|
[Sponsors] |
July 24, 2015, 07:56 |
Vertex numbering is dense
|
#1 |
Senior Member
Join Date: Mar 2015
Posts: 250
Rep Power: 12 |
Hello foamers,
I always wondered what the meaning of Code:
Vertex numbering is dense 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' Best regards, Kate |
|
July 24, 2015, 10:17 |
|
#2 |
Senior Member
|
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"); ... } 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? |
|
July 24, 2015, 10:48 |
|
#3 |
Senior Member
Join Date: Mar 2015
Posts: 250
Rep Power: 12 |
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 |
|
July 24, 2015, 11:33 |
|
#4 | ||
Senior Member
|
Hi,
Quote:
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. Quote:
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. |
|||
July 31, 2015, 10:15 |
|
#5 | ||
Senior Member
Join Date: Mar 2015
Posts: 250
Rep Power: 12 |
Hi Alexey,
Thanks for that very helpful answer. Quote:
Quote:
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) 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 Code:
Info: Region 2000 Face 14, 2 intersect What does Code:
Info: CalcLocalH: 48299 Points 0 Elements 96598 Surface Elements Code:
Info : Check subdomain 1 / 1 Info : 96598 open elements 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 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 Code:
Info : 0 open elements Info : Success ! Info : 143135 points, 761825 elements Info : Done meshing 3D (28.1425 s) Info : 189555 vertices 1044654 elements 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 |
|||
August 3, 2015, 10:28 |
|
#6 |
Senior Member
|
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. |
|
August 3, 2015, 10:35 |
|
#7 | |
Senior Member
Join Date: Mar 2015
Posts: 250
Rep Power: 12 |
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:
|
||
August 3, 2015, 10:49 |
|
#8 |
Senior Member
|
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. |
|
Thread Tools | Search this Thread |
Display Modes | |
|
|
Similar Threads | ||||
Thread | Thread Starter | Forum | Replies | Last Post |
ill defined primitive entry 'boundary' | francisco.angel | OpenFOAM Pre-Processing | 16 | September 8, 2022 06:11 |
[mesh manipulation] Mesh Refinement | Luiz Eduardo Bittencourt Sampaio (Sampaio) | OpenFOAM Meshing & Mesh Conversion | 42 | January 8, 2017 12:55 |
[blockMesh] --> foam fatal error: | lillo763 | OpenFOAM Meshing & Mesh Conversion | 0 | March 5, 2014 10:27 |
[CAD formats] my stl surface is seen as just a line | rcastilla | OpenFOAM Meshing & Mesh Conversion | 2 | January 6, 2010 01:30 |
NACA0012 geometry/design software needed | Franny | Main CFD Forum | 13 | July 7, 2007 15:57 |