Read vtk #657

LasNikas · 2024-11-10T16:17:13Z

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codecov · 2024-11-10T16:36:27Z

Codecov Report

Attention: Patch coverage is 0% with 11 lines in your changes missing coverage. Please review.

Project coverage is 68.74%. Comparing base (550b95b) to head (6710a12).

Files with missing lines	Patch %	Lines
src/preprocessing/readvtk/vtk2trixi.jl	0.00%	11 Missing ⚠️

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@@            Coverage Diff             @@
##              dev     #657      +/-   ##
==========================================
- Coverage   68.88%   68.74%   -0.15%     
==========================================
  Files          86       87       +1     
  Lines        5261     5272      +11     
==========================================
  Hits         3624     3624              
- Misses       1637     1648      +11

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LasNikas

Great work so far. Thanks a lot!
I have some initial remarks. Also, what about the files in examples/vtk-reader? Did you use these files for development? If so, and these files are not important, please remove them.
Tests are missing.

LasNikas · 2024-11-10T16:24:04Z

src/preprocessing/readvtk/vtk2trixi.jl

@@ -0,0 +1,36 @@
+using ReadVTK


Please put this in src/TrixiParticles.jl between line 20 and 21. Packages are sorted alphabetically.

LasNikas · 2024-11-10T16:24:32Z

src/preprocessing/readvtk/vtk2trixi.jl

+
+    # FluidSystem data only
+"""
+


Suggested change

LasNikas · 2024-11-10T16:27:41Z

src/preprocessing/readvtk/vtk2trixi.jl

+    Convert data from VTK-file to InitialCondition
+
+    # FluidSystem data only


Either add a TODO or elaborate more how to use the function. Look at other docs for inspiration.

LasNikas · 2024-11-10T16:32:10Z

src/preprocessing/readvtk/vtk2trixi.jl

+    # FluidSystem data only
+"""
+
+function vtk2trixi(filename)


tests are missing

LasNikas · 2024-11-10T16:35:38Z

src/preprocessing/readvtk/vtk2trixi.jl

+        velocity = vcat(velocity, zeros(1, size(velocity, 2)))
+    end
+
+    mass = ones(size(coordinates, 2))


Please create an issue that we need to write the mass per particle in trixi2vtk.

LasNikas · 2024-11-10T16:40:20Z

Project.toml

 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 StrideArrays = "d1fa6d79-ef01-42a6-86c9-f7c551f8593b"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284"
+VTKDataIO = "c6703add-1d23-52c6-9943-3ad88652b9b2"


Suggested change

VTKDataIO = "c6703add-1d23-52c6-9943-3ad88652b9b2"

Please undo all this changes in the Project.toml except ReadVTK.

LasNikas · 2024-11-10T16:44:43Z

examples/readvtk/trixi2vtk.jl

+using TrixiParticles
+using OrdinaryDiffEq
+
+ic = vtk2trixi("examples/readvtk/fluid_1_1.vtu")


please use joinpath() for this. Also it is better to store an example vtk file in examples/reprocessing/data and name it read_vtk_example.vtu or so.

LasNikas · 2024-11-10T16:49:49Z

src/preprocessing/readvtk/vtk2trixi.jl

+    # FluidSystem data only
+"""
+
+function vtk2trixi(filename)


Make this consistent with trixi2vtk. That is, please use the kwargs input_directory="out", prefix="", iter=nothing.
IMO, this makes it easier to later find the right file.

LasNikas · 2024-11-10T16:54:26Z

src/preprocessing/readvtk/vtk2trixi.jl

+    if size(velocity, 1) == 2
+        # If velocity is 2D, add 0.0 for the z component
+        velocity = vcat(velocity, zeros(1, size(velocity, 2)))
+    end


Suggested change

if size(velocity, 1) == 2

# If velocity is 2D, add 0.0 for the z component

velocity = vcat(velocity, zeros(1, size(velocity, 2)))

end

# Retrieve particle coordinates.

coordinates = get_points(vtk_file)[axes(velocity, 1), :]

Also, please add to the comment that the point coordinates are stored in 3D coordinates, but the velocity can be either 2D or 3D. I think this has something to do with the vtk data structure. You might want to read up on it.

LasNikas · 2024-11-10T16:55:55Z

src/preprocessing/readvtk/vtk2trixi.jl

+    # Retrieve particle coordinates
+    coordinates = get_points(vtk_file)


Suggested change

# Retrieve particle coordinates

coordinates = get_points(vtk_file)

LasNikas · 2024-11-13T13:36:47Z

Project.toml

 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"


Suggested change

Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"

LasNikas · 2024-11-13T13:37:09Z

Project.toml

@@ -18,17 +20,20 @@ JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"


Suggested change

OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"

* Fix callback `show` and remove hacky workaround * Reforamt code * Fix tests * Make it work for all versions

* set test up for 1.11 * add basic struct * add export * make equation available * format * typo * fix docs * add exmaple * format * fix * Increase errors for 1.11 * Fix invalidations * Fix tests * Update ci.yml * revert * Update ci.yml * Update test/validation/validation.jl Co-authored-by: Erik Faulhaber <[email protected]> * format * review fixes * add test * fix example * fix test * review comments * fix docs * Update src/schemes/fluid/weakly_compressible_sph/state_equations.jl Co-authored-by: Erik Faulhaber <[email protected]> * forgot to edit the other doc --------- Co-authored-by: Erik Faulhaber <[email protected]>

* Add tutorial for setting up a simulation * Add section about custom smoothing kernels * Implement suggestions * Add kernel plot * Try to remove warnings * Implement suggestions * Make example a dam break and plot initial condition * Fix rendering * Fix tank size * Fix range for kernel plot * Fix descriptions after changing the example * Add equation for kernel * Fix minor errors

Boundary fluid concept

* add `density_calculator` to example * add perturbation option * fix typo * implement suggestions --------- Co-authored-by: Sven Berger <[email protected]>

marcelschurer added 5 commits October 16, 2024 10:48

Update Project.toml

59d7c0b

vtk2trixi

335d3f0

vtk2trixi

4169638

example_file

550b066

Update documentation and enhance transport velocity formulation support

6710a12

LasNikas commented Nov 10, 2024

View reviewed changes

LasNikas commented Nov 13, 2024

View reviewed changes

efaulhaber assigned LasNikas Nov 14, 2024

marcelschurer and others added 17 commits November 15, 2024 12:06

add readvtk

caf9439

Merge branch 'trixi-framework:main' into custom-quantities-algorithm

4b74ef1

boundary-fluid-concept

5f37b55

Fix callback show and remove hacky workaround (trixi-framework#669)

1d007c0

* Fix callback `show` and remove hacky workaround * Reforamt code * Fix tests * Make it work for all versions

Merge branch 'trixi-framework:main' into boundary-fluid-concept

2a46613

compact-concept

f13fef2

Merge pull request #16 from marcelschurer/boundary-fluid-concept

696cf0c

Boundary fluid concept

Validation TVF (trixi-framework#640)

231e2e0

* add `density_calculator` to example * add perturbation option * fix typo * implement suggestions --------- Co-authored-by: Sven Berger <[email protected]>

integrate try and catch

e28b79b

added wall_velocity case

499e285

Merge remote-tracking branch 'origin/main' into read-vtk

0943d7c

correct ndims

e827bca

stable v1

a0e042e

delete using get_field_data()

1dbec17

update example file

642b417

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Read vtk #657

Read vtk #657

LasNikas commented Nov 10, 2024

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		Convert data from VTK-file to InitialCondition

		# FluidSystem data only

		# Retrieve particle coordinates
		coordinates = get_points(vtk_file)

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LasNikas commented Nov 10, 2024

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