Yade

Scene radius must be positive - Ignoring value

Asked by Leonard on 2019-09-05

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