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Feature gyroaverages#187

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johnomotani merged 34 commits intomastermabarnes/moment_kinetics:masterfrom feature-gyroaveragesmabarnes/moment_kinetics:feature-gyroaveragesCopy head branch name to clipboardApr 24, 2024

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Commits on Feb 28, 2024

• Addition of new module to take a gyroaverage of a spatial field, including test in the test_scripts folder. Currently this version runs but produces nonsensical results for some choices of the inpu…

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Commits on Feb 29, 2024

• Change behaviour of gyroaverage to set to zero any <field> where the gyroaverage line integral exits the domain. This change makes it easier to understand if the core numerical method is correct. C…

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• Correct position of bzeta in z and r positions taken by particles in a gyroaverage. Thanks to S. Newton for spotting the error.

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• Make phase of gyroangle consistent with notes.

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Commits on Mar 2, 2024

• Extend gyroaverge operator to support periodic boundary conditions.

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Commits on Mar 3, 2024

• Introduce test of gyroaverage based on the exact gyroaverage of a periodic function with a single wavenumber in each of the z and r dimensions. The test confirms that for reasonable resolutions (se…

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• Incomplete experimental changes adding the gyroaverage to the ion species. The gyroaverage of the fields is easily accomplished by adding new gfields which contain the necessary gyroaverages. Addin…

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Commits on Mar 6, 2024

• Refactored calculation of moments so that all diagnostic and derived moments are computed in a single function. This permits the use of a gyroaveraged distribution function in a single location in …

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• Update test script to also test the gyroaverage function used to apply the matrix to the pdf. Note that these functions require further changes to make the use the distributed and shared-memory MPI…

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• Initial check-in test for gyroaverages for periodic test functions. Catch certain errors for choosing ielement by reducing the zero value, and linking the two if statments for internal and boundary…

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• Add print statement for test output

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• Refactor order of initialisation calls to permit shared-memory MPI functions in the init_gyroaverage_operators() function. Correct some minor bugs. The code now time advances with gyrokinetic_ions …

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Commits on Mar 12, 2024

• Correct bug in choice of dummy array.

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• Update shared_utils.jl to be compatible with the new composition struct variable gyrokinetic_ions.

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Commits on Mar 13, 2024

• Add species dependence to gyroaverage operator.

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• Extend gyroaverages test to permit shared-memory MPI, extend gyroaverage functions to use shared-memory MPI. The initialisation of the gyromatrix is done in serial.

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Commits on Mar 14, 2024

• Merge branch 'geometry-upgrade' into feature-gyroaverages

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• Add example input file for studying gyroaverage operator in case with spatially periodic boundary conditions.

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• Merge branch 'geometry-upgrade' into feature-gyroaverages

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Commits on Mar 15, 2024

• Merge branch 'geometry-upgrade' into feature-gyroaverages

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Commits on Mar 17, 2024

• Modify how the summation loops over izp and irp are carried out in the gyroaverge operator. Introduce indexing arrays that record which elements of the gyromatrix are nonzero and sum only over thes…

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Commits on Mar 18, 2024

• Refactor the arrays used to index over the gyroaverage matrix so that they can be accomodated without introducing shared-memory arrays of novel types. This has the cost of introducing arrays that s…

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Commits on Mar 19, 2024

• Merge branch 'master' into feature-gyroaverages

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Commits on Mar 20, 2024

• Correct region for array copy for standard DK velocity moments calculation to make sure parallelisation over r occurs. Make sure that a standard Array rather than an MPISharedArray is used for ff_d…

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• Lower resolutions in examples/gk-ions/2D-periodic-gk.toml to reduce load on CI test.

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• Reduce resolution requirements for gyroaverages test to reduce load on CI test.

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Commits on Mar 21, 2024

• Update comments.

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Commits on Mar 22, 2024

• Merge branch 'mpi-init-only-once' into feature-gyroaverages

  

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Commits on Apr 23, 2024

• Remove commented-out code

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• Skip a couple of array copies when not gyroaveraging

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Commits on Apr 24, 2024

• Merge branch 'master' into feature-gyroaverages

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• Debug-checks test for gyroaverage operator

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• Use FFTW.ESTIMATE when generating Chebyshev-Radau integration weights

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• Add test directory so gyroaverage tests work with FFTW-wisdom-saving

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