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[azim <1774926@xxxxxxxxxxxxxxxxxx>]

Public bug reported:

Dear all
I had a problem in [1] about updating len(O.bodies) after erasing some particles.
after erasing I summoned utils.porosity and triax.porosity to check te porosity.
the former was OK but the latter was negative and it is wrong (porosity<0).
that's beacause triax.porosity (triax.boxVolume-triax.particlesVolume/triax.boxVolume) doesn't consider the erasing process and uses the particlesVolume equalse to the beggining of the simulation. sp.dim() , sp.center() and sp.aabb() have the same behaviour.
I'm using ubuntu 14.0d LTS and yadedaily 2018.02b-12211bed66~trusty.
[1] https://answers.launchpad.net/yade/+question/669845

Thanks in advance.
Azim


Script:


# -*- coding: utf-8 -*-
from yade import pack
num_spheres=1000
compFricDegree = 30
targetPorosity = 0.43
finalFricDegree = 30
rate=-0.02
damp=0.2
stabilityThreshold=0.01
young=5e6
mn,mx=Vector3(0,0,0),Vector3(1,1,1)
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()

clumps=False
if clumps:
 volume = (mx[0]-mn[0])*(mx[1]-mn[1])*(mx[2]-mn[2])
 mean_rad = pow(0.09*volume/num_spheres,0.3333)
 c1=pack.SpherePack([((-0.2*mean_rad,0,0),0.5*mean_rad),((0.2*mean_rad,0,0),0.5*mean_rad)])
 sp.makeClumpCloud(mn,mx,[c1],periodic=False)
 sp.toSimulation(material='spheres')
 O.bodies.updateClumpProperties()
else:
 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])
triax=TriaxialStressController(
 maxMultiplier=1.0+2e4/young,
 finalMaxMultiplier=1.0+2e3/young,
 thickness = 0,
 stressMask = 7,
 internalCompaction=True,
)

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,
 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

triax.internalCompaction=False
for b in O.bodies:
 if b.id>5:
  if b.state.pos[0]<.5:
   O.bodies.erase(b.id)
   
for i in range(1,200):
     print "utils.porosity= ", porosity()
     print "TriaxialStressController.porosity= ", triax.porosity
     O.run(1,1)

** Affects: yade
     Importance: Undecided
         Status: New

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https://bugs.launchpad.net/bugs/1774926

Title:
  error in porosity after erasing bodies

Status in Yade:
  New

Bug description:
  Dear all
  I had a problem in [1] about updating len(O.bodies) after erasing some particles.
  after erasing I summoned utils.porosity and triax.porosity to check te porosity.
  the former was OK but the latter was negative and it is wrong (porosity<0).
  that's beacause triax.porosity (triax.boxVolume-triax.particlesVolume/triax.boxVolume) doesn't consider the erasing process and uses the particlesVolume equalse to the beggining of the simulation. sp.dim() , sp.center() and sp.aabb() have the same behaviour.
  I'm using ubuntu 14.0d LTS and yadedaily 2018.02b-12211bed66~trusty.
  [1] https://answers.launchpad.net/yade/+question/669845

  Thanks in advance.
  Azim

  
  Script:


  # -*- coding: utf-8 -*-
  from yade import pack
  num_spheres=1000
  compFricDegree = 30
  targetPorosity = 0.43
  finalFricDegree = 30
  rate=-0.02
  damp=0.2
  stabilityThreshold=0.01
  young=5e6
  mn,mx=Vector3(0,0,0),Vector3(1,1,1)
  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()

  clumps=False
  if clumps:
   volume = (mx[0]-mn[0])*(mx[1]-mn[1])*(mx[2]-mn[2])
   mean_rad = pow(0.09*volume/num_spheres,0.3333)
   c1=pack.SpherePack([((-0.2*mean_rad,0,0),0.5*mean_rad),((0.2*mean_rad,0,0),0.5*mean_rad)])
   sp.makeClumpCloud(mn,mx,[c1],periodic=False)
   sp.toSimulation(material='spheres')
   O.bodies.updateClumpProperties()
  else:
   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])
  triax=TriaxialStressController(
   maxMultiplier=1.0+2e4/young,
   finalMaxMultiplier=1.0+2e3/young,
   thickness = 0,
   stressMask = 7,
   internalCompaction=True,
  )

  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,
   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

  triax.internalCompaction=False
  for b in O.bodies:
   if b.id>5:
    if b.state.pos[0]<.5:
     O.bodies.erase(b.id)
     
  for i in range(1,200):
       print "utils.porosity= ", porosity()
       print "TriaxialStressController.porosity= ", triax.porosity
       O.run(1,1)

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