[Yade-dev] [Bug 1813229] [NEW] Class Inheritance graphs in Yade.pdf are unreadable

[Janek Kozicki]

Public bug reported:

After documentation is generated, the inheritance graphs on the website
look good, for example:

https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.Material

but in the Yade.pdf file the class names are completely unreadable. For
example look at page 173 in pdf file.

I would like to fix this before release. If you have any hints about
where to search for place in code which causes this problem please tell!

** Affects: yade
 Importance: Undecided
 Status: New

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https://bugs.launchpad.net/bugs/1813229

Title:
  Class Inheritance graphs in Yade.pdf are unreadable

Status in Yade:
  New

Bug description:
  After documentation is generated, the inheritance graphs on the
  website look good, for example:

  https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.Material

  but in the Yade.pdf file the class names are completely unreadable.
  For example look at page 173 in pdf file.

  I would like to fix this before release. If you have any hints about
  where to search for place in code which causes this problem please
  tell!

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Re: [Yade-dev] New Yade version? Debian freeze is coming

[Janek Kozicki]

Anton,

I also plan to write some more text into ./doc/sphinx/tutorial-examples.rst

do you prefer that I make a new branch for that, or push it into fix/examples 
branch?

I will let you know about my progress. I assume that 27 January is
still a valid date for release?

best regards
Janek


Anton Gladky said: (by the date of Wed, 16 Jan 2019 22:47:10 +0100)

> Thanks all for quick responses.
> 
> > Anton, how much time do I have?  
> 
> I would then propose to make a release next weekend (26-27 of January).
> Would it be OK?
> 
> Anton
> 
> Am Mi., 16. Jan. 2019 um 13:02 Uhr schrieb Janek Kozicki :
> >
> > I agree, you can make a release.
> >
> > If you know that it is correct, then I leave it to you to remove this 
> > warning from Tesselation.ipp :)
> >
> > Tesselation.ipp:78:2: warning: #warning "It was move_point before CGAL 
> > 4.13"
> >
> > I am planning to at least fix some examples. Anton, how much time do I have?
> >
> > best regards
> > Janek
> >
> >
> > Bruno Chareyre said: (by the date of Wed, 16 Jan 2019 11:13:02 +0100)
> >  
> > > Hi Anton,
> > > I think current code is stable and it is a good time to freeze.
> > >
> > > @All
> > > Does someone have hot stuff to be included (shortly)?
> > >
> > > Bruno
> > >
> > > On 1/15/19 8:44 PM, Anton Gladky wrote:  
>  [...]  
> >
> >
> > --
> > Janek Kozicki   http://janek.kozicki.pl/  |
> >
> > ___
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[Yade-dev] [Bug 1813222] Re: GUI→Display→intrAllWire causes crash if a body is deleted

[Janek Kozicki]

proposed fix: https://gitlab.com/yade-
dev/trunk/commits/fix/crash_intrAllWire

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Title:
  GUI→Display→intrAllWire causes crash if a body is deleted

Status in Yade:
  New

Bug description:
  void OpenGLRenderer::renderAllInteractionsWire(){…} in
  OpenGLRenderer.hpp tries to draw an interaction between bodies, one of
  which has been deleted.

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[Yade-dev] [Bug 1813222] [NEW] GUI→Display→intrAllWire causes crash if a body is deleted

[Janek Kozicki]

Public bug reported:

void OpenGLRenderer::renderAllInteractionsWire(){…} in
OpenGLRenderer.hpp tries to draw an interaction between bodies, one of
which has been deleted.

** Affects: yade
 Importance: Undecided
 Status: New

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https://bugs.launchpad.net/bugs/1813222

Title:
  GUI→Display→intrAllWire causes crash if a body is deleted

Status in Yade:
  New

Bug description:
  void OpenGLRenderer::renderAllInteractionsWire(){…} in
  OpenGLRenderer.hpp tries to draw an interaction between bodies, one of
  which has been deleted.

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[Yade-dev] fixing crash after toggling intrAllWire

[Janek Kozicki]

Hi all,

While investigating examples/PotentialParticles/cubePPscaled.py I had a crash 
when toggling intrAllWire.

That was due to trying to draw an interaction to a body which has been deleted.
So in OpenGLRenderer.cpp:227 I added a safeguard to not draw such interactions.

But there is still a bug looming in there:

A body can get deleted between lines 227 and line 238 in OpenGLRenderer.cpp
And I am right now not sure what happens if we requestErase from separate 
thread.
Because OpenGLRenderer runs in separate thread.

Also this code seems to be a duplicate of similar codes in Dispatching.cpp:123
and InteractionLoop.cpp:73
Maybe better to move these four lines (check if body was deleted, then
requestErase interaction) somewhere and just call this function from
these three places?

I marked all these places in this commit, so that it will be easier to discuss 
it:

https://gitlab.com/yade-dev/trunk/commit/8eca8eb7121491df25639d8fc7b966acef1c92c0


Also these messages:

InteractionLoop.cpp:73 action: Body #76 vanished, erasing intr #76+#97!
InteractionLoop.cpp:73 action: Body #21 vanished, erasing intr #21+#96!
InteractionLoop.cpp:73 action: Body #21 vanished, erasing intr #21+#2!

Are really spamming the terminal. Yes they are nice. But we should do something
about default setting of LOG_DEBUG messages to not spam people who don't
understand what's going on. Actually that was a reason for which
I marked some examples as either suspicious or not working. And that
wasn't an error introduced by the author of the example.

best regards 
Janek Kozicki

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Re: [Yade-dev] Potential Blocks and Potential Particles - Documentation

[Janek Kozicki]

Bruno Chareyre said: (by the date of Wed, 23 Jan 2019 11:03:27 +0100)

> On 1/22/19 2:38 PM, Chia Weng Boon wrote:
> >
> > Can someone lead me to the file for polyhedra display in YADE? Maybe I 
> > can try to get the display to work in qt.  I can't recall how I made 
> > it work for Potential Particles in qt.  At one point in time, I always 
> > playing with marching cubes..but it used too much memory and the 
> > rendering was not very nice.
> >  
> 
> Hi,
> I don't know the marching cube method but if potential blocks are 
> Minkowski sums of polyhedra and spheres - as I think they are, then it 
> should be enough to combine existing functors since that's exactly how 
> PFacet polyhedra are displayed. And it should be efficient.
> Let me know.
> See the figures in [1], they are from yade GUI for most of them.
> Bruno

Actually PotentialParticles are not Minkowski sums. This would be the
case if a sphere was not added to the particle shape. Previous
sentence might sound weird, but that's actually how it works. Chia
defines a formula for the shape of the particle (declaring each side
of a polyhedral). The isosurface at which this formula==0 is the
surface of this particle. Up to this point it would be directly a
Minkowski sum. But afterwards he adds x^2+y^2+z^2-R^2 to this
formula. This means that he is adding a sphere to this formula, and
all the shapes suddenly look like cushions with soft corners instead
of polyhedral Minkowki sums.

Chia, I have discovered that setting Gl1_PotentialParticle().store=True
fixes all the display problems which I had with
examples/PotentialParticles/cubePBscaled.py
Why did you set it to false by default in C++ code?

When it was false the marching cubes algorithm was executed for every
display refresh, and when drawing just one particle it was
recalculating marching cubes for all perticles. No wonder it was
slow. Like n^2 slow.


So after setting store=True, the display now works nicely. But still
the collisions do not work. I hope that you can fix that. I made a
short video to demonstrate what I'm talking about:

https://www.youtube.com/watch?v=1XEtGrbo7lM


Regarding other two examples:

PotentialBlocks/WedgeYADE.py
PotentialBlocks/cubePBscaled.py

I could not get them to work no matter what. The particles just sit
there and never move. I will write next mail about that, because I
have done some analysis of your C++ code and it might be useful to
someone who plans to continue working on PotentailParticles, maybe
Vasileios?

best regards
Janek Kozicki

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Re: [Yade-dev] Fixing the examples

[Bruno Chareyre]

Hi Janek,
I went through list_of_examples.txt [1].
Impressive work, thanks. I just fixed two [2].

My impression is that some examples could be fixed quickly by the 
original authors, provided that they now the problem (many of them are 
probably not reading yade-dev). I'm then adding some of them in cc of 
this email for possible reaction.


Guys, you can fix thoses scripts on github or gitlab, doesn't matter. 
Please remember to insert your name and email in every script so we know 
what to do is a case like now.


FEMxDEM: Ning Guo (if this adress does not work I know Ning has 
successors in HK)
HydroForceEngine: Raphael MAURIN (postProcessing_sedim.py has a problem 
+ some scripts need move to check scripts (great!))

jointedCohesiveFrictionalPM:  Luc Scholtès and/or (?) Jérôme Duriez
OAR:  William Chèvremont  (maybe a few lines in preamble of sim.py to 
explain why - obviously - it cannot work for Janek, or maybe link back 
to where it is explained?)
SPH: Anton, is there somewhere explanation of current state of SPH? Is 
it something someone could take over one day, or should it be simply 
removed?


Thanks all.

Bruno

[1] 
https://gitlab.com/yade-dev/trunk/blob/master/examples/list_of_examples.txt
[2] 
https://gitlab.com/yade-dev/trunk/commit/46f718ee2bc3c2198809145f1446865263d1453b



On 1/20/19 10:45 PM, Janek Kozicki wrote:

Sounds great!

You can see more info in file examples/list_of_examples.txt
would be great if mark in this file those that you have fixed.

it is already merged on gitlab :)
https://gitlab.com/yade-dev/trunk/merge_requests/27

best regards
Janek


Jan Stránský said: (by the date of Sun, 20 Jan 2019 21:44:29 +0100)


Hi Janek,

thanks for the detailed look :-)


If you have any hints on how to fix any of those examples, please tell!

several mentioned not working script is from me. I think than correcting
them and pushing to gitlab is better than telling :-)


Also I see that https://yade-dem.org/doc/tutorial-examples.html looks

very strange - the youtube videos are not shown

I don't remember the reason (have read it long time ago), but the youtube
videos does work using http (not https) in the address

cheers
Jan



ne 20. 1. 2019 v 20:27 odesílatel Janek Kozicki  napsal:


Hi,

I did small or cosmetic fixes in 17 examples.
Currently 21% of examples (46 out of 215) are broken.

I tried every example in a very quick manner. I checked if it has any
explanations inside the comments, then I tried to just run it.
It is possible that some of them failed only because they need a bit
fiddling before starting them. In that case we need to explain the
fiddling inside the file, in comments. And tell me what is the fiddling to
do!

If you have any hints on how to fix any of those examples, please tell!

ResetRandomPosition.py
  : SIGSEGV/SIGABRT handler called;
  : gdb [with T = IGeomFunctor; typename
boost::detail::sp_member_access::type = IGeomFunctor*]: Assertion `px !=
0' failed.

DeformEngine/LOedometricDeform.py and OedometricDeform.py
  : NameError: name 'DeformControl' is not defined

FEMxDEM
  : ImportError: No module named esys.escript
  I am reading https://launchpad.net/escript-finley to fix this.

HydroForceEngine/twoWayCoupling/postProcessing_sedim.py
  : line:49 ValueError: operands could not be broadcast together with
shapes (900,) (901,) (900,)

LudingPM/LudingPM_1.py and LudingPM_2.py
  : NewtonIntegrator: NaN force acting on #0.

PotentialBlocks/WedgeYADE.py and cubePBscaled.py
PotentialParticles/basic.py and cubePPscaled.py
  : NameError: name 'PotentialBlock2AABB' is not defined
  I will recompile with ENABLE_POTENTIAL_BLOCKS=ON and see if they work.

agglomerate/simulation.py
  : AttributeError: 'Body' object has no attribute 'agglomerate'

capillary/liquidmigration/showcase.py
  : NameError: name 'LiqControl' is not defined
  I will recompile with LIQMIGRATION  and see if it works.

clumps/save-load-clumps.py
  : SIGSEGV/SIGABRT handler called; gdb
  : Assertion `member->isClumpMember()' failed.

deformableelem/Minimal.py
  : the graphs are empty

deformableelem/main.py
  : I suppose this file is here by mistake ?

jointedCohesiveFrictionalPM/packInGtsSurface.py and all other files
  : spams terminal with messages: UnbalancedForce=-nan, rel stress nan

mortar/modelTests/failureEnvelope.py
  : MortarMat.cpp:12 go: MortarMat not implemented for non-cohesive contacts

oar/sim.py
  : KeyError: 'Invalid key: description.'

sph/dam_break.py and all other files there
  : AttributeError: No such attribute: KernFunctionPressure.
  I will recompile with SPH and see if they work.

test/WireMatPM/net-2part-strain.py
  : UniaxialStrainer::action(): Assertion `posIds.size()==posCoords.size()
&& negIds.size()==negCoords.size() && originalLength>0 &&
crossSectionArea>0' failed.
  : SIGSEGV/SIGABRT handler called; gdb

test/batch/sim.py
  : KeyError: 'Invalid key: description.'

test/exact-rot-facet.py and exact-rot.py
  : [with T = IGeomFunctor; typename

Re: [Yade-dev] [Yade-users] [Question #676841]: the definition of porosity

[Jan Stránský]

Hi Bruno,
sorry for late answer, during Christmas I totally forgot about the topic :-)
yes, reading it once more, it sounds contradictory.. but anyway it make
sense to me and I am sure there are words that would explain/define it
better..

apparently the topic would deserve something like FAQ [1] :-)
Jan

[1] https://answers.launchpad.net/yade/+question/678055



út 18. 12. 2018 v 20:07 odesílatel Bruno Chareyre <
bruno.chare...@3sr-grenoble.fr> napsal:

>
>
> Le mar. 18 déc. 2018 16:37, Jan Stránský  a
> écrit :
>
>>
>>
>> see my previous (slightly modified):
>> - assuming the particles rigid
>> - computing the force under assumption that in reality there would be no
>> overlap and some deformation.
>>
>
> This is self contradictory, no? What would be a model where you assume the
> contrary of what you consider reality and expected result?!
> By this statement you are efficiently killing the rigid assumption.
> Obviously it doesn't fit in the general picture and it it is useless.
> Bruno
>
>
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Re: [Yade-dev] [Yade-users] [Question #676841]: the definition of porosity

[Bruno Chareyre]

Haha, no worries.
Let's see the reaction of jamespaul.
I was about to send him a link to yade doc (DEM background) in order to 
claim that yade was not assuming overlap (so _he_ would have to justify 
the concept).
Unfortunaltely it is not true: although "normal displacement", "change 
of distance", "normal strain" is used in many places (and refers to 
deformability unequivocaly) the word "overlap" still appears here and 
there. Blame me for not cleaning. :)


Bruno

On 1/24/19 2:44 PM, Jan Stránský wrote:

Hi Bruno,
sorry for late answer, during Christmas I totally forgot about the 
topic :-)
yes, reading it once more, it sounds contradictory.. but anyway it 
make sense to me and I am sure there are words that would 
explain/define it better..


apparently the topic would deserve something like FAQ [1] :-)
Jan

[1] https://answers.launchpad.net/yade/+question/678055



út 18. 12. 2018 v 20:07 odesílatel Bruno Chareyre 
> napsal:




Le mar. 18 déc. 2018 16:37, Jan Stránský
mailto:honzik.stran...@gmail.com>> a
écrit :



see my previous (slightly modified):
- assuming the particles rigid
- computing the force under assumption that in reality there
would be no overlap and some deformation.


This is self contradictory, no? What would be a model where you
assume the contrary of what you consider reality and expected result?!
By this statement you are efficiently killing the rigid
assumption. Obviously it doesn't fit in the general picture and it
it is useless.
Bruno


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