Mesh reader support for VTK high order elements [feature/vtk_high_order] #975

jonesholger · 2019-06-24T19:36:01Z

Updated PR information (Dec. 2020 – Will)

This PR adds two new features to MFEM's VTK support:

Reading XML VTK mesh files in addition to the "legacy" ASCII format
Reading high-order VTK meshes. High-order support works for both XML and legacy VTK formats.

XML parsing is done using the TinyXML2 library.

To facilitate systematic conversion between VTK's high-order node ordering and MFEM's node ordering, mappings are created that use an intermediate lexicographic ordering. Some remarks about the lexicographic ordering:

All NodalFiniteElement subclasses now support GetLexicographicOrdering, which plays the same role as TensorBasisElement::GetDofMap, but with support for all non-tensor geometries
The "refined geometry vertices" for tetrahedral elements are now lexicographically ordered in the standard reference element rather than in an "auxiliary element"
As a consequence, the lexicographic DOF ordering given by GetLexicographicOrdering always agrees with the refined geometry vertex ordering.
These orderings are tested for all geometries, for orders 1 through 6 in the unit tests.
The VTK mesh reader supports arbitrary-order Lagrange elements. The node orderings are handled using the same mappings defined for high-order ParaView output, so pre-generated data tables are not required.

As part of this PR, the handling of the VTK format for input and output are both made more systematic. The files vtk.hpp and vtk.cpp now have a lot more features that should make dealing with VTK more convenient, for instance converting from a VTK element type to MFEM Geometry::Type can now be performed using VTKGeometry:: GetMFEMGeometry instead of manual switch statements. This simplifies the code in Mesh::PrintVTK and Mesh::PrintVTU.

For testing purposes, VTK meshes of Cartesian grids with low-order and high-order elements of all types can be created in ParaView with the source "Unstructured Cell Types".

Previous information (out of date)

This mesh reader update subtask for vtk is related to MFEM issue #678 & https://blog.kitware.com/modeling-arbitrary-order-lagrange-finite-elements-in-the-visualization-toolkit/

Quads to arbitrary order vtk ascii
Hexes to arbitrary order vtk ascii
Triangles to order 6 (vtk limit) vtk ascii
Tets to order 6 (vtk limit) vtk ascii
Wedge (or prism) to order 6 (vtk limit) vtk ascii
Create static maps based on Reference Elements up to order 6 for tri/tet/wedge
Mixed cell validation -- assuming all elements are the newer Lagrange High Order Elements

Samples have been uploaded to https://github.com/mfem/data/tree/master/vtk; more will be added later

PR	Author	Editor	Reviewers	Assignment	Approval	Merge
#975	@jonesholger	@tzanio	@acfisher + @bslazarov + @mlstowell	11/30/20	01/09/21	01/24/21

jonesholger · 2019-06-24T19:36:42Z

Consolidating a few related links here:
GLVis/glvis#64
https://blog.kitware.com/modeling-arbitrary-order-lagrange-finite-elements-in-the-visualization-toolkit/
https://glvis.org/curvilinear-vtk-meshes/
https://github.com/CEED/FMS
https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf
https://lorensen.github.io/VTKExamples/site/VTKFileFormats/
https://www.visitusers.org/index.php?title=ASCII_VTK_Files
https://github.com/lorensen/VTKExamples
https://vtk.org/doc/nightly/html/vtkCellType_8h_source.html
https://github.com/agrayver/VTK_Lagrange
https://github.com/Kitware/VTK/blob/265ca48a79a36538c95622c237da11133608bbe5/Common/DataModel/vtkLagrangeQuadrilateral.cxx#L558
https://github.com/Kitware/VTK/blob/265ca48a79a36538c95622c237da11133608bbe5/Common/DataModel/vtkLagrangeHexahedron.cxx#L734
https://github.com/Kitware/VTK/blob/675adbc0feeb3f62730ecacb2af87917af124543/Filters/Sources/vtkCellTypeSource.cxx#L1307
https://github.com/Kitware/VTK/blob/675adbc0feeb3f62730ecacb2af87917af124543/Filters/Sources/vtkCellTypeSource.cxx#L345
https://github.com/Kitware/VTK/blob/5efd279913b4842bed0c1a0f2f119db89134e378/Common/DataModel/vtkCellType.h#L107-L114
https://github.com/Kitware/VTK/blob/675adbc0feeb3f62730ecacb2af87917af124543/Filters/Sources/vtkCellTypeSource.cxx#L1463
https://www.paraview.org/Wiki/ParaView_Release_Notes#Arbitrary-order_Lagrange_finite_element_support
https://github.com/Kitware/VTK/blob/675adbc0feeb3f62730ecacb2af87917af124543/Common/DataModel/vtkLagrangeInterpolation.cxx#L208

mfem/fem/fe.cpp

Lines 6878 to 6917 in 3e9a86c

    
           case 2: 
        
           { 
        
              const int p1 = p + 1; 
        
              dof_map.SetSize(p1*p1); 
        
              // vertices 
        
              dof_map[0 + 0*p1] = 0; 
        
              dof_map[p + 0*p1] = 1; 
        
              dof_map[p + p*p1] = 2; 
        
              dof_map[0 + p*p1] = 3; 
        
              // edges 
        
              int o = 4; 
        
              for (int i = 1; i < p; i++) 
        
              { 
        
                 dof_map[i + 0*p1] = o++; 
        
              } 
        
              for (int i = 1; i < p; i++) 
        
              { 
        
                 dof_map[p + i*p1] = o++; 
        
              } 
        
              for (int i = 1; i < p; i++) 
        
              { 
        
                 dof_map[(p-i) + p*p1] = o++; 
        
              } 
        
              for (int i = 1; i < p; i++) 
        
              { 
        
                 dof_map[0 + (p-i)*p1] = o++; 
        
              } 
        
              // interior 
        
              for (int j = 1; j < p; j++) 
        
              { 
        
                 for (int i = 1; i < p; i++) 
        
                 { 
        
                    dof_map[i + j*p1] = o++; 
        
                 } 
        
              } 
        
              break; 
        
           }

https://gitlab.kitware.com/vtk/vtk/blob/master/Common/DataModel/vtkUnstructuredGrid.h#L339
dealii/dealii@b029f83
dealii/dealii@e65f906
https://kitware.github.io/paraview-docs/latest/python/paraview.simple.UnstructuredCellTypes.html

mesh/mesh_readers.cpp

stale · 2020-10-08T23:44:07Z

⚠️ This issue or PR has been automatically marked as stale because it has not had any activity in the last month. If no activity occurs in the next week, it will be automatically closed. Thank you for your contributions.

pazner · 2020-10-09T00:12:37Z

We just discussed this feature this week. We should revive this PR.

stale · 2020-11-16T07:09:46Z

⚠️ This issue or PR has been automatically marked as stale because it has not had any activity in the last month. If no activity occurs in the next week, it will be automatically closed. Thank you for your contributions.

pazner · 2020-12-14T19:06:34Z

To help the reviewers, I edited the top-level comment with an updated summary of this PR — the information there was previously quite out of date.

tzanio · 2020-12-21T20:31:09Z

@acfisher, @bslazarov and @mlstowell -- can you please review?

acfisher · 2020-12-22T19:50:23Z

tests/unit/fem/test_lexicographic_ordering.cpp

+   VerifyOrdering(el);
+}
+
+TEST_CASE("Lexicographic Ordering", "[FiniteElement,Geometry]")


This is a good test to have around!

acfisher · 2020-12-22T19:57:26Z

fem/fe.cpp

@@ -8525,61 +8539,85 @@ H1_TetrahedronElement::H1_TetrahedronElement(const int p, const int btype)
   Vector shape_x(p + 1), shape_y(p + 1), shape_z(p + 1), shape_l(p + 1);
 #endif

+   auto tri = [](int k) { return (k*(k + 1))/2; };


Good use for lambdas.

mlstowell · 2020-12-30T18:57:07Z

fem/fe.hpp

@@ -731,6 +732,15 @@ class NodalFiniteElement : public ScalarFiniteElement
   virtual void ProjectDiv(const FiniteElement &fe,
                           ElementTransformation &Trans,
                           DenseMatrix &div) const;
+
+   /** @brief Get an Array<int> that maps lexicographically ordered indices to


I think we should define exactly what is meant by "lexicographically ordered". Without knowing the lexicon and the rules we use to order it this array may not be useful.

How does the updated comment look to you?

Looks perfect. Thanks!

tzanio · 2021-01-04T17:02:52Z

Extending approval due date to the end of this week...

mlstowell · 2021-01-04T22:34:18Z

fem/fe.hpp

@@ -731,6 +732,15 @@ class NodalFiniteElement : public ScalarFiniteElement
   virtual void ProjectDiv(const FiniteElement &fe,
                           ElementTransformation &Trans,
                           DenseMatrix &div) const;
+
+   /** @brief Get an Array<int> that maps lexicographically ordered indices to


Looks perfect. Thanks!

tzanio · 2021-01-10T00:20:00Z

ping: @bslazarov

tzanio · 2021-01-10T02:58:09Z

Can you please update CHANGELOG

tzanio · 2021-01-10T02:59:21Z

Merged in next for testing...

Conflicts: CHANGELOG

tzanio · 2021-01-11T18:48:48Z

Re-merged in next for testing ...

tzanio · 2021-01-13T20:52:00Z

Re-merged in next for testing ...

tzanio

@jonesholger and @pazner -- thank you so much for this important contributions. I am sure many of our users will appreciate it!

@mlstowell, @acfisher and @bslazarov -- thank you for reviewing!

add support for vtk high order elements

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jonesholger requested a review from acfisher June 24, 2019 19:41

acfisher reviewed Jun 27, 2019

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acfisher requested a review from tzanio July 3, 2019 17:20

tzanio added this to the mfem-4.1 milestone Aug 26, 2019

tzanio changed the title ~~Mesh reader support for vtk high order elements~~ Mesh reader support for VTK high order elements [feature/vtk_high_order] Aug 30, 2019

tzanio requested review from pazner and vladotomov October 21, 2019 20:47

victorsndvg mentioned this pull request Jan 21, 2020

writevtk for arbitrary order reference FEs gridap/Gridap.jl#123

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tzanio modified the milestones: mfem-4.1, mfem-4.2 Feb 27, 2020

stale bot added the stale label Oct 8, 2020

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tzanio modified the milestones: mfem-4.2, mfem-4.3 Oct 17, 2020

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camierjs added todo the mfem team will address this in the near future WIP Work in Progress and removed stale labels Nov 16, 2020

pazner added 5 commits November 17, 2020 12:34

Merge remote-tracking branch 'origin/master' into feature/vtk_high_order

30e4f99

Simplify spaceDim detection code

38d30f0

Add VTK geometry helpers

9250600

Simplify Mesh::PrintVTU and Mesh::PrintVTK

9dc9c9b

Use lexicographic vertex ordering for refined tetrahedron

b1ae8d6

v-dobrev mentioned this pull request Dec 2, 2020

Import SALOME mesh to MFEM #1867

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tzanio mentioned this pull request Dec 4, 2020

VTK xml file support with high order lagrange elements GLVis/glvis#64

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pazner self-assigned this Dec 14, 2020

acfisher reviewed Dec 22, 2020

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acfisher approved these changes Dec 22, 2020

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mlstowell reviewed Dec 30, 2020

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Add comment explaining lexicographic ordering

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tzanio added the in-next label Jan 10, 2021

pazner and others added 3 commits January 11, 2021 10:32

Fix bug reading quadratic VTK mesh

1e21230

Update CHANGELOG

e46d6be

Merge branch 'master' into feature/vtk_high_order

2550df8

Conflicts: CHANGELOG

Fix issue setting spaceDim with vertices

5d8cf0d

pazner mentioned this pull request Jan 19, 2021

Variable order finite element collections and spaces [var-order-space-dev] #1817

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minor

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Mesh reader support for VTK high order elements [feature/vtk_high_order] #975

Mesh reader support for VTK high order elements [feature/vtk_high_order] #975

jonesholger commented Jun 24, 2019 •

edited by tzanio

jonesholger commented Jun 24, 2019 •

edited

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mlstowell Dec 30, 2020

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tzanio commented Jan 4, 2021

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Mesh reader support for VTK high order elements [feature/vtk_high_order] #975

Mesh reader support for VTK high order elements [feature/vtk_high_order] #975

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jonesholger commented Jun 24, 2019 • edited by tzanio

Updated PR information (Dec. 2020 – Will)

Previous information (out of date)

jonesholger commented Jun 24, 2019 • edited

stale bot commented Oct 8, 2020

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jonesholger commented Jun 24, 2019 •

edited by tzanio

jonesholger commented Jun 24, 2019 •

edited