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Re: Potential Blocks and Potential Particles - brief analysis of the Object Oriented C++ source code



Janek thanks for the in-depth remarks on the PB (PotentialBlock) & PP (PotentialParticle) codes. It will be very useful to have a discussion on the matter and try to improve them.

Regarding the compilation warnings that stem from unused variables, I can help suppress them by commenting out the unused variables, if Chia can verify with me that he does not intend to use any them in the near future. For the other warnings, I will track them inside the code and try to suppress them as well. I will let you know if I find any difficulties.

Personally, I believe that we could unify some classes of the PB & PP, since a part of the code is overlapping; although some parts of the codes are completely different. Some comments on this -I see Chia just discussed some of these matters earlier today-. (Chia please correct me if I have misinterpreted something):

  *   The distinction between the two codes, conceptually, is that the PotentialBlocks have flat faces with no curvature, while the PotentialParticles can have curved faces and look like "cushions" (I liked that reference!). This curvature of the latter is controlled by the parameters "k" and "R" in the PotentialParticle shape class.

Also, the PotentialBlocks code has been developed to incorporate some more parameters and to be compatible with the BlockGen code, in which a PotentialBlock can be subdivided to more blocks, by intersecting the particle with discontinuity planes.

You will find in the source code that "R" is used in some parts of the PB code as well, but as a reference length unit and not as the "radius of a shadow particle", as it is in the PP class. So, in a case where the PB and PP are unified, one should choose "k=0", in order to get a particle with flat faces (like the PB) or "k>0", in order to get a particle with curved faces (like the PP). I should clarify, that when using the PB code, even if a non-zero value is given for "k", it is not used; the faces remain flat. I guess it just stayed in the code, to maintain some architectural similarity between the PB & PP classes.

  *   The most important distinction between the PB and PP codes from a programming standpoint is the contact detection algorithms used, as, in the former contact is established using linear programming (and CLP software), while in the latter contact is established using conical optimisation (either with MOSEK or Chia's second order code).

So, if we were to merge the Shape (PotentialBlock & PotentialParticle), Bound (PotentialBlock2AABB & PotentialParticle2AABB), a distinction could be made regarding the IPhys functor, so that, when k=0 (PB particles) we use the Ig2_PB_PB_ScGeom & Ip2_FrictMat_FrictMat_KnKsPBPhys functors, while if k>0 (curved faces), we use the Ig2_PP_PP_ScGeom & Ip2_FrictMat_FrictMat_KnKsPhys functors, respectivelly. As Chia said, I'm not sure we can unify the IGeom functors, as they were developed under different conceptions; though, new ideas are welcome :) .

I am interested to improve these codes, since I currently use the PotentialBlock class for my PhD. I don't think that I have the technical knowledge to apply these changes by myself. Maybe we can achieve this with some periodic consulting from Chia and some help from you Janek? Send me an email if you have the time to assist on this, I'm happy to discuss.

Chia and Janek, do you think it would be of value to merge just part of the codes, i.e. only the Shape and Bound classes for now, to simplify things?

  *   Regarding the the "heat-capacity" parameter, I'm afraid I can't help much, as I am not familiar with the topic.

These are some thoughts on my part. I'm very interested to hear more from you Janek, as you know YADE through and through and from Chia, as he is the original developer of all this work and I believe he can give us a better understanding of the conceptual design of the codes and if he thinks we should merge them.

I will go through with removing the warnings during the next days & I will also be sending a piece of documentation in .rst format regarding these codes soon.

Sorry for the long post.

Best Regards,



From: Yade-dev <yade-dev-bounces+v.angelidakis2=ncl.ac.uk@xxxxxxxxxxxxxxxxxxx> on behalf of Chia Weng Boon <chiaweng@xxxxxxxxx>
Sent: 27 January 2019 15:03:54
Cc: Yade developers
Subject: Re: [Yade-dev] Potential Blocks and Potential Particles - brief analysis of the Object Oriented C++ source code

Hi Janek,
Potential Blocks and Potential Particles are different algorithms.  Potential Blocks (PB) were developed for polygonal particles "without the spherical term".  Potential Particles (PP) were developed for general convex non-spherical particles.

The PB algorithm is based on linear programming (solved by calling linear programming libraries, now CLP ), and the contact point is calculated as the analytic centre.

The PP algorithm requires solving a nonlinear constrained optimisation problem.  The code uses second order coning programming, where there are two options.  The first is to call the function I wrote, or to call MOSEK (only free for academics).  PB is faster than PP, since PB is easier to solve.

The similar points between PB and PP are the way the contact normal is calculated (PB without the spherical term), and the way the overlap distance is calculated.

The reason why the physical contact properties were stored in the Shape file (rather than Material) is because they were originally developed for rock mechanics problems, where each face will have a different physical property.The Potential Block contact detection algorithm is compatible with the block generation algorithm here:

Vasileios and myself were in touch.  From what I know, he's using the PotentialBlock section (and also extracting the display with ParaView).  I agree there are many redundant variables that need to be removed in order to avoid confusion, and keen users may help greatly.  While I am much less active, I am still using YADE very occasionally as a hobby, and would like to see the algorithms get integrated better (eg display in QT, periodic boundaries, etc).  Hopefully in the spirit of open source, interested users will continue with this effort, leading to more possibilities.


On Sat, Jan 26, 2019 at 11:02 PM Janek Kozicki <janek_listy@xxxxx<mailto:janek_listy@xxxxx>> wrote:

I looked a bit more into PotentialBlocks, and there are some things
which surprise me, there seem to be some mistakes.

1. we strive to remove all compiler warnings. Currently when yade is
compiled without PotentialBlocks, there are only 6 warnings, and
four of them are caused by external libraries. Problem is that when
compiling with PotentialBlocks there are 198 warnings, especially
about unused variables and narrowing conversion. I've filed a
respective bug report about that:

2. material parameters (like stiffness or heat capacity) are stored
inside Shape class PotentialBlock.hpp. But they should be stored
inside a class derived from Material. My impression (I might be
wrong, in that case please correct me) is that PotentialParticle is
using default materials and default contact law. Then later you
decided that you need a more customized Material (e.g. with heat
capacity) and you have cloned PotentialParticle into PotentialBlock,
instead of adding a Material class. This error propagates down
through all my next remarks.

3. As a result of above mistake there is no IPhys (interaction
physics) functor. Its main purpose  is to calculate the physical
parameters of the contact. Eg. the heat capacity of two
PotentialBlocks that are in contact. Its contents was put into IGeom
functor Ig2_PB_PB_ScGeom.cpp

4. Ig2_PB_PB_ScGeom.cpp and Ig2_PP_PP_ScGeom.cpp are the duplicates of
each other. The code that is a difference between them is about
physics and would better go to the IPhys functor. Please do not
duplicate code. Duplicate code is the worst source of all bugs.
Because someone after a long debugging session finally corrects some
mistake, and believes that it has been corrected. And later the same
bug resurfaces in the duplicated part of the code.

5. PotentialBlock.hpp and PotentialParticle.hpp are duplicates of each
other, the difference between them is what would better go into
Material class

6. because they are duplicates the drawing of class PotentialBlock is
not implemented, while it would work perfectly well with
Gl1_PotentialParticle functor

I am sorry that my remarks are so fundamental in a sense. But this is
all in good will, I hope that fixing these problems would make the
code much more easier to work with for others, and much less prone to

After you make a class derived from Material to handle
PotentialBlocks properly, you will see that it will work best with
interaction physics (IPhys) functor which handlles this material. And
suddenly there is no need to duplicate code from
PotentialParticle.hpp into PotentialBlock.hpp. There will be only
PotentialParticle which sometimes can use the newly created material
and also will work with the default material. And this will cause
Gl1_PotentialParticle functor to draw correctly "both" of them.
"Both" in quotes, because there in fact will be inly one, but with
different material.

I hope that you can see that removing a duplicated code will suddenly
make it all simpler.

I understand that you stopped working on this topic and others are
using this code. Maybe Vasileios will want to fix this? In any case
it is good to discuss this, and if possible try to correct it.

After some discussion, maybe we should turn this Object Oriented
design problems into a bug report about PotentialBlcoks.

best regards
Janek Kozicki                               http://janek.kozicki.pl/  |

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