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Add Pyomo.DOE to contrib #2294

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ba915dc
upload package and examples
jialuw96 Aug 1, 2021
61f7f46
add a toggle for sipopt and kaug
jialuw96 Aug 3, 2021
225647e
add solver_options ma57 to sIPOPT
jialuw96 Aug 3, 2021
8fb3e82
changes according to reviews
jialuw96 Aug 5, 2021
e8fbbf4
update grid search function to support multiple dimensions
jialuw96 Aug 5, 2021
f40b99b
update grid search function to support any dimension
jialuw96 Aug 6, 2021
b5a2de0
added k_aug as a solver for calculating perturbed model output. Next …
jialuw96 Aug 7, 2021
f831918
update figure drawing function
jialuw96 Aug 9, 2021
de7c392
well commented
jialuw96 Aug 10, 2021
11c7bff
changes according to reviews
jialuw96 Aug 15, 2021
a41ce37
Merge branch 'Pyomo:main' into doe-develop1
jialuw96 Aug 15, 2021
5a43e63
some temporary files when testing k_aug
jialuw96 Aug 16, 2021
8d73a3f
fix an error in the doc string of get_dfds_dcds()
jialuw96 Aug 16, 2021
b56c897
Merge pull request #2 from jialuw96/update_sens
jialuw96 Aug 16, 2021
e3c7702
Merge branch 'Pyomo:main' into doe-develop1
jialuw96 Aug 18, 2021
1cb1195
update
jialuw96 Aug 26, 2021
b5f3326
before run sensitivity analysis with time
jialuw96 Aug 29, 2021
74a9e42
changes before reference
jialuw96 Sep 2, 2021
149e359
add three timers to fim_doe
jialuw96 Sep 4, 2021
0cc407e
update get_dsdp and get_dfds_dcds with those from IDAES repo. Only up…
jialuw96 Sep 6, 2021
ce6295a
Update all functions in this file with sens.py from IDAES repo. As lo…
jialuw96 Sep 7, 2021
e16ac15
Revert "Update all functions in this file with sens.py from IDAES rep…
jialuw96 Sep 7, 2021
d1711da
Revert "update get_dsdp and get_dfds_dcds with those from IDAES repo.…
jialuw96 Sep 7, 2021
eeed0bf
add a direct_toggle to package.
jialuw96 Sep 7, 2021
b501996
enable k_aug in package for analytical models
jialuw96 Sep 7, 2021
f5d82dc
update the kaug dsdp extraction sentences
jialuw96 Sep 7, 2021
63ff2ec
debugged for analytical problems. going to generate heatmaps to compa…
jialuw96 Sep 8, 2021
e6a2999
Debugged direct_kaug mode for DAE models
jialuw96 Sep 9, 2021
8e0c139
organize before switching branches
jialuw96 Sep 15, 2021
77ae0a2
integrate multiple versions of kinetic models to be one model. add ex…
jialuw96 Sep 16, 2021
54abe04
before changing fixed bed
jialuw96 Sep 16, 2021
d82d4e9
verify fixed bed results. going to use package for this model
jialuw96 Sep 17, 2021
7d8c85c
Temporary changes for using package to fixed bed.
jialuw96 Sep 18, 2021
45952a5
generalize the case where the design variables are not indexed by time
jialuw96 Sep 18, 2021
00fe3ce
Add extra index to measurements
jialuw96 Sep 18, 2021
2303203
Add functions so that we can choose to read measurements from pickle…
jialuw96 Sep 18, 2021
4d6e279
add a catch block for heatmap run
jialuw96 Sep 19, 2021
f77da28
end of the day commit
jialuw96 Sep 22, 2021
fb1839f
debug k_aug
jialuw96 Sep 22, 2021
51d8ad5
integrate different versions of models by adding args toggle to the p…
jialuw96 Oct 3, 2021
5133766
Merge pull request #3 from Pyomo/main
jialuw96 Oct 4, 2021
4685d98
Merge pull request #4 from Pyomo/main
jialuw96 Oct 4, 2021
7dad29d
add comments
jialuw96 Oct 4, 2021
798e8d7
Merge branch 'doe-develop1' of github.com:jialuw96/pyomo into doe-dev…
jialuw96 Oct 4, 2021
2102f24
resolve some reviews
jialuw96 Oct 5, 2021
3a57498
organize this folder
jialuw96 Oct 5, 2021
d40a618
combine measurement indexes
jialuw96 Oct 5, 2021
59ae4c7
ready to add extra index
jialuw96 Oct 6, 2021
70953d0
Merge pull request #1 from jialuw96/doe-develop1
jialuw96 Oct 6, 2021
1cefd1a
start pull request
jialuw96 Oct 6, 2021
e5e93fa
add extra index support to sequential_finite mode
jialuw96 Oct 6, 2021
5aa5fc0
debug sequential_finite mode extra index
jialuw96 Oct 6, 2021
e07c69a
update compute_FIM() with extra index support for all modes
jialuw96 Oct 7, 2021
0bda479
add extra index for simultaneous mode for optimization
jialuw96 Oct 8, 2021
d0b91fe
run No.2 fixed bed optimization
jialuw96 Oct 8, 2021
c3a6238
well commented
jialuw96 Oct 9, 2021
4bcc673
changes before review
jialuw96 Oct 11, 2021
0ad5a61
changes for fixed bed
jialuw96 Oct 17, 2021
30d671a
debug optimize_doe()
jialuw96 Oct 17, 2021
ab92500
debug other modes for FIM_results
jialuw96 Oct 18, 2021
5149708
well commented
jialuw96 Oct 18, 2021
39aee6d
update measurement class
jialuw96 Oct 23, 2021
9fea2a5
debug sequential_finite mode
jialuw96 Oct 23, 2021
fbc0980
debug sequential_sipopt
jialuw96 Oct 23, 2021
ebf0d2d
debug direct_kaug
jialuw96 Oct 24, 2021
6098b39
debug different time sets for measurements
jialuw96 Oct 24, 2021
9287505
well commented
jialuw96 Oct 24, 2021
3fc98ae
let user create measurement class; add a check_subset function to the…
jialuw96 Nov 21, 2021
15f42e4
organize measurement class. add a test file for the measurement class.
jialuw96 Nov 21, 2021
50de34c
before splitting FIM_result
jialuw96 Dec 1, 2021
1da22b9
update FIM_result class, add jac_splitter class, commentted.
jialuw96 Dec 2, 2021
d34f034
Update fim_doe.py
adowling2 Dec 2, 2021
c06aa9d
Merge pull request #6 from adowling2/patch-1
jialuw96 Dec 3, 2021
2dd88f0
before merging two classes
jialuw96 Dec 4, 2021
05d8a59
debug new FIM_result for sequential_finite mode
jialuw96 Dec 5, 2021
29ae072
changes according to comments
jialuw96 Dec 6, 2021
7144455
update all other modes
jialuw96 Dec 7, 2021
430707d
debug for simultaneous mode
jialuw96 Dec 7, 2021
b672f0b
update comments
jialuw96 Dec 7, 2021
5d7de7c
tests
jialuw96 Dec 7, 2021
37213df
before changing measurement functions
jialuw96 Dec 13, 2021
e3c25f2
eval() cannot be used in other functions without the model. This vers…
jialuw96 Dec 14, 2021
1a296b4
comment
jialuw96 Dec 14, 2021
0d1d75c
organize files
jialuw96 Jan 7, 2022
4c13a9c
organize files
jialuw96 Jan 22, 2022
908d2f0
organize
jialuw96 Feb 10, 2022
cfab61d
try to push from linux
jialuw96 Feb 16, 2022
b6b5c9f
add measurement variance
jialuw96 Feb 17, 2022
6189843
clean up kinetics case for tests
jialuw96 Feb 19, 2022
cf1c7f9
add regression test
jialuw96 Feb 20, 2022
d6b1f0a
add both tests commented
jialuw96 Feb 21, 2022
aed3f29
add a spot for copyright notice
jialuw96 Feb 21, 2022
744635b
Added copyright notice
adowling2 Feb 21, 2022
b4786c9
organize files
jialuw96 Feb 22, 2022
a54eea2
Clean up comments. Organize files.
jialuw96 Feb 23, 2022
186e588
Merge pull request #5 from jialuw96/doe-extra-index
jialuw96 Feb 23, 2022
4904b90
Merge branch 'doe-review' into patch-2
jialuw96 Feb 23, 2022
7390551
Merge pull request #7 from adowling2/patch-2
jialuw96 Feb 23, 2022
31a79cf
update copyright notice
jialuw96 Feb 23, 2022
e73cedd
add documentation
jialuw96 Feb 23, 2022
9aefc45
update sphinx documentation in index.rst
jialuw96 Feb 24, 2022
f986824
Updating copyright notice
adowling2 Feb 25, 2022
d65e6de
Updating copyright notice
adowling2 Feb 25, 2022
8129cd9
Update reactor_kinetics.py
adowling2 Feb 25, 2022
e77af1a
Update copyright notice
adowling2 Feb 25, 2022
eb41d00
add documentation, change doc strings in fim_doe for autoclass
jialuw96 Feb 28, 2022
f3de63c
Merge pull request #10 from adowling2/patch-3
jialuw96 Mar 1, 2022
90230d2
all changes in this branch
jialuw96 Mar 12, 2022
9e59dd9
solve the y_set warning.
jialuw96 Mar 12, 2022
66032ad
changes now
jialuw96 Mar 13, 2022
5acbd8e
update the notebook optimization problem
jialuw96 Mar 14, 2022
ecd62f5
update documentation
jialuw96 Mar 21, 2022
0a80c28
add uml figures
jialuw96 Mar 23, 2022
7cda901
udpate kaug objective option
jialuw96 Mar 29, 2022
c3ff1bb
add another simulation to optimization problem
jialuw96 Mar 30, 2022
a4b3f42
update documentation
jialuw96 Apr 8, 2022
a4bfecf
Merge pull request #9 from jialuw96/doe-documentation
jialuw96 Apr 8, 2022
a5dae7a
delete unused files
jialuw96 Apr 12, 2022
62a8fe5
Delete .~Regression_test.ipynb
jialuw96 Apr 12, 2022
3dd385b
organize documentation files.
jialuw96 Apr 19, 2022
315894f
fix the if_cholesky issue
jialuw96 Apr 19, 2022
f80cfec
move doc to onlinedocs
jialuw96 Apr 19, 2022
3dbd83e
index.rst conflict
jialuw96 Apr 19, 2022
331b55b
Delete .gitignore
blnicho Apr 23, 2022
5179214
Delete conf.py
blnicho Apr 23, 2022
3173806
Merge branch 'main' into doe-review
blnicho Apr 23, 2022
679dd0f
update to remove idaes, check if iPOPT is available
jialuw96 May 9, 2022
900a61f
remove idaes sentence from the test_reactor_example.py
jialuw96 May 10, 2022
7852879
add __init__.py and put tests in a folder
jialuw96 May 25, 2022
724ffef
Merge branch 'main' into doe-review
jialuw96 May 25, 2022
0993a99
add init file
jialuw96 May 25, 2022
3fe05a6
Merge branch 'doe-review' of https://github.com/jialuw96/pyomo into d…
jialuw96 May 25, 2022
2e3498a
fix the import sentence for fim_doe in tests
jialuw96 May 25, 2022
fe7faab
update .rst to fix example code error
jialuw96 Jun 1, 2022
68fee76
update .rst to fix code test bugs
jialuw96 Jun 2, 2022
a3ee7fa
fix the import numpy error
jialuw96 Jun 2, 2022
55d5d00
update the matplotlib.pyplot import
jialuw96 Jun 2, 2022
c95794d
fix the continuousset error
jialuw96 Jun 7, 2022
bd6d9c4
debug function
jialuw96 Jun 7, 2022
a0be033
delete unnecessary print sentences
jialuw96 Jun 9, 2022
ea43ce7
Merge branch 'main' into doe-review
blnicho Jun 13, 2022
b006a0b
use skipif to skip IPOPT runs
jialuw96 Jun 21, 2022
0fdcc60
skip lines in .rst
jialuw96 Jun 21, 2022
f987b68
Merge branch 'main' into doe-review
blnicho Jun 30, 2022
ab0ab4f
delete unused figures, address most comments, haven't figured out the…
jialuw96 Jul 18, 2022
516e93c
fixing autoclass error
jialuw96 Jul 18, 2022
7735abb
fixing autoclass error
jialuw96 Jul 18, 2022
4354192
fixing autoclass error
jialuw96 Jul 18, 2022
7afe0ee
fixed autoclass error
jialuw96 Jul 18, 2022
868706b
Clear test files
jialuw96 Aug 2, 2022
1571a5e
update the docstring quotes
jialuw96 Aug 2, 2022
29ba5da
address comments
jialuw96 Aug 2, 2022
17bbf4e
add a warning about the index of measurements
jialuw96 Aug 2, 2022
9332e4c
Merge branch 'main' into doe-review
blnicho Aug 2, 2022
8e65b2e
delete unneeded comments
jialuw96 Aug 2, 2022
1c55b4a
Merge branch 'doe-review' of https://github.com/jialuw96/pyomo into d…
jialuw96 Aug 2, 2022
f09d533
remove expected print sentences from docmentation
jialuw96 Aug 9, 2022
ddb7933
Removing cell ids in the Pyomo.DOE notebook example
blnicho Aug 24, 2022
644f04d
address comments - part 1
jialuw96 Sep 17, 2022
c12985e
change test folder name
jialuw96 Sep 17, 2022
ae0f71c
debug run_grid_search
jialuw96 Sep 17, 2022
963bf90
remove duplicate code
jialuw96 Sep 17, 2022
9a9af21
remove eval()s
jialuw96 Sep 17, 2022
857b1f7
split compute_FIM() to call multiple methods in it
jialuw96 Sep 18, 2022
09356c4
delete current tests
jialuw96 Sep 18, 2022
892494d
add tests
jialuw96 Sep 18, 2022
72938c8
create tests and py files for the tutorial case
jialuw96 Sep 19, 2022
2302104
debug the tests
jialuw96 Sep 19, 2022
9f562bd
add __init__ to directory
jialuw96 Sep 19, 2022
cbfa5a9
Merge branch 'main' into doe-review
blnicho Oct 11, 2022
970903d
Merge branch 'main' into doe-review
blnicho Oct 18, 2022
23876ac
changes the first solve code in fim_doe. TODO: add toggle
jialuw96 Oct 31, 2022
be22386
add skip sentence to tests
jialuw96 Oct 31, 2022
3a3468b
Merge branch 'main' into doe-review
blnicho Oct 31, 2022
657df9e
update optimize_doe test
jialuw96 Nov 1, 2022
11231b5
add initialization to L matrix
jialuw96 Nov 2, 2022
33ce678
update tests
jialuw96 Nov 2, 2022
28b795d
update test
jialuw96 Nov 2, 2022
a88f591
remove build files
jialuw96 Nov 6, 2022
e184a06
change copyright, add license
jialuw96 Nov 6, 2022
e3a2976
change print to logging
jialuw96 Nov 7, 2022
c3608d9
split files, change licsence
jialuw96 Dec 6, 2022
8d27936
address most comments; Haven't debugged yet
jialuw96 Dec 11, 2022
61aec70
finish changing.
jialuw96 Dec 11, 2022
e7d3aba
debug onlineDocs
jialuw96 Dec 11, 2022
b791e5e
Merge branch 'main' into doe-review
blnicho Dec 19, 2022
4b77d6f
Merge branch 'main' into doe-review
blnicho Dec 20, 2022
6ebb08e
update Pyomo.DoE name and import sentences
jialuw96 Jan 9, 2023
9296c39
import sentences changed
jialuw96 Jan 12, 2023
883a971
update import sentences
jialuw96 Jan 12, 2023
b7423e6
Merge branch 'main' into doe-review
blnicho Jan 13, 2023
ea25894
update tests and other changes according to reviews
jialuw96 Jan 20, 2023
5d361bc
Merge branch 'doe-review' of https://github.com/jialuw96/pyomo into d…
jialuw96 Jan 20, 2023
01c3cd6
fix the test errors about k_aug
jialuw96 Jan 23, 2023
2ebee4d
clean comments; fix test error
jialuw96 Jan 23, 2023
6e744d5
fix the cannot find pandas test error
jialuw96 Jan 23, 2023
1b610cb
Merge branch 'main' into doe-review
mrmundt Jan 24, 2023
fa6268e
Skipping the reactor kinetics example when Numpy and Pandas are not a…
blnicho Jan 25, 2023
4d504f1
fix doctest errors
jialuw96 Jan 25, 2023
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43 changes: 43 additions & 0 deletions doc/OnlineDocs/contributed_packages/doe/CCSI-license.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,43 @@
# Pyomo.DoE was originally developed as part of the Carbon Capture Simulation for Industry
# Impact (CCSI2) project under the following license:
#
# *** License Agreement ***
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#
# Pyomo.DoE Copyright (c) 2022, by the software owners: TRIAD National Security, LLC., Lawrence
# Livermore National Security, LLC., Lawrence Berkeley National Laboratory,
# Pacific Northwest National Laboratory, Battelle Memorial Institute, University of Notre Dame,
# The University of Pittsburgh, The University of Texas at Austin, University of Toledo,
# West Virginia University, et al. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted provided
# that the following conditions are met:
# (1) Redistributions of source code must retain the above copyright notice, this list of conditions and the
# following disclaimer.
# (2) Redistributions in binary form must reproduce the above copyright notice, this list of conditions and
# the following disclaimer in the documentation and/or other materials provided with the distribution.
# (3) Neither the name of the Carbon Capture Simulation for Industry Impact,
# TRIAD National Security, LLC., Lawrence Livermore National Security, LLC.,
# Lawrence Berkeley National Laboratory, Pacific Northwest National Laboratory,
# Battelle Memorial Institute, University of Notre Dame, The University of Pittsburgh,
# U.S. Dept. of Energy nor the names of its contributors may be used to endorse or promote products
# derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
# THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
# THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features,
# functionality or performance of the source code ("Enhancements") to anyone; however, if you choose to
# make your Enhancements available either publicly, or directly to Lawrence Berkeley National Laboratory,
# without imposing a separate written license agreement for such Enhancements, then you hereby grant
# the following license: a non-exclusive, royalty-free perpetual license to install, use, modify, prepare
# derivative works, incorporate into other computer software, distribute, and sublicense such
# enhancements or derivative works thereof, in binary and source code form.
#
# Lead Developers: Jialu Wang and Alexander Dowling, University of Notre Dame
424 changes: 424 additions & 0 deletions doc/OnlineDocs/contributed_packages/doe/doe.rst

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1 change: 1 addition & 0 deletions doc/OnlineDocs/contributed_packages/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ Contributed packages distributed with Pyomo:
:maxdepth: 1

community.rst
doe/doe.rst
gdpopt.rst
iis.rst
mindtpy.rst
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13 changes: 13 additions & 0 deletions pyomo/contrib/doe/__init__.py
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# ___________________________________________________________________________
#
# Pyomo: Python Optimization Modeling Objects
# Copyright 2017 National Technology and Engineering Solutions of Sandia, LLC
# Under the terms of Contract DE-NA0003525 with National Technology and
# Engineering Solutions of Sandia, LLC, the U.S. Government retains certain
# rights in this software.
# This software is distributed under the 3-clause BSD License.
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# ___________________________________________________________________________
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from .measurements import Measurements
from .doe import DesignOfExperiments
from .scenario import Scenario_generator
from .result import FisherResults, GridSearchResult
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