Code

Add Pyomo.DOE to contrib #2294

Code

Merged

blnicho merged 199 commits intoPyomo:mainPyomo/pyomo:mainfrom jialuw96:doe-reviewjialuw96/pyomo:doe-reviewCopy head branch name to clipboardJan 30, 2023

+5,614-3

Commits

Commits on Aug 1, 2021

• upload package and examples

  jialuw96

  committed
  ba915dc

Commits on Aug 3, 2021

• add a toggle for sipopt and kaug

  jialuw96

  committed
  61f7f46

• add solver_options ma57 to sIPOPT

  jialuw96

  committed
  225647e

Commits on Aug 5, 2021

• changes according to reviews

  jialuw96

  committed
  8fb3e82

• update grid search function to support multiple dimensions

  jialuw96

  committed
  e8fbbf4

Commits on Aug 6, 2021

• update grid search function to support any dimension

  jialuw96

  committed
  f40b99b

Commits on Aug 7, 2021

• added k_aug as a solver for calculating perturbed model output. Next step is using get_dsdp()

  jialuw96

  committed
  b5a2de0

Commits on Aug 9, 2021

• update figure drawing function

  jialuw96

  committed
  f831918

Commits on Aug 10, 2021

• well commented

  jialuw96

  committed
  de7c392

Commits on Aug 15, 2021

• changes according to reviews

  jialuw96

  committed
  11c7bff

• Merge branch 'Pyomo:main' into doe-develop1

  jialuw96

  authored
  a41ce37

Commits on Aug 16, 2021

• some temporary files when testing k_aug

  jialuw96

  committed
  5a43e63

• fix an error in the doc string of get_dfds_dcds()

  jialuw96

  committed
  8d73a3f

• Merge pull request #2 from jialuw96/update_sens

  Show description for b56c897
  jialuw96

  authored
  b56c897

Commits on Aug 18, 2021

• Merge branch 'Pyomo:main' into doe-develop1

  jialuw96

  authored
  e3c7702

Commits on Aug 26, 2021

• update

  jialuw96

  committed
  1cb1195

Commits on Aug 29, 2021

• before run sensitivity analysis with time

  jialuw96

  committed
  b5f3326

Commits on Sep 2, 2021

• changes before reference

  jialuw96

  committed
  74a9e42

Commits on Sep 4, 2021

• add three timers to fim_doe

  jialuw96

  committed
  149e359

Commits on Sep 6, 2021

• update get_dsdp and get_dfds_dcds with those from IDAES repo. Only updating these functions cannot make get_dsdp() work in this repo.

  jialuw96

  committed
  0cc407e

Commits on Sep 7, 2021

• Update all functions in this file with sens.py from IDAES repo. As long as it is in sensitivity toolbox repo, it cannot work for Pyomo.DAE model, but can work with analytical models.

  jialuw96

  committed
  ce6295a

• Revert "Update all functions in this file with sens.py from IDAES repo. As long as it is in sensitivity toolbox repo, it cannot work for Pyomo.DAE model, but can work with analytical models."

  Show description for e16ac15
  jialuw96

  committed
  e16ac15

• Revert "update get_dsdp and get_dfds_dcds with those from IDAES repo. Only updating these functions cannot make get_dsdp() work in this repo."

  Show description for d1711da
  jialuw96

  committed
  d1711da

• add a direct_toggle to package.

  jialuw96

  committed
  eeed0bf

• enable k_aug in package for analytical models

  jialuw96

  committed
  b501996

• update the kaug dsdp extraction sentences

  jialuw96

  committed
  f5d82dc

Commits on Sep 8, 2021

• debugged for analytical problems. going to generate heatmaps to compare and see computational time.

  jialuw96

  committed
  63ff2ec

Commits on Sep 9, 2021

• Debugged direct_kaug mode for DAE models

  jialuw96

  committed
  e6a2999

Commits on Sep 15, 2021

• organize before switching branches

  jialuw96

  committed
  8e0c139

Commits on Sep 16, 2021

• integrate multiple versions of kinetic models to be one model. add extra arguments to package

  jialuw96

  committed
  77ae0a2

• before changing fixed bed

  jialuw96

  committed
  54abe04

Commits on Sep 17, 2021

• verify fixed bed results. going to use package for this model

  jialuw96

  committed
  d82d4e9

Commits on Sep 18, 2021

• Temporary changes for using package to fixed bed.

  jialuw96

  committed
  7d8c85c

• generalize the case where the design variables are not indexed by time

  jialuw96

  committed
  45952a5

• Add extra index to measurements

  jialuw96

  committed
  00fe3ce

• Add functions so that we can choose to read measurements from pickle file and continue. Only for sequential_finite mode now, can consider to be applied to other modes after discussion.

  jialuw96

  committed
  2303203

Commits on Sep 19, 2021

• add a catch block for heatmap run

  jialuw96

  committed
  4d6e279

Commits on Sep 22, 2021

• end of the day commit

  jialuw96

  committed
  f77da28

• debug k_aug

  jialuw96

  committed
  fb1839f

Commits on Oct 3, 2021

• integrate different versions of models by adding args toggle to the package

  jialuw96

  committed
  51d8ad5

Commits on Oct 4, 2021

• Merge pull request #3 from Pyomo/main

  Show description for 5133766
  jialuw96

  authored
  5133766

• Merge pull request #4 from Pyomo/main

  Show description for 4685d98
  jialuw96

  authored
  4685d98

• add comments

  jialuw96

  committed
  7dad29d

• Merge branch 'doe-develop1' of github.com:jialuw96/pyomo into doe-develop1

  jialuw96

  committed
  798e8d7

Commits on Oct 5, 2021

• resolve some reviews

  jialuw96

  committed
  2102f24

• organize this folder

  jialuw96

  committed
  3a57498

• combine measurement indexes

  jialuw96

  committed
  d40a618

Commits on Oct 6, 2021

• ready to add extra index

  jialuw96

  committed
  59ae4c7

• Merge pull request #1 from jialuw96/doe-develop1

  Show description for 70953d0
  jialuw96

  authored
  70953d0

• start pull request

  jialuw96

  committed
  1cefd1a

• add extra index support to sequential_finite mode

  jialuw96

  committed
  e5e93fa

• debug sequential_finite mode extra index

  jialuw96

  committed
  5aa5fc0

Commits on Oct 7, 2021

• update compute_FIM() with extra index support for all modes

  jialuw96

  committed
  e07c69a

Commits on Oct 8, 2021

• add extra index for simultaneous mode for optimization

  jialuw96

  committed
  0bda479

• run No.2 fixed bed optimization

  jialuw96

  committed
  d0b91fe

Commits on Oct 9, 2021

• well commented

  jialuw96

  committed
  c3a6238

Commits on Oct 11, 2021

• changes before review

  jialuw96

  committed
  4bcc673

Commits on Oct 17, 2021

• changes for fixed bed

  jialuw96

  committed
  0ad5a61

• debug optimize_doe()

  jialuw96

  committed
  30d671a

Commits on Oct 18, 2021

• debug other modes for FIM_results

  jialuw96

  committed
  ab92500

• well commented

  jialuw96

  committed
  5149708

Commits on Oct 23, 2021

• update measurement class

  jialuw96

  committed
  39aee6d

• debug sequential_finite mode

  jialuw96

  committed
  9fea2a5

• debug sequential_sipopt

  jialuw96

  committed
  fbc0980

Commits on Oct 24, 2021

• debug direct_kaug

  jialuw96

  committed
  ebf0d2d

• debug different time sets for measurements

  jialuw96

  committed
  6098b39

• well commented

  jialuw96

  committed
  9287505

Commits on Nov 21, 2021

• let user create measurement class; add a check_subset function to the measurement class

  jialuw96

  committed
  3fc98ae

• organize measurement class. add a test file for the measurement class.

  jialuw96

  committed
  15f42e4

Commits on Dec 1, 2021

• before splitting FIM_result

  jialuw96

  committed
  50de34c

Commits on Dec 2, 2021

• update FIM_result class, add jac_splitter class, commentted.

  jialuw96

  committed
  1da22b9

• Update fim_doe.py

  Show description for d34f034
  adowling2

  authored
  d34f034

Commits on Dec 3, 2021

• Merge pull request #6 from adowling2/patch-1

  Show description for c06aa9d
  jialuw96

  authored
  c06aa9d

Commits on Dec 4, 2021

• before merging two classes

  jialuw96

  committed
  2dd88f0

Commits on Dec 5, 2021

• debug new FIM_result for sequential_finite mode

  jialuw96

  committed
  05d8a59

Commits on Dec 6, 2021

• changes according to comments

  jialuw96

  committed
  29ae072

Commits on Dec 7, 2021

• update all other modes

  jialuw96

  committed
  7144455

• debug for simultaneous mode

  jialuw96

  committed
  430707d

• update comments

  jialuw96

  committed
  b672f0b

• tests

  jialuw96

  committed
  5d7de7c

Commits on Dec 13, 2021

• before changing measurement functions

  jialuw96

  committed
  37213df

Commits on Dec 14, 2021

• eval() cannot be used in other functions without the model. This version is for tests if needed.

  jialuw96

  committed
  e3c25f2

• comment

  jialuw96

  committed
  1a296b4

Commits on Jan 7, 2022

• organize files

  jialuw96

  committed
  0d1d75c

Commits on Jan 22, 2022

• organize files

  jialuw96

  committed
  4c13a9c

Commits on Feb 10, 2022

• organize

  jialuw96

  committed
  908d2f0

Commits on Feb 16, 2022

• try to push from linux

  jialuw96

  committed
  cfab61d

Commits on Feb 17, 2022

• add measurement variance

  jialuw96

  committed
  b6b5c9f

Commits on Feb 19, 2022

• clean up kinetics case for tests

  jialuw96

  committed
  6189843

Commits on Feb 20, 2022

• add regression test

  jialuw96

  committed
  cf1c7f9

Commits on Feb 21, 2022

• add both tests commented

  jialuw96

  committed
  d6b1f0a

• add a spot for copyright notice

  jialuw96

  committed
  aed3f29

• Added copyright notice

  adowling2

  authored
  744635b

Commits on Feb 22, 2022

• organize files

  jialuw96

  committed
  b4786c9

Commits on Feb 23, 2022

• Clean up comments. Organize files.

  jialuw96

  committed
  a54eea2

• Merge pull request #5 from jialuw96/doe-extra-index

  Show description for 186e588
  jialuw96

  authored
  186e588

• Merge branch 'doe-review' into patch-2

  jialuw96

  authored
  4904b90

• Merge pull request #7 from adowling2/patch-2

  Show description for 7390551
  jialuw96

  authored
  7390551

• update copyright notice

  jialuw96

  committed
  31a79cf

• add documentation

  jialuw96

  committed
  e73cedd

Commits on Feb 24, 2022

• update sphinx documentation in index.rst

  jialuw96

  committed
  9aefc45

Commits on Feb 25, 2022

• Updating copyright notice

  adowling2

  authored
  f986824

• Updating copyright notice

  adowling2

  authored
  d65e6de

• Update reactor_kinetics.py

  adowling2

  authored
  8129cd9

• Update copyright notice

  adowling2

  authored
  e77af1a

Commits on Feb 28, 2022

• add documentation, change doc strings in fim_doe for autoclass

  jialuw96

  committed
  eb41d00

Commits on Mar 1, 2022

• Merge pull request #10 from adowling2/patch-3

  Show description for f3de63c
  jialuw96

  authored
  f3de63c

Commits on Mar 12, 2022

• all changes in this branch

  jialuw96

  committed
  90230d2

• solve the y_set warning.

  jialuw96

  committed
  9e59dd9

Commits on Mar 13, 2022

• changes now

  jialuw96

  committed
  66032ad

Commits on Mar 14, 2022

• update the notebook optimization problem

  jialuw96

  committed
  5acbd8e

Commits on Mar 21, 2022

• update documentation

  jialuw96

  committed
  ecd62f5

Commits on Mar 23, 2022

• add uml figures

  jialuw96

  committed
  0a80c28

Commits on Mar 29, 2022

• udpate kaug objective option

  jialuw96

  committed
  7cda901

Commits on Mar 30, 2022

• add another simulation to optimization problem

  jialuw96

  committed
  c3ff1bb

Commits on Apr 8, 2022

• update documentation

  jialuw96

  committed
  a4b3f42

• Merge pull request #9 from jialuw96/doe-documentation

  Show description for a4bfecf
  jialuw96

  authored
  a4bfecf

Commits on Apr 12, 2022

• delete unused files

  jialuw96

  committed
  a5dae7a

• Delete .~Regression_test.ipynb

  jialuw96

  authored
  62a8fe5

Commits on Apr 19, 2022

• organize documentation files.

  jialuw96

  committed
  3dd385b

• fix the if_cholesky issue

  jialuw96

  committed
  315894f

• move doc to onlinedocs

  jialuw96

  committed
  f80cfec

• index.rst conflict

  jialuw96

  committed
  3dbd83e

Commits on Apr 23, 2022

• Delete .gitignore

  blnicho

  authored
  331b55b

• Delete conf.py

  blnicho

  authored
  5179214

• Merge branch 'main' into doe-review

  blnicho

  authored
  3173806

Commits on May 9, 2022

• update to remove idaes, check if iPOPT is available

  jialuw96

  committed
  679dd0f

Commits on May 10, 2022

• remove idaes sentence from the test_reactor_example.py

  jialuw96

  committed
  900a61f

Commits on May 25, 2022

• add __init__.py and put tests in a folder

  jialuw96

  committed
  7852879

• Merge branch 'main' into doe-review

  jialuw96

  authored
  724ffef

• add init file

  jialuw96

  committed
  0993a99

• Merge branch 'doe-review' of https://github.com/jialuw96/pyomo into doe-review

  jialuw96

  committed
  3fe05a6

• fix the import sentence for fim_doe in tests

  jialuw96

  committed
  2e3498a

Commits on Jun 1, 2022

• update .rst to fix example code error

  jialuw96

  committed
  fe7faab

Commits on Jun 2, 2022

• update .rst to fix code test bugs

  jialuw96

  committed
  68fee76

• fix the import numpy error

  jialuw96

  committed
  a3ee7fa

• update the matplotlib.pyplot import

  jialuw96

  committed
  55d5d00

Commits on Jun 7, 2022

• fix the continuousset error

  jialuw96

  committed
  c95794d

• debug function

  jialuw96

  committed
  bd6d9c4

Commits on Jun 9, 2022

• delete unnecessary print sentences

  jialuw96

  committed
  a0be033

Commits on Jun 13, 2022

• Merge branch 'main' into doe-review

  blnicho

  authored
  ea43ce7

Commits on Jun 21, 2022

• use skipif to skip IPOPT runs

  jialuw96

  committed
  b006a0b

• skip lines in .rst

  jialuw96

  committed
  0fdcc60

Commits on Jun 30, 2022

• Merge branch 'main' into doe-review

  blnicho

  authored
  f987b68

Commits on Jul 18, 2022

• delete unused figures, address most comments, haven't figured out the autoclass bug

  jialuw96

  committed
  ab0ab4f

• fixing autoclass error

  jialuw96

  committed
  516e93c

• fixing autoclass error

  jialuw96

  committed
  7735abb

• fixing autoclass error

  jialuw96

  committed
  4354192

• fixed autoclass error

  jialuw96

  committed
  7afe0ee

Commits on Aug 2, 2022

• Clear test files

  jialuw96

  committed
  868706b

• update the docstring quotes

  jialuw96

  committed
  1571a5e

• address comments

  jialuw96

  committed
  29ba5da

• add a warning about the index of measurements

  jialuw96

  committed
  17bbf4e

• Merge branch 'main' into doe-review

  blnicho

  authored
  9332e4c

• delete unneeded comments

  jialuw96

  committed
  8e65b2e

• Merge branch 'doe-review' of https://github.com/jialuw96/pyomo into doe-review

  jialuw96

  committed
  1c55b4a

Commits on Aug 9, 2022

• remove expected print sentences from docmentation

  jialuw96

  committed
  f09d533

Commits on Aug 24, 2022

• Removing cell ids in the Pyomo.DOE notebook example

  blnicho

  committed
  ddb7933

Commits on Sep 17, 2022

• address comments - part 1

  jialuw96

  committed
  644f04d

• change test folder name

  jialuw96

  committed
  c12985e

• debug run_grid_search

  jialuw96

  committed
  ae0f71c

• remove duplicate code

  jialuw96

  committed
  963bf90

• remove eval()s

  jialuw96

  committed
  9a9af21

Commits on Sep 18, 2022

• split compute_FIM() to call multiple methods in it

  jialuw96

  committed
  857b1f7

• delete current tests

  jialuw96

  committed
  09356c4

• add tests

  jialuw96

  committed
  892494d

Commits on Sep 19, 2022

• create tests and py files for the tutorial case

  jialuw96

  committed
  72938c8

• debug the tests

  jialuw96

  committed
  2302104

• add __init__ to directory

  jialuw96

  committed
  9f562bd

Commits on Oct 11, 2022

• Merge branch 'main' into doe-review

  blnicho

  authored
  cbfa5a9

Commits on Oct 18, 2022

• Merge branch 'main' into doe-review

  blnicho

  authored
  970903d

Commits on Oct 31, 2022

• changes the first solve code in fim_doe. TODO: add toggle

  jialuw96

  committed
  23876ac

• add skip sentence to tests

  jialuw96

  committed
  be22386

• Merge branch 'main' into doe-review

  blnicho

  authored
  3a3468b

Commits on Nov 1, 2022

• update optimize_doe test

  jialuw96

  committed
  657df9e

Commits on Nov 2, 2022

• add initialization to L matrix

  jialuw96

  committed
  11231b5

• update tests

  jialuw96

  committed
  33ce678

• update test

  jialuw96

  committed
  28b795d

Commits on Nov 6, 2022

• remove build files

  jialuw96

  committed
  a88f591

• change copyright, add license

  jialuw96

  committed
  e184a06

Commits on Nov 7, 2022

• change print to logging

  jialuw96

  committed
  e3a2976

Commits on Dec 6, 2022

• split files, change licsence

  jialuw96

  committed
  c3608d9

Commits on Dec 11, 2022

• address most comments; Haven't debugged yet

  jialuw96

  committed
  8d27936

• finish changing.

  jialuw96

  committed
  61aec70

• debug onlineDocs

  jialuw96

  committed
  e7d3aba

Commits on Dec 19, 2022

• Merge branch 'main' into doe-review

  blnicho

  authored
  b791e5e

Commits on Dec 20, 2022

• Merge branch 'main' into doe-review

  blnicho

  authored
  4b77d6f

Commits on Jan 9, 2023

• update Pyomo.DoE name and import sentences

  jialuw96

  committed
  6ebb08e

Commits on Jan 12, 2023

• import sentences changed

  jialuw96

  committed
  9296c39

• update import sentences

  jialuw96

  committed
  883a971

Commits on Jan 13, 2023

• Merge branch 'main' into doe-review

  blnicho

  authored
  b7423e6

Commits on Jan 20, 2023

• update tests and other changes according to reviews

  jialuw96

  committed
  ea25894

• Merge branch 'doe-review' of https://github.com/jialuw96/pyomo into doe-review

  jialuw96

  committed
  5d361bc

Commits on Jan 23, 2023

• fix the test errors about k_aug

  jialuw96

  committed
  01c3cd6

• clean comments; fix test error

  jialuw96

  committed
  2ebee4d

• fix the cannot find pandas test error

  jialuw96

  committed
  6e744d5

Commits on Jan 24, 2023

• Merge branch 'main' into doe-review

  mrmundt

  authored
  1b610cb

Commits on Jan 25, 2023

• Skipping the reactor kinetics example when Numpy and Pandas are not available

  blnicho

  authored
  fa6268e

• fix doctest errors

  jialuw96

  committed
  4d504f1