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Advection of arbitrary fields#668

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timspainNERSC wants to merge 126 commits intodevelopnextsimhub/nextsimdg:developfrom issue99_337_advectionnextsimhub/nextsimdg:issue99_337_advectionCopy head branch name to clipboard

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Commits on Mar 22, 2024

• Add the advected fields array.

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• Add Tice and Hsnow for advection.

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Commits on Jul 26, 2024

• Add the advected fields array.

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• Add Tice and Hsnow for advection.

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• Merge branch 'issue99_337_advection' of [email protected]:nextsimhub/nextsimdg.git into issue99_337_advection

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• Add the advected fields array.

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• Add Tice and Hsnow for advection.

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• Merge branch 'issue99_337_advection' of [email protected]:nextsimhub/nextsimdg.git into issue99_337_advection

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Commits on Jul 31, 2024

• Merge branch 'issue608_emptymodules' into issue99_337_advection

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• Add a common advection timestep length.

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• Restarting directly from CG is no longer being considered.

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• Add a flag that checks the advection has been prepared.

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Commits on Aug 2, 2024

• Add an advection-only dynamics kernel.

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• Advect a field in DynamicsKernel.

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• Test the advection of a ModelArray field.

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Commits on Aug 6, 2024

• Don't zero out all the DG components.

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• A test for advection of an arbitrary field.

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Commits on Aug 7, 2024

• Make the advection test actually test what we want to see.

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• Set higher DG components to zero where necessary.

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• IDynamics interface to advecting fields.

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Commits on Aug 9, 2024

• Add a function to set a block of data to a ModelArray.

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• Add advectField for DummyDynamics.

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• Advect >2 dimensional fields.

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• Add an advection test for 3D fields.

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• Advect the remaining prognostic fields.

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Commits on Aug 19, 2024

• Ensure that the advection is signalled ready.

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• Store the type of each advected field (to call the correct ma2dg()).

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• Start implementing a Fourier-like test.

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Commits on Aug 20, 2024

• Test the advection with a hand-rolled, one component Fourier transform.

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Commits on Aug 21, 2024

• Test 3D ModelArrays actual get set to zero.

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• Fix the contiguous data setter in ModelArray.

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• Test copying between DGVector and 3D ModelArrays.

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• Remove code superfluous to the doctest test.

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• Add template parameters to MA<->DG function calls.

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Commits on Aug 22, 2024

• Merge remote-tracking branch 'origin/develop' into issue99_337_advection

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• Reverse the order of thermodynamics and dynamics in PrognosticData.

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Commits on Aug 28, 2024

• Add a setData that assigns data with start indices.

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• Move splitting higher dimensional fields for advection from the kernels.

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• Remove the higher dimensional DGModelArray features.

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• Remove the field advection test.

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• Remove splitting >2D dimensional fields for advection from the kernels.

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• Remove the suffix generator.

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• clang formatting

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• clang formatting

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• clang formatting dynamics

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Commits on Aug 29, 2024

• Reinstate full functionality of the advection.

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• Add back the test of dynamics kernel advection.

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• Move the u/vice registration fo IDynamics.

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• Quotes, not guillemots.

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Commits on Aug 30, 2024

• Add a test for the advection at the module level.

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• Merge remote-tracking branch 'origin/develop' into issue99_337_advection

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• Remove a definition duplicated in the merge.

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• Final clean up of the advection test.

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• Faster advection tests.

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• Fasterer advection tests.

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• Zero out the higher DG components, as ma2dg doesn't any longer.

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• Remove the advectedFields variable.

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Commits on Oct 14, 2024

• Zero out the high DG components when setting forcing data.

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Commits on Oct 30, 2024

• Merge branch 'develop_rescue' into issue99_337_advection

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Commits on Nov 5, 2024

• Add hsnow to the list of fields to advect.

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• Break out the indexing from ModelArray to an external function.

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Commits on Nov 6, 2024

• Add the Slice class and an initial test.

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• Single element in one dimension.

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• Multidimensional indexing.

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• Test for dimensional mismatch.

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• Default to the beginning of the slice.

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Commits on Nov 7, 2024

• Slice to the end of the array if stop is present but undefined.

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• Multidimensional slicing.

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Commits on Nov 8, 2024

• Add a function that reverses the behaviour of indexer.

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• Test higher dimension slicing.

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• Test running to the end of the range in 2 dimensions.

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• Implement striding.

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• Create the outline of the ModelArraySlice class.

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Commits on Nov 11, 2024

• Make slice immuutable and bounds directly accessible.

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• Increment dimensions other than the first.

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• Assign a scalar value to a slice.

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• Remove dimSteps.

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• Spell 'ceil' correctly.

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• Test the shape of the slices.

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• Start Slice to Slice assignment.

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Commits on Nov 12, 2024

• Functions for calculating the actual bounds.

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• Slice to Slice assignment.

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• Replace stop() by nElements().

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Commits on Nov 13, 2024

• Make indices signed everywhere.

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• Add one-dimensional versions of start(), nElements(), stop().

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• Deal with the default start position if the step is negative.

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• Handle negative steps.

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• Test multidimensional backwards steps.

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• Test negative step size.

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Commits on Nov 14, 2024

• Break out the actual copying of ModelArraySlices.

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• Copy a whole ModelArray to a similarly sized Slice.

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• Assign a Slice to a ModelArray.

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• Delete commented code.

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Commits on Nov 15, 2024

• Allow the ModelArray indexing operator to accept a Slice argument.

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• Reduce the number of assertions when testing the 8D array.

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• Implement copying ModelArraySlices to and from buffers.

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• Rearrange classes and namespaces.

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Commits on Nov 18, 2024

• Implement the logic equivalent to numpy a[:].

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Commits on Nov 19, 2024

• Negative indices including testing.

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• Negative indices.

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• Throw on zero step.

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• Clang formatting on all the changed files.

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• Adding printing for SliceIter.

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• Implement SliceIter equality.

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• clang formatting

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Commits on Nov 21, 2024

• Make atEnd iterators equally regardless of positions.

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Commits on Nov 26, 2024

• Add a test to check confusion with multi-dimensional indexing.

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• Test extracting a single row slice.

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• Copy to and from the underlying ModelArray data type (usu. Eigen).

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• Add iterators to ModelArraySlice.

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Commits on Nov 27, 2024

• Correct indexing when setting the iterator end.

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• Clean up iterator tests.

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• clang formatting

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• Syntax description for the Slice class.

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• Slice and SliceIter documentation.

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• Add size() and position() member functions to Slice.

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• Merge branch 'slicer' into issue99_337_advection

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Commits on Nov 29, 2024

• Add array slicing to the advection calculation.

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• Add the header file header and include guards(!).

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• Merge branch 'slicer' into issue99_337_advection

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• Halve the testing timestep, test sines as well.

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Commits on Dec 2, 2024

• Halve the testing timestep, test the sines as well (for core).

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• Remove extra trailing newline.

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• Merge branch 'develop' into issue99_337_advection

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• Don't include the ModelArrayDetails twice.

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• Remove the duplicate advection of hsnow.

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