Re: [Yade-users] [Question #293179]: 'Name error' while calling function

[subha]

Question #293179 on Yade changed:
https://answers.launchpad.net/yade/+question/293179

subha posted a new comment:
Thanks Klaus,

For some reason, option#1 resulted in a segmentation fault (core dumped)
however option#2 worked but obviously at the expense of increased
simulation time as you previously indicated.

SM

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Re: [Yade-users] [Question #293179]: 'Name error' while calling function

[Klaus Thoeni]

Question #293179 on Yade changed:
https://answers.launchpad.net/yade/+question/293179

Klaus Thoeni posted a new comment:
add #10: you have two options: 
1. execute the line plot.saveDataTxt('file2.txt.bz2') in the terminal after you 
have finished the simulation
2. put the line back where you had it at the beginning, it was only a 
suggestion to move it outside the PyRunner for better performance

K

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Re: [Yade-users] [Question #293179]: 'Name error' while calling function

[subha]

Question #293179 on Yade changed:
https://answers.launchpad.net/yade/+question/293179

subha posted a new comment:
Hi Jerome,

Thanks for your comment. How do I define the scope of a function local
or global in the script?

Thanks,

SM

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Re: [Yade-users] [Question #293179]: 'Name error' while calling function

[subha]

Question #293179 on Yade changed:
https://answers.launchpad.net/yade/+question/293179

subha posted a new comment:
Hi Klaus,

I noticed that if O.run(N,False) is used, the script does not write the
data in the text file, but saves the images.

SM

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Re: [Yade-users] [Question #293345]: capillary files

[Jérôme Duriez]

Question #293345 on Yade changed:
https://answers.launchpad.net/yade/+question/293345

Status: Open => Answered

Jérôme Duriez proposed the following answer:
Hello,

"r" stands for the radii ratio (greater radius divided by smaller radius) 
between two capillary bonded spheres. 
The very first lines of each file include
- the r value
- the number Nd of dimensionless interparticle distances in this file
- a number Nuc of dimensionless capillary pressure values

Then, you have Nuc lines describing Nuc capillary bridge configurations in 
terms of 6 columns with :
- the dimensionless distance value (constant along these Nuc lines)
- a dimensionless capillary pressure value
- a dimensionless liquid volume volume
- a dimensionless force value
- a filling angle on the smallest particle (in degrees)
- a filling angle on the biggest particle (in degrees)

(This scheme repeats Nd times)

If you're interested in these files, I'd recommend you give a look to
https://bugs.launchpad.net/yade/+bug/1440887, and especially #4 that
gives a MATLAB file to plot the capillary files data.

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[Yade-users] [Question #293345]: capillary files

[Seungcheol Yeom]

New question #293345 on Yade:
https://answers.launchpad.net/yade/+question/293345

Hello all,

I have a quick question regarding the capillary files.
There are ten files named like M(r=numbers).
What does r stand for?
Also, in the file, can someone please tell me what each column of data stands 
for?
Thank you.

Sincerely,

Seungcheol

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Re: [Yade-users] [Question #293342]: Problem with simulation

[Jérôme Duriez]

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

Status: Open => Answered

Jérôme Duriez proposed the following answer:
Hi,

According to the name of Ig2_Sphere_ChainedCylinder_CylScGeom6D(), the
interaction between Sphere and chainedCylinder has a "geom" of
CylScGeom6D type

Thus, you need to include in your simulations a "Law2" that can handle
such interactions, wich is not the case here (none of your Law2 functors
include CylScGeom6D in its name).

I'd advice you to give a close look to https://yade-
dem.org/doc/user.html#functors-choice, instead of using brute force and
stuffing as many functors as possible (without the right one, by lack of
luck) into your simulation ;-) ;-)

PS: the title of your question is not so original

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[Yade-users] [Question #293342]: Problem with simulation

[Alex]

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

Hello friends,

I created the simulation below and I had a problem. 

My objective is to make the cylinder collide with spheres. But, I can't do 
this. When I run the simulation the cylinder goes inside the spheres.

I ask if someone could help in this problem.


import sys
from yade import ymport, utils , plot
import math


 Material microproperties -> SHALE!
intR=1.22955
DENS=2659.6453 
YOUNG=40e9 
FRICT=25
ALPHA=0.25  
TENS=10e5 
COH=10e6
aRes=1e-3 
damp=0.2 
jointFRICT=25 
jointDIL=15 

 material definition
def sphereMat(): return JCFpmMat(type=1,density=DENS,young=YOUNG,poisson = 
ALPHA,frictionAngle=radians(FRICT), 
  
tensileStrength=TENS,cohesion=COH,jointNormalStiffness=YOUNG/10.,jointShearStiffness=0.2*YOUNG/10.,
  
jointTensileStrength=0.,jointCohesion=0.,jointFrictionAngle=radians(jointFRICT),jointDilationAngle=radians(jointDIL))


O.engines=[
ForceResetter(),
InsertionSortCollider([
Bo1_ChainedCylinder_Aabb(),
Bo1_Sphere_Aabb()
]),
InteractionLoop(
# Geomeetric interactions
[Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D(),
Ig2_Sphere_ChainedCylinder_CylScGeom6D(),
Ig2_Sphere_Sphere_ScGeom6D(),   
Ig2_Sphere_Sphere_L3Geom(),Ig2_Facet_Sphere_L3Geom()
],

[Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=True),
Ip2_FrictMat_FrictMat_FrictPhys()
],
[Law2_ScGeom6D_CohFrictPhys_CohesionMoment(label='law'),
 Law2_ScGeom_FrictPhys_CundallStrack(), 
 Law2_L3Geom_FrictPhys_ElPerfPl(),
]
),
## Motion equation
NewtonIntegrator(damping=0.4,gravity=[0,0,0]),
PyRunner(command='main()',iterPeriod=10)
]

O.dt=1e-7

# create a cylinder
cil = chainedCylinder(begin=Vector3(0.3,0.4,2.02), 
end=Vector3(0.3,0.6,2.02),radius=0.025,color=Vector3(0.6,0.5,0.5))

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

yade.qt.View();

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


 

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Re: [Yade-users] [Question #293216]: Creating Ellipse or Ellipsoid

[Jan Stránský]

Question #293216 on Yade changed:
https://answers.launchpad.net/yade/+question/293216

Jan Stránský proposed the following answer:
Hi Mohsen,

if you have different question than the original problem, please open a new
question.

your 2) comes from 1). I always use randomDensePack with spheresInCell
parameter, usually with value between 300 and 2000. Then your example
(memoizeDb, too) works OK.

cheers
Jan


2016-05-05 9:17 GMT+02:00 mohsen :

> Question #293216 on Yade changed:
> https://answers.launchpad.net/yade/+question/293216
>
> mohsen posted a new comment:
> Hi Felipe and Jan
> Jan i also have some trouble with making a predicate!
> generally when i using randomDensePack, i encounter some errors or
> warnings that i can not understand their meanings!
> Jan can you help us about "memoizeDb"? I think some errors is because of
> this.
>
> in the following is my simple code and warnings:
>
> ###
> ## construct the predicate first
> pred=pack.inCylinder(centerBottom=(0,0,-.1),centerTop=(0,0,.1),radius=.05)
> ## alternatively: pack.inHyperboloid((0,0,-.1),(0,0,.1),.05,.03)
>
> ## pack the predicate with spheres (will be explained later)
> spheres=pack.randomDensePack(pred,radius=8.5e-3)
>
> ## add spheres to simulation
> O.bodies.append(spheres)
>
> 
> Warnings:
> WARN
> /build/yadedaily-1.20.0-126-e3271e8~trusty/pkg/dem/SpherePack.cpp:104
> makeCloud: porosity must be >0, changing it for you. It will be ineffective
> if rMean>0.
> /usr/lib/x86_64-linux-gnu/yadedaily/py/yade/pack.py:296: FutureWarning:
> The default behavior will change; specify returnSpherePack=True for the new
> behavior, and False to get rid of this warning (your code will break in the
> future, however). The returned SpherePack object can be added to the
> simulation using SpherePack.toSimulation()
>   warnings.warn('The default behavior will change; specify
> returnSpherePack=True for the new behavior, and False to get rid of this
> warning (your code will break in the future, however). The returned
> SpherePack object can be added to the simulation using
> SpherePack.toSimulation()',category=FutureWarning)
> /usr/lib/x86_64-linux-gnu/yadedaily/py/yade/pack.py:301: UserWarning:
> Packing's dimension
> (Vector3(0.09220547603362886,0.09204759935856582,0.1700020579236124))
> doesn't fully contain dimension of the predicate (Vector3(0.1,0.1,0.2)).
>   if dimP[0]>dimS[0] or dimP[1]>dimS[1] or dimP[2]>dimS[2]:
> warnings.warn("Packing's dimension (%s) doesn't fully contain dimension of
> the predicate (%s)."%(dimS,dimP))
>
> 
>
> 2- another problem is that the spheres in generated pack have overlap!!
> How can we avoid this? ( I know that the over lap is removed if we give a
> number to spheresInCell, i.e activating periodic condition. but is there
> any other way to have a aperiodic scene without overlap)
> Is there another method to construct a cylinder filled with spheres with
> no initial overlap?
>
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Re: [Yade-users] [Question #291202]: Clumping - angl of repose

[Seti]

Question #291202 on Yade changed:
https://answers.launchpad.net/yade/+question/291202

Status: Answered => Open

Seti is still having a problem:
Yes, I have even tried O.dt=.1*utils.PWaveTimeStep() , no different !

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Re: [Yade-users] [Question #291202]: Clumping - angl of repose

[Seti]

Question #291202 on Yade changed:
https://answers.launchpad.net/yade/+question/291202

Seti gave more information on the question:
Yes, I have even tried O.dt=.1*utils.PWaveTimeStep() , no difference!

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Re: [Yade-users] [Question #291202]: Clumping - angl of repose

[Jérôme Duriez]

Question #291202 on Yade changed:
https://answers.launchpad.net/yade/+question/291202

Status: Open => Answered

Jérôme Duriez proposed the following answer:
Have you tried to play with (decrease) the timestep ? Excessively high
timesteps are a classical reason for "explosion"

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Re: [Yade-users] [Question #291202]: Clumping - angl of repose

[Seti]

Question #291202 on Yade changed:
https://answers.launchpad.net/yade/+question/291202

Seti gave more information on the question:
I think this explosion is depended on percentage of clumping . I mean by 
increasing the ratio of clumping the sample explode sooner. I am not sure what 
is the conflict.
Does anybody experience in this regard.

Thanks 
Seti

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Re: [Yade-users] [Question #291202]: Clumping - angl of repose

[Seti]

Question #291202 on Yade changed:
https://answers.launchpad.net/yade/+question/291202

Status: Answered => Open

Seti is still having a problem:
Hi Kalus, 
Thanks for your response . I have tried to use mackeCloud , easily as per 
below, However I have the same problem. Would you please?

from yade import pack,utils, qt, plot

#create material
soil1 = 
CohFrictMat(young=30e9,poisson=0.3,frictionAngle=radians(30),density=2600.0,normalCohesion=1e6,
 shearCohesion=80e6,label='soil')
#color=(1,0,0) red color

O.materials.append(soil1)
O.bodies.append(utils.wall(0,axis=1,sense=1))
O.materials.append(CohFrictMat(young=30e9,poisson=0.3, frictionAngle = 
radians(30) , label='wallmat'))
wallmat = O.materials[-1]

sp=SpherePack()
sp.makeCloud((0,0,0),(14.5,14.5,14.5),rMean=0.5,rRelFuzz=0.0)
#sp.makeCloud((0,0,0),(14.5,14.5,14.5),rMean=0.2,rRelFuzz=0.0,False,0.95,[0.2,0.3,0.4,0.5,0.6,0.7,0.8],[0.14,0.28,0.34,0.50,0.65,0.85,1.00])
#spheres.toSimulation()
sp.toSimulation()
#O.bodies.append(spheres)

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Re: [Yade-users] [Question #292846]: Particle packing - How to avoid overlap

[Jan Stránský]

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

Status: Open => Answered

Jan Stránský proposed the following answer:
Hi Varun,
yes, you are right. The s[1]-particle_radius in old and s[1] in new version
should do the same.
cheers
Jan


2016-05-04 23:07 GMT+02:00 VG :

> Question #292846 on Yade changed:
> https://answers.launchpad.net/yade/+question/292846
>
> VG posted a new comment:
> Also, I got the latest update of yadedaily which has the change you
> mentioned above. The point you mentioned above:
>
> "in pack.inSphere, it was a real bug. Of course, you can play with settings
>  like using s[1] or s[1]-particle_radius, but this is different point."
>
> With the new version of yadedaily, it generates the exact same number of
> particles in an aggregate, as generated when I used
> "s[1]-particle_radius"  instead of "s[1]" with the previous version of
> yadedaily.
>
> In my opinion, your fix in the code and the use of
> "s[1]-particle_radius" while generating randomDensepack  are doing the
> exact same things.
>
>
> For example, in the above script, using a sample_diameter of 2e-4 and
> particle diameter of 1e-5, results in 3732 particles within an agglomerate
> results in a packing ratio of 0.466, whereas the previous version lead to
> 4372 particles and a packing ratio of 0.55.
>
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Re: [Yade-users] [Question #293247]: Physic interaction betweem particles and polyhedra

[Jérôme Duriez]

Question #293247 on Yade changed:
https://answers.launchpad.net/yade/+question/293247

Jérôme Duriez proposed the following answer:
Yes, this is what I meant (in case your non-spherical bodies are all of
the same type, either Facet or Box, you may remove either Bo1_Box_Aabb()
; Ig2_Box_Sphere_ScGeom() or Bo1_Facet_Aabb() ;
Ig2_Facet_Sphere_ScGeom())

This being said, I realize my lengthy answer may not be directly related
to your initial problem, I am sorry...

I now understand you have different material parameters (these en,es)
for different bodies. Usually, YADE handles this at the bodies
"material" properties level [1].

For instance, simulations with "FrictPhys" handle like a charm different
friction angles for sphere-sphere and sphere-box interactions. We just
put different values for the frictionAngle attribute of the sphere or
box bodies' Material [2], and one unique Ip2
(Ip2_FrictMat_FrictMat_FrictPhys) does the job giving different local
friction angles for sphere-sphere and sphere-box interactions.

Here, the design of Ip2_FrictMat_FrictMat_MindlinPhys is flawed in my
point of view (I'm not used to MindlinPhys, though) if these en,es,krot
are material parameters that can be different among bodies. Because
including these parameters in Ip2_FrictMat_FrictMat_MindlinPhys prevents
playing with different parameters the same way as frictionAngle within
FrictPhys (hence your problem)..

I see two possible solutions to your problem, both involving modifying
the source code

- either modifying the source code of Ip2_FrictMat_FrictMat_MindlinPhys
to detect the shape of interacting bodies and assign distinct en,es in
accordance. From my point of view, this would not conform the classical
YADE design I exposed in #6, I agree thus with Jan it would be "hacky"

- removing these en,es from Ip2_FrictMat_FrictMat_MindlinPhys to insert
them in a (new ?) material class. Which would make more sense, from my
point of view.


Further discussion would require other people more used to MindlinPhys than me. 
Hope it still helps

[1] https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.Body.material
[2] 
https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.FrictMat.frictionAngle

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Re: [Yade-users] [Question #293247]: Physic interaction betweem particles and polyhedra

[Jonathan Pergoli]

Question #293247 on Yade changed:
https://answers.launchpad.net/yade/+question/293247

Jonathan Pergoli posted a new comment:
Hi Jérome,

you mean this:
O.engines=[
ForceResetter(),

InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),Bo1_Box_Aabb()]),
InteractionLoop(

[Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_MindlinPhys(en=.55,es=.55,krot=3)],
[Law2_ScGeom_MindlinPhys_Mindlin(includeMoment=True)]
),
NewtonIntegrator(gravity=(0,0,-2.5e-4),damping=.2)
]
?

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Re: [Yade-users] [Question #293216]: Creating Ellipse or Ellipsoid

[mohsen]

Question #293216 on Yade changed:
https://answers.launchpad.net/yade/+question/293216

mohsen posted a new comment:
Hi Felipe and Jan
Jan i also have some trouble with making a predicate!
generally when i using randomDensePack, i encounter some errors or warnings 
that i can not understand their meanings!
Jan can you help us about "memoizeDb"? I think some errors is because of this.

in the following is my simple code and warnings:

###
## construct the predicate first
pred=pack.inCylinder(centerBottom=(0,0,-.1),centerTop=(0,0,.1),radius=.05)
## alternatively: pack.inHyperboloid((0,0,-.1),(0,0,.1),.05,.03)

## pack the predicate with spheres (will be explained later)
spheres=pack.randomDensePack(pred,radius=8.5e-3)

## add spheres to simulation
O.bodies.append(spheres)


Warnings:
WARN  /build/yadedaily-1.20.0-126-e3271e8~trusty/pkg/dem/SpherePack.cpp:104 
makeCloud: porosity must be >0, changing it for you. It will be ineffective if 
rMean>0.
/usr/lib/x86_64-linux-gnu/yadedaily/py/yade/pack.py:296: FutureWarning: The 
default behavior will change; specify returnSpherePack=True for the new 
behavior, and False to get rid of this warning (your code will break in the 
future, however). The returned SpherePack object can be added to the simulation 
using SpherePack.toSimulation()
  warnings.warn('The default behavior will change; specify 
returnSpherePack=True for the new behavior, and False to get rid of this 
warning (your code will break in the future, however). The returned SpherePack 
object can be added to the simulation using 
SpherePack.toSimulation()',category=FutureWarning)
/usr/lib/x86_64-linux-gnu/yadedaily/py/yade/pack.py:301: UserWarning: Packing's 
dimension (Vector3(0.09220547603362886,0.09204759935856582,0.1700020579236124)) 
doesn't fully contain dimension of the predicate (Vector3(0.1,0.1,0.2)).
  if dimP[0]>dimS[0] or dimP[1]>dimS[1] or dimP[2]>dimS[2]: 
warnings.warn("Packing's dimension (%s) doesn't fully contain dimension of the 
predicate (%s)."%(dimS,dimP))



2- another problem is that the spheres in generated pack have overlap!! 
How can we avoid this? ( I know that the over lap is removed if we give a 
number to spheresInCell, i.e activating periodic condition. but is there any 
other way to have a aperiodic scene without overlap)
Is there another method to construct a cylinder filled with spheres with no 
initial overlap?

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