Re: [Yade-dev] : Compilation on K/Ubuntu 18.04

[Janek Kozicki (yade-dev)]

Hi Klaus, this looks very much like the errors which I have been fixing two 
months ago. It seems that Robert and Luc were not aware that to compile with 
CGAL 4.11 we have to use Tri.locate(CGT::Sphere(…)) and when writing ->point() 
we should instead write ->point().point() (regardless of how silly it looks, 
this is the correct way in CGAL).

I have just committed the compilation fix for this. Have a look at this diff, 
and you will see what I mean. Please try again to compile with CGAL 4.11 and 
let us know if it works for you.

best regards
Janek


On 14 May 2018, 09:20 +0200, Klaus Thoeni , wrote:
> Hi guys,
>
> I remember a discussion with a CGAL problem to get yade ready for 18.04 LTS. 
> From the discussion it looks that everything is solved. However, I just did a 
> fresh install of Kubuntu 18.04 and tried to compile the code (latest trunk 
> version).
>
> cmake went fine but compilation didn't work as expected. I got an error 
> related to some CGAL commands used in DFNFlow.cpp:
>
> /home/yade/YADE-git/trunk/pkg/pfv/DFNFlow.cpp: In member function ‘void 
> DFNFlowEngine::interpolateCrack(TemplateFlowEngine_DFNFlowEngineT  DFNVertexInfo, CGT::_Tesselation DFNCellInfo> >, DFNBoundingSphere>::Tesselation&, 
> TemplateFlowEngine_DFNFlowEngineT CGT::_Tesselation >, 
> DFNBoundingSphere>::Tesselation&)’:
> /home/yade/YADE-git/trunk/pkg/pfv/DFNFlow.cpp:216:136: error: no match for 
> ‘operator-’ (operand types are 
> ‘CGAL::Regular_triangulation_vertex_base_3 CGAL::Triangulation_ds_vertex_base_3  CGAL::Triangulation_vertex_base_with_info_3 CGAL::Regular_triangulation_vertex_base_3 >, 
> CGAL::Boolean_tag, CGAL::Boolean_tag >, 
> CGAL::Alpha_shape_cell_base_3 CGAL::Triangulation_cell_base_with_info_3 CGAL::Regular_triangulation_cell_base_3 >, 
> CGAL::Boolean_tag, CGAL::Boolean_tag >, CGAL::Sequential_tag> > 
> >::Point {aka CGAL::Weighted_point_3}’ and ‘const CGAL::Origin’)
>    if (newCell->info().fictious()==0) for (int k=0;k<4;k++) center = center + 
> 0.25*(Tes.vertex(newCell->vertex(k)->info().id())->point()-CGAL::ORIGIN);
>   
>   ^
>
>
> /home/yade/YADE-git/trunk/pkg/pfv/DFNFlow.cpp:218:71: error: no matching 
> function for call to ‘CGAL::Regular_triangulation_3 CGAL::Triangulation_data_structure_3  CGAL::Triangulation_vertex_base_with_info_3 CGAL::Regular_triangulation_vertex_base_3 >, 
> CGAL::Boolean_tag, CGAL::Boolean_tag >, 
> CGAL::Alpha_shape_cell_base_3 CGAL::Triangulation_cell_base_with_info_3 CGAL::Regular_triangulation_cell_base_3 >, 
> CGAL::Boolean_tag, CGAL::Boolean_tag >, CGAL::Sequential_tag>, 
> CGAL::Default>::locate(Point)’
>    CellHandle oldCell = Tri.locate(Point(center[0],center[1],center[2]));
>    ^
> In file included from /usr/include/CGAL/Regular_triangulation_3.h:45:0,
>  from 
> /home/yade/YADE-git/trunk/lib/triangulation/RegularTriangulation.h:13,
>  from 
> /home/yade/YADE-git/trunk/lib/triangulation/Tesselation.h:9,
>  from 
> /home/yade/YADE-git/trunk/pkg/dem/TesselationWrapper.hpp:15,
>  from 
> /home/yade/YADE-git/build/pkg/pfv/FlowEngine_DFNFlowEngineT.hpp:38,
>  from /home/yade/YADE-git/trunk/pkg/pfv/DFNFlow.cpp:20:
> /usr/include/CGAL/Triangulation_3.h:1012:3: note: candidate: 
> CGAL::Triangulation_3::Cell_handle 
> CGAL::Triangulation_3::locate(const Point&, 
> CGAL::Triangulation_3::Vertex_handle, bool*) 
> const [with GT = CGAL::Epick; Tds_ = 
> CGAL::Triangulation_data_structure_3  CGAL::Triangulation_vertex_base_with_info_3 CGAL::Regular_triangulation_vertex_base_3 >, 
> CGAL::Boolean_tag, CGAL::Boolean_tag >, 
> CGAL::Alpha_shape_cell_base_3 CGAL::Triangulation_cell_base_with_info_3 CGAL::Regular_triangulation_cell_base_3 >, 
> CGAL::Boolean_tag, CGAL::Boolean_tag >, CGAL::Sequential_tag>; 
> Lock_data_structure_ = CGAL::Default; CGAL::Triangulation_3 Lock_data_structure>::Cell_handle = 
> CGAL::internal::CC_iterator  CGAL::Triangulation_cell_base_with_info_3 

Re: [Yade-dev] Odp: Re: Yade for LTS Ubuntu 18.04

[Janek Kozicki (yade-dev)]

Awesome! Thank you! :-)

On 22 Feb 2018, 21:12 +0100, Anton Gladky , wrote:
> Dear Yade developers,
>
> the new minor Yade 2018.02b was released on 20-th of February.
> It allows us to compile Yade against CGAL_4.11 and fixes some
> bugs. Tarballs are available on GitHub [1] and Launchpad [2].
>
> Also the new version was uploaded to Debian [3] and even synced
> into the Ubuntu LTS 18.04 Bionic [4] and successfully built for all
> relevant platforms.
>
> Thanks all for the great work!
>
> [1] https://github.com/yade/trunk/releases
> [2] https://launchpad.net/yade/+download
> [3] https://buildd.debian.org/status/package.php?p=yade
> [4] https://launchpad.net/ubuntu/+source/yade/2018.02b-1
>
> Anton
>
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Re: [Yade-dev] Ip2_FrictMat_FrictMat_FrictPhys doc

[Janek Kozicki (yade-dev)]

When it comes to documentation, for me it’s: never remove anything, always 
improve :)

On 21 Feb 2018, 22:25 +0100, Robert Caulk , wrote:
> Hello Jérôme,
>
> I support clarifying the meaning of particle young in the class reference as 
> you suggest. There is no doubt that newcomers to DEM and Yade confuse micro 
> young's modulus with macro young's modulus all the time.
>
> I would vote for clarifying the general doc instead of full removal of 
> stiffness and normal stiffness section in general doc, I think they provide 
> good examples of how Yade treats micro stiffness. If we decide to keep the 
> sections I can look into improving their clarity. But if others think removal 
> is best, I am not against it :-)
>
> Best,
>
> Robert
>
> > On Wed, Feb 21, 2018 at 8:59 AM, Jerome Duriez  
> > wrote:
> > > Hi,
> > >
> > > After seeing Yet Another Doubts on "young" meaning / 
> > > Ip2_FrictMat_FrictMat_FrictPhys contact model (a PhD student in my 
> > > institute), I'm proposing to explicitly mention the underlying equations 
> > > in the doc, once for all.
> > > The corresponding would-be diff appears at the end of the email, you may 
> > > also compare the attached screenshot with 
> > > https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.Ip2_FrictMat_FrictMat_FrictPhys.
> > > From the diff, you will see I'm also proposing to remove the "harmonic 
> > > average stiffness" comment, for instance because there actually is a "2" 
> > > factor missing/extra between the comment and the actual code.
> > >
> > >
> > > In the case of the above-mentioned PhD student, confusion also arose 
> > > because of https://yade-dem.org/doc/formulation.html#stiffnesses and 
> > > https://yade-dem.org/doc/formulation.html#normal-stiffness.
> > > As such, I would also propose to simply remove these two sections from 
> > > the doc.
> > > From my point of view, they actually are too Ip2-specific to appear in 
> > > the general doc.
> > >
> > >
> > > If necessary, a reference to the (equivalent) 2.2.1 and 2.2.1.1. sections 
> > > from Vaclav's thesis ([Smilauer2010b] reference) could be introduced e.g. 
> > > in Ip2_CpmMat_CpmMat_CpmPhys and Ip2_FrictMat_FrictMat_FrictPhys 
> > > docstrings, to keep track of these comments that could be made concerning 
> > > the Ip2 equations.
> > >
> > >
> > > This email probably is Yet Another non-critical one, but since it deals 
> > > about (the doc of) central pieces of code, and lines probably written by 
> > > Vaclav, I'm opening a possible discussion here before performing the 
> > > changes.
> > >
> > >
> > > Jérôme
> > >
> > > PS: next step would be to move 
> > > https://yade-dem.org/doc/formulation.html#strain-evaluation to Ig2 
> > > docstrings but I'm not planning on it...
> > >
> > >
> > > ** Diff herein proposed for commit **
> > >
> > > diff --git a/pkg/dem/FrictPhys.cpp b/pkg/dem/FrictPhys.cpp
> > > index cb904da..4f8ffe8 100644
> > > --- a/pkg/dem/FrictPhys.cpp
> > > +++ b/pkg/dem/FrictPhys.cpp
> > > @@ -26,9 +26,7 @@ void Ip2_FrictMat_FrictMat_FrictPhys::go( const 
> > > shared_ptr& b1
> > >     Real Va = mat1->poisson;
> > >     Real Vb = mat2->poisson;
> > >
> > > -   //harmonic average of the two stiffnesses when (2*Ri*Ei) is the 
> > > stiffness of a contact point on sphere "i"
> > >     Real Kn = 2*Ea*Ra*Eb*Rb/(Ea*Ra+Eb*Rb);
> > > -   //same for shear stiffness
> > >     Real Ks = 2*Ea*Ra*Va*Eb*Rb*Vb/(Ea*Ra*Va+Eb*Rb*Vb);
> > >
> > >     Real frictionAngle = (!frictAngle) ? 
> > > std::min(mat1->frictionAngle,mat2->frictionAngle) : 
> > > (*frictAngle)(mat1->id,mat2->id,mat1->frictionAngle,mat2->frictionAngle);
> > >
> > > diff --git a/pkg/dem/FrictPhys.hpp b/pkg/dem/FrictPhys.hpp
> > > index eeb2ef4..12c85ee 100644
> > > --- a/pkg/dem/FrictPhys.hpp
> > > +++ b/pkg/dem/FrictPhys.hpp
> > > @@ -44,7 +44,7 @@ class Ip2_FrictMat_FrictMat_FrictPhys: public 
> > > IPhysFunctor{
> > >     const shared_ptr& b2,
> > >     const shared_ptr& interaction);
> > >     FUNCTOR2D(FrictMat,FrictMat);
> > > -   
> > > YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictMat_FrictMat_FrictPhys,IPhysFunctor,"Create
> > >  a :yref:`FrictPhys` from two :yref:`FrictMats`. The compliance 
> > > of one sphere under point load is defined here as $1/(E.D)$, with $E$ the 
> > > stiffness of the sphere and $D$ its diameter. The compliance of the 
> > > contact itself will be the sum of compliances from each sphere, i.e. 
> > > $1/(E_1.D_1)+1/(E_2.D_2)$ in the general case, or $2/(E.D)$ in the 
> > > special case of equal sizes and equal stiffness. Note that summing 
> > > compliances corresponds to an harmonic average of stiffnesss (as in e.g. 
> > > [Scholtes2009a]_), which is how kn is actually computed in the 
> > > :yref:`Ip2_FrictMat_FrictMat_FrictPhys` functor:\n\n $k_n = 
> > > \\frac{E_1D_1*E_2D_2}{E_1D_1+E_2D_2}=\\frac{k_1*k_2}{k_1+k_2}$, 

Re: [Yade-dev] Yade for LTS Ubuntu 18.04

[Janek Kozicki (yade-dev)]

Hi Anton and Bruno,

I am glad that I can help, and use this opportunity to get back in track ;) So 
I will do this entire Saturday after I get back home on friday night.

Should I work on latest yade trunk?

BTW: I'm writing this from an airport ;)

Best regards,
Janek

On 8 Feb 2018, 19:10 +0100, Anton Gladky <gladky.an...@gmail.com>, wrote:
> Hi Bruno,
>
> CGAL_ 4.11 is the only version now for Debian (testing) [1]
> and upcoming Ubuntu 18.04 [2]. The shipped Yade does
> not support CGAL due to compilation problems.
>
> I am preparing the new Yade upload, but we have a chance
> to patch the Yade within the next two weeks or prepare
> the 2018.02b release with CGAL-support and upload it.
>
> [1] https://tracker.debian.org/pkg/cgal
> [2] https://launchpad.net/ubuntu/+source/cgal
>
> Anton
>
>
> 2018-02-08 18:45 GMT+01:00 Bruno Chareyre <bruno.chare...@grenoble-inp.fr>:
> > Hi Anton,
> > Thank you very much.
> > I'm not so sure what we are speaking about here.
> > Yade 2018.02a is the candidate source code for producing a binary
> > yade-stable in Ubuntu 18.04, correct (approximately)?
> > If yes, can we build yade-stable with CGAL at the moment?
> > Bruno
> >
> >
> >
> > On 02/08/2018 06:35 PM, Anton Gladky wrote:
> > >
> > > Well, if we find a way to fix it within the next 2 weeks,
> > > I think there is a chance to get it pushed into Debian->Ubuntu.
> > >
> > > Regards
> > >
> > > Anton
> > >
> > >
> > > 2018-02-08 15:23 GMT+01:00 Bruno Chareyre
> > > <bruno.chare...@grenoble-inp.fr>:
> > > >
> > > >
> > > > On 02/07/2018 05:35 PM, Janek Kozicki (yade-dev) wrote:
> > > > >
> > > > >
> > > > > Regarding compiling yade with CGAL 4.11, I can look into it on 
> > > > > Saturday,
> > > > > if my last patches didn't work for you?
> > > >
> > > > I did not test it yet I'm afraid. :-/
> > > > It sounds like a critical issue for a 18.04 release. Is it?
> > > > Would that mean to skip the whole CGAL related code in the binary
> > > > release?
> > > > I'll go back to this asap, thanks for pinging.
> > > >
> > > > Bruno
> > > >
> > > >
> > > >
> > > >
> > > > ___
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> >
> >
> >
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Re: [Yade-dev] Yade for LTS Ubuntu 18.04

[Janek Kozicki (yade-dev)]

This is a great effort, I saw you squashed dozens of bugs yesterday. Great!

Regarding compiling yade with CGAL 4.11, I can look into it on Saturday, if my 
last patches didn't work for you? I am currently on a trip and have with me 
just a small laptop. The last patches I've sent is what I currently have at the 
moment. Yade was compiling, and seemed to work, except that one test after the 
compilation was hanging idefinitely. Not sure why - I still didn't look into 
it. Did you try to reproduce what I reported?

best regards
Janek

On 6 Feb 2018, 10:02 +0100, Bruno Chareyre , 
wrote:
>
>
> On 02/05/2018 08:42 PM, Anton Gladky wrote:
> > I also want to ask everybody to have a look at the bug-tracker [1].
> Good point. I'll check the one you mentioned at least.
> It would be great to fix some more.
> B
>
>
>
>
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Re: [Yade-dev] Yade related publication?

[Janek Kozicki (yade-dev)]

Hi Robert,

I think that it’s a great idea. Especially if we could use it to directly 
improve the documentation. I suppose that virtually everything that we could 
write about using yade could be somehow fit into the sphinx docs. Like in 
Jerome said, my specific answers to two of your questions are "no” at the 
moment. Mostly because whatever I do, I plan to release it either as a paper, 
or on the documentation. However some specific scripts to calculate this, or 
that - they usually grow organically over time, and I guess that those would 
fit greatly into what you are proposing to do.

best regards
Janek

On 5 Feb 2018, 16:40 +0100, Bruno Chareyre , 
wrote:
> Hi Robert,
>
> On 02/02/2018 07:37 PM, Robert Caulk wrote:
> > Hey Yade Devs,
> >
> > I am wondering if we have the demand to create a Yade related white
> > paper publication. The publication would document very Yade specific
> > functionalities and I imagine some papers might even highlight pieces
> > code. I think the format would be very flexible, some releases might
> > be 3 pages with brief summary and figures, while others might be
> > formatted similarly to a conference paper. In all cases, I think we
> > could maintain a quality archive by incorporating CrossRef, reviewing
> > the writing/work, and laying out the documents consistently.
> >
> I think it makes complete sense, I would support the initiative, thanks.
> I would point out one risk though: it may distract one from writing an
> actual documentation (with sphinx) while we know that writing the doc is
> of highest importance.
> I feel that the benefits could be more than the risk, but the issue
> should be kept in mind. Actually the possibility of converting some of
> these white papers into sphinx documents (to be included directly as doc
> pages) could be systematically considered, and the white paper could be
> just a step in that direction.
>
> This page is a good example of a short paper that was converted into a
> doc page.
> https://yade-dem.org/doc/FEMxDEM.html
>
> I think you know this one to: ;)
> https://yade-dem.org/doc/amazonEC2.html
>
> Bruno
>
>
>
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Re: [Yade-dev] Yade with CGAL 4.11

[Janek Kozicki (yade-dev)]

Uh, Bruno :-) I was thinking to ask you whether you have given my diff to Anton 
after you have modified it. Please do it, or just confirm that the one which I 
sent is good to go (which isn’t optimal due to too many #ifdefs as you 
mentioned earlier).

best regards
Janek

On 27 Nov 2017, 20:04 +0100, Anton Gladky , wrote:
> Hi all,
>
> is there any progress on fixing this issue? I have disabled CGAL for
> Debian builds, but it would be good to switch it on again.
>
> Also the stable Yade version is almost one year old. It is time to release
> something newer soon. If there are some volunteers to go through
> existing bugs on launchpad [1] and fix/close/react on some of them,
> it would be good.
>
> I will probably be able to prepare a release at the beginning of 2018.
>
> [1] https://bugs.launchpad.net/yade
>
> Best regards
>
> Anton
>
>
> 2017-11-07 19:35 GMT+01:00 Bruno Chareyre :
> >
> >
> > On 11/07/2017 06:47 PM, Janek Kozicki wrote:
> > >
> > > I just feel a little uneasy about cross_product of two
> > > (sphere-sphere) pairs ;)
> >
> >
> > Well... after admitting that spheres can be mutually orthogonal (which is
> > really the case) cross product is fine... :)
> > But you are right, here cross product is really ordinary cross_product.
> > Bruno
> >
> >
> >
> >
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