Yade

Asking help for implementing TesselationWrapper()

Asked by Shenyang Cai

Hi all,

I was able to put TesselationWrapper() in my script months ago, but now I can't anymore.

When I try running the TesselationWrapper example given on the GitHub:

tt=TriaxialTest()
tt.generate("test.yade")
O.load("test.yade")
O.run(100,True)
TW=TesselationWrapper()
TW.triangulate() #compute regular Delaunay triangulation, don’t construct tesselation
TW.computeVolumes() #will silently tesselate the packing, then compute volume of each Voronoi cell
TW.volume(10) #get volume associated to sphere of id 10
TW.setState(0) #store current positions internaly for later use as the "0" state
O.run(100,True) #make particles move a little (let's hope they will!)
TW.setState(1) #store current positions internaly in the "1" (deformed) state

the terminal gives me this:

python: /tmp/buildd/yadedaily-1.14.0-54-f44c022~trusty/lib/triangulation/Tesselation.ipp:66: CGT::_Tesselation<TT>::VertexHandle CGT::_Tesselation<TT>::insert(CGT::Real, CGT::Real, CGT::Real, CGT::Real, unsigned int, bool) [with TT = CGT::TriangulationTypes<CGT::SimpleVertexInfo, CGT::SimpleCellInfo>; CGT::_Tesselation<TT>::VertexHandle = CGAL::internal::CC_iterator<CGAL::Compact_container<CGAL::Triangulation_vertex_base_with_info_3<CGT::SimpleVertexInfo, CGAL::Regular_triangulation_euclidean_traits_3<CGAL::Epick>, CGAL::Triangulation_vertex_base_3<CGAL::Regular_triangulation_euclidean_traits_3<CGAL::Epick>, CGAL::Triangulation_ds_vertex_base_3<CGAL::Triangulation_data_structure_3<CGAL::Triangulation_vertex_base_with_info_3<CGT::SimpleVertexInfo, CGAL::Regular_triangulation_euclidean_traits_3<CGAL::Epick>, CGAL::Triangulation_vertex_base_3<CGAL::Regular_triangulation_euclidean_traits_3<CGAL::Epick>, CGAL::Triangulation_ds_vertex_base_3<void> > >, CGAL::Triangulation_cell_base_with_info_3<CGT::SimpleCellInfo, CGAL::Regular_triangulation_euclidean_traits_3<CGAL::Epick>, CGAL::Triangulation_cell_base_3<CGAL::Regular_triangulation_euclidean_traits_3<CGAL::Epick>, CGAL::Triangulation_ds_cell_base_3<void> > >, CGAL::Sequential_tag> > > >, CGAL::Default, CGAL::Default, CGAL::Default>, false>; CGT::Real = double]: Assertion `vertexHandles.size()>id' failed.

I wonder why this happens.

Thanks a lot!

Shenyang

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Revision history for this message
Shenyang Cai (sycai) said : 		#1

Yade 1.07 works well with the function. Problem solved.

Sorry for the trouble.

Revision history for this message
Bruno Chareyre (bruno-chareyre) said : 		#2

I can confirm that it was broken after some revisions, then fixed subsequently.
Good to hear that your problem is solved.
Bruno

Revision history for this message
Kneib François (francois-kneib) said : 		#3

Hi Bruno,

I'm afraid I still experience this issue (with the exact same error message as Shenyang). Here is exactly what I have done :
- install a clean kubuntu 14.04 trusty (we never know ...);
- update the system (apt-get update && apt-get dist-upgrade);
- added yade repository (deb http://www.yade-dem.org/packages/ trusty/) because we need libeigen3-dev 3.2.1 but default trusty repository has 3.1.8 only;
- apt-get update;
- install dependencies according to the online doc command line : sudo apt-get install cmake git freeglut3-dev libloki-dev libboost-all-dev fakeroot dpkg-dev build-essential g++ python-dev ipython python-matplotlib libsqlite3-dev python-numpy python-tk gnuplot libgts-dev python-pygraphviz libvtk5-dev python-scientific libeigen3-dev python-xlib python-qt4 pyqt4-dev-tools gtk2-engines-pixbuf python-argparse libqglviewer-dev python-imaging libjs-jquery python-sphinx python-git python-bibtex libxmu-dev libxi-dev libcgal-dev help2man libbz2-dev zlib1g-dev python-minieigen
- mkdir yade ; cd yade;
- https clone : git clone https://github.com/yade/trunk.git
- create folders : mkdir install ; mkdir build ; cd build
- cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk
- make -j6 install
- run the tesselation script in the examples -> crash

My CGAL version is : libcgal-dev 4.5-2~trusty1 (same for libcgal10)

Do you have an idea ?

Revision history for this message
Kneib François (francois-kneib) said : 		#4

Here is the cmake log : https://drive.google.com/file/d/0B7rHPgDZcbBPRXlUYVRBUWtJZUE/view?usp=sharing
And here the make log : https://drive.google.com/file/d/0B7rHPgDZcbBPOVdjR0pndzh5WFU/view?usp=sharing

Revision history for this message
Anton Gladky (gladky-anton) said : 		#5

Hi Francois,

it looks like the problem in the last line of the script:

TW.defToVtk("strain.vtk")

At least it crashes in this point. Please file a corresponding bug
for that.

Best regards

Anton

2015-11-09 15:47 GMT+01:00 Kneib François
<email address hidden>:
> Question #272636 on Yade changed:
> https://answers.launchpad.net/yade/+question/272636
>
> Kneib François posted a new comment:
> Here is the cmake log : https://drive.google.com/file/d/0B7rHPgDZcbBPRXlUYVRBUWtJZUE/view?usp=sharing
> And here the make log : https://drive.google.com/file/d/0B7rHPgDZcbBPOVdjR0pndzh5WFU/view?usp=sharing

Revision history for this message
Kneib François (francois-kneib) said : 		#6

Thanks Anton, I will do it.
I can add that it doesn't work with yadedaily neither.

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