<div dir="ltr"><div>Dear colleages, dear Ugis <br></div><div><br></div><div>Thank you for your suggestions to solve the problem about bad orientated elements.</div><div><br></div><div>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)<br></div><div><br></div><div>5665 vertices<br>closing file 24009 6078<br>24009 tetrahedrons<br>6078 triangles<br>30459 numElements<br> -- GMesh3 , n V: 5665 , n Elm: 24009 , n B Elm: 6078mes 877 674.198 , bb: (-5 -15 -5) , (5 3 0)<br> -- BuildAdj:nva= 3 4 6078<br> -- warning true boundary element 102 is no in correct orientation <br> -- warning true boundary element 103 is no in correct orientation <br> -- warning true boundary element 104 is no in correct orientation <br> -- warning true boundary element 105 is no in correct orientation <br> -- warning true boundary element 106 is no in correct orientation <br> -- warning true boundary element 107 is no in correct orientation <br> -- warning true boundary element 108 is no in correct orientation <br> -- warning true boundary element 109 is no in correct orientation <br> -- warning true boundary element 110 is no in correct orientation <br> Warning change orientation of 1938 faces <br> Warning error in boundary oriention 1938 faces <br></div><div><br></div><div>I have written to the FreeFem++ community also.<br></div><div>If you have any other idea, it will be welcomed!</div><div>Thank you very much in advance,</div><div><br></div><div>Jose<br></div><div><br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El vie., 15 may. 2020 a las 9:44, Ugis Lacis (<<a href="mailto:ugis.lacis@gmail.com">ugis.lacis@gmail.com</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
Hi Jose,<br>
<br>
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<br>
"gmsh pentagono.geo -3"<br>
And then loaded and displayed the mesh with FreeFEM++<br>
"FreeFem++ test_load.edp"<br>
<br>
Seemed to work fine for me. I use FreeFEM 4.1, and GMSH v4.3.0.<br>
<br>
Overall, these questions might be more suitable for FreeFEM mailing
list / forum.<br>
<br>
/Ugis<br>
<br>
<div>On 15/05/2020 08:55, Jose Juan Alonso
del Rosario wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Dear Ugis and colleages of GMSH,</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>"read mesh ok 0Mesh3, num Tetra:= 24011, num Vertice:= 5665
num boundary Triangles:= 6078<br>
Mesh3::meshS, num Triangles:= 6078, num Vertice:= 3039 num
boundary Edges:= 354<br>
read mesh ok 0Mesh3, num Tetra:= 24011, num Vertice:= 5665 num
boundary Triangles:= 6078<br>
Mesh3::meshS, num Triangles:= 6078, num Vertice:= 3039 num
boundary Edges:= 354<br>
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? <br>
S, num Triangles:= 6078, num Vertice:= 3039 num boundary
Edges:= 354<br>
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? "</div>
<div><br>
</div>
<div>This is after several Optimize3D and Optimize 3d with
NetGen and reading it with freefem++<br>
</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Thanks in advance!!!</div>
<div><br>
</div>
<div>Jose<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">El jue., 14 may. 2020 a las
13:54, Ugis Lacis (<<a href="mailto:ugis.lacis@gmail.com" target="_blank">ugis.lacis@gmail.com</a>>)
escribió:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div> Dear Jose,<br>
<br>
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.<br>
<br>
Maybe it can be helpful for you.<br>
<br>
Best regards,<br>
Ugis Lacis<br>
Researcher<br>
KTH Mechanics<br>
<br>
------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
-------- Forwarded Message --------
<table cellspacing="0" cellpadding="0" border="0">
<tbody>
<tr>
<th valign="BASELINE" nowrap align="RIGHT">Subject:
</th>
<td>Re: [Freefempp] Issue with loading mesh from GMSH.</td>
</tr>
<tr>
<th valign="BASELINE" nowrap align="RIGHT">Date:
</th>
<td>Fri, 3 Aug 2018 09:41:29 +0200</td>
</tr>
<tr>
<th valign="BASELINE" nowrap align="RIGHT">From:
</th>
<td>Uģis Lācis <a href="mailto:ugis.lacis@gmail.com" target="_blank"><ugis.lacis@gmail.com></a></td>
</tr>
<tr>
<th valign="BASELINE" nowrap align="RIGHT">To:
</th>
<td>FreeFem mailing list <a href="mailto:freefempp@ljll.math.upmc.fr" target="_blank"><freefempp@ljll.math.upmc.fr></a></td>
</tr>
</tbody>
</table>
<br>
<br>
Hi everyone,<br>
<br>
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.,<br>
change<br>
Line Loop(5) = {18, 19, 20, 12, 7, 8};<br>
to<br>
Line Loop(5) = {-18, -19, -20, -12, -7, -8};<br>
<br>
Maybe this helps to someone at some point.<br>
<br>
Best,<br>
Ugis<br>
<br>
On 02/08/18 15:30, Uģis Lācis wrote:<br>
Dear FreeFEM++ users and developers,<br>
<br>
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:<br>
<br>
Assertion fail : (area>0)<br>
line :281, in file ./include/fem.hpp<br>
<br>
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.<br>
<br>
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...<br>
<br>
Do you have any suggestions on how to solve this issue?<br>
<br>
Best regards,<br>
Ugis Lacis<br>
Researcher<br>
KTH Mechanics<br>
------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
<br>
<br>
<div>On 14/05/2020 12:03, Jose Juan Alonso del Rosario
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Dear colleages</div>
<div><br>
</div>
<div>I am trying to build the mesh for a slice with a
pentagonal hole.</div>
<div>GMSH runs properly with good quality tets but when
trying to read it from freefem++ the error is:</div>
<div><br>
</div>
<div>" 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? <br>
current line = 12 mpirank 1 / 2<br>
</div>
<div>"</div>
<div>Can you give any advice on this?</div>
<div><br>
</div>
<div>Thanks in advance<br>
</div>
<div><br>
</div>
<div>Jose<br>
</div>
<div><br>
-- <br>
<div dir="ltr">
<div dir="ltr">Prof. Dr. Jose Juan Alonso del
Rosario<br>
Applied Physics Dept.,
<div>Naval and Oceanic Engineering. </div>
<div>University of Cadiz.<br>
Avda Rep Saharaui s/n. Puerto Real, 11510,
Cadiz, Spain<br>
Tlf: +34 956 016054<br>
Fax: +34 956016079<br>
Secretary: +34 956016078<br>
<br>
</div>
<div>"All I wanna say is that they don't really
care about us", Michael Jackson<br>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
<pre>_______________________________________________
gmsh mailing list
<a href="mailto:gmsh@onelab.info" target="_blank">gmsh@onelab.info</a>
<a href="http://onelab.info/mailman/listinfo/gmsh" target="_blank">http://onelab.info/mailman/listinfo/gmsh</a>
</pre>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br clear="all">
<br>
-- <br>
<div dir="ltr">
<div dir="ltr">Prof. Dr. Jose Juan Alonso del Rosario<br>
Applied Physics Dept.,
<div>Naval and Oceanic Engineering. </div>
<div>University of Cadiz.<br>
Avda Rep Saharaui s/n. Puerto Real, 11510, Cadiz, Spain<br>
Tlf: +34 956 016054<br>
Fax: +34 956016079<br>
Secretary: +34 956016078<br>
<br>
</div>
<div>"All I wanna say is that they don't really care about
us", Michael Jackson<br>
</div>
</div>
</div>
</blockquote>
<br>
</div>
</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr">Prof. Dr. Jose Juan Alonso del Rosario<br>Applied Physics Dept., <div>Naval and Oceanic Engineering. </div><div>University of Cadiz.<br>Avda Rep Saharaui s/n. Puerto Real, 11510, Cadiz, Spain<br>Tlf: +34 956 016054<br>Fax: +34 956016079<br>Secretary: +34 956016078<br><br></div><div>"All I wanna say is that they don't really care about us", Michael Jackson<br></div></div></div>