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[Leonard <question683821@xxxxxxxxxxxxxxxxxxxxx>]

New question #683821 on Yade:
https://answers.launchpad.net/yade/+question/683821

Hi,
I'm trying to generate a cylinder sample with target porosity, the MWE comes from [1]. The main changes are:
1. changed the sphere material from FrictMat to CohFrictMat, as well as corresponding engines,
2. cut the cubic sample to fulfil a cylinder shape after target porosity is reached.
The problem is after the simulation finished (run about 30 seconds), I can not find any particles in the scene, while I use 'len(O.bodies)' to check, I can get that there are 870 bodies. Here is the MWE:
########
from yade import pack
num_spheres=1000
key='_triax_base_'
targetPorosity = 0.43
compFricDegree = 30
finalFricDegree = 30
rate=-0.02
damp=0.2
stabilityThreshold=0.01
young=5e6
mn,mx=Vector3(0,0,0),Vector3(0.07,0.07,0.14)

cement = CohFrictMat(young=30e9,poisson=0.3,frictionAngle=radians(30),density=2650.0,isCohesive=True,normalCohesion=1e8, shearCohesion=1e8,label='cement')
walls = FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls')

O.materials.append(cement)
O.materials.append(walls)

walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
sp=pack.SpherePack()

x=[5.0,6.0005088055510125,6.807147320174279,7.200507128170075,7.399996645238125,7.604595185078019,7.809172757656196,8.008676252898724,8.20306373628217,8.41275033163219,9.005096442414814]
y=[0,9.972588799847912,20.08747541588565,29.9397121334748,39.93424666725376,50.065627529175956,59.78605006143409,70.0545568149891,80.04923113051282,89.9064999909142,100.0]

#### change the size units 
psdSizes=x
for i in range(0,len(x)):
    psdSizes[i]=x[i]*0.001

## change the unit to percentage
psdCumm=y
for i in range(0,len(y)):
    psdCumm[i]=y[i]*0.01

sp.makeCloud(mn,mx,psdSizes=psdSizes,psdCumm=psdCumm,distributeMass=True,seed=1)
sp.toSimulation(material='cement')

Gl1_Sphere.quality=3

triax=TriaxialStressController(
	maxMultiplier=1.+2e4/young,
	finalMaxMultiplier=1.+2e3/young,
	thickness = 0,
	stressMask = 7,
	internalCompaction=False,
)

newton=NewtonIntegrator(damping=damp)

O.engines=[
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Box_Sphere_ScGeom()],
		[Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(),Ip2_FrictMat_FrictMat_FrictPhys()],
		[Law2_ScGeom6D_CohFrictPhys_CohesionMoment(),Law2_ScGeom_FrictPhys_CundallStrack()]
	),
	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
	triax,
	TriaxialStateRecorder(iterPeriod=100,file='WallStresses'+key),
	newton
]
triax.goal1=triax.goal2=triax.goal3=-10000

while 1:
  O.run(1000, True)
  unb=unbalancedForce()
  print 'unbalanced force:',unb,' mean stress: ',triax.meanStress
  if unb<stabilityThreshold and abs(-10000-triax.meanStress)/10000<0.001:
    break

print "###      Isotropic state saved      ###"

import sys
while triax.porosity>targetPorosity:
	compFricDegree = 0.95*compFricDegree
	setContactFriction(radians(compFricDegree))
	print "\r compFrictionDegree: ",compFricDegree," porosity:",triax.porosity,
	sys.stdout.flush()
	O.run(500,1)

print "###    Compacted state saved      ###"

aabb=utils.aabbExtrema()
predX=(aabb[0][0]+aabb[1][0])/2
predY=(aabb[0][1]+aabb[1][1])/2
predR=min((aabb[1][0]-aabb[0][0])/2,(aabb[1][1]-aabb[0][1])/2)

pred=pack.inCylinder((predX,predY,0),(predX,predY,0.14),predR)

## erase Walls and spheres which is not in cylinder
def cylinderShape():
	for i in O.bodies:
		if not isinstance(i.shape,Sphere):
			O.bodies.erase(i.id)
		if isinstance(i.shape,Sphere):
				if not pred(i.state.pos, i.shape.radius):  # if sphere with c,r is in pred(cylinder), then add this sphere into bodies.
					O.bodies.erase(i.id)
cylinderShape()
########

Could you please help me with this problem?
Thanks,
Leonard

[1]https://github.com/yade/trunk/blob/master/examples/triax-tutorial/script-session1.py

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