[Gmsh] bad orientation

Jose Juan Alonso del Rosario josejuan.alonso at gm.uca.es
Sun May 17 08:29:14 CEST 2020 

Dear colleages, dear Ugis

Thank you for your suggestions to solve the problem about bad orientated
elements.

I have tried all what you suggested. The mesh generation with GMSH gave no
issues but when reading the mesh file with FreeFem++ the message is
(changing the verbosity level)

5665 vertices
closing file 24009 6078
24009 tetrahedrons
6078 triangles
30459 numElements
  -- GMesh3 , n V: 5665 , n Elm: 24009 , n B Elm: 6078mes 877 674.198 , bb:
(-5 -15 -5) , (5 3 0)
   -- BuildAdj:nva= 3 4 6078
  --  warning true  boundary element 102 is no in correct orientation
  --  warning true  boundary element 103 is no in correct orientation
  --  warning true  boundary element 104 is no in correct orientation
  --  warning true  boundary element 105 is no in correct orientation
  --  warning true  boundary element 106 is no in correct orientation
  --  warning true  boundary element 107 is no in correct orientation
  --  warning true  boundary element 108 is no in correct orientation
  --  warning true  boundary element 109 is no in correct orientation
  --  warning true  boundary element 110 is no in correct orientation
 Warning change orientation of 1938 faces
 Warning error in boundary oriention  1938 faces

I have written to the FreeFem++ community also.
If you have any other idea, it will be welcomed!
Thank you very much in advance,

Jose




El vie., 15 may. 2020 a las 9:44, Ugis Lacis (<ugis.lacis at gmail.com>)
escribió:

> Hi Jose,
>
> In general, You should be careful with mesh formats and element types when
> using GMSH and FreeFEM++. I checked your geo file and modified the mesh
> format and version definition (see attached files). I tested the geo file
> by producing the mesh using
> "gmsh pentagono.geo -3"
> And then loaded and displayed the mesh with FreeFEM++
> "FreeFem++ test_load.edp"
>
> Seemed to work fine for me. I use FreeFEM 4.1, and GMSH v4.3.0.
>
> Overall, these questions might be more suitable for FreeFEM mailing list /
> forum.
>
> /Ugis
>
> On 15/05/2020 08:55, Jose Juan Alonso del Rosario wrote:
>
> Dear Ugis and colleages of GMSH,
>
> Thank you for your suggestions. I have changed the loop orientation of the
> upper and lower faces of the pentagon and the whole volumen was meshed (no
> hole at the end). In addition the same error still happens.
>
> "read mesh ok 0Mesh3, num Tetra:= 24011, num Vertice:= 5665 num boundary
> Triangles:= 6078
> Mesh3::meshS, num Triangles:= 6078, num Vertice:= 3039 num boundary
> Edges:= 354
> read mesh ok 0Mesh3, num Tetra:= 24011, num Vertice:= 5665 num boundary
> Triangles:= 6078
> Mesh3::meshS, num Triangles:= 6078, num Vertice:= 3039 num boundary
> Edges:= 354
>  Bad orientation: The adj border element  defined by [  3 210 ]  is
> oriented in the same direction in element 3519 and in the element 367
> ****** bug in mesh construction? orientation parameter?
> S, num Triangles:= 6078, num Vertice:= 3039 num boundary Edges:= 354
>  Bad orientation: The adj border element  defined by [  3 210 ]  is
> oriented in the same direction in element 3519 and in the element 367
> ****** bug in mesh construction? orientation parameter? "
>
> This is after several Optimize3D and Optimize 3d with NetGen and reading
> it with freefem++
>
> I include the .geo code. It is a thick slice with a pentagonal hole. The
> gmsh is now 4.5.6 and the meshing options are MeshAdapt and Frontal. I have
> played with the signs of plane surfaces 14 and 15.
>
> Thanks in advance!!!
>
> Jose
>
>
>
>
>
> El jue., 14 may. 2020 a las 13:54, Ugis Lacis (<ugis.lacis at gmail.com>)
> escribió:
>
>> Dear Jose,
>>
>> I think I have had similar error, when importing GMSH mesh into
>> FreeFEM++, few years ago (although it seems that the error message might
>> have changed). It turned out that the direction of loop definition in GMSH
>> was the issue for me. See below my exchange with FreeFEM++ mailing list.
>>
>> Maybe it can be helpful for you.
>>
>> Best regards,
>> Ugis Lacis
>> Researcher
>> KTH Mechanics
>>
>>
>> ------------------------------------------------------------------------------------------------------------------------------------------------------------------
>> -------- Forwarded Message --------
>> Subject: Re: [Freefempp] Issue with loading mesh from GMSH.
>> Date: Fri, 3 Aug 2018 09:41:29 +0200
>> From: Uģis Lācis <ugis.lacis at gmail.com> <ugis.lacis at gmail.com>
>> To: FreeFem mailing list <freefempp at ljll.math.upmc.fr>
>> <freefempp at ljll.math.upmc.fr>
>>
>> Hi everyone,
>>
>> I managed to solve the issue myself. It turned out that the direction of
>> GMSH loop was surviving till FreeFEM++ and while GMSH did not complain
>> about anything, FreeFEM++ couldn't use the mesh. mesh2 could be fixed by
>> changing signs in all lines within the line loop, i.e.,
>> change
>> Line Loop(5) = {18, 19, 20, 12, 7, 8};
>> to
>> Line Loop(5) = {-18, -19, -20, -12, -7, -8};
>>
>> Maybe this helps to someone at some point.
>>
>> Best,
>> Ugis
>>
>> On 02/08/18 15:30, Uģis Lācis wrote:
>> Dear FreeFEM++ users and developers,
>>
>> I have run into an issue which I am unable to solve by myself. I have
>> been using FreeFEM++ together with GMSH without any problems for quite some
>> time. Now, however, trying to load a 2D mesh generated by GMSH, gives me
>> following error:
>>
>> Assertion fail : (area>0)
>>     line :281, in file ./include/fem.hpp
>>
>> I attach the corresponding geo and msh files of two meshes (mesh1 -
>> working fine, mesh2 - does not load), as well as edp file for reading and
>> plotting the mesh.
>>
>> I have carefully checked that physical tags are applied correctly, I have
>> tried exporting both in MSH and MESH (medit) formats, using GMSH versions
>> 3.06 and 2.16.0, as well as using FreeFEM++ versions 3.560000 and 3.610002,
>> all try has led me to the same behaviour. I have identified that the issue
>> comes from the surface mesh, if I export only line mesh (comment out
>> "Physical Surface(11) = {3,4};" from mesh2.geo and run "gmsh -2
>> mesh2.geo"), then it loads fine. But checking the mesh within GMSH,
>> everything seems to be perfectly fine...
>>
>> Do you have any suggestions on how to solve this issue?
>>
>> Best regards,
>> Ugis Lacis
>> Researcher
>> KTH Mechanics
>>
>> ------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>>
>> On 14/05/2020 12:03, Jose Juan Alonso del Rosario wrote:
>>
>> Dear colleages
>>
>> I am trying to build the mesh for a slice with a pentagonal hole.
>> GMSH runs properly with good quality tets but when trying to read it from
>> freefem++ the error is:
>>
>> " Bad orientation: The adj border element  defined by [  16 246 ]  is
>> oriented in the same direction in element 3922 and in the element 446
>> ****** bug in mesh construction? orientation parameter?
>>   current line = 12 mpirank 1 / 2
>> "
>> Can you give any advice on this?
>>
>> Thanks in advance
>>
>> Jose
>>
>> --
>> Prof. Dr. Jose Juan Alonso del Rosario
>> Applied Physics Dept.,
>> Naval and Oceanic Engineering.
>> University of Cadiz.
>> Avda Rep Saharaui s/n. Puerto Real, 11510, Cadiz, Spain
>> Tlf: +34 956 016054
>> Fax: +34 956016079
>> Secretary: +34 956016078
>>
>> "All I wanna say is that they don't really care about us", Michael Jackson
>>
>> _______________________________________________
>> gmsh mailing listgmsh at onelab.infohttp://onelab.info/mailman/listinfo/gmsh
>>
>>
>>
>
> --
> Prof. Dr. Jose Juan Alonso del Rosario
> Applied Physics Dept.,
> Naval and Oceanic Engineering.
> University of Cadiz.
> Avda Rep Saharaui s/n. Puerto Real, 11510, Cadiz, Spain
> Tlf: +34 956 016054
> Fax: +34 956016079
> Secretary: +34 956016078
>
> "All I wanna say is that they don't really care about us", Michael Jackson
>
>
>

-- 
Prof. Dr. Jose Juan Alonso del Rosario
Applied Physics Dept.,
Naval and Oceanic Engineering.
University of Cadiz.
Avda Rep Saharaui s/n. Puerto Real, 11510, Cadiz, Spain
Tlf: +34 956 016054
Fax: +34 956016079
Secretary: +34 956016078

"All I wanna say is that they don't really care about us", Michael Jackson
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://onelab.info/pipermail/gmsh/attachments/20200517/4f275f02/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: pentagonV2.geo
Type: application/octet-stream
Size: 1892 bytes
Desc: not available
URL: <http://onelab.info/pipermail/gmsh/attachments/20200517/4f275f02/attachment.geo>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test_loadv2.edp
Type: application/octet-stream
Size: 379 bytes
Desc: not available
URL: <http://onelab.info/pipermail/gmsh/attachments/20200517/4f275f02/attachment.edp>

More information about the gmsh mailing list