[Yade-users] [Question #293600]: Periodic Cell and Periodic Boundary

[Felipe]

New question #293600 on Yade:
https://answers.launchpad.net/yade/+question/293600

Hello Everybody,

I would like to know how i can get more information about periodic cell and 
also periodic boundary.

I have studied about this topic with the help of Sullivan - Particulate 
Discrete Element Modelling  book and others paper wich focus on interaction 
between the spheres.

Moreover, I was seeing on DEM Background (YADE) if i would get more information 
but I did not understand how i can use this concept on the simulations.

By the way, I have been asking in this question if it would be possible to 
explain with more details how to use:

-> Periodic Cell;

-> Periodic Boundary;

Both of topics above, what is mean of use these concept on the simulation? Will 
it have to save time on the simulation? What will it be the difference when i 
am using these concepts or not?

Thank you for attention.

Please, let me know if you have more information about it and also links to 
learn more about periodic cell.

Best Regards,

Felipe

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Re: [Yade-users] [Question #293295]: Want to connect all the particles in an aggregate using cohesive bond

[VG]

Question #293295 on Yade changed:
https://answers.launchpad.net/yade/+question/293295

VG posted a new comment:
Thanks Bruno, that solved the issue I was facing.

Also, can you please recommend me a good reference for the CohFrictMat
and cohesive model ?

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Re: [Yade-users] [Question #293295]: Want to connect all the particles in an aggregate using cohesive bond

[VG]

Question #293295 on Yade changed:
https://answers.launchpad.net/yade/+question/293295

Status: Answered => Solved

VG confirmed that the question is solved:
Thanks Bruno Chareyre, that solved my question.

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

[Hicham BENNIOU]

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

Hicham BENNIOU posted a new comment:
Thanks Anton,

By deleting /usr/local/lib/libcholmod.a and recompiling a fresh build,
it worked perfectly !

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

[Hicham BENNIOU]

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

Hicham BENNIOU posted a new comment:
Thanks Anton,

By deleting /usr/local/lib/libcholmod.a and recompiling a fresh build,
it worked perfectly !

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

[Hicham BENNIOU]

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

Status: Answered => Solved

Hicham BENNIOU confirmed that the question is solved:
Thanks Anton Gladky, that solved my question.

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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 #293445]: Polyhedra Elements, Infinite Loop.

[Bruno Chareyre]

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

Status: Open => Needs information

Bruno Chareyre requested more information:
Hi,
Thanks for the script but in fact it does not show the bug, since you add 
"After calling O.step() for several times, this bug will occur."
It may sound like a dumb question but can you really try to make the script 
hang by itself? The reason could be there.
Bruno

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

[Hicham BENNIOU]

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

Hicham BENNIOU posted a new comment:
Hi Anton,

I'm on Ubuntu 14.04

By the way, here is the cmake "produce"

-- The C compiler identification is GNU 4.8.4
-- The CXX compiler identification is GNU 4.8.4
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found PythonInterp: /usr/bin/python (found version "2.7.6") 
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake (found version "4.8.6") 
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.26") 
-- Version is set to 2016-05-09.git-145e975
-- Looking for XOpenDisplay in 
/usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so
-- Looking for XOpenDisplay in 
/usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /usr/lib/x86_64-linux-gnu/libX11.so
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.so  
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found GL2PS: /usr/lib/libgl2ps.so  
-- Found CGAL: /usr/include/CGAL, /usr/lib/libCGAL.so
-- Found NumPy: version "1.8.2" 
/usr/lib/python2.7/dist-packages/numpy/core/include
-- Found Loki: /usr/include  
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0 and -save-temps
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   python
--   thread
--   filesystem
--   iostreams
--   regex
--   serialization
--   system
--   date_time
--   Boost_VERSION: 105400
--   Boost_LIB_VERSION: 1_54
--   Boost_INCLUDE_DIRS: /usr/include
--   Boost_LIBRARIES: 
/usr/lib/x86_64-linux-gnu/libboost_python.so/usr/lib/x86_64-linux-gnu/libboost_thread.so/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/libpthread.so
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6") 
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - found
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found version 
"2.7.6") 
-- Found Eigen3, version: 3.2.1
-- Disable vectorization
-- Found VTK
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- checking for one of the modules 'glib-2.0'
-- Found GLib2: glib-2.0 
/usr/include/glib-2.0;/usr/lib/x86_64-linux-gnu/glib-2.0/include
-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - not found
-- Found GTS
-- Found GLUT: /usr/lib/x86_64-linux-gnu/libglut.so  
-- Found QGLVIEWER: /usr/include/QGLViewer  
-- Found Qt4: /usr/bin/qmake (found version "4.8.6") 
-- Found GUI-LIBS
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so 
/usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found GMP: /usr/include/x86_64-linux-gnu  
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so 
/usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found CGAL
-- Found Cholmod: /usr/local/lib/libcholmod.a  
-- Found OpenBlas: /usr/lib/libopenblas.so  
-- Found Metis: /usr/include/metis  
-- Found Cholmod
-- Found OpenBlas
-- Found Metis
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own 
risk!
Yade will be installed to /home/3S-LAB/hbenniou/Yade/install
-- Suffix is set to -2016-05-09.git-145e975
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/3S-LAB/hbenniou/Yade/install
-- Found gts: /usr/lib/python2.7/dist-packages/gts  
-- Use system gts version
-- Found minieigen: /usr/lib/python2.7/dist-packages/minieigen.so  

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 #293500]: Undefined symbol : zpotrf_

[Hicham BENNIOU]

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

Hicham BENNIOU posted a new comment:
Thanks Jan for the answer.

However, after multiple verification, everything seems installed and up
to date.

other versions run with no problem. I think I'll stick with an older
version for now.

I'll post here if I find the problem.

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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
:
> 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 #293342]: Problem with simulation

[Alex]

Question #293342 on Yade changed:
https://answers.launchpad.net/yade/+question/293342

Status: Answered => Open

Alex is still having a problem:
Hello Jérôme and Klauss,

Thank you for the answers. They have helped a lot. I'm sorry for the
delay in replying and for the title... The next time I will be more
specific and more original. ;-)

I rewrote my code and I continue with the same problem, that is, when I
run the simulation the cylinder goes inside the spheres and that's not
what I want.

Once again, I ask if someone could help in this problem. Below is my new
code.

import sys
from yade import ymport
from yade import qt
from numpy import linspace

 material definition 
def sphereMat(): 
return  CohFrictMat(young=8e5,poisson=0.3,density=4e3,

frictionAngle=radians(30),normalCohesion=4e4,shearCohesion=1e5,momentRotationLaw=False,label='sphereMat')

def gridNodeMat():
return 
CohFrictMat(young=8e5,poisson=0.3,density=4e3,frictionAngle=radians(30),

normalCohesion=1e5,shearCohesion=1e5,momentRotationLaw=True,label='gridNodeMat')

def gridCoMat():
return CohFrictMat(young=8e5,poisson=0.3,density=4e3, 
frictionAngle=radians(30),

normalCohesion=1e5,shearCohesion=1e5,momentRotationLaw=True,label='gridCoMat')
 end material definition ### 


O.engines=[
ForceResetter(),
InsertionSortCollider([
Bo1_GridConnection_Aabb(),
Bo1_Sphere_Aabb()
]),
InteractionLoop(
 Geometric interactions
[
Ig2_GridNode_GridNode_GridNodeGeom6D(),
Ig2_Sphere_GridConnection_ScGridCoGeom()

],


[Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=True),
],

[Law2_ScGeom6D_CohFrictPhys_CohesionMoment(label='law'),
 Law2_ScGridCoGeom_CohFrictPhys_CundallStrack() 
]
),
 Motion equation
NewtonIntegrator(damping=0.4,gravity=[0,0,0]),
PyRunner(command='main()',iterPeriod=10)
]

O.dt=1e-7

rCyl=0.025
nL= 2
L=0.3

 Create all nodes first :
nodesIds=[]
for i in linspace(0,L,nL):
  nodesIds.append( O.bodies.append(
gridNode([0.3,i + 
0.4,2.02],rCyl,wire=False,fixed=False,material=gridNodeMat) ) )

 Now create connection between the nodes
for i,j in zip( nodesIds[:-1], nodesIds[1:]):
  O.bodies.append( gridConnection(i,j,rCyl,
  material=gridCoMat
  ) )

 read a sphere's package 
PACKING = '10K_P1'
O.bodies.append(ymport.text(PACKING+'.spheres',scale=1.,shift=Vector3(0,0,0),material=sphereMat))

qt.View();

def main():
global Fn,Ft
O.bodies[0].dynamic=False
O.bodies[0].state.vel[2]=-500.0
O.bodies[1].state.vel[2]=-500.0
O.bodies[2].state.vel[2]=-500.0

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

[Raphaël Maurin]

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 #293295]: Want to connect all the particles in an aggregate using cohesive bond

[Bruno Chareyre]

Question #293295 on Yade changed:
https://answers.launchpad.net/yade/+question/293295

Bruno Chareyre proposed the following answer:
Changing the adhesion of existing interactions is not a problem at all.
After the first iteration:
i.phys.normalAdhesion = something
i.phys.shearAdhesion = another thing
i.phys.unp = 0 #to make it initially force free, as in the link quoted in #3

The only problem was that you were changing material parameters instead
of changing interaction parameters (as found by whr, even if he suggests
a different workaround).

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