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Trapping, extended to (a) enstrophy, and (b) local trapping #536

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merged 100 commits into from
Jul 31, 2024
Merged

Trapping, extended to (a) enstrophy, and (b) local trapping #536

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312f0c2
Made a new branch where the generalized trapping SINDy work will go.
Jan 11, 2022
2478bd4
Added example 16 with all the new trapping investigations
Feb 14, 2022
7eaf249
Still working on trapping example.
Feb 15, 2022
8da5db4
Added some more changes. Going to merge the main branch in
Feb 20, 2022
95217b1
Merged in the main branch.
Feb 20, 2022
b4b53a1
Adding the new trapping examples, consolidated trapping SR3 algorithm…
Feb 23, 2022
5be87a2
Deleted the older trapping generalized sr3 file, and think I fixed th…
Feb 23, 2022
675fa06
Still working on getting some of the new trapping loss functions work…
Feb 25, 2022
b326ccb
Added new file to get Mai started on this branch. Merging in main bra…
Nov 4, 2022
7abb697
merged in the main branch
Nov 4, 2022
e5ad333
Cleaned up a notebook for Mai to work on.
Nov 6, 2022
483f8f4
PT_ added and fix the PQ_tensor
MPeng5 Feb 8, 2023
695af36
Committing current version of the trapping notebook so I can move to …
Feb 14, 2023
ba435e0
P modified for continuing working on the optimizer
Feb 17, 2023
51bfc4e
P modified to work on the optimizer
Feb 17, 2023
7c11d12
some TODOs updated, follow the TODOs
MPeng5 Feb 21, 2023
e15a07e
Merge branch 'master' into trapping_extended
MPeng5 Feb 21, 2023
1f00e03
modified optimizer now works for Lorenz and MHD model, wait for poten…
MPeng5 Feb 23, 2023
0742399
fix PT check
MPeng5 Feb 23, 2023
7f307fc
Simplified and reran the trapping notebook, which is looking good. Al…
Feb 24, 2023
e7ecae1
updated stability check in notebook
MPeng5 Feb 26, 2023
831d15e
Fixed some bugs. Continue to work on the radius next week
MPeng5 Feb 27, 2023
7f0d95a
updated the definition for constraints
MPeng5 Mar 1, 2023
80d3c92
Merge branch 'trapping_extended' of https://github.com/dynamicslab/py…
Mar 7, 2023
631c51e
fixed small bugs in _reduce
MPeng5 Mar 9, 2023
187eb67
tried with suitable beta values
MPeng5 Mar 9, 2023
77baf32
added stability radius drawing after 'soft constraint'
MPeng5 Mar 10, 2023
023744e
Merge branch 'trapping_extended' of https://github.com/dynamicslab/py…
Mar 14, 2023
6178df9
Added a fix to the soft constraints functionality. Issue was the resh…
Mar 17, 2023
d31556c
Think I fixed the sphinx issue and added unit tests for python3.9 to …
Mar 17, 2023
330a28d
added a projection operator for the bias term
MPeng5 Mar 25, 2023
d02f4c2
fixed a bug in the optimizer. Continue to work on the notebook
MPeng5 Mar 27, 2023
3106d8c
Merge branch 'trapping_extended' of https://github.com/dynamicslab/py…
Mar 27, 2023
bad090d
Updated the example 16 notebook for the enstrophy.
Apr 7, 2023
1d27108
Merge branch 'trapping_extended' of https://github.com/dynamicslab/py…
Apr 12, 2023
902bf57
fixed the stability radius and continue work on the notebook on Friday
MPeng5 Apr 14, 2023
7a63b2c
Merge branch 'trapping_extended' of https://github.com/dynamicslab/py…
Apr 14, 2023
c68b873
local stability radius well defined. More examples to show
MPeng5 Apr 19, 2023
0d90a86
Merge branch 'trapping_extended' of https://github.com/dynamicslab/py…
Apr 19, 2023
5adc7f0
Removed TODOs
Apr 19, 2023
78b4645
Updated some plots
Apr 21, 2023
2efe993
Renamed and reorganized some scripts. Added the von karman example us…
Apr 23, 2023
ba71846
Merge branch 'trapping_extended' of https://github.com/dynamicslab/py…
Apr 23, 2023
3ec8481
Reorganized the trapping files under a single directory 8_trapping_si…
Apr 26, 2023
4327510
cleaned repeating variables/definitions in functions
MPeng5 Apr 27, 2023
46ac661
Added the plot of trapping region of Lorenze. Renamed some of the fun…
MPeng5 May 9, 2023
7358911
Added noise to the Lorenz example. Need to fix the std
MPeng5 May 19, 2023
6c66c97
A contour of the evolution of the kinetic energy of 2d globally stabl…
May 23, 2023
e9d64c9
More levels added
May 23, 2023
6aa3e76
Updating notebook but not done comparing the lorenz noisy data perfor…
Jun 22, 2023
59a335b
Played around with the enstrophy version of the trapping theorem and …
Jun 25, 2023
e956ce7
when check stability, print out the max deviation from having zero to…
MPeng5 Aug 6, 2023
497de09
fixed the trap_progress_plots: legend 'unstable -> possibly unstable'
MPeng5 Aug 17, 2023
8d46f27
updated some results
MPeng5 Dec 24, 2023
d6ee083
Fixed issue seen for local trapping theorem with enstrophy on the von…
akaptano Jan 11, 2024
ff30661
added switch to control the bias term in making constraints
Apr 2, 2024
779eb10
Merge master CI
Jacob-Stevens-Haas Apr 17, 2024
ef9c63e
CLN: Fix mispelling of 'trajectories'
Jacob-Stevens-Haas Apr 17, 2024
90e0f75
BLD: Remove conflict with master pyproject.toml
Jacob-Stevens-Haas Apr 17, 2024
61120d9
CLN: extract PQ and PL to mirror trapping-resolve
Jacob-Stevens-Haas May 13, 2024
60ab879
CLN (trapping): No need to check matrix we just created
Jacob-Stevens-Haas May 13, 2024
2654a8a
CLN: Extract building the PC tensor
Jacob-Stevens-Haas May 13, 2024
b8d8feb
CI: Change test strategy from fail-fast to run always
Jacob-Stevens-Haas May 7, 2024
3dd8ea2
BLD: add trapping requirements to their own file
Jacob-Stevens-Haas May 25, 2024
7126b0e
Merge pull request #499 from dynamicslab/trapping_extended-jake
Jacob-Stevens-Haas May 26, 2024
b8faec0
feat (trapping): change initialization to match master
Jacob-Stevens-Haas May 26, 2024
c69e247
cln: align simple initialization and admin work with master
Jacob-Stevens-Haas May 26, 2024
afa25db
cln: offload some of _solve_sparse_relax_and_split() to ConstrainedSR3
Jacob-Stevens-Haas May 26, 2024
f463b18
Backport polynomial library fixes to trapping_extended
Jacob-Stevens-Haas May 30, 2024
3436aed
Backport changes to BaseOptimizer, SR3, and ConstrainedSR3
Jacob-Stevens-Haas May 30, 2024
2d141d9
CLN: specify nonsparse rs steps as "if local trapping"
Jacob-Stevens-Haas May 30, 2024
02b5a8a
CLN: Align a few bits and pieces to trapping-resolve
Jacob-Stevens-Haas May 30, 2024
ecdd800
fix: some function calls
Jacob-Stevens-Haas Jun 1, 2024
0254032
Add option to make PMatrix using global stability
Jacob-Stevens-Haas Jun 2, 2024
70fbb67
update objective to align with trapping-resolve
Jacob-Stevens-Haas Jun 2, 2024
4426965
cln: Split global/local math in _solve_m_relax_and_split
Jacob-Stevens-Haas Jun 2, 2024
11dcb02
Merge pull request #513 from dynamicslab/trapping_extended-jake
Jacob-Stevens-Haas Jun 2, 2024
39870b4
Merge branch 'trapping_extended-jake' into trapping-resolve
Jacob-Stevens-Haas Jun 3, 2024
7fcd5de
Merge pull request #516 from dynamicslab/trapping-resolve
Jacob-Stevens-Haas Jun 4, 2024
fd51517
test (trapping): adjust trap test params to compatible _include_bias
Jacob-Stevens-Haas Jun 4, 2024
76b7dbf
fix: Make Gradient descent on current point
Jacob-Stevens-Haas Jun 19, 2024
a7b1464
NBK: Add notebook scripts to examples
Jacob-Stevens-Haas Jun 19, 2024
bc0a98c
NBK: Restore Mai's value of alpha_m in VK Street (revert accident)
Jacob-Stevens-Haas Jun 19, 2024
ab7c344
NBK: Lorenz needs accel=False
Jacob-Stevens-Haas Jun 19, 2024
872d014
TST: Add much more robust testing for trapping constraint
Jacob-Stevens-Haas Jun 28, 2024
6444890
BUG: Create correct number of a_i, a_j^2 constraints in trapping
Jacob-Stevens-Haas Jun 28, 2024
e6013cd
Removed the if statements between global and local so they use the sa…
akaptano Jun 28, 2024
037afd3
Got the other example files working reasonably well again.
akaptano Jun 28, 2024
280869a
Increasing rcond parameter in the constrained pinv solve immediately …
akaptano Jun 28, 2024
76f18a2
NBK: Add script for von Karman street
Jacob-Stevens-Haas Jun 30, 2024
8b301b7
NBK: Fixed trapping extended, dysts notebooks
Jacob-Stevens-Haas Jul 11, 2024
acc72e5
test: Remove obsolete accel Trapping arg from tests
Jacob-Stevens-Haas Jul 23, 2024
958e246
tst: Add enstrophy tests
Jacob-Stevens-Haas Jul 23, 2024
263dea1
fix: Apply correct constraints to enstrophy trapping
Jacob-Stevens-Haas Jul 23, 2024
45754aa
Merge branch 'trapping_extended-jake' into trapping_extended
Jacob-Stevens-Haas Jul 23, 2024
8eab533
TST: Improve conditioning of enstrophy test
Jacob-Stevens-Haas Jul 29, 2024
4f5f172
DOC: Fix doc build with new trapping notebooks
Jacob-Stevens-Haas Jul 29, 2024
d3214b9
Merge branch 'trapping_extended-jake' into trapping_extended
Jacob-Stevens-Haas Jul 29, 2024
a65b801
TST: Skip testing notebook 8, which requires additional packages
Jacob-Stevens-Haas Jul 30, 2024
94febf9
NBK: Save updated versions of all notebooks
Jacob-Stevens-Haas Jul 31, 2024
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4 changes: 4 additions & 0 deletions .gitattributes
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# Interpret Jupyter notebooks as Python
*.ipynb linguist-language=Python

*.ipynb diff=jupyternotebook

*.ipynb merge=jupyternotebook
1 change: 1 addition & 0 deletions examples/8_trapping_sindy_examples/.gitignore
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*.pdf
1,070 changes: 1,070 additions & 0 deletions examples/8_trapping_sindy_examples/dysts_examples.ipynb
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