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[Leonard <question683679@xxxxxxxxxxxxxxxxxxxxx>]

New question #683679 on Yade:
https://answers.launchpad.net/yade/+question/683679

Hello:
I'm trying to generate a cylinder sample with target porosity, the MWE comes from [1], after I run the MWE, I click "show 3D" then click "Reference" or "Center" to show the model in different direction, there will be:
In [1]: Scene radius must be positive - Ignoring value
With this notification, the scene moves strange when I adjust it through mouse.
My yade version is 2018.02b with Ubuntu 18.04, here is the MWE:
################
from yade import pack
num_spheres=1000
key='_triax_base_'
targetPorosity = 0.45
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)
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
sp=pack.SpherePack()
sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1)
O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp])
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_ScGeom(),Ig2_Box_Sphere_ScGeom()],
		[Ip2_FrictMat_FrictMat_FrictPhys()],
		[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):
					O.bodies.erase(i.id)
cylinderShape()
###############
Could you please help me with this problem?
Thanks in advance!
Leonard

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

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