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[gmsh] Vertex numbering is dense

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Old   July 24, 2015, 07:56
Default [gmsh] Vertex numbering is dense
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Hello foamers,

I always wondered what the meaning of

Code:
Vertex numbering is dense
is, when importing a *.msh file into gmsh. Is this an error message? What does ist mean?

Here you can find my complete output:

Code:
Info    : -------------------------------------------------------
Info    : Gmsh version   : 2.9.3
Info    : Build OS       : MacOSX
Info    : Build options  : 64Bit Ann Bamg Bfgs Blas(VecLib) Blossom Chaco DIntegration Dlopen Fltk Gmm Jpeg(Fltk) Kbipack Lapack(VecLib) MathEx Med Mesh Metis Mmg3d Mpeg NativeFileChooser Netgen ONELAB ONELABMetamodel OpenCascade OpenGL OptHom PETSc Parser Plugins Png(Fltk) Post SLEPc Salome Solver Tetgen(1.5) Voro3D Zlib
Info    : Build date     : 20150418
Info    : Build host     : Christophes-Mac.local
Info    : Packager       : geuzaine
Info    : Executable     : /Applications/Gmsh.app/Contents/MacOS/gmsh
Info    : Home directory : /Users/kateeisenhower/
Info    : Launch date    : Fri Jul 24 13:43:41 2015
Info    : Command line   : /Applications/Gmsh.app/Contents/MacOS/gmsh
Info    : -------------------------------------------------------
Info    : Reading '/Users/kateeisenhower/Documents/gmsh/Daten/cone/test.geo'...
Info    : Reading '/Users/kateeisenhower/Documents/gmsh/Daten/cone/cone.msh'...
Info    : 64 vertices
Info    : Vertex numbering is dense
Info    : 64 elements
Info    : Done reading '/Users/kateeisenhower/Documents/gmsh/Daten/cone/cone.msh'
Info    : Creating topology from mesh...
Info    : Removing duplicate mesh vertices...
Info    : Found 0 duplicate vertices 
Info    : No duplicate vertices found
Info    : Done creating topology from mesh (0.002625 s)
Info    : Done reading '/Users/kateeisenhower/Documents/gmsh/Daten/cone/test.geo'
And as an additional question: Why can't I see my 64 imported vertices in the tree browser tab of the visibility window?

Best regards,

Kate
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Old   July 24, 2015, 10:17
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Alexey Matveichev
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Hi,

If you look into GModelIO_MSH2.cpp:

Code:
      // If the vertex numbering is dense, transfer the map into a
      // vector to speed up element creation
      if((int)vertexMap.size() == numVertices &&
         ((minVertex == 1 && maxVertex == numVertices) ||
          (minVertex == 0 && maxVertex == numVertices - 1))){
        Msg::Info("Vertex numbering is dense");
                ...
      }
I guess what author would like to say is "vertex numbering is contiguous". I.e. there is no gaps in vertex numbering and we can use vector instead of map to store them.

Concerning second question: could you provide example file? Just opened MSH file and all entities were in visibility tree browser. Or should I merge MSH file from GEO file?
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Old   July 24, 2015, 10:48
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Hi Alexey,

Thank you for your answer. Regarding the vertex numbering, that's what I assumed too. Only it looks like some kind of error message in gmsh. I googled for vertex numbering is dense but couldn't find anything useful. How do you search for such a term in the source code? This would be very helpful for the future.

I attached cone.zip to this post which contains my *.stl file which I created in Blender (cone.stl). I opened this file in gmsh and hit save mesh. The cone.msh file is also attached, as well as my test.geo.
When i open the cone.msh file with a text edit app, I can see 64 vertices, which is the same number as the points I can count in Blender. In the gmsh tree browser in the visibility window, I can only see 17 points. Some of these were created in the geo file to define the wind tunnel. Point 1 and 2 are on the cone I guess but why they have that exact position or what they are here for, I never found out. And I can't even find point 5 and 9.
I don't really get the logic how gmsh handles geometry imported as stl. But it's getting better every day.

Best regards and thanks for your help,

Kate
Attached Files
File Type: zip cone.zip (3.5 KB, 3 views)
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Old   July 24, 2015, 11:33
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Alexey Matveichev
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Hi,

Quote:
Originally Posted by KateEisenhower View Post
How do you search for such a term in the source code? This would be very helpful for the future.
I use grep, nothing fancy. So to find the lines from previous post I used:

Code:
alexey at daphne in gmsh$ grep -r 'is dense' *
Geo/GModel.cpp:  // if the vertex numbering is dense, transfer the map into a vector to speed
Geo/GModel.cpp:    Msg::Info("Vertex numbering is dense");
Geo/GModelIO_DIFF.cpp:      // If the vertex numbering is dense, tranfer the map into a
Geo/GModelIO_DIFF.cpp:        Msg::Info("Vertex numbering is dense");
Geo/GModelIO_MSH.cpp:      // if the vertex numbering is dense, transfer the map into a vector to
Geo/GModelIO_MSH.cpp:        Msg::Info("Vertex numbering is dense");
Geo/GModelIO_MSH2.cpp:      // If the vertex numbering is dense, transfer the map into a
Geo/GModelIO_MSH2.cpp:        Msg::Info("Vertex numbering is dense");
contrib/gmm/gmm_precond_ildltt.h:// the matrix is dense. In this case the fill-in is K on each line.
Since you question was about MSH, I have chosen Geo/GModelIO_MSH2.cpp file.

Quote:
I attached cone.zip to this post which contains my *.stl file which I created in Blender (cone.stl).
Well, STL and Gmsh is something special and in fact a little bit beyond my knowledge. Yet, Google helped me to find:

1. It is not enough to call CreateTopology, you need to create compound lines and surfaces. Like in t13.geo from demos.

2. If you use the same procedure as in t13.geo on your cone.stl (or cone.msh) Gmsh finds only 2 vertices.

3. There is "Reclassify 2D" tool in Gmsh GUI. It greatly improves handling of STL (see attached screenshots). Unfortunately it is not accessible through the scripting interface.
Attached Images
File Type: png 1-.png (52.5 KB, 7 views)
File Type: png 2-.png (70.9 KB, 9 views)
File Type: png 3-.png (69.1 KB, 9 views)
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Old   July 31, 2015, 10:15
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Hi Alexey,

Thanks for that very helpful answer.

Quote:
Originally Posted by alexeym View Post
Hi,



I use grep, nothing fancy. So to find the lines from previous post I used:

Code:
alexey at daphne in gmsh$ grep -r 'is dense' *
Geo/GModel.cpp:  // if the vertex numbering is dense, transfer the map into a vector to speed
Geo/GModel.cpp:    Msg::Info("Vertex numbering is dense");
Geo/GModelIO_DIFF.cpp:      // If the vertex numbering is dense, tranfer the map into a
Geo/GModelIO_DIFF.cpp:        Msg::Info("Vertex numbering is dense");
Geo/GModelIO_MSH.cpp:      // if the vertex numbering is dense, transfer the map into a vector to
Geo/GModelIO_MSH.cpp:        Msg::Info("Vertex numbering is dense");
Geo/GModelIO_MSH2.cpp:      // If the vertex numbering is dense, transfer the map into a
Geo/GModelIO_MSH2.cpp:        Msg::Info("Vertex numbering is dense");
contrib/gmm/gmm_precond_ildltt.h:// the matrix is dense. In this case the fill-in is K on each line.
Since you question was about MSH, I have chosen Geo/GModelIO_MSH2.cpp file.
I have a few questions about this. In which directory do you execute this command? What does daphne mean? Is this possible when running gmsh on OS X too?

Quote:


Well, STL and Gmsh is something special and in fact a little bit beyond my knowledge. Yet, Google helped me to find:

1. It is not enough to call CreateTopology, you need to create compound lines and surfaces. Like in t13.geo from demos.

2. If you use the same procedure as in t13.geo on your cone.stl (or cone.msh) Gmsh finds only 2 vertices.

3. There is "Reclassify 2D" tool in Gmsh GUI. It greatly improves handling of STL (see attached screenshots). Unfortunately it is not accessible through the scripting interface.
Yes, I have played around with this "Reclassify 2D" tool too. Originally my question was aiming at why gmsh handles stl files this way? What is the logic behind it? But thanks anyway!

I have still problems with a default patch which appears after using gmshToFoam. This patch contains some undefined faces which are located at a problematic location of the mesh (cut trailing edge of an airfoil). When I view this default patch in ParaView, the cells seem to be part of my prismatic region. I am not allowed to share my files here but I try to create a minimal example over the weekend.

In the meantime I am trying to understand the gmsh output better:

Code:
Info    : Reading '/Users/kateeisenhower/Documents/gmsh/Daten/Kante2mm_13_hk1element_enGridmsh/fluegel.msh'...
Info    : 46420 vertices
Info    : Vertex numbering is dense
Info    : 92355 elements
Info    : Done reading '/Users/kateeisenhower/Documents/gmsh/Daten/Kante2mm_13_hk1element_enGridmsh/fluegel.msh'
Info    : Creating topology from mesh...
Info    : Removing duplicate mesh vertices...
Info    : Found 0 duplicate vertices 
Info    : No duplicate vertices found
Info    : Done creating topology from mesh (1.0721 s)
Info    : Done reading '/Users/kateeisenhower/Documents/gmsh/Daten/Kante2mm_13_hk1element_enGridmsh/test.geo'
Info    : Done
Info    : Meshing 1D...
Info    : Meshing curve 15 (Line)
Info    : Meshing curve 16 (Line)
Info    : Meshing curve 17 (Line)
Info    : Meshing curve 18 (Line)
Info    : Meshing curve 22 (Line)
Info    : Meshing curve 23 (Line)
Info    : Meshing curve 24 (Line)
Info    : Meshing curve 25 (Line)
Info    : Meshing curve 26 (Line)
Info    : Meshing curve 27 (Line)
Info    : Meshing curve 28 (Line)
Info    : Meshing curve 29 (Line)
Info    : Done meshing 1D (0.004893 s)
Info    : Meshing 2D...
Info    : 0 dependencies in mesh of source faces
Info    : Meshing curve 15 (Line)
Info    : Meshing curve 16 (Line)
Info    : Meshing curve 17 (Line)
Info    : Meshing curve 18 (Line)
Info    : Meshing curve 22 (Line)
Info    : Meshing curve 23 (Line)
Info    : Meshing curve 24 (Line)
Info    : Meshing curve 25 (Line)
Info    : Meshing curve 26 (Line)
Info    : Meshing curve 27 (Line)
Info    : Meshing curve 28 (Line)
Info    : Meshing curve 29 (Line)
Info    : Meshing curve 4
Info    : Meshing curve 4 (extruded)
Info    : Meshing curve 5
Info    : Meshing curve 5 (extruded)
Info    : Meshing curve 7
Info    : Meshing curve 7 (extruded)
Info    : Meshing curve 11
Info    : Meshing curve 11 (extruded)
Info    : Meshing surface 14 (extruded)
Info    : Meshing surface 21 (Plane, Delaunay)
Info    : Meshing surface 31 (Plane, Delaunay)
Info    : Meshing surface 33 (Plane, Delaunay)
Info    : Meshing surface 35 (Plane, Delaunay)
Info    : Meshing surface 37 (Plane, Delaunay)
Info    : Meshing surface 40 (Plane, Delaunay)
Info    : Meshing surface 9 (extruded)
Info    : Meshing surface 13 (extruded)
Info    : Meshing surface 9 (Boundary layer surface)
Info    : Meshing surface 9 (extruded)
Info    : Meshing surface 13 (Boundary layer surface)
Info    : Meshing surface 13 (extruded)
Info    : Meshing surface 14 (Boundary layer surface)
Info    : Meshing surface 14 (extruded)
Info    : Done meshing 2D (1.03019 s)
Everything up to here is clear.

Code:
Info    : 94719 vertices 190474 elements
Info    : Meshing 3D...
Info    : Meshing volume 1 (extruded)
Info    : Meshing volume 2000 (Frontal)
Info    : Region 2000 Face 14, 2 intersect
Info    : Region 2000 Face 21, 1 intersect
Info    : Region 2000 Face 31, 0 intersect
Info    : Region 2000 Face 33, 1 intersect
Info    : Region 2000 Face 35, 1 intersect
Info    : Region 2000 Face 37, 0 intersect
Info    : Region 2000 Face 40, 1 intersect
Info    : CalcLocalH: 48299 Points 0 Elements 96598 Surface Elements
Volume 1 is my extruded prismatic layer. Volume 2 is my farfield from the extruded surface 14 to the boundaries of my wind tunnel. What does
Code:
Info: Region 2000 Face 14, 2 intersect
mean then?
What does
Code:
Info: CalcLocalH: 48299 Points 0 Elements 96598 Surface Elements
mean? Does this mean that there are no volume elements before the 3D meshing? Well, this is obvious, isn't it?

Code:
Info    : Check subdomain 1 / 1 
Info    : 96598 open elements
This means that all of my Surface Elements are open. So my assumption is that this is okay?
Code:
Info    : Meshing subdomain 1 of 1 
Info    : 96598 open elements 
Info    : Use internal rules 
Info    : 96598 open elements 
Info    : Delaunay meshing 
Info    : number of points: 48299 
Info    : blockfill local h 
Info    : number of points: 147786 
Info    : Points: 147786 
Info    : Elements: 917243 
Info    : 388 open elements 
Info    : Num open: 388 
Info    : free: 4836, fixed: 912407 
Info    : SwapImprove  
Info    : 843 swaps performed 
Info    : 24 open elements 
Info    : Num open: 24 
Info    : free: 425, fixed: 916503 
Info    : SwapImprove  
Info    : 25 swaps performed 
Info    : 13 degenerated elements removed 
Info    : Remove intersecting 
Info    : Remove outer 
Info    : tables filled 
Info    : outer removed 
Info    : 96598 open elements 
Info    : 143090 points, 761358 elements 
Info    : 242 open elements 
Info    : 242 open faces 
Info    : start tetmeshing 
Info    : Use internal rules
What are internal rules?
What is blockfill local h?
What is SwapImprove?
At the end I have 242 open elements. I guess these are 2D elements. How does an open 2D element look like?
The meshed than starts tetmeshing with 242 open faces? Doesn't gmsh need to close them first?
Code:
 
Info    : El: 0 faces: 242 vol = 100 
Info    : El: 1 faces: 244 vol = 99.6836 
Info    : El: 2 faces: 240 vol = 99.674 
Info    : El: 3 faces: 236 vol = 99.4231 
Info    : El: 4 faces: 234 vol = 99.3117 
Info    : El: 5 faces: 230 vol = 99.2368 
Info    : El: 6 faces: 226 vol = 98.9873 
Info    : El: 8 faces: 228 vol = 98.9099 
Info    : El: 9 faces: 230 vol = 98.4964 
Info    : El: 10 faces: 230 vol = 98.4773 
Info    : El: 12 faces: 232 vol = 98.1052 
Info    : El: 13 faces: 232 vol = 98.0222 
Info    : El: 14 faces: 232 vol = 97.9299 
Info    : El: 15 faces: 232 vol = 97.9131 
Info    : El: 16 faces: 230 vol = 97.8938 
Info    : El: 18 faces: 232 vol = 97.548 
Info    : El: 19 faces: 232 vol = 97.3348 
Info    : El: 21 faces: 234 vol = 97.1164 
Info    : El: 22 faces: 236 vol = 96.8727 
Info    : El: 23 faces: 234 vol = 96.7858 
Info    : El: 24 faces: 234 vol = 96.6404 
Info    : El: 25 faces: 230 vol = 96.5812 
Info    : El: 26 faces: 228 vol = 96.3466 
Info    : El: 27 faces: 230 vol = 96.2778 
Info    : El: 28 faces: 230 vol = 96.0911 
Info    : El: 30 faces: 232 vol = 95.2821 
Info    : El: 31 faces: 232 vol = 95.1339 
Info    : El: 32 faces: 232 vol = 94.8947 
Info    : El: 33 faces: 232 vol = 94.8266 
Info    : El: 34 faces: 232 vol = 94.7491 
Info    : El: 35 faces: 232 vol = 94.6145 
Info    : El: 36 faces: 232 vol = 94.1144 
Info    : El: 37 faces: 232 vol = 93.9356 
Info    : El: 38 faces: 230 vol = 93.722 
Info    : El: 39 faces: 232 vol = 93.3295 
Info    : El: 41 faces: 234 vol = 92.8613 
Info    : El: 43 faces: 236 vol = 92.7953 
Info    : El: 45 faces: 238 vol = 92.666 
Info    : El: 47 faces: 240 vol = 92.595 
Info    : El: 48 faces: 242 vol = 92.4929 
Info    : El: 50 faces: 244 vol = 92.2974 
Info    : El: 51 faces: 244 vol = 92.2702 
Info    : El: 52 faces: 242 vol = 92.1424 
Info    : El: 53 faces: 244 vol = 91.9445 
Info    : El: 54 faces: 244 vol = 91.6564 
Info    : El: 56 faces: 246 vol = 91.5494 
Info    : El: 57 faces: 248 vol = 91.4719 
Info    : El: 59 faces: 250 vol = 91.3639 
Info    : El: 60 faces: 248 vol = 91.1938 
Info    : El: 61 faces: 246 vol = 90.7731 
Info    : El: 62 faces: 248 vol = 90.5932 
Info    : El: 63 faces: 248 vol = 90.3011 
Info    : El: 64 faces: 248 vol = 90.0146 
Info    : El: 65 faces: 250 vol = 89.2982 
Info    : El: 66 faces: 250 vol = 88.4385 
Info    : El: 67 faces: 252 vol = 87.5789 
Info    : El: 68 faces: 250 vol = 87.0057 
Info    : El: 69 faces: 246 vol = 86.4326 
Info    : El: 70 faces: 248 vol = 86.0028 
Info    : El: 72 faces: 250 vol = 85.5387 
Info    : El: 73 faces: 250 vol = 85.2946 
Info    : El: 74 faces: 250 vol = 84.4349 
Info    : El: 75 faces: 250 vol = 84.2031 
Info    : El: 76 faces: 252 vol = 84.0599 
Info    : El: 77 faces: 252 vol = 83.2002 
Info    : El: 78 faces: 250 vol = 82.3405 
Info    : El: 79 faces: 252 vol = 82.2022 
Info    : El: 80 faces: 252 vol = 82.016 
Info    : El: 82 faces: 254 vol = 81.7547 
Info    : El: 83 faces: 254 vol = 81.3249 
Info    : El: 84 faces: 256 vol = 80.4652 
Info    : El: 85 faces: 254 vol = 80.2503 
Info    : El: 86 faces: 254 vol = 80.0354 
Info    : El: 88 faces: 256 vol = 78.5481 
Info    : El: 89 faces: 258 vol = 78.2956 
Info    : El: 90 faces: 256 vol = 78.224 
Info    : El: 91 faces: 258 vol = 78.0807 
Info    : El: 92 faces: 258 vol = 77.5076 
Info    : El: 93 faces: 258 vol = 77.221 
.
.
.
Info    : El: 459 faces: 8 vol = 0.00284852 
Info    : El: 463 faces: 8 vol = 0.00226242 
Info    : El: 464 faces: 8 vol = 0.00209685 
Info    : El: 465 faces: 6 vol = 0.00203621 
Info    : El: 466 faces: 4 vol = 0.00196921
I don't understand this peace of code. El stands for element? Can someone explain these lines? Is a smaller volume better?

Code:
Info    : 0 open elements 
Info    : Success ! 
Info    : 143135 points, 761825 elements 
Info    : Done meshing 3D (28.1425 s)
Info    : 189555 vertices 1044654 elements
This looks promising in the first place. But as I wrote already, checkMesh complains about the mesh.

I am aware of this being a huge post with a lot of questions. If you, Alexey, or anyone else could provide some answers, I would be very grateful!
Sadly the gmsh Guide doesn't.

Best regards,

Kate
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Old   August 3, 2015, 10:28
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Alexey Matveichev
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Hi,

Since the messages are from particular meshing algorithm (guess, they will change if you select different values in Options -> Mesh -> General -> 2D and 3D algorithm drop-downs), it is possible to locate the reason for concrete message in source code, but there is almost no comments in the code

Guess, the easiest way to find meaning of the messages is to use Gmsh mailing list (http://www.geuz.org/mailman/listinfo/gmsh/) and ask authors of software directly.
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Old   August 3, 2015, 10:35
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Hi Alexey,

I've previously posted on the mailing list but sadly I almost never got an answer. However, I'll give it another try.

Can you please answer the first of my questions?

Quote:

Hi Alexey,

Thanks for that very helpful answer.

Quote:
Originally Posted by alexeym View Post
Hi,



I use grep, nothing fancy. So to find the lines from previous post I used:

Code:
alexey at daphne in gmsh$ grep -r 'is dense' *
Geo/GModel.cpp: // if the vertex numbering is dense, transfer the map into a vector to speed
Geo/GModel.cpp: Msg::Info("Vertex numbering is dense");
Geo/GModelIO_DIFF.cpp: // If the vertex numbering is dense, tranfer the map into a
Geo/GModelIO_DIFF.cpp: Msg::Info("Vertex numbering is dense");
Geo/GModelIO_MSH.cpp: // if the vertex numbering is dense, transfer the map into a vector to
Geo/GModelIO_MSH.cpp: Msg::Info("Vertex numbering is dense");
Geo/GModelIO_MSH2.cpp: // If the vertex numbering is dense, transfer the map into a
Geo/GModelIO_MSH2.cpp: Msg::Info("Vertex numbering is dense");
contrib/gmm/gmm_precond_ildltt.h:// the matrix is dense. In this case the fill-in is K on each line.
Since you question was about MSH, I have chosen Geo/GModelIO_MSH2.cpp file.


I have a few questions about this. In which directory do you execute this command? What does daphne mean? Is this possible when running gmsh on OS X too?
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Old   August 3, 2015, 10:49
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Hi,

Oh, sorry, overlooked these questions.

1. I execute the command in project's root folder. I.e. if I checked out sources in $HOME/Sources/gmsh, I execute command in $HOME/Sources/gmsh. See read-only svn clause in http://www.geuz.org/gmsh/#Download, on how to get project sources.

2. daphne is the host name of my laptop, so it is irrelevant to the problem. 'alexey at daphne in gmsh' is a prompt of my shell, which consists of user name, host name and current folder.

3. Since project sources and OS X compiled binaries are separate entities, you can search source code on any platform you like.
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