particles partially in the wall

Hi John,
please provide a MWE. E.g., the used time step could affect this
thanks
Jan

Hello,
the used timestep is
  O.dt=.8*PWaveTimeStep()
and the initialization deletes all the particles that are initially partly or fully inside the walls

minimal working example follows

def run(name,boundaries,r,gap,numStepsPerIteration):

  facets = ymport.stl(name)

  rod1 = O.bodies.append(facets)

  # converts facets to gts (see the other question)

  s = gts.Surface()

  for facet in facets:

     vs = [facet.state.pos + facet.state.ori*v for v in facet.shape.vertices]

     vs = [gts.Vertex(v[0],v[1],v[2]) for v in vs]

     es = [gts.Edge(vs[i],vs[j]) for i,j in ((0,1),(1,2),(2,0))]

     f = gts.Face(es[0],es[1],es[2])

     s.add(f)

  print s.is_closed()

  threshold = 1e-3

  s.cleanup(threshold)

  print s.is_closed()

  assert s.is_closed()

  # use gts to filter spheres

  pred = inGtsSurface(s)

   sp=pack.regularHexa(pack.inAlignedBox((boundaries[0],boundaries[2],boundaries[4]),(boundaries[1],boundaries[3],boundaries[5])),radius=r,gap=gap)

  # remove spheres completely inside walls

  for b in sp:

     if pred(b.state.pos,0):

        continue

     O.bodies.append(b)

  # remove spheres partially inside walls

  O.dt = 0

  O.step() # interactions are created afterwards

  toErase = set()

  for i in O.interactions:

     b1,b2 = [O.bodies[i] for i in (i.id1,i.id2)]

     if any(isinstance(b.shape,Facet) for b in (b1,b2)): # if facet is involved, delete

        toErase.add(b1)

        toErase.add(b2)

  toErase = [b for b in toErase if isinstance(b.shape,Sphere)] # delete just spheres

  if not restart:

   for b in toErase: # delete the spheres

      O.bodies.erase(b.id)

  #generate the initial global index list

  for b in O.bodies:

      if isinstance(b.shape,Sphere):

   loc2glob.append(b.id)

  O.engines=[

     ForceResetter(),

     InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),

     InteractionLoop(

  # handle sphere+sphere and facet+sphere collisions

        [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()],

        [Ip2_FrictMat_FrictMat_FrictPhys()],

        [Law2_ScGeom_FrictPhys_CundallStrack()]

     ),

     NewtonIntegrator(gravity=(0,-9.81,0),damping=0.4, label='newtonInt'),

  ]

  O.dt=.8*PWaveTimeStep()

  O.step()

minimal working example follows

def run(name,boundaries,r,gap,numStepsPerIteration):

  facets = ymport.stl(name)

  rod1 = O.bodies.append(facets)

  # converts facets to gts (see the other question)

  s = gts.Surface()

  for facet in facets:

     vs = [facet.state.pos + facet.state.ori*v for v in facet.shape.vertices]

     vs = [gts.Vertex(v[0],v[1],v[2]) for v in vs]

     es = [gts.Edge(vs[i],vs[j]) for i,j in ((0,1),(1,2),(2,0))]

     f = gts.Face(es[0],es[1],es[2])

     s.add(f)

  print s.is_closed()

  threshold = 1e-3

  s.cleanup(threshold)

  print s.is_closed()

  assert s.is_closed()

  # use gts to filter spheres

  pred = inGtsSurface(s)

   sp=pack.regularHexa(pack.inAlignedBox((boundaries[0],boundaries[2],boundaries[4]),(boundaries[1],boundaries[3],boundaries[5])),radius=r,gap=gap)

  # remove spheres completely inside walls

  for b in sp:

     if pred(b.state.pos,0):

        continue

     O.bodies.append(b)

  # remove spheres partially inside walls

  O.dt = 0

  O.step() # interactions are created afterwards

  toErase = set()

  for i in O.interactions:

     b1,b2 = [O.bodies[i] for i in (i.id1,i.id2)]

     if any(isinstance(b.shape,Facet) for b in (b1,b2)): # if facet is involved, delete

        toErase.add(b1)

        toErase.add(b2)

  toErase = [b for b in toErase if isinstance(b.shape,Sphere)] # delete just spheres

  if not restart:

   for b in toErase: # delete the spheres

      O.bodies.erase(b.id)

  #generate the initial global index list

  for b in O.bodies:

      if isinstance(b.shape,Sphere):

   loc2glob.append(b.id)

  O.engines=[

     ForceResetter(),

     InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),

     InteractionLoop(

  # handle sphere+sphere and facet+sphere collisions

        [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()],

        [Ip2_FrictMat_FrictMat_FrictPhys()],

        [Law2_ScGeom_FrictPhys_CundallStrack()]

     ),

     NewtonIntegrator(gravity=(0,-9.81,0),damping=0.4, label='newtonInt'),

  ]

  O.dt=.8*PWaveTimeStep()

  O.step()

Please also provide the stl file
thanks
Jan

http://dropmefiles.com/zwMDt

But the issue appears almost randomly after some rotations.

thanks for the file. Now please make the example working :-D i.e. with what arguments do you call run(...)?
thx
Jan

boundaries = [-75.0, 75.4, -75.013, 75.387, 0.0, 15.200000000000001]

 Yadesimulation.run("maze1.stl",boundaries2,0,100)

So the problem is, this will propably not show the error. The thing that causes it ironically i dont have the right to give.
I was hoping more on a general method on how to extract particles from the wall the fastest with the least amount of unphysical behaviour possible for a general case

I appreciate the difficulty of the question and i really appreciate your help so far

Thanks for that, wall stiffness helped considerable
regards
John

Thanks Jan Stránský, that solved my question.