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

2016-06-21 Thread 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 :
> 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 #295531]: Cohesion/Moment only work with TriaxialCompressionEngine?

2016-06-21 Thread Jérôme Duriez 
Question #295531 on Yade changed:
https://answers.launchpad.net/yade/+question/295531

Status: Open => Needs information

Jérôme Duriez requested more information:
Hi,

Your issue sounds rather strange to me. The data saved (by
TriaxialStateRecorder() engine) in 'WallStresses' obviously should not
be affected by the contact law used, or the choice of
TriaxialStressController vs TriaxialCompressionEngine as a boundary
controller.

Apart for the (always possible) existence of a weird bug, it may also happen 
that your simulation is inconsistently defined when you try to include moment 
law in HM or "setCohesionNow" in "Cundall-Strack". 
In fact, please be more specific here as "setCohesionNow" is part of the 
"CohFrictMat" model (in terms of Ip2_CohFrictMat_CohFrictMat_CohFrictPhys -- 
Law2_ScGeom6D_CohFrictPhys_CohesionMoment) but is not part of the 
"CundallStrack" model (in terms of Ip2_FrictMat_FrictMat_FrictPhys -- 
Law2_ScGeom_FrictPhys_CundallStrack)


In order to help us to look at your issue, a first recommendation would be to 
provide us with a minimal working script that is
- minimal (we do not care about VTK things, particle size distribution, and so 
on...)
- and working: it will be impossible for anyone to try your script because of 
sp.load('sp.txt'), for instance.
;-)

Jerome

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Re: [Yade-users] [Question #295527]: CohFrictMat model

2016-06-21 Thread Jérôme Duriez 
Question #295527 on Yade changed:
https://answers.launchpad.net/yade/+question/295527

Status: Open => Answered

Jérôme Duriez proposed the following answer:
Hi Paula,

In fact you're lucky because the CohFrictMat model is well documented
from my point of view, see

- https://yade-
dem.org/doc/yade.wrapper.html#yade.wrapper.Ip2_CohFrictMat_CohFrictMat_CohFrictPhys

- https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.CohFrictMat
(whose documentation is the one that could be slightly improved, I
confess)

- https://yade-
dem.org/doc/yade.wrapper.html#yade.wrapper.Law2_ScGeom6D_CohFrictPhys_CohesionMoment

See also this recent question:
https://answers.launchpad.net/yade/+question/295225

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[Yade-users] [Question #295531]: Cohesion/Moment only work with TriaxialCompressionEngine?

2016-06-21 Thread Gary Pekmezi 
New question #295531 on Yade:
https://answers.launchpad.net/yade/+question/295531

This was an issue I ran into before with the Cundall-Strack law, and I am now 
also seeing with Hertz-Mindlin law.
If I have:

triax=TriaxialStressController(...)

then the "Wallstresses" file shows all stresses and porosity as "NaN" for 
Hertz-Mindlin, or I get a core dump for Cundall-Strack. This happens only when 
I set "includeMoment" to True for Hertz-Mindlin, or "setCohesionNow" to True 
for Cundall-Strack.  It's fairly simple to get my models to run, all I have to 
do is to switch to :

triax=TriaxialCompressionEngine(...)

So is the moment law and cohesion not supported with TriaxialStressController, 
is it a bug, or (probably most likely) am I doing something wrong?

I should add that I tested this with the latest version released last week and 
saw the same behavior

I am pasting my Hertz-Mindlin input below for completeness.

Thanks,
Gary



import math, os, sys
from yade import plot
from yade import pack

### DEFINE VARIABLES AND MATERIALS   ###

readParamsFromTable(krot=1.0,noTableOk=True)
from yade.params.table import *
desc='description'
key=O.tags[desc]
print key, krot

os.mkdir(key)

finalFricDegree=14.5
rate=-25.0 # loading rate (strain rate)
damp=0.2 # damping coefficient
stabilityThreshold=0.02
triaxialThreshold=0.005
young=20e9
poisson=0.33
triaxial_p = -5.0e6 

sp=pack.SpherePack()
sp.load('sp.txt')
print "Saved Confined State Loaded"
box=sp.aabb()
print box
print (sp.psd(bins=10))
# ###
# ###   DEFINE THE SCENE  ###
# ###
O.materials.append(FrictMat(young=young,
poisson=poisson,
frictionAngle=radians(finalFricDegree),
density=2600,
label='spheres'))
O.materials.append(FrictMat(young=young,
poisson=poisson,
frictionAngle=0,
density=0,
label='walls'))
walls=aabbWalls(box,thickness=0,oversizeFactor=2.0,material='walls')
wallIds=O.bodies.append(walls)
sp.toSimulation(material='spheres')

###   DEFINING ENGINES   ###

triax=TriaxialStressController( #replace 
with#TriaxialCompressionEngine(#
  maxMultiplier=1.005, # spheres growing factor (fast growth)
  finalMaxMultiplier=1.5, # spheres growing factor (slow growth)
  thickness = -1,
  stressMask = 7,
  internalCompaction=True,
  autoCompressionActivation=False,
  sigmaIsoCompaction=triaxial_p,
  sigmaLateralConfinement=triaxial_p,
  )
triax.goal1=triax.goal2=triax.goal3=confinement_p
  
newton=NewtonIntegrator(damping=damp)
  
vtkrec=VTKRecorder(recorders=['spheres','boxes','stress'],)
vtkrec.fileName=key+'/'+'vtkHC'
  
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
InteractionLoop(
   [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
   [Ip2_FrictMat_FrictMat_MindlinPhys(krot=krot,eta=1.0)],
   
[Law2_ScGeom_MindlinPhys_Mindlin(includeMoment=True,label="mindlinLaw2")],  
 ),

GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
triax,
newton,
TriaxialStateRecorder(iterPeriod=100,file=key+'/'+'WallStresses'),
vtkrec, 
 ]
#
###Record and plot data ###
#
def history():
plot.addData(e1=triax.strain[1]*-100.0,
ev=-100.0*triax.volumetricStrain,
pDiff=pDiff,
i=O.iter)
vtkrec.fileName=key+'/'+'vtkTriaxial'
f=open(key+'/'+'./zout.txt', 'w+')
# ###
# ###   APPLYING TRIAXIAL PRESSURE   ###
# ###
triax.goal1=triax.goal2=triax.goal3=triaxial_p
while 1:
  O.run(1000, True)
  unb=unbalancedForce()
  triDiff=abs((triax.goal1-triax.meanStress)/(triax.goal1))
  print >>f,'unb:',unb,' triDiff: ',triDiff,' meanS: ',triax.meanStress,' 
porosity: ',triax.porosity,'pMult',triax.previousMultiplier
  sys.stdout.flush()
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Re: [Yade-users] [Question #295520]: Exception occured: std::bad_alloc

2016-06-21 Thread Yor1 
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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[Yade-users] [Question #295527]: CohFrictMat model

2016-06-21 Thread paula 
New question #295527 on Yade:
https://answers.launchpad.net/yade/+question/295527

Please please please can someone help me?, I'm using the CohFrictMat contact 
model and I'm trying to get a certain behavior of the material but I need to 
understand the CohFrictMat contact model to modify the variables of it. 
Thanks for all the help that you can provide.

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

2016-06-21 Thread Bruno Chareyre 
Question #295520 on Yade changed:
https://answers.launchpad.net/yade/+question/295520

Bruno Chareyre proposed the following answer:
There should not be any memory cost for this function.

Why is there an indentation before "O" in:
### add top box

O.bodies.append(utils.box(center=(xinf-thickness+Rmean/10,3*(ysup/4)+2*Rmean,zsup/2)

It could be a problem.

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Re: [Yade-users] [Question #295486]: Using CpmMat to simulate the hysteretic curve of concrete

2016-06-21 Thread liukeqi 
Question #295486 on Yade changed:
https://answers.launchpad.net/yade/+question/295486

Status: Answered => Solved

liukeqi confirmed that the question is solved:
Thanks Jan Stránský. It solved my question.

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Re: [Yade-users] [Question #295486]: Using CpmMat to simulate the hysteretic curve of concrete

2016-06-21 Thread liukeqi 
Question #295486 on Yade changed:
https://answers.launchpad.net/yade/+question/295486

liukeqi posted a new comment:
Thanks Jérôme Duriez.

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

2016-06-21 Thread Yor1 
Question #295520 on Yade changed:
https://answers.launchpad.net/yade/+question/295520

Yor1 posted a new comment:
Hello Bruno,

I think that is a problem of memory.
In the engines i think tha 
"PyRunner(iterPeriod=1,initRun=True,command='servoController()',label='servo')" 
take a lot of memory and after 1000 iterations i don't have memory.
In order to preserve memory for the simulation, i think that the solution is 
iterPeriod must be important for example iterPeriod=100 or iterPeriod=1000.

Best regards.
Jabrane.

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Re: [Yade-users] [Question #295521]: contact-normal in Yade

2016-06-21 Thread Bruno Chareyre 
Question #295521 on Yade changed:
https://answers.launchpad.net/yade/+question/295521

Status: Open => Answered

Bruno Chareyre proposed the following answer:
>[1] Are there anything wrong in my understanding of contact normal
distribution?

Looking at fig.2, your maths are wrong for sure. I can't tell where exactly.
Even figs.3 and 4 are weird, the extrema are like shifted by pi/4 from what is 
expected with vertical+horizontal walls.

>[2] Or Yade has its own pattern in defining the contact normal?

Not at all.

Bruno

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

2016-06-21 Thread Bruno Chareyre 
Question #295520 on Yade changed:
https://answers.launchpad.net/yade/+question/295520

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
Can you compile&run a debug build and post more information here?
Bruno

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[Yade-users] [Question #295521]: contact-normal in Yade

2016-06-21 Thread Fu zuoguang 
New question #295521 on Yade:
https://answers.launchpad.net/yade/+question/295521

Dear Prof. Chareyre and all users,

Fabric analysis is one of the most common methods for detecting those 
micro-level natures of such granular materials. Recently I have tried to do it 
in 2D-simulation task in Yade-1.14-daily version with the simplest isotropic 
condition. But unfortunately, I’m lost in getting the same results as that in 
Ref.[1]. All the details of my simulation are in Fig.1

Fig dir: http://tinypic.com/view.php?pic=2dwhukl&s=9#.V2kZvbEs-VU

After the consolidation process finished, I listed all the directional data I 
want to use as the following mode:

#
Body_Numbers,  Body_Cur_P_x,  Body_Cur_P_y,  Body_Cur_P_z,
   1,  -1.28536e-01,   0.0e+00,   0.0e+00,
   2,   1.28528e-01,   0.0e+00,   0.0e+00,
   3,   0.0e+00,  -1.28642e-01,   0.0e+00,
   4,   0.0e+00,   1.28632e-01,   0.0e+00,
   5,   0.0e+00,   0.0e+00,  -5.0e-01,
   6,   0.0e+00,   0.0e+00,   5.0e-01,
   7,   1.20924e-01,   6.60472e-02,   0.0e+00,
   8,  -1.22713e-01,   1.02525e-01,   0.0e+00,
   9,   4.91498e-02,   1.84187e-02,   0.0e+00,
  10,-4.19541e-02,  -3.18193e-02,   0.0e+00,
   .
###

So，I firstly summarized the contact-normal as the vector variable and 
transformed it from Cartesian to polar axis (using format 1-1) but got a 
strange result as shown in Fig.2. All the contact-normals are not symmetrically 
distributed around the origin of principle axes, but most of them are located 
in the area of (math.pi to 3/2math.pi).

Then, I respectively used the particle position and the contact-point position 
to execute the same process as above for ensuring that I got a correct output 
of those data, and plotted them in the same style as in Fig.3 and Fig.4. Now, 
the statistical results of the two group data show me the same trend. They are 
distributed axisymmetrically around the principle axes. And in the same 
quadrant, the number of data located in diagonal area is more than that in 
others, which can meet the deviatoric-shear condition.

Why is only the contact normal showing the non-symmetric distribution here? 
[1] Are there anything wrong in my understanding of contact normal distribution?
[2] Or Yade has its own pattern in defining the contact normal?

Seeking your help!

Ref.
[1] Distribution of directional data and fabric tensors. 1984_Int.J.Eng.Sci


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

2016-06-21 Thread Yor1 
New question #295520 on Yade:
https://answers.launchpad.net/yade/+question/295520

Hello everybody !

I try to simulate a simple shear test.
I simulate the simple shear test with 40 iterations.
The problem is when the simulation is between 1000 and 1100 iterations i 
obtained this error message:

"FATAL /home/hamdi/YADE/sources/trunk/core/ThreadRunner.cpp:30 run: Exception 
occured: 
std::bad_alloc"

I don't undersatand the origin of the error.

Best regards!
Jabrane

P.S this is my script


# -*- coding: utf-8 -*-
O=Omega()

from yade import ymport, utils, plot

## parameters definition
PACKING='X1Y1Z1_1k'
DAMPING=0.5
dtCOEFF=0.5
normalSTRESS=5e5
normalVEL=normalSTRESS/1e8 # 0.001 for 100kPa // optimized for 
normalVEL=normalSTRESS/1e8?
shearVEL=1*normalVEL # try different values to ensure quasi-static conditions
intR=1.263 #1.263 for X1Y1Z1_5k
DENS=3000
YOUNG=50e9
FRICT=18
ALPHA=0.3
TENS=45e5
COH=45e6
iterMAX=40
OUT='shearTest_'+PACKING+'_K10_D3000_Y50e9A03F18T45e5C45e6_500kPa_shearVel1'

## Import of the sphere assembly
### material definition
def sphereMat(): return JCFpmMat(type=1,density=DENS,young=YOUNG,poisson = 
ALPHA,frictionAngle=radians(FRICT),tensileStrength=TENS,cohesion=COH)
def wallMat(): return 
JCFpmMat(type=0,density=DENS,young=YOUNG,frictionAngle=radians(0))
## copy spheres from the packing into the scene
O.bodies.append(ymport.text(PACKING+'.spheres',scale=1.,shift=Vector3(0,0,0),material=sphereMat))

## preprocessing to get dimensions
dim=utils.aabbExtrema()
xinf=dim[0][0]
xsup=dim[1][0]
X=xsup-xinf
yinf=dim[0][1]
ysup=dim[1][1]
Y=ysup-yinf
zinf=dim[0][2]
zsup=dim[1][2]
Z=zsup-zinf
## initial surface
S0=X*Z

## spheres factory
R=0
Rmax=0
numSpheres=0.
for o in O.bodies:
 if isinstance(o.shape,Sphere):
   o.shape.color=(0.7,0.5,0.3)
   numSpheres+=1
   R+=o.shape.radius
   if o.shape.radius>Rmax:
 Rmax=o.shape.radius
Rmean=R/numSpheres

## creation of shear box
thickness=Y/100
oversizeFactor=1.3

### loading platens
O.bodies.append(utils.box(center=(xinf+X/2.,yinf-thickness+Rmean/10.,zinf+Z/2.),extents=(oversizeFactor*X/2,thickness,oversizeFactor*Z/2),material=wallMat,fixed=True))
bottomPlate=O.bodies[-1]
O.bodies.append(utils.box(center=(xinf+X/2.,ysup+thickness-Rmean/10.,zinf+Z/2.),extents=(oversizeFactor*X/2,thickness,oversizeFactor*Z/2),material=wallMat,fixed=True))
topPlate=O.bodies[-1]


O.engines=[

 ForceResetter(),
 
InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=intR,label='aabb'),Bo1_Box_Aabb()]),
 InteractionLoop(
  
[Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intR,label='ss2d3dg'),Ig2_Box_Sphere_ScGeom()],
  
[Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1,label='interactionPhys')],
  
[Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(recordCracks=True,Key=OUT,label='interactionLaw')]
 ),

 
GlobalStiffnessTimeStepper(defaultDt=0.1*PWaveTimeStep(),timestepSafetyCoefficient=dtCOEFF),
 
TranslationEngine(ids=[topPlate.id],translationAxis=(0.,-1.,0.),velocity=0.,label='yTranslation'),
 PyRunner(iterPeriod=1,initRun=True,command='servoController()',label='servo'),
 NewtonIntegrator(damping=DAMPING,gravity=(0,0,0),label='damper'),
 PyRunner(iterPeriod=100,initRun=True,command='dataCollector()'),
]

## Engines definition ( servoController() and 
dataCollector() )
shearing=False
sigmaN=0
tau=0
Fs1=0
Fs2=0
Xdispl=0
px0=0
Ydispl=0
py0=topPlate.state.pos[1]
prevTranslation=0
n=0

def servoController():
global px0, py0, sigmaN, n, Fn1, Fn2, shearing, butee, piston1, piston2
Fn1=abs(O.forces.f(topPlate.id)[1])
Fn2=abs(O.forces.f(bottomPlate.id)[1])
sigmaN=Fn1/(S0-2*Xdispl*Z) # necessary?
#print yTranslation.velocity, sigmaN
if shearing==False:
  if yTranslation.velocity(0.9*normalSTRESS):
yTranslation.velocity=normalVEL*((normalSTRESS-sigmaN)/normalSTRESS)
if shearing==False and abs((normalSTRESS-sigmaN)/normalSTRESS)<0.001 and 
unbalancedForce()<0.01:
  yTranslation.velocity=0
  n+=1
  if n>1000 and abs((sigmaN-normalSTRESS)/normalSTRESS)<0.001:
print 'stress on joint plane = ', 
utils.forcesOnPlane((X/2,Y/2,Z/2),(0,1,0))/S0

 ### add top box

O.bodies.append(utils.box(center=(xinf-thickness+Rmean/10,3*(ysup/4)+2*Rmean,zsup/2),extents=(thickness,Y/4,oversizeFactor*Z/2),material=wallMat,fixed=True))
butee=O.bodies[-1]

O.bodies.append(utils.box(center=(xsup+thickness-Rmean/10,3*(ysup/4)+2*Rmean,zsup/2),extents=(thickness,Y/4,oversizeFactor*Z/2),material=wallMat,fixed=True))
 

O.bodies.append(utils.box(center=(xsup/2,3*(ysup/4)+2*Rmean,zinf-thickness+Rmean/10),extents=(oversizeFactor*X/2,Y/4,thickness),material=wallMat,fixed=True,wire=True))
 

O.bodies.append(utils.box(center=(xsup/2,3*(ysup/4)+2*Rmean,zsup+thickness-Rmean/10),extents=(oversizeFactor*X/2,Y/4,thickness),material=wallMat,fixed=True,wire=True))
 ### add bottom box

O.bodies.append(utils.box(center=(xsup+thickness-R

Re: [Yade-users] [Question #295464]: Calculation of damping energy on chosen particles of a sample

2016-06-21 Thread Yor1 
Question #295464 on Yade changed:
https://answers.launchpad.net/yade/+question/295464

Status: Answered => Solved

Yor1 confirmed that the question is solved:
Hi Jan!

Thank you for the response.
I got a method to choose the particle in which I want to calculate the damping 
energy.
For the uniaxial test : i choose the particles which state.vel[0]!=0 and 
state.vel[2]!=0.
For the shear test : i choose the particle which state.vel!=(0,0,0)

Best regards.
Jabrane.

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