Re: [Yade-users] [Question #290950]: Particles crossing the wall

[VG]

Question #290950 on Yade changed:
https://answers.launchpad.net/yade/+question/290950

VG posted a new comment:
I am using version 1.07.0

The output of the two commands are as follows:

O.bodies[top_id].state.mass
0.0

O.bodies[top_id].state.inertia
Vector3(nan,nan,nan)

Thanks
Varun

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Re: [Yade-users] [Question #292258]: An error message when I use multiple cores

[behzad]

Question #292258 on Yade changed:
https://answers.launchpad.net/yade/+question/292258

behzad posted a new comment:
Please ignore the last message! That was sent by mistake

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Re: [Yade-users] [Question #292258]: An error message when I use multiple cores

[behzad]

Question #292258 on Yade changed:
https://answers.launchpad.net/yade/+question/292258

Status: Answered => Open

behzad is still having a problem:
http://www.linuxfromscratch.org/blfs/view/systemd/general/qtchooser.html

On Mon, Apr 25, 2016 at 8:47 PM, behzad <
question292...@answers.launchpad.net> wrote:

> Your question #292258 on Yade changed:
> https://answers.launchpad.net/yade/+question/292258
>
> behzad posted a new comment:
> I installed qt5 and I use the option USE-QT5 as:
>
>
> cmake -DCMAKE_INSTALL_PREFIX=~/yade2/install ~/yade2/trunk
> -DOPTION1=USE_QT5
>
>
> but I still get
>
>
> -- Found VTK
> -- Found OpenMP
> -- GTS using gts-config /usr/bin/gts-config
> -- Using GTS from /usr
> -- Found GTS
> -- Found Qt4: /usr/bin/qmake (found version "4.8.6")
> -- Found GUI-LIBS
> -- GMP libs: /usr/lib/i386-linux-gnu/libgmp.so
> /usr/lib/i386-linux-gnu/libgmpxx.so
> -- GMP libs: /usr/lib/i386-linux-gnu/libgmp.so
> /usr/lib/i386-linux-gnu/libgmpxx.so
> -- Found CGAL
> -- 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/behzad/yade2/install
> -- Suffix is set to -2016-04-23.git-806ecaa
> -- LIBRARY_OUTPUT_PATH is set to lib/i386-linux-gnu
> -- runtimePREFIX is set to /home/behzad/yade2/install
> -- Could NOT find gts (missing:  PY_gts)
> -- Use embedded version of gts. Please, consider installing the
> corresponding package
> -- ===
> -- Yade configured with following features: Odeint VTK OpenMP GTS GUI CGAL
> PFVFLOW LINSOLV GL2PS LBMFLOW
> -- Disabled features: SPH LIQMIGRATION MASK_ARBITRARY PROFILING
> PotentialParticles
> -- Optimized build
> -- ===
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/behzad/yade2/build
>
>
> in which I`ve got:
>
> Found Qt4: /usr/bin/qmake (found version "4.8.6")
>
> You received this question notification because you asked the question.
>


-- 
Behzad Majidi

Research Student
Aluminium Research Centre
REGAL-Université Laval
Québec, QC, Canada



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Re: [Yade-users] [Question #290950]: Particles crossing the wall

[Jan Stránský]

Question #290950 on Yade changed:
https://answers.launchpad.net/yade/+question/290950

Jan Stránský proposed the following answer:
The script works fine for me (at least nothing disappears).
What version of Yade do you use?
What is the output of "O.bodies[top_id].state.mass" and
"O.bodies[top_id].state.inertia"?
thanks
Jan


2016-04-26 2:21 GMT+02:00 VG :

> Question #290950 on Yade changed:
> https://answers.launchpad.net/yade/+question/290950
>
> VG posted a new comment:
> Thanks Jan!
> I modified the generation of top and bottom boxes as you suggested. The
> boxes seem to be generated the way they should be. However, as soon as the
> simulation starts, those boxes just disappear. I am not sure what is
> causing this behavior. Here is the updated MWE script:
>
>
> # Generate a periodic cell with few super-particles.
> # Each superparticle consists of smaller sub-particles of 75 microns
> # bonded with cohesive bonds.
>
> from yade import pack,qt,plot,utils,export,ymport
> from math import *
> from pylab import rand
> import datetime
> import os,shutil
>
>
> #
> # Set up run
>
> #
> run_name="PeriodicCohesive_MWE"
> data_root_dir="."
> if not os.path.exists(data_root_dir):
>   print "The data root directory you specified:"
>   print data_root_dir
>   print "does not exist. Exiting..."
>   exit()
> timestamp=datetime.datetime.now().strftime("%Y.%m.%d-%H%M%S")
> run_dir_name=timestamp+'-'+run_name
> data_dir_path=os.path.join(data_root_dir,run_dir_name)
> if not os.path.exists(data_dir_path):
>   os.makedirs(data_dir_path)
> else:
>   print("Something is really wrong if you get this message. Exiting...\n")
>   exit()
>
> run_name_base_path=os.path.join(data_dir_path,run_name+'-')
> # opts.script is defined in yade, which inserts the script file (e.g.
> # this file) into itself.
> this_script=os.path.abspath(opts.script)
> shutil.copy(this_script,data_dir_path)
>
>
>
> #
> # Materials
>
> #
> plate_material=CohFrictMat(
> young=200e9
>,poisson=0.3
>,density=8000
>,frictionAngle=radians(30)
>,normalCohesion=1e10
>,shearCohesion=1e10
>,momentRotationLaw=True
>,label='plate_mat')
> O.materials.append(plate_material)
>
>
> sample_material=CohFrictMat(
> young=4e9
>,poisson=0.25
>,density=1400
>,frictionAngle=radians(30)
>,normalCohesion=1e8*1.2
>,shearCohesion=.4e8*1.2
>,momentRotationLaw=True
>,label='sample_mat')
> O.materials.append(sample_material)
>
>
>
> #
> # Component dimensions and operating condition
>
> #
> # Granular material dimension
> sample_diameter=2e-4
> sample_radius=sample_diameter/2.0
> # Sub-particle dimension
> particle_diameter=74.e-6
> particle_radius=particle_diameter/2.
>
>
> #
> # grinding plate dimension
>
> #
>
> rotvel=2./3.*pi*(1.5+0.5)*.254
>
>
> #
> # Periodic Geometry
>
> #
>
>
> # Set up periodic boundary conditions
> O.periodic=True
> xExt=4*sample_diameter
> yExt=3.*sample_diameter*2 #to block the periodicity in y direction
> zExt=xExt
> xLim=xExt
> yLim=yExt/4
> zLim=zExt
> O.cell.hSize=Matrix3(
>   xExt, 0, 0,
>   0, yExt, 0,
>   0, 0, zExt)
>
>
> length=xExt
> height=yExt
> width=zExt
>
> # Top and bottom plate thickness
> thickness=0.1*height
>
>
> #
> # Bottom
> #
> #bottom=box(
> #center=(length/2.0,yLim - thickness/2.0,width/2.0)
> #   ,extents=(4*length,thickness/2.0,width)
> #   ,wire=False
> #   ,material='plate_mat'
> #   )
>
> bottomBoxes = []
> for ix in (0,1,2):
>  for iz in (0,1,2):
>bottomBoxes.append(box( # create 3x3 boxes with 1/3 cell size
>center=(xExt/6.*(1+2*ix),yLim - thickness/2.0,zExt/6.*(1+2*iz))
>,extents=(xExt/6.,thickness/2.0,zExt/6.)
>,wire=False
>,material='plate_mat'
>))
>
> bottom_id,bottom_ids = O.bodies.appendClumped(bottomBoxes) # bottom_id
> is the clump id,
>
>
> O.bodies[bottom_id].state.blockedDOFs='xyzXYZ'
>
>
>
> #
> # Particle Packing
>
> #
>
> min_corner= (0,yLim,0)
> max_corner= (xLim, yExt-yLim, zLim)
>
> sp=pack.SpherePack()
> sp.makeCloud( min_corner,max_corner, rMean=sample_radius, 

Re: [Yade-users] [Question #290950]: Particles crossing the wall

[VG]

Question #290950 on Yade changed:
https://answers.launchpad.net/yade/+question/290950

VG posted a new comment:
Thanks Jan!
I modified the generation of top and bottom boxes as you suggested. The boxes 
seem to be generated the way they should be. However, as soon as the simulation 
starts, those boxes just disappear. I am not sure what is causing this 
behavior. Here is the updated MWE script:


# Generate a periodic cell with few super-particles.
# Each superparticle consists of smaller sub-particles of 75 microns
# bonded with cohesive bonds.

from yade import pack,qt,plot,utils,export,ymport
from math import *
from pylab import rand
import datetime
import os,shutil

#
# Set up run
#
run_name="PeriodicCohesive_MWE"
data_root_dir="."
if not os.path.exists(data_root_dir):
  print "The data root directory you specified:"
  print data_root_dir
  print "does not exist. Exiting..."
  exit()
timestamp=datetime.datetime.now().strftime("%Y.%m.%d-%H%M%S")
run_dir_name=timestamp+'-'+run_name
data_dir_path=os.path.join(data_root_dir,run_dir_name)
if not os.path.exists(data_dir_path):
  os.makedirs(data_dir_path)
else:
  print("Something is really wrong if you get this message. Exiting...\n")
  exit()

run_name_base_path=os.path.join(data_dir_path,run_name+'-')
# opts.script is defined in yade, which inserts the script file (e.g.
# this file) into itself.
this_script=os.path.abspath(opts.script)
shutil.copy(this_script,data_dir_path)


#
# Materials
#
plate_material=CohFrictMat(
young=200e9
   ,poisson=0.3
   ,density=8000
   ,frictionAngle=radians(30)
   ,normalCohesion=1e10
   ,shearCohesion=1e10
   ,momentRotationLaw=True
   ,label='plate_mat')
O.materials.append(plate_material)


sample_material=CohFrictMat(
young=4e9
   ,poisson=0.25
   ,density=1400
   ,frictionAngle=radians(30)
   ,normalCohesion=1e8*1.2
   ,shearCohesion=.4e8*1.2
   ,momentRotationLaw=True
   ,label='sample_mat')
O.materials.append(sample_material)


#
# Component dimensions and operating condition
#
# Granular material dimension
sample_diameter=2e-4
sample_radius=sample_diameter/2.0
# Sub-particle dimension
particle_diameter=74.e-6
particle_radius=particle_diameter/2.

# 
# grinding plate dimension
#

rotvel=2./3.*pi*(1.5+0.5)*.254

#
# Periodic Geometry
#


# Set up periodic boundary conditions
O.periodic=True
xExt=4*sample_diameter
yExt=3.*sample_diameter*2 #to block the periodicity in y direction
zExt=xExt
xLim=xExt
yLim=yExt/4
zLim=zExt
O.cell.hSize=Matrix3(
  xExt, 0, 0,
  0, yExt, 0,
  0, 0, zExt)


length=xExt
height=yExt
width=zExt

# Top and bottom plate thickness
thickness=0.1*height


#
# Bottom
#
#bottom=box(
#center=(length/2.0,yLim - thickness/2.0,width/2.0)
#   ,extents=(4*length,thickness/2.0,width)
#   ,wire=False
#   ,material='plate_mat'
#   )

bottomBoxes = []
for ix in (0,1,2):
 for iz in (0,1,2):
   bottomBoxes.append(box( # create 3x3 boxes with 1/3 cell size
   center=(xExt/6.*(1+2*ix),yLim - thickness/2.0,zExt/6.*(1+2*iz))
   ,extents=(xExt/6.,thickness/2.0,zExt/6.)
   ,wire=False
   ,material='plate_mat'
   ))

bottom_id,bottom_ids = O.bodies.appendClumped(bottomBoxes) # bottom_id
is the clump id,


O.bodies[bottom_id].state.blockedDOFs='xyzXYZ'


#
# Particle Packing
#

min_corner= (0,yLim,0)
max_corner= (xLim, yExt-yLim, zLim)

sp=pack.SpherePack()
sp.makeCloud( min_corner,max_corner, rMean=sample_radius, periodic=False)

print "Generated ",len(sp)," aggregates"

###
# Sample
###
for s in sp:
  sphere=pack.inSphere((s[0][0],s[0][1],s[0][2]),s[1])
  sp1=pack.randomDensePack(
  sphere
 ,spheresInCell=2000
 ,radius=particle_radius
 ,memoizeDb='/tmp/triaxPackCache.sqlite'
 ,returnSpherePack=True
 )

  sp1.toSimulation(material='sample_mat',color=(0.9,0.8,0.6))
  print 'Generated ',len(sp1),' particles'

Gl1_Sphere(stripes=True)

#
# Top
#
#top=box(
#center=(length/2.0,yExt - yLim + thickness*2,width/2.0)
#   ,extents=(0.16*length,thickness/2.0,0.16*width)
#   ,wire=False
# 

Re: [Yade-users] [Question #290950]: Particles crossing the wall

[Jan Stránský]

Question #290950 on Yade changed:
https://answers.launchpad.net/yade/+question/290950

Jan Stránský proposed the following answer:
Hi Varun,
change the creation of your top box in the following way. To be sure it
works, I would modify also the bottom in the same way.

to get a force reaction, O.forces.f(top_id) will return only the prescribed
force. Use the following command instead (maybe +- plate_downforce, you can
play a bit)
sum( ( O.forces.f(i) for i in top_ids ), Vector3.Zero )

cheers
Jan

#
# Top
#
topBoxes = []
for ix in (0,1,2):
for iz in (1,2,3):
topBoxes.append(box( # create 3x3 boxes with 1/3 cell size
center=(xExt/6.*(1+2*ix),yExt - yLim + thickness/2.0,zExt/6.*(1+2*iz))
,extents=(xExt/6.,thickness/2.0,zExt/6.)
,wire=False
,material='plate_mat'
))
top_id,top_ids = O.bodies.appendClumped(topBoxes) # top_id is the clump id,
top_ids is its members id
O.bodies[top_id].state.blockedDOFs='xzXYZ'
##


2016-04-25 22:47 GMT+02:00 VG :

> Question #290950 on Yade changed:
> https://answers.launchpad.net/yade/+question/290950
>
> VG posted a new comment:
> Hello Jan,
>
> Thanks for your response. I tried what you suggested, i.e. one small box
> (1/3 of the periodic cell), but it still seems to have the same problem
> and the top box is just flying through the particles. I don't know if
> there is a way to attach images here, so I have sent you screenshot of
> the simulation through email. Is there something in my set up that I am
> missing ?
>
> Thanks
> Varun
>
> --
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> an answer contact for Yade.
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Re: [Yade-users] [Question #292258]: An error message when I use multiple cores

[behzad]

Question #292258 on Yade changed:
https://answers.launchpad.net/yade/+question/292258

behzad posted a new comment:
It's Ubuntu  14.04

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Re: [Yade-users] [Question #292258]: An error message when I use multiple cores

[Anton Gladky]

Question #292258 on Yade changed:
https://answers.launchpad.net/yade/+question/292258

Anton Gladky proposed the following answer:
You did not answer the question about operating system.
QMake is not used for Yade compilation.

Regards

Anton

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Re: [Yade-users] [Question #290950]: Particles crossing the wall

[VG]

Question #290950 on Yade changed:
https://answers.launchpad.net/yade/+question/290950

VG posted a new comment:
Hello Jan,

Thanks for your response. I tried what you suggested, i.e. one small box
(1/3 of the periodic cell), but it still seems to have the same problem
and the top box is just flying through the particles. I don't know if
there is a way to attach images here, so I have sent you screenshot of
the simulation through email. Is there something in my set up that I am
missing ?

Thanks
Varun

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Re: [Yade-users] [Question #292258]: An error message when I use multiple cores

[behzad]

Question #292258 on Yade changed:
https://answers.launchpad.net/yade/+question/292258

behzad posted a new comment:

I've got QMake version of 2.01a using Qt version 4.8.6.
I don't know how can I check  the version of libqglviewer

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Re: [Yade-users] [Question #290950]: Particles crossing the wall

[Jan Stránský]

Question #290950 on Yade changed:
https://answers.launchpad.net/yade/+question/290950

Jan Stránský proposed the following answer:
Just reformulating Bruno's and Jerome's answers. Instead of one big box,
try to use e.g. clump of 3x3 boxes, each with dimensions 1/3 of cell size.
The simulation is periodic, so you don't need to have this "top" larger
than one periodic cell.

I just tried with one small box (using your script, just making "top"
approx. 1/3 of periodic cell) and it works ok, all interactions seems to be
detected.

cheers
Jan


2016-04-25 20:22 GMT+02:00 VG :

> Question #290950 on Yade changed:
> https://answers.launchpad.net/yade/+question/290950
>
> VG posted a new comment:
> Hi Bruno,
>
> Thanks for your response.
>
> I tried to incorporate the changes you suggested, but the problem still
> doesn't seem to go away. Also, another perplexing thing I notice from
> the simulation that as soon as it starts, some individual particles seem
> to be just flying in the domain even though they should be part of
> aggregates connected by cohesive bonds.
>
> Is there a work around or something I could change in the problem set up
> that would help me resolve this issue ?
>
> I just simply need to compress the granular material with a constant
> force or leading to a constant compressive stress and then apply shear
> force.
>
> Regards
> Varun
>
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Re: [Yade-users] [Question #292258]: An error message when I use multiple cores

[behzad]

Question #292258 on Yade changed:
https://answers.launchpad.net/yade/+question/292258

behzad posted a new comment:

I downloaded the trunk and then, I added two files for the new material that I 
use and I compiled all. 
If this is what you call self compiled so it's a self compiled YADE. 

The new material has nothing to do with this problem and even without
having that the problem exist.

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Re: [Yade-users] [Question #291114]: virtual time and time step

[Jan Stránský]

Question #291114 on Yade changed:
https://answers.launchpad.net/yade/+question/291114

Jan Stránský posted a new comment:
Your welcome, I solved nothing :-) it is exactly the reason why a script
reproducing the error should be attached :-)
cheers
Jan


2016-04-25 20:37 GMT+02:00 VG :

> Question #291114 on Yade changed:
> https://answers.launchpad.net/yade/+question/291114
>
> VG confirmed that the question is solved:
> Thanks Jan Stránský, that solved my question.
>
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Re: [Yade-users] [Question #292258]: An error message when I use multiple cores

[Anton Gladky]

Question #292258 on Yade changed:
https://answers.launchpad.net/yade/+question/292258

Anton Gladky proposed the following answer:
Hi,

do you use the packaged or self-compiled Yade?

Anton

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Re: [Yade-users] [Question #290933]: Particles fall through facets in periodic simulation

[VG]

Question #290933 on Yade changed:
https://answers.launchpad.net/yade/+question/290933

VG posted a new comment:
Thanks for your response, Bettina!
Yes the work around which Bruno suggested doesn't work for me either.

May be I will have to change the problem set up, but at this point I
don't know how I could achieve that and still keep it physically
realistic. I need to compress the granular material with a constant
force or leading to a constant compressive stress and then induce shear
stress (currently doing it through the velocity of plate) to study the
breakage of granular material. Please let me know if you have any
suggestions.

Thanks
Varun

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Re: [Yade-users] [Question #292258]: An error message when I use multiple cores

[behzad]

Question #292258 on Yade changed:
https://answers.launchpad.net/yade/+question/292258

behzad posted a new comment:

Hi Jan

It's 2016-04-15.git-c671ce7

By the way I had this issue with older versions as well.

thanks,
Behzad

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Re: [Yade-users] [Question #290950]: Particles crossing the wall

[VG]

Question #290950 on Yade changed:
https://answers.launchpad.net/yade/+question/290950

VG posted a new comment:
Hi Bruno,

Thanks for your response.

I tried to incorporate the changes you suggested, but the problem still
doesn't seem to go away. Also, another perplexing thing I notice from
the simulation that as soon as it starts, some individual particles seem
to be just flying in the domain even though they should be part of
aggregates connected by cohesive bonds.

Is there a work around or something I could change in the problem set up
that would help me resolve this issue ?

I just simply need to compress the granular material with a constant
force or leading to a constant compressive stress and then apply shear
force.

Regards
Varun

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Re: [Yade-users] [Question #292258]: An error message when I use multiple cores

[Jan Stránský]

Question #292258 on Yade changed:
https://answers.launchpad.net/yade/+question/292258

Status: Open => Answered

Jan Stránský proposed the following answer:
Hi Behzad,
see [1]. What version of Yade do you use?
cheers
Jan

[1] https://bugs.launchpad.net/yade/+bug/1559098


2016-04-25 19:57 GMT+02:00 behzad :

> Question #292258 on Yade changed:
> https://answers.launchpad.net/yade/+question/292258
>
> behzad posted a new comment:
>
> This is an example of the script causing the error message most of the
> time:
>
> https://www.dropbox.com/s/zrpi7c4nkl7nsm5/G8-14.py?dl=0
>
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Re: [Yade-users] [Question #292258]: An error message when I use multiple cores

[behzad]

Question #292258 on Yade changed:
https://answers.launchpad.net/yade/+question/292258

behzad posted a new comment:

This is an example of the script causing the error message most of the time:

https://www.dropbox.com/s/zrpi7c4nkl7nsm5/G8-14.py?dl=0

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[Yade-users] [Question #292258]: An error message when I use multiple cores

[behzad]

New question #292258 on Yade:
https://answers.launchpad.net/yade/+question/292258


Hi folks,

I get this error message maybe 50% of the time I use multiple cores. Any idea 
that where does it come from?

*** Error in `/usr/bin/python': free(): invalid next size (fast): 0x09268828 ***
Aborted (core dumped)

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Re: [Yade-users] [Question #290933]: Particles fall through facets in periodic simulation

[Jérôme Duriez]

Question #290933 on Yade changed:
https://answers.launchpad.net/yade/+question/290933

Linked to bug: #1112763
https://bugs.launchpad.net/bugs/1112763
"interaction not detected in a VERY specific (body size = period size) case"

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Re: [Yade-users] [Question #290950]: Particles crossing the wall

[Jérôme Duriez]

Question #290950 on Yade changed:
https://answers.launchpad.net/yade/+question/290950

Linked to bug: #1112763
https://bugs.launchpad.net/bugs/1112763
"interaction not detected in a VERY specific (body size = period size) case"

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Re: [Yade-users] [Question #290950]: Particles crossing the wall

[Bruno Chareyre]

Question #290950 on Yade changed:
https://answers.launchpad.net/yade/+question/290950

Status: Open => Answered

Bruno Chareyre proposed the following answer:
You found a known bug for large objects in periodic simulations.
The bug seems to show up especially when some interactions exist at iteration 
0, those ones are not detected correctly (this is your case, where you have 
large overlaps in the initial geometry).
I find that the problem disappear in your case if line 149 is changed as 
follows:

top=box(
center=(length/2.0,yExt - yLim + thickness*2,width/2.0)
   ,extents=(4*length,thickness/2.0,width)
   ,wire=False
   ,material='plate_mat'
   )

Besides, there is absolutely no need to define a thickness for your
plates. Thickness zero is ok (mind that the default will be zero
though).

Bruno

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Re: [Yade-users] [Question #292180]: Finding Scripts

[Seti]

Question #292180 on Yade changed:
https://answers.launchpad.net/yade/+question/292180

Status: Answered => Solved

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

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