[Yade-users] New version of Yade release, release plan

[Anton Gladky]

Dear Yade users and developers,

As is customary at the beginning of January, we aim to release a new version
of Yade. The release process takes some time, so we kindly request that you
commit all your planned features by the *end of the day on January 19, 2023*
,
so that we can prepare the tarball, test it on all supported architectures,
and
upload it into the package archives.

The version 2024.01 is intended to be included in the next Long-term-support
Ubuntu Release 24.04, scheduled for release in April 2024 and will be
supported
until 2029.

Please plan your work accordingly.

Thanks and best regards,

Anton
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[Yade-users] Yade 2023.02a released

[Anton Gladky]

Dear Yade users and developers,

We are excited to announce the release of Yade 2023.02a!
This latest version comes with several new features and improvements
that we hope will enhance your experience with the software.

Thanks to all our developers and users for their contributions to this
release.
Special thanks to Janek for his contribution and for preparing the release
notes.

Debian packages are now available in the current Debian Testing and
have also been synced to the Ubuntu archive. Daily packages are also
available and provide all the new features for most active platforms.
Please see the installation page in the documentation.

Thank you for your continued support and contributions to Yade.

Anton


Changelog:

==
yade-2023.02a

Short summary of 2023.02a release:
short title (Merge Request count, until !912)

Documentation / Comments  (26 MRs)
Bug fixes (12 MRs)
LevelSet  (12 MRs)
Small improvements( 9 MRs)
Fluid & thermal & particle saturation ( 7 MRs)
High precision RealHP ComplexHP ( 7 MRs)
PotentialParticles / Blocks   ( 5 MRs)
Examples  ( 4 MRs)
Tests & checks & CI   ( 4 MRs)
Polyhedra / Facets( 3 MRs)
Clumps( 3 MRs)
Packaging improvements & building ( 2 MRs)
Alpha shapes  ( 2 MRs)
clang-format & reorganize ( 7 MRs)
OpenMPI calculations  ( 0 MRs)
GUI   ( 0 MRs)


Documentation / Comments  (26 MRs)
  remove link to wiki in homepage + mention the generic  adress for paid
support in another place (!822)
  GnuplotHyperlink (!824)
  Peace in Ukraine (!833)
  a valid link to russian scientists protesting war (it  disappeared from
russian websites) (!834)
  trunk | new thesis (!837)
  Fix doc: import error in make doc (!840)
  Reintroducing git version number in doc index (!842)
  Doc updates (installation, ViscEl, makeClumpCloud) (!841)
  VTKRecorder doc typo and +1 paper (!854)
  Update information about yadedaily installation (!855)
  Doc: missing new line in raw docstring (!860)
  Fix broken link to pdf docs (!863)
  New publications (!875)
  clarify options and packages (!861)
  Remove google-analytics script #280 (!873)
  Py3 related comment in one capillary script (!876)
  Add short-course guides and slides to website (!871)
  Add news about Yade hackathon (!879)
  Modifying Installation page, merging indications of  features and
external packages (!870)
  Fix #286, replace frontpage Changelog link + other  homepage
modifications (!882)
  clarify a FIXME which has been partly fixed. (!903)
  Doc updates regarding Clump and OAR compilation option  (!900)
  New publications (!905)
  +1 paper (!912)
  mention ubuntu20.04 virtual machine (!915)
  Yade on Twitter (!920)

Bug fixes (12 MRs)
  small fix: correct shebang and follow XDG specification  (!831)
  fix #256 (!852)
  fix #259 (!850)
  fix #264 - Failed screenshot tests in test_22_04 (!853)
  workaround bug  https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1009739
(!858)
  Revert "workaround bug
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1009739; (!867)
  reimplement flipCell, fix
https://answers.launchpad.net/yade/+question/701782 (!864)
  Fix compilation with g++ 12 (!885)
  One more g++ 12 fix. (!886)
  Fix ppc64el and i386 (!890)
  Remove last trace of libloki-dev (!888)
  FIX #290, binding functions should not use 'def_readonly'  (!898)

LevelSet  (12 MRs)
  Level set visualisation (!828)
  Reflecting recent qt visualization of LevelSet in the doc  (!836)
  Level set Periodic Boundary Conditions (!832)
  LevelSet Updates (!865)
  A better definition of LS grids for superquadrics (back  to [Duriez2021b]
behavior) (!883)
  Smeared Heaviside step function for level sets (!881)
  Level-set DEM periodic boundary conditions update (!897)
  LS updates (!908)
  Correcting location of LS-LS ScGeom contactPoint (!911)
  Avoiding a brutal throw when boost root finding algorithm does not find
any in LevelSet (!928)
  LevelSet new discharge example, updates in smearing considerations and
formal changes (!914)
  fabricTensor for non-spherical particles through extrema argument (!916)

Small improvements( 9 MRs)
  Removing unused Body.chain (!825)
  add support for python 3.10 and add new find paths for  CLP, CuBlas and
freeglut with  new archlinux image (!830)
  Introducing capillary files in yade-data. (!877)
  Fix urls to input data in the benchmark scripts, and set
 preventGranularRatcheting=False, hertzian=True (!895)
  use precomputed shearIncrement: faster and compatible  with all Ig2
functors,... (!893)
  ensure randomColor() uses utils func (!909)
  Removing unused chain attribute from facet() Python  signature (!913)
  

Re: [Yade-users] [Yade-dev] Upcoming Yade Release 2023.01

[Anton Gladky]

Thanks for your work, Janek! I really appreciate it!

I will start preparing for a release this week, but will wait
until next week for some upcoming features.

Regards

Anton


Am Mi., 18. Jan. 2023 um 23:20 Uhr schrieb Janek Kozicki (yade) <
jkozicki-y...@pg.edu.pl>:

> Hi,
>
> I created update Changelog MR for this:
>
> https://gitlab.com/yade-dev/trunk/-/merge_requests/917/diffs
>
> best regards
> Janek
>
> Anton Gladky said: (by the date of Mon, 16 Jan 2023 21:16:59 +0100)
>
> > Dear all,
> >
> > as always at the beginning of the year we are preparing
> > the stable Yade Release.
> >
> > Please, push your changes through merge requests till this Friday,
> > 20.01.2023 and think about adding some more notes into the
> > Changelog [1].
> >
> > [1] https://pad.systemli.org/p/yade-2023-changelog
> >
> > Thank you
> >
> > Anton
> >
> > ___
> > Mailing list: https://launchpad.net/~yade-dev
> > Post to : yade-...@lists.launchpad.net
> > Unsubscribe : https://launchpad.net/~yade-dev
> > More help   : https://help.launchpad.net/ListHelp
>
>
> --
> --
> Janek Kozicki, PhD. DSc. Arch. Assoc. Prof.
> Gdansk University of Technology (Gdansk Tech)
> Faculty of Applied Physics and Mathematics
> Institute of Physics and Applied Computer Science
> Division of Theoretical Physics and Quantum Information
> --
> http://yade-dem.org/
> http://pg.edu.pl/p/jan-kozicki-19725
> http://mostwiedzy.pl/en/jan-kozicki,19725-1
>
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[Yade-users] Upcoming Yade Release 2023.01

[Anton Gladky]

Dear all,

as always at the beginning of the year we are preparing
the stable Yade Release.

Please, push your changes through merge requests till this Friday,
20.01.2023 and think about adding some more notes into the
Changelog [1].

[1] https://pad.systemli.org/p/yade-2023-changelog

Thank you

Anton

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[Yade-users] TODO-List for Yade

[Anton Gladky]

Dear all,

As discussed during the last meeting of yade-devs, I have prepared
a list of TODO-tasks [1] for Yade, which can be completed during the student
works, Google summer of code and other similar contests and springs.

Feel free to add new ideas (even crazy ones!) into this list. If somebody
will work on the particular task, it will be separated into the extra-task to be
tracked.

[1] https://gitlab.com/yade-dev/trunk/-/issues/251

Thanks and best regards

Anton

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Re: [Yade-users] [Question #700411]: Aborted (core dumped) occured when I use the Hertz-Minlin contact law with non-zero krot and eta

[Anton Gladky]

Question #700411 on Yade changed:
https://answers.launchpad.net/yade/+question/700411

Anton Gladky posted a new comment:
It would also be good if you compile yade with debug symbols, so we can
get more information about the crash.

Could you also please create an issue on gitlab [1] with this
information about this problem?

[1] https://gitlab.com/yade-dev/trunk/-/issues

Thanks

Anton

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[Yade-users] Yade 2022.01a released

[Anton Gladky]

Dear Yade users and developers,

As always at the beginning of the year we are releasing the new Yade version.
Yade 2022.01a has just been released [1]!

Thanks all developers and users for contributions! Special thanks to Janek for
his contribution and preparing the release notes!

Last year we started regular online meetings of Yade members. Feel free to join
us (more details are here [2]).

[1] https://gitlab.com/yade-dev/trunk/-/releases/2022.01a
[2] https://lists.launchpad.net/yade-dev/msg15105.html

Best regards

Anton


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Description: OpenPGP digital signature
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Re: [Yade-users] [Question #699714]: Python problems in Yade 2021.01a

[Anton Gladky]

Question #699714 on Yade changed:
https://answers.launchpad.net/yade/+question/699714

Anton Gladky proposed the following answer:
Please file a bug here [1] with a minimal working example, so we will
have a change to fix it before the next release.

[1] https://gitlab.com/yade-dev/trunk/-/issues

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Re: [Yade-users] [Question #699714]: Python problems in Yade 2021.01a

[Anton Gladky]

Question #699714 on Yade changed:
https://answers.launchpad.net/yade/+question/699714

Status: Open => Answered

Anton Gladky proposed the following answer:
Definitely update your scripts to 3rd python version and switch to a
newer Yade. We are not supporting older Yade version, so there is no
chance to fix an error in those versions, if they are detected.

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[Yade-users] New version of Yade, 2022. Release plan

[Anton Gladky]

Dear Yade users and developers,

as always at the beginning of January we want to release a new Yade version.
Release process takes some time, so please commit all your planned features
till the end of the December 2021, so we can prepare tarball, test it on all
supported architectures and upload it into the package archives.

The version 2022.01 should go into the next Long-term-support Ubuntu Release,
which is planned to be released in April 2022 and will be supported till 2027,
and even with Extended Security Maintenance till 2032.

Please plan your work accordingly.

Thanks and best regards

Anton

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Re: [Yade-users] [Question #699190]: Problem Install Yade Daily

[Anton Gladky]

Question #699190 on Yade changed:
https://answers.launchpad.net/yade/+question/699190

Status: Open => Answered

Anton Gladky proposed the following answer:
We are supporting only LTS-Ubuntu versions. 21.04 is not
a LTS version, thus is not supported. See the list of suported
versions here [1].

[1] https://yade-dem.org/doc/installation.html#packages

Best regards

Anton

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Re: [Yade-users] [Question #699190]: Problem Install Yade Daily

[Anton Gladky]

Question #699190 on Yade changed:
https://answers.launchpad.net/yade/+question/699190

Status: Open => Answered

Anton Gladky proposed the following answer:
What is your operating system? What version?


Anton

Am Fr., 22. Okt. 2021 um 18:01 Uhr schrieb Chiara Gigoli
:
>
> A question was asked in a language (Italian) spoken by
> none of the registered Yade answer contacts.
>
> https://answers.launchpad.net/yade/+question/699190
>
> Hi,
> First of all, excuse me for my english. I'm new on Linux and on Yade.
> I have some problems installing Yade daily. Some weeks ago I installed Yade 
> and it works.
> In my university recommended to install yadedaily, because we are only users 
> of the software, so I want to follow their suggestion. So I remove Yade and 
> tried to install yadedaily.
> I followed instruction in https://yade-dem.org/doc/installation.html
> But when I arrived at step
> Add the PGP-key AA915EEB as trusted and install yadedaily
> there is a warning:
> Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead 
> (see apt-key(8)).
> If I ignore this warning and go over, terminal restitutes that to me:
> Alcuni pacchetti non possono essere installati. Questo può voler dire
> che è stata richiesta una situazione impossibile oppure, se si sta
> usando una distribuzione in sviluppo, che alcuni pacchetti richiesti
> non sono ancora stati creati o sono stati rimossi da Incoming.
> Le seguenti informazioni possono aiutare a risolvere la situazione:
>
> I seguenti pacchetti hanno dipendenze non soddisfatte:
>  libyadedaily : Dipende: libboost-python1.71.0-py38 ma non è installabile
> Dipende: libboost-regex1.71.0-icu66 ma non è installabile
> Dipende: libpython3.8 (>= 3.8.2) ma non è installabile
>  python3-yadedaily : Dipende: libboost-python1.71.0-py38 ma non è installabile
>  Dipende: libboost-regex1.71.0-icu66 ma non è installabile
>  Dipende: libpython3.8 (>= 3.8.2) ma non è installabile
> E: Impossibile correggere i problemi, ci sono pacchetti danneggiati bloccati.
>
> (it's in italian, but maybe that's pretty clear the meaning).
> I search here and online in general if somone else had the same problem, but 
> I didn't find anyone, so I think that post this question could be helpful for 
> other users.
> Thank you in advance for the help, and sorry again (maybe it's a banal 
> problem).
> Chiara
>
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Re: [Yade-users] [Question #698654]: libopenblas problem after updating to Ubuntu 20

[Anton Gladky]

Question #698654 on Yade changed:
https://answers.launchpad.net/yade/+question/698654

Anton Gladky posted a new comment:
OK, I am glad that the problem is fixed. But I do not really know, why
it libopenblas0 package was not installed on your system.

>From here [1]: libyade strictly depends on libopenblas0, so it HAS to be 
>installed by the package manager.
>From here [2] libopenblas0 can be provided by libopenblas0-pthread,
>libopenblas0-openmp or  libopenblas0-serial and all of them are providing 
>libopenblas0.so

No idea, what was wrong there.

[1] https://packages.debian.org/unstable/libyade
[2] https://packages.debian.org/sid/libopenblas0

Anton

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Re: [Yade-users] [Question #698654]: libopenblas problem after updating to Ubuntu 20

[Anton Gladky]

Question #698654 on Yade changed:
https://answers.launchpad.net/yade/+question/698654

Status: Needs information => Answered

Anton Gladky proposed the following answer:
It is very strange. Could you please check, whether maybe
LD_LIBRARY_PATH is set in your environment?

echo $LD_LIBRARY_PATH

And please check, how libyade is linked:

ldd /usr/lib/x86_64-linux-gnu/yade/libyade.so | grep -i openblas

>>> libopenblas.so.0 => /lib/x86_64-linux-gnu/libopenblas.so.0
(0x7f409ddb)

I have just installed yade in Ubuntu 20.04 docker-container and it works
as it should. Please also show all your environmental variables:

env

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Re: [Yade-users] [Question #696708]: no X rendring on WSl ubuntu

[Anton Gladky]

Question #696708 on Yade changed:
https://answers.launchpad.net/yade/+question/696708

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

it is interesting to know that Yade can be running on Windows. 
As far as I understand Microsoft has just started to port Linux GUI on Windows 
and they reported about it yesterday [1].

It would be useful if you share your experience compiling/running Yade
on Windows even without GUI.

[1] https://devblogs.microsoft.com/commandline/the-initial-preview-of-
gui-app-support-is-now-available-for-the-windows-subsystem-for-linux-2/

Regards

Anton

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Re: [Yade-users] [Question #696307]: Recompile Haustein Source code

[Anton Gladky]

Question #696307 on Yade changed:
https://answers.launchpad.net/yade/+question/696307

Anton Gladky proposed the following answer:
As far as I remember we integrated the complete code into the Yade main branch 
[1].
Just try, by enabling YADE_DEFORM feature. 

[1] https://gitlab.com/yade-
dev/trunk/-/tree/master/examples/DeformEngine

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Re: [Yade-users] [Question #696131]: Problem MPI_CXX during default Compilation

[Anton Gladky]

Question #696131 on Yade changed:
https://answers.launchpad.net/yade/+question/696131

Anton Gladky proposed the following answer:
It looks like you are using clang, which has problems with MPI. Please
use gcc instead.

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[Yade-users] Yade 2021.01a is released

[Anton Gladky]

Dear Yade users and developers,

As always at the beginning of the year we are releasing
the newer Yade version. A couple of days ago Yade 2021.01a
was released [1]! Thanks all for contributions!

Special thanks to Janek for his contribution and preparing the
release notes! French team thanks for pushing MPI version of the
Yade and other features and fixes!

[1] https://gitlab.com/yade-dev/trunk/-/releases/2021.01a

Best regards

Anton
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Re: [Yade-users] [Question #695082]: Yadedaily installation and mpmath error (focal)

[Anton Gladky]

Question #695082 on Yade changed:
https://answers.launchpad.net/yade/+question/695082

Anton Gladky posted a new comment:
I have added the dependency into yadedaily

https://gitlab.com/yade-
dev/trunk/-/commit/fcd4d709a16ffaac3422d79dfc9926f67ee349c2

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[Yade-users] Yade_2020.01a for Debian 10 Buster and Debian 9 Stretch

[Anton Gladky]

Dear Yade users and developers,

backport repositories of Debian 10 Buster (stable) [1]
and Debian 9 Stretch (oldstable) [2] have got an updated
yade_2020.01a.

If you use one of those distributions, you can install updated
Yade from backports:

sudo apt-get install yade -t stretch-backports

or

sudo apt-get install yade -t buster-backports.

If you have any questions or troubles with it, please let me know.

[1] https://buildd.debian.org/status/package.php?p=yade=buster-backports
[2] https://buildd.debian.org/status/package.php?p=yade=stretch-backports

Best regards

Anton

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[Yade-users] New Yade version, beginning of January 2021

[Anton Gladky]

Dear Yade users and developers,

As always at the beginning of January I am planning to prepare
a release of a new Yade version.

Please try to push your changes inyo the code at least till the mid
of December, so we will have enough time to test it on different
platforms during the Christmas period and release it on time.
Also please try not to push too much breaking changes at that
period..

The new Debian Bullseye release is scheduled already [1]. So we
should not be too late to prepare a new Yade for the next stable
Debian version.

Also it would be good to prepare short but meaningful release notes.
Current git-workflow has too many small log-messages, so it is
difficult to get meaningful information from there. Please use this
link to add some notes [2].

[1] https://wiki.debian.org/DebianBullseye
[2] https://pad.systemli.org/p/yade-2021-release-notes

Thank you

Anton Gladky

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Re: [Yade-users] [Question #693698]: Trouble when compiling with g++-9 or g++-7

[Anton Gladky]

Question #693698 on Yade changed:
https://answers.launchpad.net/yade/+question/693698

Anton Gladky proposed the following answer:
I am working on VTK 9 for Debian. It is difficult. piece of software
for packaging.. Not sure it will get into the Debian Bullseye though.

Anton

Am So., 1. Nov. 2020 um 17:16 Uhr schrieb Janek Kozicki
:
> Yes, it seems that cmake is discovering VTK 9. And reinstalling VTK 6 is
> not affecting cmake which prefers VTK 9. I am not sure why linking with
> VTK 9 somehow goes wrong. However this is the first time when yade
> encounters VTK 9. Latest version which we have in the pipeline is 8.2.
> It is now difficult to include VTK 9 in the pipeline, because it is not
> in any of the linux distros which we have in the CI. This problem could
> be solved by fiddling with cmake or cmake invocation:

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Re: [Yade-users] [Question #693698]: Trouble when compiling with g++-9 or g++-7

[Anton Gladky]

Question #693698 on Yade changed:
https://answers.launchpad.net/yade/+question/693698

Anton Gladky proposed the following answer:
Hi,

you are compiling with clang, not with gcc:

-- The C compiler identification is Clang 6.0.0
-- The CXX compiler identification is Clang 6.0.0

Be sure to have empty CC and CXX environmental variables.
Or set them explicitly.

Regards

Anton

Am Do., 29. Okt. 2020 um 18:41 Uhr schrieb Sacha Duverger
:
>
> Question #693698 on Yade changed:
> https://answers.launchpad.net/yade/+question/693698
>
> Sacha Duverger posted a new comment:
> Thank you for your answers,
>
> Before trying to compile with g++-7 I emptied the "build" and "install"
> directories (with "rm -r build/* install/*"), this counts has a fresh
> directory right? Anyway, I tried to start from a really fresh directory
> (with another name) and had the same problem.
>
> The g++-9 installed on my machine worked well when I used it to compile
> another package (this package is the reason why I upgraded g++ in the
> first place). Can there still be a problem with g++-9's necessary
> packages while it already worked for another package than YADE?
>
> I tried to compile YADE with clang but I don't see where I can identify
> which package cause problems with g++. See [1] for the outputs of cmake
> and make install.
>
> I also tried to uninstall and reinstall all of my g++ versions, hoping
> that it could fix problems on the necessary packages, but it still
> doesn't work.
>
> 
> [1] : Running cmake and make with clang
>
> ## cmake command
>
> cmake -DENABLE_GUI=ON -DENABLE_MPI=OFF -DENABLE_PFVFLOW=OFF
> -DENABLE_TWOPHASEFLOW=OFF -DENABLE_LBMFLOW=OFF
> -DENABLE_POTENTIAL_BLOCKS=OFF -DCMAKE_CXX_COMPILER=clang
> -DCMAKE_INSTALL_PREFIX=../install ../trunk
>
> ## cmake output
>
> -- The C compiler identification is Clang 6.0.0
> -- The CXX compiler identification is Clang 6.0.0
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working C compiler: /usr/bin/cc - skipped
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Check for working CXX compiler: /usr/bin/clang - skipped
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Version is set to 2020-10-20.git-427f64c
> -- GCC Version >= 4.8. Adding -save-temps
> -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0")
> -- Log filtering: enabled
> -- Enabling boost::log library and DEBUG=OFF. Logging will work nicely, 
> backtraces will not have debug info, files will be small.
> Loop on the following python versions and check available 
> dependencies:3.8;3.7;3.6;3.5;3.4;3.3;3.2;3.1;3.0;2.7;2.6
> -- Found PythonInterp: /usr/bin/python (found version "2.7.17")
> -- Found PythonInterp: /usr/bin/python3.6 (found version "3.6.9")
> Python version 3.6.9 found, try to import dependencies...
> -- Found NumPy: version "1.18.4" 
> /home/sacha.duverger/.local/lib/python3.6/site-packages/numpy/core/include
> -- Found IPython: /usr/lib/python3/dist-packages/IPython
> -- Found matplotlib: 
> /home/sacha.duverger/.local/lib/python3.6/site-packages/matplotlib
> -- Found pygraphviz: /usr/lib/python3/dist-packages/pygraphviz
> -- Found Xlib: /usr/lib/python3/dist-packages/Xlib
> -- Found future: /usr/lib/python3/dist-packages/future
> -- Found past: /usr/lib/python3/dist-packages/past
> -- Found tkinter: /usr/lib/python3.6/tkinter
> --   Boost_VERSION: 106501
> --   Boost_LIB_VERSION: 1_65_1
> --   Boost_INCLUDE_DIRS: /usr/include
> --   Boost_LIBRARIES: 
> /usr/lib/x86_64-linux-gnu/libboost_python3-py36.so/usr/lib/x86_64-linux-gnu/libboost_thread.so-lpthread/usr/lib/x86_64-linux-gnu/libboost_filesystem.so/usr/lib/x86_64-linux-gnu/libboost_iostreams.so/usr/lib/x86_64-linux-gnu/libboost_regex.so/usr/lib/x86_64-linux-gnu/libboost_serialization.so/usr/lib/x86_64-linux-gnu/libboost_system.so/usr/lib/x86_64-linux-gnu/libboost_date_time.so/usr/lib/x86_64-linux-gnu/libboost_log.so/usr/lib/x86_64-linux-gnu/libboost_chrono.so/usr/lib/x86_64-linux-gnu/libboost_atomic.so/usr/lib/x86_64-linux-gnu/libboost_log_setup.so
> Found all python dependencies with version 3.6.9, will compile yade with that.
> -- Chosen compiler flags are: CMAKE_CXX_FLAGS =   -Werror -Wformat 
> -Wformat-security -Wformat-nonliteral -Wall -Wextra -Wnarrowing -Wreturn-type 
> -Wuninitialized -Wfloat-conversion -Wcast-align -Wdisabled-optimizat

Re: [Yade-users] [Question #690925]: corrupted double-linked list

[Anton Gladky]

Question #690925 on Yade changed:
https://answers.launchpad.net/yade/+question/690925

Status: Needs information => Answered

Anton Gladky proposed the following answer:
Smells like a heap corruption. Please create an issue on gitlab with the
script which reproduces the problem. Thanks.

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Re: [Yade-users] [Question #690051]: eccentric motor vibration

[Anton Gladky]

Question #690051 on Yade changed:
https://answers.launchpad.net/yade/+question/690051

Status: Open => Answered

Anton Gladky proposed the following answer:
Please check BicyclePedalEngine [1]

[1] https://yade-
dem.org/doc/yade.wrapper.html?highlight=bicycle#yade.wrapper.BicyclePedalEngine

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Re: [Yade-users] [Question #684881]: Introducing viscous forces in a liquid bridge

[Anton Gladky]

Question #684881 on Yade changed:
https://answers.launchpad.net/yade/+question/684881

Status: Open => Answered

Anton Gladky proposed the following answer:
I would recommend you to extend an existing law instead of writing a new
one, if it is possible. Thus you can escape the code duplication and
pain of adding new files from scratch.

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Re: [Yade-users] [Question #684063]: Yade cannot startup. Segmentation fault. 0x00007fffdbce42a9 in GlobalError::PushToStack() () from /usr/lib/x86_64-linux-gnu/libapt-pkg.so.5.0

[Anton Gladky]

Question #684063 on Yade changed:
https://answers.launchpad.net/yade/+question/684063

Anton Gladky posted a new comment:
Looks like a similar error here was described [1]. Did you install self-comiled 
boost?
Anyway, you can try to fix it here [2]. 


[1] 
https://stackoverflow.com/questions/57064962/boost-python-own-module-throws-segmentation-fault-globalerrorpushtostack
[2] 
https://gitlab.com/yade-dev/trunk/blob/master/cMake/YadePythonHelpers.cmake#L59

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Re: [Yade-users] [Question #684226]: install yadedaily in Ubuntu16.04

[Anton Gladky]

Question #684226 on Yade changed:
https://answers.launchpad.net/yade/+question/684226

Status: Open => Answered

Anton Gladky proposed the following answer:
Please wait a bit, it is updating now. New instructions how to update
yadedaily are coming.

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Re: [Yade-users] [Question #670453]: yadedaily- broken packages

[Anton Gladky]

Question #670453 on Yade changed:
https://answers.launchpad.net/yade/+question/670453

Status: Needs information => Answered

Anton Gladky proposed the following answer:
> 2018.02b-15189a57e8~xenial-1)

18.04 is the "bionic"-release. You have xenial (16.04) in
/etc/apt/sources.list

Anton

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Re: [Yade-users] [Question #670374]: segmentation fault (core dumped)

[Anton Gladky]

Question #670374 on Yade changed:
https://answers.launchpad.net/yade/+question/670374

Anton Gladky proposed the following answer:
My 2 cts. "core dumped" just means that Yade-process crashed and the
operating system has recorded the state of the memory before the crash,
which can be helpful for Post-Mortem analyze.

If you used the Yade, shipped with the Ubuntu, and you can provide this
core file it is possible to try to understand the reason of the crash, using
the gdb.

Regards

Anton


2018-06-21 18:27 GMT+02:00 Bruno Chareyre
:
> Question #670374 on Yade changed:
> https://answers.launchpad.net/yade/+question/670374
>
> Status: Open => Answered
>
> Bruno Chareyre proposed the following answer:
> Hi,
> Please note that "segmentation fault (core dumped)" is a very common yet 
> hardly informative error message.
> So basically what we know is that you have ubuntu 18.04 on a computer and a 
> problem with "a" script. Obviously a bit short to guess anything.
> Please read [1], especially point 6.
> Also, you may have better luck with the yadedaily package since "yade" is 
> stable package and is usually a bit old.
> Bruno
>
> [1] https://yade-dem.org/wiki/Howtoask
>
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[Yade-users] Yade 2018.02a released

[Anton Gladky]

Dear Yade users and developers,

After almost 13 months of development I am glad to announce
the next Yade version 2018.02a. The complete changelog
you will find as always at the end of this message.
The list of committers is presented in alphabetical order.

Tarballs are available on GitHub [1] and on Launchpad [2].

Thanks all for contributions!

[1] https://github.com/yade/trunk/releases/tag/2018.02a
[2] https://launchpad.net/yade/trunk/yade-1.00.0/+download/yade-2018.02a.tar.gz

Anton

==

# yade-2018.02a #
_Wed, Feb 7 20:06:30 2018 +0100_

**Anton Gladky (15):**
* Remove RELEASE file.
* Initialize gui in IPython 5.
* Add dependency on python-pyqt5.qtsvg.
* Fix PDF-compilation with sphinx>=1.4.9
* Remove comented lines in CMakeLists
* Test commit number two.
* Do not enable LINSOLV if CGAL not found
* Fix missing AND operator in prevoius commit
* Extend polyhedra breakage model by Mohr-Coulomb-Weibull failure criterion.
* Add examples for the PolyhedraBreak model
* Add one more Yade-Paper
* Update .gitignore
* Make newly added labels consistent with other labels.
* One more thesis, where Yade is mentioned
* Add RELEASE file

**Bruno Chareyre (73):**
* Fix https://bugs.launchpad.net/yade/+bug/1666339 (thx Robert)
* +5 journal papers
* +2 journal papers
* + Christian Jakob's PhD in references
* Put brackets in the right place (thx Robert).
* +4 journal papers
* 1+ journal paper by V. Lapcevic
* Add editor to Yade workshop proceedings (me!)
* missing comma (sorry)
* turn ERROR into WARNING when ISCollider does not find spheres to
determine verletDist
* +2 journal papers
* +2 journal papers
* +11 conference papers
* add missing year in a bibtex entry
* Fix kineticEnergy() for clumps
* fix the flipCell() function
* fix compile error
* flipping periodic cell -> small/doc fix
* move PBC example scripts
* cleaning examples
* documentation on changing the boundary conditions in FlowEngine and
derivatives
* Robert Caulk's guide to cloud computing inserted in doc
* return a consistent set of constrictions in the periodic case (some
constrictions were previsously skipped inconsistenty)
* re-apply the fix of rev 26efbec to getConstrictionFull()
* fix a compile warning
* fix an indentation problem in shinx document - hopefully fixing the buildbot
* fix unicode warning (documentation build)
* add a reference url
* fix compiler warning
* small fix in getConstriction() + a typo
* new logic for interating on facets in periodic triangulations
(following ref. Rev.26efbec and followers)
* new data 'crackArea' added to DFNFlow cells and updated
automatically - first step toward solving the artificial
compressibility of fluids in cracks
* #define DFNFLOW commented out
* small updates in doc, fixing compile errors and some warnings
* add exemple script for two-phase flow with 2PFV technique, related
to Yuan and Chareyre (2017)
* extended version of ForceEngine with its own fluid solver (by J. Chauchat)
* move HydroForceEngine to independent source files.
* Minor changes in authorship and inline comments
* Critical bugfix for collision detection in periodic boundary
conditions. Bounds lists were left partially unordered, then some
interactions were never detected (my toughest yade debugging until
now).
* Minors & cosmetic.
* fix feature NewtonIntegrator::densityScaling
* Introduce a tolerance on overlap determination (in periodic BC
only), avoiding false negative due to round-off errors. (usage in a
separate commit).
* A simpler and faster version of spatialOverlapPeri. Only one call to
floor(), ~20% speedup for ISCollider::action. Tolerance introduced to
fix detection failures.
* Keep the values of sorted bounds in the [0,size] range in ISCollider.
* small scale optimization in ISCollider
* Fix collision detection again (amending commit c7c8e6f62d452c8).
Don't move bounds below the starting point of the sort, else partial
(only) ordering can occure.
* Don't start blinking the 0-body when opening inspector + make it
possible to un-highlight before/after closing the inspector by
selecting empty space.
* Fix miscommit in d2211bd747d74eaea569ac88e.
* remove a function that was declared but undefined (leading to runtime error)
* cite recent reference on timestep
* TwoPhaseFlowEngine::getNeighbors now returning less than 4 neighbor
cells if some of them are infinite (normally only one)
* a function + python wrap for invading one single pore and updating
the clusters
* fix cluster invasion/update (thx Son for spotting the bug)
* fix doctest's target following b5ca352
* fix doctest in addData (re-apply c011decc36)
* fix doctest indentation (after 36c016bd)
* TesselationWrapper wrapping CGAL's AlphaShapes for defining an alpha-contour
* remove function definitions from FlowEngine.hpp
* preliminary version of 'extended' alpha shape contour
* further extension and debugging of alphaShape code
* nearly working version of the extended alpha-contour
* small fix
* proper calculation of alpha

Re: [Yade-users] [Question #661824]: PyQt4 issue on a Cray

[Anton Gladky]

Question #661824 on Yade changed:
https://answers.launchpad.net/yade/+question/661824

Status: Open => Answered

Anton Gladky proposed the following answer:
img_rc.py is generated by cmake-function [1].
Please check whether you have pyrcc5 (or installed. Because it is the
only program needed for this step.

[1] https://github.com/yade/trunk/blob/master/gui/CMakeLists.txt#L20

Cheers

Anton


2017-12-20 18:42 GMT+01:00 Gary Pekmezi <question661...@answers.launchpad.net>:
> Question #661824 on Yade changed:
> https://answers.launchpad.net/yade/+question/661824
>
> Status: Answered => Open
>
> Gary Pekmezi is still having a problem:
> Thanks for the suggestion Jan,
>
> It took my a few days to get Yade to compile [1] after building a recent
> version of QT5, libQGLviewer, and PyQT5. After all that, I unfortunately
> found that I received the same error upon issuing "make install". Is
> there perhaps some environment variable that must be set when building
> the GUI libraries locally?
>
> Thanks,
> Gary
>
> [1] CMake command and output:

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Re: [Yade-users] [Question #661824]: PyQt4 issue on a Cray

[Anton Gladky]

img_rc.py is generated by cmake-function [1].
Please check whether you have pyrcc5 (or installed. Because it is the
only program needed for this step.

[1] https://github.com/yade/trunk/blob/master/gui/CMakeLists.txt#L20

Cheers

Anton


2017-12-20 18:42 GMT+01:00 Gary Pekmezi :
> Question #661824 on Yade changed:
> https://answers.launchpad.net/yade/+question/661824
>
> Status: Answered => Open
>
> Gary Pekmezi is still having a problem:
> Thanks for the suggestion Jan,
>
> It took my a few days to get Yade to compile [1] after building a recent
> version of QT5, libQGLviewer, and PyQT5. After all that, I unfortunately
> found that I received the same error upon issuing "make install". Is
> there perhaps some environment variable that must be set when building
> the GUI libraries locally?
>
> Thanks,
> Gary
>
> [1] CMake command and output:

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Re: [Yade-users] [Question #661256]: yade installation issues

[Anton Gladky]

Question #661256 on Yade changed:
https://answers.launchpad.net/yade/+question/661256

Status: Open => Answered

Anton Gladky proposed the following answer:
2017-11-30 0:02 GMT+01:00 george <question661...@answers.launchpad.net>:
>  gtk2-engines-pixbuf : Depends: libgtk2.0-0 (= 2.24.30-1ubuntu1) but 
> 2.24.30-1ubuntu1.16.04.2 is to be installed

This is the source of the problem. Is it i386 package on amd64 box?
Try to force install of libgtk2.0-0=2.24.30-1ubuntu1 and then
gtk2-engines-pixbuf
Pay attention on what the system responses. There is a risk to
uninstall half of the system.

Cheers

Anton

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Re: [Yade-users] [Question #660024]: Chunksize use and compilation errors

[Anton Gladky]

Question #660024 on Yade changed:
https://answers.launchpad.net/yade/+question/660024

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

you can compare lib5.cpp and and lib10.cpp and try to find the
identical lines there.

Anton


2017-10-26 18:10 GMT+02:00 Jérôme Duriez <question660...@answers.launchpad.net>:
> New question #660024 on Yade:
> https://answers.launchpad.net/yade/+question/660024
>
> Hello,
>
> I just tried (for the first time) to play with chunksize for source 
> compilation. I downloaded the source code as of today, defined one cmake 
> option as -DCHUNKSIZE=X (I tested for now X=1, 2, 4, 8) and enjoyed to see 
> "-- CHUNKSIZE is set to X" in cmake output.
>
> This being said, most of my "make install" (with -j Y, Y = 1, 2, 4 or 8) then 
> faced compilation errors, depending on X (the chunksize value)
>
> E.g., for X = chunksize = 8
> [ 11%] Building CXX object CMakeFiles/yade.dir/pkg.4.cpp.o
> In file included from /usr/include/CGAL/boost/graph/iterator.h:28:0,
>  from 
> /usr/include/CGAL/boost/graph/graph_traits_HalfedgeDS.h:34,
>  from 
> /usr/include/CGAL/boost/graph/graph_traits_Polyhedron_3.h:23,
>  from /usr/include/CGAL/Polyhedron_3.h:1540,
>  from 
> /home/jerome.duriez/Yade/myTrunk/pkg/dem/Polyhedra.hpp:28,
>  from 
> /home/jerome.duriez/Yade/myTrunk/pkg/dem/Polyhedra.cpp:9,
>  from /home/jerome.duriez/Yade/myBuild/pkg.4.cpp:5:
> /usr/include/x86_64-linux-gnu/qt5/QtCore/qglobal.h:975:21: error: 
> ‘boost::Q_FOREACH’ has not been declared
>  #define foreach Q_FOREACH
>
>
> Or , for X = chunksize = 4
> [ 50%] Linking CXX shared library lib/x86_64-linux-gnu/libyade.so
> CMakeFiles/yade.dir/lib.5.cpp.o: In function `Real_timer::Real_timer()':
> lib.5.cpp:(.text+0x160): multiple definition of `Real_timer::Real_timer()'
> CMakeFiles/yade.dir/lib.10.cpp.o:lib.10.cpp:(.text+0x0): first defined here
> CMakeFiles/yade.dir/lib.5.cpp.o: In function `Real_timer::Real_timer()':
> lib.5.cpp:(.text+0x160): multiple definition of `Real_timer::Real_timer()'
> CMakeFiles/yade.dir/lib.10.cpp.o:lib.10.cpp:(.text+0x0): first defined here
> (and plenty of other multiple definition errors)
>
>
> I think compilation completed successfully only once with chunksize>1 (for 
> chunksize=2), with a comparable/identical compilation time than chunksize=1, 
> which was also a disappointment.
> Anyway, I start to doubt about this one: I actually wonder whether 
> compilation could be chunksize-path-dependent ?... (in some aspects like the 
> live output, at least)
>
>
> Needless to say that the compilation of the exact same code completes 
> successfully when chunksize = 1...
>
>
> Would you have any explanations / advices ? Thanks,
>
> Jérôme
>
> PS: cmake version 3.5.1, and ubuntu 16.04
>
>
>
>
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Re: [Yade-users] [Question #658070]: from start: Segmentation fault (core dumped)

[Anton Gladky]

Question #658070 on Yade changed:
https://answers.launchpad.net/yade/+question/658070

Anton Gladky posted a new comment:
That;s just mean that libqglviewer in OpenSuse is compiled against Qt4.
So you are not able to swith to Qt5 in Yade without recompiling
libqglviwer against qt5 and installing it.

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Re: [Yade-users] [Question #654435]: Yade breaks terminal

[Anton Gladky]

Hi Jan,

as far as I remember this incompatibility with
specific ipython version was fixed after 1.20
release.

Cheers

Anton

Am Dienstag, 1. August 2017 schrieb Jan Stránský :

> New question #654435 on Yade:
> https://answers.launchpad.net/yade/+question/654435
>
> Hello,
> on Ubuntu 16.04 I have installed Yade packaged version (1.20.0) by
> sudo apt-get install yade
> When I run it without script, it works as expected.
> When I run a script (even an empty one), the terminal is broken. It shows
> (in default color)
> [0;34mYade [[1;34m1[0;34m]: [0m
> instead of blue "Yade [1]:"
> The IPython does not work as expected (e.g. no auto-completion).
> After yade exit, the terminal itself does not work as expected (pressing
> enter does not create a new line).
>
> on previous computer with Ubuntu 16.04 I did not have this problem.
> The same problem is present in Yade compiled from source.
>
> Do you know what could be the problem / how to solve it?
> I remember reading about such problem, but was not able to find the
> corresponding discussion..
>
> thanks
> Jan
>
>
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Re: [Yade-users] [Question #654435]: Yade breaks terminal

[Anton Gladky]

Question #654435 on Yade changed:
https://answers.launchpad.net/yade/+question/654435

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi Jan,

as far as I remember this incompatibility with
specific ipython version was fixed after 1.20
release.

Cheers

Anton

Am Dienstag, 1. August 2017 schrieb Jan Stránský :

> New question #654435 on Yade:
> https://answers.launchpad.net/yade/+question/654435
>
> Hello,
> on Ubuntu 16.04 I have installed Yade packaged version (1.20.0) by
> sudo apt-get install yade
> When I run it without script, it works as expected.
> When I run a script (even an empty one), the terminal is broken. It shows
> (in default color)
> [0;34mYade [[1;34m1[0;34m]: [0m
> instead of blue "Yade [1]:"
> The IPython does not work as expected (e.g. no auto-completion).
> After yade exit, the terminal itself does not work as expected (pressing
> enter does not create a new line).
>
> on previous computer with Ubuntu 16.04 I did not have this problem.
> The same problem is present in Yade compiled from source.
>
> Do you know what could be the problem / how to solve it?
> I remember reading about such problem, but was not able to find the
> corresponding discussion..
>
> thanks
> Jan
>
>
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Re: [Yade-users] [Question #643703]: Installation on centOS7 (loki pb)

[Anton Gladky]

Question #643703 on Yade changed:
https://answers.launchpad.net/yade/+question/643703

Status: Open => Answered

Anton Gladky proposed the following answer:
Please be careful. The link was just an example, that the RPM package
exist. You should install it from your repo! Just find the package in
your package manager. Sorry for confusion.

Regards

Anton

2017-06-13 20:08 GMT+02:00 Cédric <question643...@answers.launchpad.net>:
> But your reply provided me a different vision on the topic: I think I simply 
> can download the .rpm and install it without breaking any dependancies :)
> Am I right ?

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Re: [Yade-users] [Question #643703]: Installation on centOS7 (loki pb)

[Anton Gladky]

Question #643703 on Yade changed:
https://answers.launchpad.net/yade/+question/643703

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

well, loki library should probably replaced by standard C++
constructions in Yade. But now you need to install it from
RPM-packages [1].

Regards

[1] https://rpms.remirepo.net/rpmphp/zoom.php?rpm=loki-lib

Anton

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Re: [Yade-users] [Question #643154]: installing prerequisites on Ubuntu 14.0.4

[Anton Gladky]

Question #643154 on Yade changed:
https://answers.launchpad.net/yade/+question/643154

Anton Gladky proposed the following answer:
Hi, do you really need to compile it? Is it not enough for you to use
packaged version?

Cheers

Anton


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Re: [Yade-users] [Question #635850]: Trouble linking Trilinos shared libraries

[Anton Gladky]

Question #635850 on Yade changed:
https://answers.launchpad.net/yade/+question/635850

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi Robert,

as a workaround you can try to add
/usr/local/lib/trilinos2/install/lib/ into LD_LIBRARY_PATH.

export
LD_LIBRARY_PATH=/usr/local/lib/trilinos2/install/lib/:$LD_LIBRARY_PATH

It should help your operating system to find the shared library.
Long-term solution would be
to use the package trllinois [1]. You can choose exactly the needed
library (there are a lot of
them) and escape LD_LIBRARY_PATH hack.

[1] https://tracker.debian.org/pkg/trilinos

Best regards


Anton


2017-05-28 5:23 GMT+02:00 Robert Caulk <question635...@answers.launchpad.net>:
> Question #635850 on Yade changed:
> https://answers.launchpad.net/yade/+question/635850
>
> Description changed to:
> Hello Yade community,
>
> I am trying to incorporate some tools from the Trilinos tool box into
> yade, but I am running into an issue with linking shared libraries. If
> you have any experience linking shared libraries with yade (or other
> software), I would greatly appreciate some advice here.

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Re: [Yade-users] [Question #631650]: Export the model as stl format

[Anton Gladky]

Question #631650 on Yade changed:
https://answers.launchpad.net/yade/+question/631650

Anton Gladky proposed the following answer:
Hi,

you can use export.gmshGeo [1] to export spheres in geo-file. It can be than
imported into the GMSH, which is a three-dimensional finite element mesh 
generator [2].

Generated mesh exports in any available format, including STL,

[1] https://github.com/yade/trunk/blob/master/py/export.py#L894
[2] http://gmsh.info/

Cheers,

Anton

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Re: [Yade-users] [Question #631403]: 'make' error during compilation

[Anton Gladky]

Question #631403 on Yade changed:
https://answers.launchpad.net/yade/+question/631403

Status: Open => Answered

Anton Gladky proposed the following answer:
You should point the source directory at the end of cmake-command.

Cheers

Anton

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Re: [Yade-users] [Question #631403]: 'make' error during compilation

[Anton Gladky]

Question #631403 on Yade changed:
https://answers.launchpad.net/yade/+question/631403

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

as far as I remember, there was a bug in gcc. Your code
falis to compile due to VTK. If you do not need VTK
just disable it: -DENABLE_VTK=0.

Another option is to update your system, maybe it is fixed
already.

Regards

Anton

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Re: [Yade-users] [Question #482687]: make doc error

[Anton Gladky]

Question #482687 on Yade changed:
https://answers.launchpad.net/yade/+question/482687

Anton Gladky posted a new comment:
Well, it was planned to replace the documentation generation by a a
simple "make doc". I do not remember why, but it did not worked well
everywhere. That is why we still have "yade yadeSphinx"  magic in
debian builds.

"make doc" is supposed to be executed __only__ in build directory, and
it must not be the same as a source one.

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Re: [Yade-users] [Question #482687]: make doc error

[Anton Gladky]

Question #482687 on Yade changed:
https://answers.launchpad.net/yade/+question/482687

Status: Open => Answered

Anton Gladky proposed the following answer:
You do not need to install Sphinx from external repository.
That requirement in README is obsolete and only for
very old distributions.

Regards

Anton

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Re: [Yade-users] [Question #455151]: compilation problems

[Anton Gladky]

Question #455151 on Yade changed:
https://answers.launchpad.net/yade/+question/455151

Anton Gladky proposed the following answer:
If you use 14.04, you have to add -DUSE_QT5=0 into the cmake
configuration step.

Anton

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Re: [Yade-users] [Question #455151]: compilation problems

[Anton Gladky]

Question #455151 on Yade changed:
https://answers.launchpad.net/yade/+question/455151

Status: Open => Answered

Anton Gladky proposed the following answer:
You have to instlal QT5-dev packages. Have a look at the installation
page of the Yade documentation.

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Re: [Yade-users] [Question #432848]: yade compiled installation in a redhat cluster

[Anton Gladky]

Question #432848 on Yade changed:
https://answers.launchpad.net/yade/+question/432848

Status: Open => Answered

Anton Gladky proposed the following answer:
Debug mode just means that the debug-symbols will not
be stripped. So, before the crash you should get some
stacktrace in the console. There is no special command
line option for debugging.

Anton

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[Yade-users] Yade 2017.01a released

[Anton Gladky]

Dear Yade users and developers,

After almost 7 months of development I am glad to announce
the next Yade version 2017.01a. The complete changelog
you will find as always at the end of this message.

Tarballs are available on GitHub and on Launchpad..

Thanks all for contributions!

Anton

==
yade-2017.01a
Thu, Jan 19 22:07:25 2017 +0100
Anton Gladky (20):
  Remove RELEASE file.
  Add some notes about how to make releases.
  Make Yade compatible with VTK7.
  Use C++11 constructions for InteractionLoop.
  Optimize using of ndarray.
  Partly fix webpage help show. LP:1598174
  Final fix for LP:1598174
  Add missing dependency on python-pyqt5.qtwebkit.
  Fix load/save in GUI-QT5.
  Drop unused typedef.
  Disable LAW2_SCGEOM_CAPILLARYPHYS_Capillarity1 by default.
  Remove some deprecated scripts.
  Increase the size of force container.
  +1 paper.
  Provide a proper functioning with IPython5.
  Add -fext-numeric-literals to fix FTBFS against boost_1.62
  Fix yade with IPython5.
  Update distro names in documentation
  Add missing header include 
  Add RELEASE file.

Bruno Chareyre (12):
  +2 articles (thanks to Bettina Suhr)
  + 1 proceedings (thanks to Bettina Suhr)
  Update citing_yade.bib
  revert the revert ca0e29ac57
  list authors of the doc as in doi:10.5281/zenodo.34073
  a note on using distcc and ccache
  minor editing of installation page
  Master thesis Morales2012a
  Introduce Network::surfaceSolidThroatInPore() for partial solid
surfaces per half-throat
  make the recursion conditional for invasion in multiphase flow
  push a file missing in commit e91ff135b7
  Yade bibtex: "and others" invalid for less than 9 authors

Chao Yuan (4):
  Add cell label for phase cluster. NW-res label 0, W-res label 1,
disconnected w-clusters start from 2. label can be saved in
savePhaseVtk.
  fix comment on label.
  clean UnsaturatedEngine, move all functions to TwoPhaseFlowEngine.
  Revert DryingEngine.

Francois Kneib (1):
  Fix O.engines in examples/cylinders/cylinderconnection-roots.py

Jan Stránský (11):
  fixed a small bug in shear force computation in CPM model
  Added PolyhedraSplitter example
  Changed L3Geom to ScGeom in tutorial example scripts
  fixed a minor compilation issue in ConcretePM
  Fixed call of _utils.interactionAnglesHistogram with default arduments
  making all Law2::go virtual
  Matrix_computeUnitaryPositive, changed computeThinX to computeFullX flags
  User's manual, added how to visualize force chain in Paraview
  UnstructuredGrid: fiexd little bug in manual setting of facet
position from vertices
  added pack.inHalfSpace and pack.inConvexPolygon + example script
  fixed another little bug in utils.UnstructuredGrid

Jerome Duriez (11):
  Doc clarification for TriaxialStressController.externalWork
(http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg12083.html)
  Doc of utils.readParamsFromTable() hopefully improved
  Friendlier BibTex entries for 2015 doc. To avoid Smilauer and et
al in manuscripts
  Doc Getting help section updated to reflect current practice
  Including interface orientation data in CapillaryPhys code
  Capillary scripts commit
(http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg12103.html).
Located in a new examples/capillaryLaplaceYoung folder intended to
illustrates capillary Law2. With one new simulation script example and
another old one, moved here
  Typo and minor corrections of previous capillary commit
  Capillary law2: erasing when necessary sphere-non sphere
interactions (bug LP: #1628273) + minor changes
  Capillary law2: restricting test shape. Plus minor change in
capillaryLaplaceYoung/README text file
  Doc: small updates in PartialEngine and KinematicEngines
  References .bib files: including new entries

Raphael Maurin (4):
  HydroForceEngine: add a condition to ignore particles fixed on
the sideWalls.
  Add an example for the use of HydroForceEngine
  HydroForceEngine: new fluctuation model for the example script +
small correction Add new simple discrete random walk fluctuation
model, to be used with the new example script fluidizedBed.py Change
the condition for applying the fluid force from p>0 to p>=0, which is
more appropriate
  Add two example scripts for the use of HydroForceEngine One
simple example to get familiar with the application of buoyancy
(buoyantParticles.py). One example simulating a fluidized bed
configuration to get familiar with both the application of a fluid
velocity profile and of turbulent fluctuation with the DRW models
(fluidizedBed.py)

bchareyre (19):
  fix invalid pointer, thanks Jerome
(https://lists.launchpad.net/yade-dev/msg12791.html)
  (doc) clarify the meaning of Triaxial

Re: [Yade-users] [Question #432848]: yade compiled installation in a redhat cluster

[Anton Gladky]

Question #432848 on Yade changed:
https://answers.launchpad.net/yade/+question/432848

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

missing header was added. Thanks. It would be good to get
a feedback from people, using different OSs and (better)
pull request.

It looks like the you have some path problems. There are some
info here [1].

[1] http://stackoverflow.com/questions/5216399/usr-lib-libstdc-so-6
-version-glibcxx-3-4-15-not-found

Regards

Anton


2017-01-19 13:57 GMT+01:00 hanzj <question432...@answers.launchpad.net>:
> Question #432848 on Yade changed:
> https://answers.launchpad.net/yade/+question/432848
>
> Status: Answered => Open
>
> hanzj is still having a problem:
> hello,flomine and all,
>
> thank you for your reply,It works,it can make install and finished well , but 
> after install I can not use yade
> the error as follows:
> [luxy@ln1 bin]$ ./yade
> Welcome to Yade 2016.06a
> Traceback (most recent call last):
>   File "./yade", line 129, in 
> import yade
>   File "/home/luxy/Yade/install/lib64/yade/py/yade/__init__.py", line 65, in 
> 
> import boot
> ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found 
> (required by /home/luxy/Yade/install/lib64/yade/py/yade/boot.so)
>
> have you come across that?
>
>
>
> At 2017-01-19 18:57:52, "flomine" <question432...@answers.launchpad.net> 
> wrote:
>>Question #432848 on Yade changed:
>>https://answers.launchpad.net/yade/+question/432848
>>
>>Status: Open => Answered
>>
>>flomine proposed the following answer:
>>Hi Hanzj,
>>I had a similar issue on archlinux.
>>Try to had
>>   #include 
>>at the beginning of /home/luxy/Yade/trunk/py/wrapper/yadeWrapper.cpp
>>
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Re: [Yade-users] [Question #439709]: Compilation problematic. Provide generic binaries please.

[Anton Gladky]

Question #439709 on Yade changed:
https://answers.launchpad.net/yade/+question/439709

Status: Open => Answered

Anton Gladky proposed the following answer:
Yade-binaries with statically linked libraries are not possible, because
one need to compile statically all dependent libs, which is a nightmare.
Now there is a good trend in distros to drop all static binaries and it
makes sense.

Volunteers for creating RPM-packages are always welcome.

Best regards

Anton

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Re: [Yade-users] [Question #432848]: yade compiled installation in a redhat cluster

[Anton Gladky]

Question #432848 on Yade changed:
https://answers.launchpad.net/yade/+question/432848

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

you just need to find the same RPM-packages. Their name
can differ from DEB-names. After that you should follow
instructions from "install" section of documentation.

If I remember correctly, somebody used Yade on similar
platform. You can search in questions.

Best regards

Anton

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Re: [Yade-users] [Question #407563]: yadedaily installation does not contain ymport module

[Anton Gladky]

Question #407563 on Yade changed:
https://answers.launchpad.net/yade/+question/407563

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

Linux Mint is not in supported distributions for yadedaily. Please use
appropriate distribution or compile from source.

Best Regards

Anton

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Re: [Yade-users] [Question #404651]: missing: PY_minieigen (already installed minieigen)

[Anton Gladky]

Question #404651 on Yade changed:
https://answers.launchpad.net/yade/+question/404651

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

just a workaround. Check, whether python -c"import minieigen" does
not return an error. If it is so, you can comment the line 465 to enable
compilation.

Anton


2016-12-05 10:33 GMT+01:00 Lei Zhang <question404...@answers.launchpad.net>:
> New question #404651 on Yade:
> https://answers.launchpad.net/yade/+question/404651
>
> Dear all,
>
> I am new to Yade and trying to install Yade on my workstation with CentOS 
> 6.7. I have checked out the questions in this forum, it seems the reason is 
> that I did not install minieigen. However, I have tried "pip install 
> minieigen" in the command line, and also downloaded the package from
> https://pypi.python.org/pypi/minieigen, and installed minieigen by "python 
> setup.py install", both installation seems to succeed, but cmake still 
> reports missing minieigen. I would great appreciate if someone here can 
> provide me an answer.
>
> Many thanks!
> Lei
>
> Here is the output for cmake,
> -- Found Qt4: /usr/bin/qmake-qt4 (found version "4.6.2")
> -- Version is set to 1.20.0
> -- GTS using gts-config /usr/local/bin/gts-config
> -- Using GTS from /usr/local
> -- Boost version: 1.46.1
> -- Found the following Boost libraries:
> --   python
> --   thread
> --   filesystem
> --   iostreams
> --   regex
> --   serialization
> --   system
> --   date_time
> --   Boost_VERSION: 104601
> --   Boost_LIB_VERSION: 1_46_1
> --   Boost_INCLUDE_DIRS: /usr/local/include
> --   Boost_LIBRARIES: 
> /usr/local/lib/libboost_python.so/usr/local/lib/libboost_thread.so/usr/local/lib/libboost_filesystem.so/usr/local/lib/libboost_iostreams.so/usr/local/lib/libboost_regex.so/usr/local/lib/libboost_serialization.so/usr/local/lib/libboost_system.so/usr/local/lib/libboost_date_time.so
> -- Found Eigen3, version: 3.3.0
> -- Disable vectorization
> -- Boost Odeint can be enabled, only if Boost>=1.53 is used
> -- Found VTK
> -- Found OpenMP
> -- GTS using gts-config /usr/local/bin/gts-config
> -- Using GTS from /usr/local
> -- Found GTS
> -- Found Qt4: /usr/bin/qmake-qt4 (found version "4.6.2")
> -- Found GUI-LIBS
> -- GMP libs: /usr/lib64/libgmp.so /usr/lib64/libgmpxx.so
> -- GMP libs: /usr/lib64/libgmp.so /usr/lib64/libgmpxx.so
> -- Found CGAL
> -- Could NOT find Cholmod (missing:  CHOLMOD_LIBRARIES CHOLMOD_INCLUDE_DIR 
> AMD_LIBRARY CAMD_LIBRARY COLAMD_LIBRARY CCOLAMD_LIBRARY)
> -- Could NOT find Metis (missing:  METIS_INCLUDE_DIR METIS_LIBRARY)
> -- Missing dependency for LINSOLV, disabled
> -- Found GL2PS
> LBMFLOW is still experimental, building and running LBM engine are at your 
> own risk!
> Yade will be installed to /home/lzhang/Downloads/myYade/install
> -- Suffix is set to -1.20.0
> -- LIBRARY_OUTPUT_PATH is set to lib64
> -- runtimePREFIX is set to /home/lzhang/Downloads/myYade/install
> -- Could NOT find gts (missing:  PY_gts)
> -- Use embedded version of gts. Please, consider installing the corresponding 
> package
> CMake Error at 
> /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:108 (message):
>   Could NOT find minieigen (missing: PY_minieigen)
> Call Stack (most recent call first):
>   /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:315 
> (_FPHSA_FAILURE_MESSAGE)
>   cMake/FindPythonModule.cmake:22 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
>   CMakeLists.txt:465 (find_python_module)
>
> -- Configuring incomplete, errors occurred!
>
>
>
>
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Re: [Yade-users] [Question #404455]: damping in ViscElMat

[Anton Gladky]

Question #404455 on Yade changed:
https://answers.launchpad.net/yade/+question/404455

Anton Gladky proposed the following answer:
Another option is to use restituion coefficient instead
of direct setting of cn and cs parameters.

Best regards

Anton

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Re: [Yade-users] [Question #404070]: about adding an new InsertionSortCollider

[Anton Gladky]

Question #404070 on Yade changed:
https://answers.launchpad.net/yade/+question/404070

Anton Gladky proposed the following answer:
If you just added files and did not "touch CMakeLists.txt"
the file list for compilation is not regenerated.

Anton

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Re: [Yade-users] [Question #404070]: about adding an new InsertionSortCollider

[Anton Gladky]

Question #404070 on Yade changed:
https://answers.launchpad.net/yade/+question/404070

Anton Gladky proposed the following answer:
Hi,

did you see that the newly created files were compiled? To be sure,
you should "touch CMakeLists.txt" to regenerate the list of cpp-files
and run compilation process again.

Best regards

Anton

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Re: [Yade-users] Yade installation questions

[Anton Gladky]

Hi David,

2016-11-15 15:45 GMT+01:00 Baker D.J. :
> I have just finished installing Yade from source on our RedHat 6.3 cluster.
> That is, to be more precise, I installed Yade with the GUI component
> switched off. The build was eventually successful and I was then able to run
> both “yade –check” and “yade –test” without any issues. On the other hand
> when I tested a script provided by the user I noticed that my Yade could not
> find the Gl1_Sphere attribute/command. Is that because I build Yade with
> GUI=OFF?

Pay attention, if you switched off the GUI, the user-script should not
contain any GUI-related code.

> I then attempted to build the GUI version. The build (make) process
> completed successfully, however I found that “make install” failed looking
> for a file called “img_rc.py”. I cannot find any trace of this file in the

img_rc.py is generated in gui/CMakeLists.txt. during the configuration
step of the build. It would be good to read the output from CMake on
this stage.

> Yale source distribution, and so I have no idea how to progress the GUI
> build. In this respect I have installed qt v4, however not PyQt4 – is the
> latter package required?

For GUI-enabled builds - yes, you need it and for build time and for runtime.

Cheers,

Anton

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Re: [Yade-users] [Question #402702]: Problem since I installed Ubuntu 16 Xenial

[Anton Gladky]

Question #402702 on Yade changed:
https://answers.launchpad.net/yade/+question/402702

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

what Yade version do you use? Try to use at least the latest stable or
the trunk.

Anton

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Re: [Yade-users] [Question #402288]: Compiling

[Anton Gladky]

Question #402288 on Yade changed:
https://answers.launchpad.net/yade/+question/402288

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi Seti,

2016-09-26 14:43 GMT+02:00 Seti <question402...@answers.launchpad.net>:
> scons PREFIX=/home/elaheh/YADE-1

where have you found such an old way to build yade, which is not actual for
many years?

Use cmake to configure and then make to build yade [1]. Or use packages, if
you do not need to modify the source code.

[1] https://yade-dem.org/doc/installation.html#compilation

Cheers,

Anton

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Re: [Yade-users] [Question #402260]: Rotate pack

[Anton Gladky]

Question #402260 on Yade changed:
https://answers.launchpad.net/yade/+question/402260

Status: Open => Answered

Anton Gladky proposed the following answer:
2016-09-25 14:37 GMT+02:00 Luis Barbosa <question402...@answers.launchpad.net>:
> ag = 
> pack.regularHexa(pack.inSphere((0,0,r),r),oriBody,radius=rad,gap=gap,color=(0,0,1))

It looks like inSphere does not have orientation parameter [1]. That
is logical, because
there is no sense to rotate the sphere in general case.

To escape such errors in the future, list parameters in "name=value" format:
ag = 
pack.regularHexa(pack.inSphere((0,0,r),r),orientation=oriBody,radius=rad,gap=gap,color=(0,0,1))

So, you will get an error instead of silence.

[1] https://yade-
dem.org/doc/yade.pack.html?highlight=insphere#yade._packPredicates.inSphere

Best regards

Anton

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Re: [Yade-users] [Question #390174]: No to_python (by-value) converter found for C++ type: boost:: ...

[Anton Gladky]

2016-09-16 16:08 GMT+02:00 Luc Sibille :
> Note that gcc-4.9 is consequently required for the compilation.

Consider to update your operating system. gcc_4.9 is pretty old and if we
switch to C++-14, you will unlikely be able to compile the code due to a
weak support of this standard version in 4.9.

Cheers

Anton

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Re: [Yade-users] [Question #364940]: problem with using Clump

[Anton Gladky]

Question #364940 on Yade changed:
https://answers.launchpad.net/yade/+question/364940

Anton Gladky proposed the following answer:
Try to use yadedaily. A very important bug was fixed
yesterday. The fix is available on github and in
yadedaily_2016.06a-24-0557faf

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Re: [Yade-users] [Question #364940]: problem with using Clump

[Anton Gladky]

Question #364940 on Yade changed:
https://answers.launchpad.net/yade/+question/364940

Anton Gladky proposed the following answer:
At what iteration?

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Re: [Yade-users] [Question #364940]: problem with using Clump

[Anton Gladky]

Question #364940 on Yade changed:
https://answers.launchpad.net/yade/+question/364940

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

what yade version do you use and how long do you simulate
to get an error?

I started the script on 2016.06a and there is no error at least
till the step 22 000.

Such problem can also happen due to unstable simulation
(high forces->velocities->displacement).

Regards

Anton

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Re: [Yade-users] [Question #355386]: Can not instal Yadedaily on Ubuntu 16.04

[Anton Gladky]

Question #355386 on Yade changed:
https://answers.launchpad.net/yade/+question/355386

Status: Open => Answered

Anton Gladky proposed the following answer:
You are using "xenial" distribution already, not "trusty".
You need to replace the corresponding distribution name in 
/etc/apt/sources.lists

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Re: [Yade-users] [Question #327433]: Installation Yade on Ubuntu 16.04 Xenial

[Anton Gladky]

Question #327433 on Yade changed:
https://answers.launchpad.net/yade/+question/327433

Anton Gladky proposed the following answer:
Should be fixed already.

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Re: [Yade-users] [Question #327518]: install yadedaily on Ubuntu 14.04

[Anton Gladky]

Question #327518 on Yade changed:
https://answers.launchpad.net/yade/+question/327518

Status: Open => Answered

Anton Gladky proposed the following answer:
Should be fixed already.

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Re: [Yade-users] [Question #327433]: Installation Yade on Ubuntu 16.04 Xenial

[Anton Gladky]

Question #327433 on Yade changed:
https://answers.launchpad.net/yade/+question/327433

Status: Open => Answered

Anton Gladky proposed the following answer:
There are some problems already on our side. Will be fixed in a couple
of days.

Anton

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Re: [Yade-users] [Question #327433]: Installation Yade on Ubuntu 16.04 Xenial

[Anton Gladky]

Question #327433 on Yade changed:
https://answers.launchpad.net/yade/+question/327433

Status: Open => Answered

Anton Gladky proposed the following answer:
You have to remove this line:

deb http://www.yade-dem.org/packages/ xenial xerus/

Also last 2 duplicating lines should be shortened to one.

Regards

Anton

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Re: [Yade-users] [Question #327433]: Installation Yade on Ubuntu 16.04 Xenial

[Anton Gladky]

Question #327433 on Yade changed:
https://answers.launchpad.net/yade/+question/327433

Status: Open => Answered

Anton Gladky proposed the following answer:
Please, show your /etc/apt/sources.list

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Re: [Yade-users] [Question #326649]: when "make install" , an error appears

[Anton Gladky]

Question #326649 on Yade changed:
https://answers.launchpad.net/yade/+question/326649

Anton Gladky proposed the following answer:
Hi,

you are using an old Yade version. This issue was fixed several months ago.
Also, are you able to use a newer compiler? 4.8.x is pretty antic.

Regards

Anton

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Re: [Yade-users] [Question #297855]: AttributeError: 'module' object has no attribute 'inGtsSurface'

[Anton Gladky]

Question #297855 on Yade changed:
https://answers.launchpad.net/yade/+question/297855

Status: Open => Answered

Anton Gladky proposed the following answer:
Could you please provide the output of cmake-step and also CmakeCache.txt file, 
which is in build-folder?
Also please run "yade --test" and "yade --check".

Anton

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Re: [Yade-users] [Question #300740]: -Wdeprecated_declarations: where to put it?

[Anton Gladky]

Question #300740 on Yade changed:
https://answers.launchpad.net/yade/+question/300740

Anton Gladky proposed the following answer:
One need to have a closer look, but it seems that the most of warnings
are coming from eigen or (and) boost.

If you want to investigate it further, please create a small c++-program and 
include:
#include 

Check whether you get the same warning.

Regards

Anton

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Re: [Yade-users] [Question #300740]: -Wdeprecated_declarations: where to put it?

[Anton Gladky]

Question #300740 on Yade changed:
https://answers.launchpad.net/yade/+question/300740

Anton Gladky proposed the following answer:
One need to have a closer look, but it seems that the most of warnings
are coming from eigen or (and) boost.

If you want to investigate it further, please create a small c++-program and 
include:
#include 

Check whether you get the same warning.

Regards

Anton

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Re: [Yade-users] [Question #300740]: -Wdeprecated_declarations: where to put it?

[Anton Gladky]

Question #300740 on Yade changed:
https://answers.launchpad.net/yade/+question/300740

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

as far as I see, those warnings are originated from
Eigen and boost. Please provide versions of both.
Also it would be good to see the full compilation
log.

Regards,

Anton


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Re: [Yade-users] [Question #295827]: Latest Yade Installation Fron Source

[Anton Gladky]

Question #295827 on Yade changed:
https://answers.launchpad.net/yade/+question/295827

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

first of all please try to install Yade from packages (sudo apt-get
install yade) and check, whether it works for you.

Cheers
Anton

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Re: [Yade-users] [Question #295520]: Exception occured: std::bad_alloc

[Anton Gladky]

Question #295520 on Yade changed:
https://answers.launchpad.net/yade/+question/295520

Anton Gladky proposed the following answer:
You are adding bodies at each call of servoController()?
Could you please check the number of bodies during the
simulation?

Anton


2016-06-21 18:37 GMT+02:00 Yor1 <question295...@answers.launchpad.net>:
> Question #295520 on Yade changed:
> https://answers.launchpad.net/yade/+question/295520
>
> Yor1 posted a new comment:
> Hi Bruno,
>
> We have the indentation before "O"  because this line is included
> in the recorder servoController().
>
> Best regards.
> Jabrane.
>
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Re: [Yade-users] [Question #295309]: Use of GID for Yade

[Anton Gladky]

Question #295309 on Yade changed:
https://answers.launchpad.net/yade/+question/295309

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

the common way is to convert your surfaces to STL and then import them
into Yade. GID is not supported by Yade due to its commercial nature.

Cheerrs,

Anton

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[Yade-users] Yade 2016.06a released

[Anton Gladky]

Dear Yade users and developers,

After almost 8 months of development I am glad to announce
the next Yade version 2016.06a. The complete changelog
you will find as always at the end of this message.

The versioning of releases is changed and now is in the
form .MMx. Where x is the letter, which can be
changed by minor updates in the stable releases.

Thanks all for contributions!

Anton

==
yade-2016.06a
Tue, Jun 14 20:30:53 2016 +0200

Anton Gladky (88):
  Remove release.
  Clean some unused macroses (old wm3-stuff)
  Remove some global headers
  Raise minimal boost version to 1.47
  Add -DNDEBUG if compiling in release mode
  Tiny code refactoring
  Clean some warnings and old stuff.
  Return removed header back.
  Fix warning in newer matplotlib.
  Drop old commented stuff in python-scrips.
  Remove flags and preSteps from scene
  Remove deprecated findBoundDispatcherInEnginesIfNoFunctorsAndWarn
  Remove PISC_DEBUG.
  Fix typo in installation sections of doce. Thanks to Jan.
  Export normal and viscous part of the visco-elastic contact
  Remove confusing part in installation part of documentation regarding Qt5.
  Fix typo in CMakeLists
  Tiny updates of examples of LudingPM.
  Fix compilation warnings.
  Update formatting in SpherePack
  Fix an order of calculation of c in SpherePack
  Fix some compilation warnings.
  Fix cappitalization typo in Lapack (case-sensitive in this case).
  Respect VTK6 in PotentialParticles.
  Add .travis.yml for CI.
  Remove version restriction on sphinx.
  Use trusty as build-env.
  Add -y parameter to apt-get install.
  Fix numpy import on travis.
  Fix segfault during save/load of CapViscModels
  Add one more check-script (capillary models)
  Fix typo in check-script.
  Fix crash in Ig2_Facet_Polyhedra_PolyhedraGeom
  vtkExporter: increase number of leading zeros to 8
  Move implementation of methods of ForceContainer in cpp.
  Split implementation of ForceContainer in parallel and serial.
  Add zero-forces to the youngest body after simulation load.
Closes LP:1560171
  Drop parallel execution in replaceByClumps. Closes LP:1559098
  Add import of polyhedras from the file.
  Add an opportunity to shift, scale and rotate imported polyhedrons
  Minor fixes in Polyhedra_splitter.
  Fix division by zero crash in Polyhedra
  Add CGAL_DISABLE_ROUNDING_MATH_CHECK, -frounding-math when CGAL
is enabled.
  Fix some formatting issues.
  Non-invasive fixes in polyhedra_splitter.
  Get max-min coefs in polyhedra_splitter simpler.
  Use tuple as a parameter for SplitPolyhedraDouble
  Add check script for polyhedra crash.
  Use explicitly -DNDEBUG instead of CMAKE_CXX_FLAGS_RELEASE
  Check isnan in some coordinates before calling CGAL.
  Minor formatting fixes in Polyhedra.
  Add check-script for save/load of clumps.
  Disable checkPolyhedraCrush. It is unstable now.
  Fix checkPolyhedraCrush
  Remove polyhedra_utils import from "ymport"
  Add prefix std:: to isnan and isinf.
  Update checkPolyhedraCrush
  Update files for ppa-infrastructure.
  Undef NDEBUG in all polyhedra files.
  Add pause for checkSaveLoadClumps to escape race condition.
  Use variadic arguments in DynLibDispatcher.
  Fix crash in polyhedra, if maxFs=0.
  Fix checkPolyhedraCrush (remove qt)
  Remove unused functionality in Dispatcher.
  Set Qt5 by default.
  Add mathcmaker for normalCohesion and shearCohesion.
  Split QGLViewer.cmake on qt4 and qt5 versions.
  Add .gitattributes to ignore line endings.
  Migrate buildppa to python3.
  Replace some "#define"(s) by functions.
  Remove some machine-specific items in documentation.
  Add unit test for matchmaker.
  Replace vector by unordered_map data structure in Matchmaker.
  Minor fix in documentation.
  Replace some "defines" by functions.
  Remove numpy.hpp.
  Fix bug in polyhedra_splitter.
  Some cosmetic fixes in core-files.
  Enable C++14.
  Revert 2dc99 and ed8dcb.
  Use unordered_map instead of map for MapId2IntrT
  Use unordered_map only for Boost >= 1.56
  Back to C++11.
  Revert using unordered_map in Body.
  Scale mass and inertia in spheresModify.
  Reduce size of flags in Bounds of InsertionSortCollider
  Fix bug in MatchMaker.
  Add RELEASE file.

Bruno Chareyre (16):
  add labels to default engines for easier showcases
  fix ambiguous syntax, fixing https://bugs.launchpad.net/bugs/1514477
  introduce 2nd edition of the documentation and contact for
consuting (in homepage)
  update the webpage about citation with 2nd edition, add 1st
edition as an external reference, update pdf metadata
  fix one

Re: [Yade-users] [Question #295158]: Can we create a rigid body using only particles, rather than importing a gts surface.

[Anton Gladky]

Question #295158 on Yade changed:
https://answers.launchpad.net/yade/+question/295158

Anton Gladky proposed the following answer:
2016-06-13 19:22 GMT+02:00 A Dinesh <question295...@answers.launchpad.net>:
> As I am trying to write my own code to implement DEM, please suggest me which 
> visualization tool kit should I use to visualize the spheres, Box, and rigid 
> bodies as they move with time? Thank you sir.

That is what that I would strongly not recommend to do. There are many
open source DEM codes, which you can use as a basis, if YADE is not
suitable for your needs (just google it). Many thousands of man-hours were
spent by many people polishing programs, trying to do them bug-free.
Writing the new code from the scratch is not always a good idea.

Regards

Anton

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Re: [Yade-users] [Question #295170]: Problem with MatchMaker

[Anton Gladky]

Question #295170 on Yade changed:
https://answers.launchpad.net/yade/+question/295170

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

I caused this bug during MatchMaker refactoring, sorry. It was fixed yesterday 
[1].
Yadedaily will be updated tonight.

[1]
https://github.com/yade/trunk/commit/e2e5a4cfbcf8bdd62d17c30637c299804a1b02af

Regards

Anton

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Re: [Yade-users] [Question #294845]: Multicore Yade

[Anton Gladky]

Question #294845 on Yade changed:
https://answers.launchpad.net/yade/+question/294845

Anton Gladky proposed the following answer:
I have a gut feeling that the bottle neck of your simulations are
many python-functions executed by PyRunner. All of them are
normally executed by one thread.

Anton

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Re: [Yade-users] [Question #294822]: img_rc.py not found

[Anton Gladky]

Question #294822 on Yade changed:
https://answers.launchpad.net/yade/+question/294822

Status: Open => Answered

Anton Gladky proposed the following answer:
Yade_1.14.0 had no qt5 support yet. No need to switch
off it there. Just install necessary packages.

Anton

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Re: [Yade-users] [Question #294790]: YADE-1.20.0 compiled with Intel Compiler

[Anton Gladky]

Question #294790 on Yade changed:
https://answers.launchpad.net/yade/+question/294790

Status: Open => Answered

Anton Gladky proposed the following answer:
The purpose of compiling with gcc is just to check,
whether gcc is able to produce the working binaries
for your platform.

You can theoretically write a simple C++ code, link it
against libyade and use this C++ program without
python bindings. But it can also be not so easy
and bug-free though

Cheers

Anton

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Re: [Yade-users] [Question #294790]: YADE-1.20.0 compiled with Intel Compiler

[Anton Gladky]

Question #294790 on Yade changed:
https://answers.launchpad.net/yade/+question/294790

Status: Open => Answered

Anton Gladky proposed the following answer:
Difficult to say. Looks like a problem in Boost. Try to use
another boost-version. Can you try to compile with gcc?

Anton


2016-06-02 22:17 GMT+02:00 Feng Chen <question294...@answers.launchpad.net>:
> Question #294790 on Yade changed:
> https://answers.launchpad.net/yade/+question/294790
>
> Status: Answered => Open
>
> Feng Chen is still having a problem:
> Hi, Anton, thanks for your quick reply, I attached here the debug info
> for the run, it seems quite long, do you have any idea which part went
> wrong?
>
> [fchen14@host003 bin]$ ./yade-1.20.0 >err.log 2>&1
> Segmentation fault

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Re: [Yade-users] [Question #294790]: YADE-1.20.0 compiled with Intel Compiler

[Anton Gladky]

Question #294790 on Yade changed:
https://answers.launchpad.net/yade/+question/294790

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

you need to compile Yade in debug-mode to get debugging symbols:
-DDEBUG=1 option on the cmake-step.

After that you start Yade and should get a lot of information during 
the crash, which can be useful to understand the source the problems. 

Regards

Anton

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Re: [Yade-users] [Question #294529]: random orientation of chained cylinders

[Anton Gladky]

Question #294529 on Yade changed:
https://answers.launchpad.net/yade/+question/294529

Anton Gladky proposed the following answer:
There is a peace of code which i used to generate a random orientation
of clumps in python-yade-script:

 oriBody = Quaternion(Vector3(1,0,0),random.random()*(pi/2))
 oriBody *= Quaternion(Vector3(0,1,0),random.random()*(pi/2))
 oriBody *= Quaternion(Vector3(0,0,1),random.random()*(pi/2))
 clpId,sphId =
O.bodies.appendClumped(bodiesHandling.spheresModify(pack1,shift=(x,y,z),orientation=oriBody,copy=True))

It can also be modified for any other body.

Ceers

Anton

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Re: [Yade-users] [Question #294209]: Belt Conveyor create

[Anton Gladky]

Question #294209 on Yade changed:
https://answers.launchpad.net/yade/+question/294209

Anton Gladky proposed the following answer:
I do not quite understand, what you mean. Here [1] you go
through all facets and set the constant velocity. If it must
be a function of a time - it should not be a problem too.

[1]
https://github.com/yade/trunk/blob/master/examples/conveyor/conveyor.py#L32

Anton


2016-05-25 15:13 GMT+02:00 paula <question294...@answers.launchpad.net>:
> Thanks Anton, but I need to give an specific velocity to the belt. Anyway 
> thanks again.
> Paula

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Re: [Yade-users] [Question #294209]: Belt Conveyor create

[Anton Gladky]

Question #294209 on Yade changed:
https://answers.launchpad.net/yade/+question/294209

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

you can try this example [1]. The conveyor will not move itself,
but it will give the particles the necessary velocity components.

[1] https://github.com/yade/trunk/tree/master/examples/conveyor

Regards

Anton

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Re: [Yade-users] [Question #293576]: yade from source on Ubuntu 16.04

[Anton Gladky]

Question #293576 on Yade changed:
https://answers.launchpad.net/yade/+question/293576

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi Rafael,

first of all, I do not clearly understand, whether you recompiled
libqglviewer or not. You do not need to do it. Just install libqglviewer-dev
from standard repository.

An error, which you refer just means that you probably missed
python-pyqt5 or pyqt5-dev-tools. Please install them and try again.

Regards

Anton

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Re: [Yade-users] [Question #293500]: Undefined symbol : zpotrf_

[Anton Gladky]

Question #293500 on Yade changed:
https://answers.launchpad.net/yade/+question/293500

Anton Gladky proposed the following answer:
> Found Cholmod: /usr/local/lib/libcholmod.a

That is probably the source of  your problems. You are statically
link cholmod, which is not shipped by packages. But I assume,
that headers for compilation are taken from packaged version. One need
to decide, what version you want to use and let cmake configure
MakeFile according to your needs.

Regards

Anton

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Re: [Yade-users] [Question #293500]: Undefined symbol : zpotrf_

[Anton Gladky]

> Found Cholmod: /usr/local/lib/libcholmod.a

That is probably the source of  your problems. You are statically
link cholmod, which is not shipped by packages. But I assume,
that headers for compilation are taken from packaged version. One need
to decide, what version you want to use and let cmake configure
MakeFile according to your needs.

Regards

Anton
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Re: [Yade-users] [Question #293500]: Undefined symbol : zpotrf_

[Anton Gladky]

Question #293500 on Yade changed:
https://answers.launchpad.net/yade/+question/293500

Anton Gladky proposed the following answer:
Please specify an operating system, which you use.

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Re: [Yade-users] [Question #293576]: yade from source on Ubuntu 16.04

[Anton Gladky]

Question #293576 on Yade changed:
https://answers.launchpad.net/yade/+question/293576

Status: Open => Answered

Anton Gladky proposed the following answer:
Hi,

python-scientific is deprecated. Use python-numpy instead.
But it is not obligatory (we need to update installation section
in doc). Also one need to use libvtk6-dev.  -DUSE_QT5=1
option is mandatory for 16.04. I will update installation page
tonight.

Regards

Anton


2016-05-11 13:47 GMT+02:00 Raphaël Maurin
<question293...@answers.launchpad.net>:
> New question #293576 on Yade:
> https://answers.launchpad.net/yade/+question/293576
>
> Hi everyone,
>
> After installing yadedaily (which works) on my new computer running with  
> Ubuntu 16.04 (with xfce interface), I am trying to install Yade from the 
> source code. I suceeded to install all the necessary packages except the 
> "python-scientific" one, which give the error (in french sorry):
>
> "sudo apt-get install  python-scientific
> Lecture des listes de paquets... Fait
> Construction de l'arbre des dépendances
> Lecture des informations d'état... Fait
> Aucune version du paquet python-scientific n'est disponible, mais il existe 
> dans la base
> de données. Cela signifie en général que le paquet est manquant, qu'il est 
> devenu obsolète
> ou qu'il n'est disponible que sur une autre source
>
> E: Le paquet « python-scientific » n'a pas de version susceptible d'être 
> installée"
>
> meaning that the package is missing or out of date or available only on 
> another source.
>
> I tried to continue the installation without this package, it is compiling 
> and create the executable of yade (after cmake, make and make install), but 
> when I run it I get a long error:
>
> "*** Error in `/usr/bin/python': realloc(): invalid pointer: 
> 0x7fbab345a820 ***
> === Backtrace: =
> /lib/x86_64-linux-gnu/libc.so.6(+0x77725)[0x7fbabc43c725]
> /lib/x86_64-linux-gnu/libc.so.6(realloc+0x348)[0x7fbabc448f88]
> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(_ZN9QListData7reallocEi+0x1f)[0x7fbaa3f34a5f]
> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(_ZN9QListData6appendEi+0x81)[0x7fbaa3f34b31]
> /usr/lib/x86_64-linux-gnu/libQt5Core.so.5(+0x1d7018)[0x7fbaa4001018]
>
> ..."
>
> ending with:
> "
> 7fba9d434000-7fba9d435000 r--p c000 08:01 5514583
> /usr/lib/x86_64-linux-gnu/libgsm.so.1.0.12
> 7fba9d435000-7fba9d436000 rw-p d000 08:01 5514583
> /usr/lib/x86_64-linux-gnu/libgsm.so.1.0.12
> 7fba9d436000-7fba9d47b000 r-xp  08:01 5514811
> /usr/lib/x86_64-linux-gnu/libmp3lame.so.0.0.0Abandon (core dumped)"
>
>
> First, can you confirm that it is due to the absence of the package 
> python-scientific ? If it is the case, is there a way to install it on Ubuntu 
> 16.04 ? If it is not the case and the problem is more complex, do you believe 
> it is better for me to come back to Ubuntu 14.04, or would yade from source 
> be compatible soon with Ubuntu16.04?
>
> Thanks,
>
> Raphael
>
>
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Re: [Yade-users] [Question #293445]: Polyhedra Elements, Infinite Loop.

[Anton Gladky]

Question #293445 on Yade changed:
https://answers.launchpad.net/yade/+question/293445

Anton Gladky proposed the following answer:
You can try yadedaily which is updating permanently now
for most supported Debian-based distributions.

Best regards

Anton

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Re: [Yade-users] [Question #293235]: Update algorithm of shear displacement

[Anton Gladky]

Question #293235 on Yade changed:
https://answers.launchpad.net/yade/+question/293235

Anton Gladky proposed the following answer:
Hi Jibril,

thanks a lot for the checking and analyzing the code and documentation.
As Jan said, we need to update outdated documentation. If you have
a wish to do it, feel free to join us. We are always opened for new
collaborators.

Regarding the correctness of ScGeom, we need to discuss it in more
details.

Best regards

Anton


2016-05-04 11:13 GMT+02:00 Jibril Coulibaly
<question293...@answers.launchpad.net>:
> New question #293235 on Yade:
> https://answers.launchpad.net/yade/+question/293235
>
> Hi everyone,
>
> My questions concern the algorithm used for the shear dispalcement update and 
> its implementation is the class ScGeom. I would like to fully understand the 
> update procedure but it seems like there are discrepancies between the 
> documentation and the code.
>
> In the documentation ( https://yade-dem.org/doc/formulation.html#fig-shear-2d 
> ), the update is said to be "done by perpendicular projection to the plane 
> first (which might decrease |\uT|) and adding what corresponds to spatial 
> rotation of the interaction instead". The formulae for the corresponding 
> increments don't indicate a projection and look more like infinitesimal 
> rotations. These 2 rotations, acting of the previous shear dispalcement 
> vector, are eventually linearly added, not composed, to form the current 
> shear dispalcement vector.
>
> Getting into the corresponding code from the class ScGeom ( 
> https://github.com/yade/trunk/blob/master/pkg/dem/ScGeom.cpp ), the 
> ScGeom::rotate function clearly performs the composition of the two 
> approximate rotations, not the addition, about what is defined as the 
> orthonormal axis first (line 17) and the twist axis second (line 18).
> The determination of these axes is performed in the ScGeom::precompute 
> function. While the definition of the orthonormal axis (line 27) corresponds 
> to what the documentation says, the definition of the twist angle and axis 
> (lines 28,29) differs from the formula in the documentation in that is uses 
> the variable "normal" for the current normal vector n° and not 
> "currentNormal".
>
> Regarding the documentation, shouldn't the second rotation of the shear 
> dispalcement (around the twist axis) be applied to the shear displacement 
> already updated by the first rotation (around the orthonormal axis), as it is 
> in the function ScGeom::rotate ? That is :
>
> (\Delta \uT)_2&=-(\prevuT + (\Delta \uT)_1) \times\left(\frac{\Delta t}{2} 
> \currn \cdot (\pprev{\vec{\omega}}_1+\pprev{\vec{\omega}}_2)\right) \currn
>
> instead of
>
> (\Delta \uT)_2&=-\prevuT\times\left(\frac{\Delta t}{2} \currn \cdot 
> (\pprev{\vec{\omega}}_1+\pprev{\vec{\omega}}_2)\right) \currn
>
> And keeping the summation of the 3 increments as it is.
>
> Regarding the ScGeom::precompute function, shouldn't the twist axis be around 
> the current normal vector n° as it is in the documentation ? That is 
> replacing the variable "normal" by "currentNormal" in lines (28,29) ? This 
> way the rotations would be properly composed :
> - rotation around the orthonormal axis first brings the previous normal 
> vector together with the current normal vector.
> - rotation around the twist axis (that is colinear to the current normal) 
> then performs the remaining rotation.
>
> I would really appreciate your help and hope I have been understandable and 
> clear.
>
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Re: [Yade-users] [Question #292846]: Particle packing - How to avoid overlap

[Anton Gladky]

Question #292846 on Yade changed:
https://answers.launchpad.net/yade/+question/292846

Anton Gladky proposed the following answer:
Yadedaily should be relatively updated.
Last week there were 2 uploads.

Anton

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