values calls to code to truncate arrays etc.

  AdityaSavara

  committed
  d7f14fb

• Moved more of the Bayesian_Dict fields population to init

  AdityaSavara

  committed
  5ead861

• Cleaning up print statements

  AdityaSavara

  committed
  4e514aa

• Fixing rate_constants_parameters_bnds_exist for multiple rate constants

  AdityaSavara

  committed
  faec7f6

• Update CheKiPEUQ_integration_notes.txt

  AdityaSavara

  committed
  542b47c

• Merge branch 'CheKiPEUQ_integration_v3' into CheKiPEUQ_integration_v3

  tsikes

  authored
  a8d26f1

• Che ki peuq integration v3 (#8)

  Show description for bf82a60
  

  AdityaSavara

  and

  tsikes

  authored
  bf82a60

Commits on Jan 25, 2021

• Residual Optimization Update

  Show description for 9e8d7b4
  tsikes

  committed
  9e8d7b4

• More Loss Function Changes

  tsikes

  committed
  f7740d3

• Oops

  tsikes

  committed
  eeceeb7

• Bayesian Obj Func Change

  Show description for 5eb584e
  tsikes

  committed
  5eb584e

• Bounds Error Fix

  tsikes

  committed
  e147519

• Update

  Show description for 0cf9a9c
  tsikes

  committed
  0cf9a9c

• Trying new fonts for log

  tsikes

  committed
  969099a

Commits on Jan 26, 2021

• ChekiPEUQ: First attempt to implement variance per response for too long

  AdityaSavara

  committed
  c29daa0

• Linear scaling working now, but some 'iterations' of Frhodo are freezing during CheKiPEUQ's PE_object init.

  Show description for 7c6d209
  AdityaSavara

  committed
  7c6d209

• Reduced the slowdown to the extent of not freezing

  Show description for 718c175
  AdityaSavara

  committed
  718c175

• Printing shows that the weighting array shape going into CheKiPEUQ is correct.

  AdityaSavara

  committed
  231b30b

• Fixed shape of weighting arrray passed to CheKiPEUQ

  Show description for 8dc7548
  AdityaSavara

  committed
  8dc7548

• Removing excess print statements and cleaning up.

  AdityaSavara

  committed
  1563ee1

Commits on Jan 27, 2021

• Improving heuristic slightly

  AdityaSavara

  committed
  a2e306a

• Updating version number and fixing minor error from the recent edits.

  AdityaSavara

  committed
  cec457c

• Added automatic copy rates to optimize

  tsikes

  committed
  b5b32d4

• Merge branch 'CheKiPEUQ_integration_v3' into CheKiPEUQ_integration_v3

  tsikes

  authored
  b4d5a5e

• Merge pull request #9 from AdityaSavara/CheKiPEUQ_integration_v3

  Show description for 0fe5bff
  tsikes

  authored
  0fe5bff

Commits on Jan 28, 2021

• Cleaning up the merge conflict that was dropped

  Show description for 16240dd
  AdityaSavara

  committed
  16240dd

• Remoing print statement from CheKiPUEQ_local

  AdityaSavara

  committed
  abead3e

• Weights Work

  tsikes

  committed
  a28e5cb

• Merge pull request #10 from AdityaSavara/CheKiPEUQ_integration_v3

  Show description for 0710579
  tsikes

  authored
  0710579

• Style Changes

  tsikes

  committed
  48d818a

• Silly Math Error

  tsikes

  committed
  ddc336a

Commits on Jan 29, 2021

• CheKiPEUQ changes

  Show description for 72c1374
  tsikes

  committed
  72c1374

Commits on Jan 30, 2021

• Minor fixes

  tsikes

  committed
  87ee291

• Update fit_fcn.py

  tsikes

  committed
  81012b3

Commits on Jan 31, 2021

• Nomenclature Change

  tsikes

  committed
  595a9d0

Commits on Feb 2, 2021

• Refactoring

  Show description for 8241fa2
  tsikes

  committed
  8241fa2

• Preliminary Signal Plot Changes

  tsikes

  committed
  fd3d969

Commits on Feb 3, 2021

• Weight Function Update

  Show description for 7567229
  tsikes

  committed
  7567229

Commits on Feb 4, 2021

• Implemented Uncertainty in Observable Data

  Show description for 0b71f96
  tsikes

  committed
  0b71f96

Commits on Feb 5, 2021

• Bayesian Opt Uncertainty Working

  Show description for 115b860
  tsikes

  committed
  115b860

Commits on Feb 6, 2021

• Added Shaded Unc

  Show description for 4470c12
  tsikes

  committed
  4470c12

• Uncertainty Shading

  Show description for 1cce77d
  tsikes

  committed
  1cce77d

Commits on Feb 7, 2021

• Added Abs Uncertainty

  tsikes

  committed
  23d4104

Commits on Feb 8, 2021

• Modifications to absolute uncertainty

  Show description for 743e749
  tsikes

  committed
  743e749

• Axes update in draggable

  Show description for b15fed4
  tsikes

  committed
  b15fed4

• Merge pull request #11 from tsikes/CheKiPEUQ_integration_v3

  Show description for a86576a
  tsikes

  authored
  a86576a

• GUI falloff/pressure dependent uncertainty

  tsikes

  committed
  68c9592

• Implementing rate coef/bnds on Plogs and falloff eqns

  tsikes

  committed
  e944a66

Commits on Jan 17, 2022

• Troe Optimization

  Show description for 0626afa
  tsikes

  committed
  0626afa