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Add beam eigenemittances to reduced diagnostics. #702

Merged
merged 54 commits into from
Oct 10, 2024
Merged

Add beam eigenemittances to reduced diagnostics. #702

merged 54 commits into from
Oct 10, 2024

Commits on Sep 13, 2024

  1. Add eigenemittance calculation.

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  3. Update CovarianceMatrixMath.H 

    Clean Doxygen and delete unused function TestMult (used for benchmarking).
    @cemitch99
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  4. Update EmittanceInvariants.cpp 

    Clean Doxygen
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  5. Update EmittanceInvariants.H 

    Clean Doxygen
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  6. Update EmittanceInvariants.cpp 

    Remove duplicate Doxygen comments in EmittanceInvariants.cpp/h
    @cemitch99
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  7. Treat special case of vanishing discriminant in Cardano's formula.

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  8. Test from ReducedDiagnostics; update ej ordering.

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  10. Add diagnostic output.

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  12. Comment print statements used for debugging.

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    cemitch99 authored Sep 13, 2024
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  13. Update ReducedBeamCharacteristics.cpp 

    Comment benchmarking call to Eigenemittance to avoid unused variable errors.
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Commits on Sep 14, 2024

  1. Add benchmark example.

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  3. Add documentation.

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  5. Update CMakeLists.txt 

    Corrected path to benchmark test files.
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  6. Update CMakeLists.txt 

    Update path for analysis scripts.
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  7. Normalize momenta by mc (dynamical units) for eigenemittances.

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Commits on Sep 16, 2024

  1. Add alternative routine for cubic roots.

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  2. Update EmittanceInvariants.cpp 

    Update default cubic roots alg.
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  3. Update CovarianceMatrixMath.H 

    Avoid subtracting complex and double types.
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  4. Temporarily comment pytest test_transformation.

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  5. Update test_transformation.py 

    Modify comment syntax c++ -> Python.
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  7. Delete commented debugging print statements.

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  8. Update EmittanceInvariants.H 

    Add literature citations.
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  9. Update EmittanceInvariants.cpp 

    Add literature citations.
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Commits on Sep 19, 2024

  1. Apply suggestions from code review 

    Correct typo; avoid possible NaN resulting from sqrt.
    @cemitch99
    cemitch99 authored Sep 19, 2024
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  2. Update src/particles/diagnostics/EmittanceInvariants.cpp 

    Use amrex::abs
    @cemitch99
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  3. Update EmittanceInvariants.cpp 

    Revert to std
    @cemitch99
    cemitch99 authored Sep 19, 2024
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Commits on Sep 24, 2024

  1. Add emittance_1,2,3 print.

    @cemitch99
    cemitch99 committed Sep 24, 2024
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  2. Finalize print of emittance_1,2,3.

    @cemitch99
    cemitch99 committed Sep 24, 2024
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  3. Add ParmParse for optional calculation.

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  5. Update test_transformation.py 

    Re-enable test_transformation.py.
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Commits on Sep 25, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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    cemitch99 and ax3l authored Sep 25, 2024
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  2. Update EmittanceInvariants.cpp 

    Add PROFILE header.
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Commits on Sep 26, 2024

  1. Update CovarianceMatrixMath.H 

    Use math functions from std::  (sqrt, pow, sin, cos, etc) -> (std::sqrt, std::pow, std::sin, std::cos, etc).
    @cemitch99
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  2. Update src/particles/diagnostics/CovarianceMatrixMath.H 

    Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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  3. Update CovarianceMatrixMath.H

    @cemitch99
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  4. Update CovarianceMatrixMath.H 

    Remove std::math for complex functions.
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  5. Use amrex:: math for complex functions.

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Commits on Oct 2, 2024

  1. Avoid copying matrices

    @ax3l
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  2. Formatting: Whitespaces 

    Only spaces
    @ax3l
    ax3l authored Oct 2, 2024
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  3. More general odd-ness test

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    ax3l authored Oct 2, 2024
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Commits on Oct 5, 2024

  1. Add conditional emittance output columns.

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  3. Add documentation for user-facing input control.

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    cemitch99 committed Oct 5, 2024
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  4. Update dataanalysis documentation of eigenemittances.

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Commits on Oct 8, 2024

  1. Update CovarianceMatrixMath.H 

    Update treatment of warnings.
    @cemitch99
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  2. Apply suggestions from code review 

    Changes to test_transformation.py were not intentional.  These were reversed per code review.

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
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Commits on Oct 10, 2024

  1. Update tests/python/test_transformation.py

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