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Add Pyomo.DOE to contrib #2294

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

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Commits on Aug 1, 2021

• upload package and examples

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Commits on Aug 3, 2021

• add a toggle for sipopt and kaug

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• add solver_options ma57 to sIPOPT

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Commits on Aug 5, 2021

• changes according to reviews

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• update grid search function to support multiple dimensions

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Commits on Aug 6, 2021

• update grid search function to support any dimension

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Commits on Aug 7, 2021

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

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Commits on Aug 9, 2021

• update figure drawing function

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Commits on Aug 10, 2021

• well commented

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Commits on Aug 15, 2021

• changes according to reviews

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

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Commits on Aug 16, 2021

• some temporary files when testing k_aug

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

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• Merge pull request #2 from jialuw96/update_sens

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Commits on Aug 18, 2021

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

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Commits on Aug 26, 2021

• update

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Commits on Aug 29, 2021

• before run sensitivity analysis with time

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Commits on Sep 2, 2021

• changes before reference

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Commits on Sep 4, 2021

• add three timers to fim_doe

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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.

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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.

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• 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."

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• 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."

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• add a direct_toggle to package.

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• enable k_aug in package for analytical models

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• update the kaug dsdp extraction sentences

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Commits on Sep 8, 2021

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

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Commits on Sep 9, 2021

• Debugged direct_kaug mode for DAE models

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Commits on Sep 15, 2021

• organize before switching branches

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Commits on Sep 16, 2021

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

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• before changing fixed bed

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Commits on Sep 17, 2021

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

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Commits on Sep 18, 2021

• Temporary changes for using package to fixed bed.

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

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• Add extra index to measurements

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• 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.

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Commits on Sep 19, 2021

• add a catch block for heatmap run

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Commits on Sep 22, 2021

• end of the day commit

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• debug k_aug

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Commits on Oct 3, 2021

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

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Commits on Oct 4, 2021

• Merge pull request #3 from Pyomo/main

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• Merge pull request #4 from Pyomo/main

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• add comments

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

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Commits on Oct 5, 2021

• resolve some reviews

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• organize this folder

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• combine measurement indexes

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Commits on Oct 6, 2021

• ready to add extra index

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

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• start pull request

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• add extra index support to sequential_finite mode

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• debug sequential_finite mode extra index

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Commits on Oct 7, 2021

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

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Commits on Oct 8, 2021

• add extra index for simultaneous mode for optimization

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• run No.2 fixed bed optimization

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Commits on Oct 9, 2021

• well commented

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Commits on Oct 11, 2021

• changes before review

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Commits on Oct 17, 2021

• changes for fixed bed

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• debug optimize_doe()

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Commits on Oct 18, 2021

• debug other modes for FIM_results

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• well commented

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Commits on Oct 23, 2021

• update measurement class

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• debug sequential_finite mode

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• debug sequential_sipopt

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Commits on Oct 24, 2021

• debug direct_kaug

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• debug different time sets for measurements

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• well commented

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Commits on Nov 21, 2021

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

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

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Commits on Dec 1, 2021

• before splitting FIM_result

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Commits on Dec 2, 2021

• update FIM_result class, add jac_splitter class, commentted.

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• Update fim_doe.py

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Commits on Dec 3, 2021

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

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Commits on Dec 4, 2021

• before merging two classes

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Commits on Dec 5, 2021

• debug new FIM_result for sequential_finite mode

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Commits on Dec 6, 2021

• changes according to comments

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Commits on Dec 7, 2021

• update all other modes

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• debug for simultaneous mode

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• update comments

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• tests

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Commits on Dec 13, 2021

• before changing measurement functions

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Commits on Dec 14, 2021

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

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• comment

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Commits on Jan 7, 2022

• organize files

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• organize files

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• organize

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Commits on Feb 16, 2022

• try to push from linux

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Commits on Feb 17, 2022

• add measurement variance

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Commits on Feb 19, 2022

• clean up kinetics case for tests

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• add regression test

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• add both tests commented

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• Added copyright notice

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Commits on Feb 22, 2022

• organize files

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• Clean up comments. Organize files.

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

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

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

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Commits on Feb 24, 2022

• update sphinx documentation in index.rst

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• Updating copyright notice

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• Updating copyright notice

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Commits on Feb 28, 2022

• add documentation, change doc strings in fim_doe for autoclass

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Commits on Mar 1, 2022

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

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Commits on Mar 12, 2022

• all changes in this branch

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• solve the y_set warning.

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Commits on Mar 13, 2022

• changes now

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• update the notebook optimization problem

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• udpate kaug objective option

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• add another simulation to optimization problem

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• update documentation

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Commits on Apr 19, 2022

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• Merge branch 'main' into doe-review

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Commits on May 9, 2022

• update to remove idaes, check if iPOPT is available

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• remove idaes sentence from the test_reactor_example.py

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• Merge branch 'main' into doe-review

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• use skipif to skip IPOPT runs

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Commits on Jul 18, 2022

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

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• fixing autoclass error

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• fixing autoclass error

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• fixing autoclass error

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• fixed autoclass error

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• add a warning about the index of measurements

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• Merge branch 'main' into doe-review

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

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Commits on Aug 9, 2022

• remove expected print sentences from docmentation

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Commits on Aug 24, 2022

• Removing cell ids in the Pyomo.DOE notebook example

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Commits on Sep 17, 2022

• address comments - part 1

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Commits on Sep 18, 2022

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Commits on Sep 19, 2022

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