User-Defined Linear Map #743

cemitch99 · 2024-10-15T18:06:04Z

This is a duplicate of the draft PR #714 owned by cemitch99. Close #538

Follow-up PR will add

return transport matrices in each element
push for covariance matrix
- add: ImpactX::track_envelope

General structure. Co-authored-by: Chad Mitchell <[email protected]>

Update initialization of LinearMap element.

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Finish implementation of LinearMap element push.

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Initialize covariance matrix from distribution parameters.

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…ance-and-transport-maps

Remove unnecessary ,.

Correct naming in elements.cpp binding for LinearMap.

ax3l · 2025-01-13T06:49:45Z

src/particles/elements/mixin/lineartransport.H

+        {
+        }
+
+        //LinearTransport () = default;


After thinking a bit more about this for the follow-up PR: we want to probably create a function that returns R for each element, but we do not want to store R as a member variable -- at least not with the same class we use for pushing. Can explain in more detail after this PR, but it's mainly about the size of the class we copy to GPU for tracking purposes not not to bloat that.

Correct argument declaration for Python bindings of LinearMap in elements.cpp.

Document "Name" parameter in LinearMap.

src/initialization/InitDistribution.cpp

Modify zero-initialization of CovarianceMatrix cv.

Correct name of Rmat/R.

Fix naming of R again.

Fix number of periods.

ax3l

That's a very cool example, thank you!

examples/linear_map/README.rst

examples/linear_map/input_map.in

docs/source/usage/parameters.rst

docs/source/usage/python.rst

examples/CMakeLists.txt

Co-authored-by: Chad Mitchell <[email protected]>

docs/source/usage/workflows/add_element.rst

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docs/source/usage/python.rst

docs/source/usage/workflows/add_element.rst

Taken over from generalized version we merged to WarpX.

src/initialization/InitElement.cpp

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src/python/elements.cpp

src/initialization/InitElement.cpp

examples/CMakeLists.txt

ax3l

That looks great to me :)

src/python/elements.cpp

ax3l and others added 14 commits September 24, 2024 15:34

[Draft] Transport and Covariance Matrices

4e2a733

General structure. Co-authored-by: Chad Mitchell <[email protected]>

Update InitElement.cpp

5d09112

Update initialization of LinearMap element.

[pre-commit.ci] auto fixes from pre-commit.com hooks

7d95ca5

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Update LinearMap.H

65c9bd0

Finish implementation of LinearMap element push.

[pre-commit.ci] auto fixes from pre-commit.com hooks

2ad47d2

for more information, see https://pre-commit.ci

Update InitDistribution.cpp

c2fe2be

Initialize covariance matrix from distribution parameters.

Add Drift return linear map.

a5df0a3

Use LinearMap struct in Drift.H.

b2f158c

Merge branch 'development' into topic-covariance-and-transport-maps

0044f78

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cd4c989

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Merge remote-tracking branch 'mainline/development' into topic-covari…

a9888ce

…ance-and-transport-maps

Transport/Covariane: Use SmallMatrix

817cc51

Add Python bindings for LinearMap element.

1ef158e

Update elements.cpp

ccad983

Remove unnecessary ,.

cemitch99 changed the title ~~Topic covariance and transport maps~~ Transport and Covariance Matrices Oct 15, 2024

Update elements.cpp

2b288db

Correct naming in elements.cpp binding for LinearMap.

github-advanced-security bot found potential problems Oct 15, 2024

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cemitch99 and others added 4 commits October 23, 2024 15:15

Update elements.cpp

06718d8

Correct argument declaration for Python bindings of LinearMap in elements.cpp.

Add LinearMap to 'Named' elements.

2e57e91

Update LinearMap.H

911fbec

Document "Name" parameter in LinearMap.

Modify LinearMap Python bindings.

ac6556c

cemitch99 commented Nov 5, 2024

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Update src/initialization/InitDistribution.cpp

0444b5d

cemitch99 commented Nov 5, 2024

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cemitch99 added 2 commits November 5, 2024 11:44

Update src/initialization/InitDistribution.cpp

fa67921

Update InitDistribution.cpp

d460272

Modify zero-initialization of CovarianceMatrix cv.

This was referenced Jan 3, 2025

[Draft] Transport and Covariance Matrices #714

Closed

Small Matrix (6x6, F) AMReX-Codes/pyamrex#399

Merged

ax3l self-requested a review January 6, 2025 04:48

ax3l self-assigned this Jan 6, 2025

cemitch99 added 3 commits January 11, 2025 17:49

Update run_map.py

04be1fb

Correct name of Rmat/R.

Update run_map.py

1a36a89

Fix naming of R again.

Update input_map.in

4fa891b

Fix number of periods.