Initial support for P4estMesh #593

sloede · 2021-05-22T10:13:57Z

No description provided.

* Add P4estMesh and implement unstructured calc_interface_flux! * Comment indexfunction_reduced * Save cell geometry in interpolation nodes instead of a mapping function * Use P4est to compute node coordinates * Extract interface information from p4est * Make indexfunction_surface type stable * Downgrade P4est_jll to 2.2 * Add P4est_jll as dependency * Update Project.toml * Update Project.toml * Fix node_coordinates interpolation * Add kwarg initial_refinement_level * Add documentation of P4estMesh * Remove trees_per_dimension to make P4estMesh truly unstructured * Add proper show function * Remove P4est_jll from dependencies * Improve comments * Destroy p4est data structures on exit * Add test case for P4estMesh * Implement suggestions * Implement suggestions * Revise constructor of P4estMesh to use kwargs * Improve performance of indices2direction * Fix mesh polydegs and stepsize for non-constant speeds * Implement suggestions

sloede · 2021-05-22T12:28:02Z

@efaulhaber I think you need to replace @timeit_debug with @timed to fix the non-Windows errors.

efaulhaber · 2021-05-22T12:38:52Z

Yes, I already did this while working on the BCs.

@timed

* Replace @timeit_debug with @timed * Implement save/restart for P4estMesh * Return node_coordinates * Change parameter basis to nodes to reuse function in Trixi2Vtk * Add Trixi2Vtk dev tips to docs * Fix docs * Update docs/src/visualization.md Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * Update src/mesh/mesh_io.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * Implement suggestions Co-authored-by: Michael Schlottke-Lakemper <[email protected]>

@timed

* Replace @timeit_debug with @timed * Extract orientation from face info * Reuse code from UnstructuredQuadMesh to implement non-periodic boundaries * Fix save/restart * Add nonperiodic example * Add assertion * Remove periodicity from P4estMesh * Fix loading meshes from different paths * Add constructor to build P4estMeshes from ABAQUS files * Allow initial_refinement_level > 1 * Add mapping as additional parameter to P4estMesh from file * Rename calc_node_coordinates! to avoid ambiguity * Add curved p4est Euler FSP example * Add documentation to new constructor * Check BCs for integrity * Add EOC test for non-periodic Euler on unstructured mesh * Implement suggestions * Implement suggestions * Fix tests * Implement suggestions * Fix spacing

codecov · 2021-05-28T07:47:40Z

Codecov Report

❗ No coverage uploaded for pull request base (main@8b67f66). Click here to learn what that means.
The diff coverage is 95.84%.

@@           Coverage Diff           @@
##             main     #593   +/-   ##
=======================================
  Coverage        ?   93.36%           
=======================================
  Files           ?      155           
  Lines           ?    15353           
  Branches        ?        0           
=======================================
  Hits            ?    14334           
  Misses          ?     1019           
  Partials        ?        0

Flag	Coverage Δ
unittests	`93.36% <95.84%> (?)`

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
...es/2d/elixir_advection_amr_solution_independent.jl	`100.00% <ø> (ø)`
src/callbacks_step/save_solution_dg.jl	`95.89% <ø> (ø)`
src/mesh/mesh.jl	`84.50% <ø> (ø)`
src/solvers/dg_curved/dg_2d.jl	`96.66% <ø> (ø)`
src/auxiliary/auxiliary.jl	`86.66% <60.00%> (ø)`
src/solvers/dg_tree/dg_2d.jl	`96.84% <66.66%> (ø)`
src/solvers/dg_tree/dg_3d.jl	`97.50% <66.66%> (ø)`
src/callbacks_step/amr_dg2d.jl	`98.84% <85.71%> (ø)`
src/callbacks_step/amr.jl	`94.27% <91.30%> (ø)`
src/solvers/dg_p4est/containers.jl	`91.66% <91.66%> (ø)`
... and 21 more

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* Prepare data structures for non-conforming meshes * Implement prolong2mortars * Implement mortar flux (not working yet) * Fix mortar flux calculation * Use global number of quadrants * Include tests for P4estMesh * Implement suggestions * Add test for non-conforming P4estMesh * Use Downloads.download * Implement suggestions * Fix tests * Fix CI tests on macOS

src/mesh/p4est_mesh.jl

ranocha

Do you have a test where you use a different polynomial degree for the solver and the mesh? If not, could you please add such a test?

* Implement AMR with p4est (needs debugging) * Fix TreeMesh AMR * Fix print_amr_information * Fix refinement * Fix CurvedMesh * Fix AMR with p4est * Add general print_amr_information for non-AMR meshes * Fix boundary conditions with AMR * Fix AMR on unstructured meshes * Add tests for AMR with p4est * Use Downloads: download * Improve performance of P4estMesh * Prepare PR * Fix 2279806 * Remove some allocations from count_required functions * Remove more allocations * Implement suggestions * Implement more suggestions * Fix polydeg in show(P4estMesh) * Destroy p4est data structures in inner constructor * Update examples/2d/elixir_advection_amr_p4est_unstructured_flag.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update examples/2d/elixir_advection_p4est_non_conforming_flag.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Make AMR controllers independent of the mesh * Implement suggestions * Fix e71913f * Implement suggestions * Fix 6a6a183 Co-authored-by: Hendrik Ranocha <[email protected]>

ranocha · 2021-06-10T04:35:36Z

We should be ready to merge this once

conflicts are resolved
a test of different polynomial degrees (solver/mesh) is added
tests pass

sloede

@efaulhaber @ranocha I have two small questions, but after that, I think we can merge it once the tests pass and coverage is ok

sloede · 2021-06-10T09:07:33Z

test/test_special_elixirs.jl

@@ -22,6 +22,9 @@ const EXAMPLES_DIR = joinpath(pathof(Trixi) |> dirname |> dirname, "examples")
    mean_eoc = convergence_test(@__MODULE__, joinpath(EXAMPLES_DIR, "2d", "elixir_advection_extended_curved.jl"), 3)
    @test isapprox(mean_eoc[:l2], [4.0], rtol=0.01)

+    mean_eoc = convergence_test(@__MODULE__, joinpath(EXAMPLES_DIR, "2d", "elixir_euler_nonperiodic_p4est.jl"), 3)
+    @test isapprox(mean_eoc[:l2], [3.54, 3.50, 3.50, 3.52], rtol=0.01)


@efaulhaber Can you tell me agian why the EOCs are so low?

I guess that's because it's using an unstructured mesh, but I'm not an expert.
It's this one:

@andrewwinters5000 could we get your take on this? Such a mesh with straight sides should give us the full EOC, shouldn't it?

There are lots of kite-like elements (when one of the angles is very obtuse and the element is approaching a triangle) in this mesh which can mess with the quality of the EOCs.

How does the EOC look in the last few refinement levels? Sometimes the mean EOC can get polluted with sub-optimal values from too coarse resolution

Something is fishy here...does this use calc_interface_flux! from dg_unstructured or did you write a new one?

I wrote a new one, but it's very similar to yours.

Okay, I am still trying to track down the EOCs issue in my implementation (so it could have a bug in it). I was thinking that the problem was the mapping, but your EOCs seem to indicate that it is also a problem for straight-sided elements

Can you convert my .inp mesh file to one that you can read somehow? Then you could use the same mesh with your solver (maybe even make it periodic?).

This is the second (less crazy) mesh.

src/callbacks_step/amr.jl

sloede · 2021-06-10T10:39:14Z

All tests have passed, but coverage is still not optimal. Do you see an easy way to increase test coverage by looking at the "New missed lines in diff" at https://coveralls.io/builds/40470257? Maybe by removing something that is not necessary or by slightly modifying an existing test? OTOH, the difference (-0.03%) is not so big as to require fundamental changes with a big effort, but it would be good to check for some low-hanging fruits.

efaulhaber · 2021-06-10T10:45:44Z

Most of these are the "passive solver" stuff in amr.jl. That is used by the Euler gravity stuff, right? Should I add a test there that uses P4estMesh, or should I just remove the passive solver stuff?
The line

@inline nboundaries(container::UnstructuredQuadSortedBoundaryTypes) = sum(length, container.boundary_indices)

is now unused. Do you want me to remove this line in a new PR? I used to test if the numbers of boundaries in the types container matches the number of boundaries of the boundary container, but this is not correct. Adding two boundaries on the left and removing two on the right would still require the container to be reinitialized.

sloede · 2021-06-10T11:06:57Z

Most of these are the "passive solver" stuff in amr.jl. That is used by the Euler gravity stuff, right? Should I add a test there that uses P4estMesh, or should I just remove the passive solver stuff?

Have you tested whether it works? If not, I'd rather not have it in there but maybe an error message somewhere in the beginning saying that this has not been implemented or tested yet.

There's also a bunch of untested lines here and it seems like there is no test for the "structured" P4est ctor for non-periodic cells (see here). The former seems like it can be just removed, while for the latter I think it would be good to have it tested in case someone would like to use it - it seems like a reasonable use case.

efaulhaber · 2021-06-10T11:19:08Z

Oops, I missed that. I'll add a test for a non-periodic structured mesh.

efaulhaber · 2021-06-10T11:39:08Z

Alright, Euler gravity works with P4estMesh and produces only slightly different L2 errors and even slightly smaller Linf errors.
The first uncovered lines that you linked are the 3D version of evaluate_index_surface, which will be used when I implement 3D.

* Add test for non-periodic structured P4estMesh * Add Euler gravity test with P4estMesh * Remove nboundaries(UnstructuredQuadSortedBoundaryTypes) * Move p4est Euler gravity tests to other p4est tests * Add news entry for P4estMesh

sloede

LGTM!

efaulhaber and others added 4 commits May 22, 2021 07:11

Merge branch 'main' into dev

844d13c

Merge branch 'main' into dev

9728666

Merge branch 'main' into dev

89f76c1

efaulhaber and others added 5 commits May 23, 2021 07:03

Merge branch 'main' into dev

39879c3

Merge branch 'main' into dev

cb49f5c

Update P4est [compat] version to pass Windows/macOS tests (#619)

fcb5dda

ranocha reviewed Jun 5, 2021

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src/mesh/p4est_mesh.jl Outdated Show resolved Hide resolved

ranocha requested changes Jun 9, 2021

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ranocha and others added 2 commits June 10, 2021 06:54

Merge branch 'main' into dev

2bc28f7

Add test with different geometry and solver polydeg (#634)

98d9b44

sloede changed the title ~~WIP: Initial support for P4estMesh~~ Initial support for P4estMesh Jun 10, 2021

sloede marked this pull request as ready for review June 10, 2021 08:48

sloede requested a review from ranocha June 10, 2021 08:51

ranocha previously approved these changes Jun 10, 2021

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sloede commented Jun 10, 2021

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Increase coverage with P4estMesh (#635)

a85c087

* Add test for non-periodic structured P4estMesh * Add Euler gravity test with P4estMesh * Remove nboundaries(UnstructuredQuadSortedBoundaryTypes) * Move p4est Euler gravity tests to other p4est tests * Add news entry for P4estMesh

sloede dismissed ranocha’s stale review via a85c087 June 10, 2021 12:35

sloede commented Jun 10, 2021

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sloede enabled auto-merge June 10, 2021 12:42

Fix a85c087 (#636)

7b39097

sloede disabled auto-merge June 10, 2021 15:23

sloede merged commit 7374f63 into main Jun 10, 2021

sloede deleted the dev branch June 10, 2021 15:24

sloede restored the dev branch June 10, 2021 15:24

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Initial support for P4estMesh #593

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Initial support for P4estMesh #593

Initial support for P4estMesh #593

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