New question #401525 on Yade:
https://answers.launchpad.net/yade/+question/401525

Hi guys,

I'm trying to model shear dilation in a granular system. I'd like to have 
periodic walls in x boundaries only. Boundaries in y and z directions are walls 
which apply strain or stress to material.
The problem is when I define periodicity as:

O.periodic=True
O.cell.refSize=(3,3,3)


This also affects the interaction of spheres with the walls. In particular, if 
you run the following script the first layer of the spheres will pass the upper 
and lower plates (for whatever the reason). But if we remove the periodicity, 
material get compacted as expected.
Periodic cell is big enough to not affect the plate interactions in z 
direction. So, what I'm missing here? 

Thank you


#=================================================================


from yade import pack,plot, qt

#-----------------------------materials---------------------------------

O.materials.append(CohFrictMat(normalCohesion= 1e4, shearCohesion= 1e4, 
isCohesive= True, young=4.0e9, 
density=1523.6, poisson=0.3, frictionAngle= 0.28, fragile=False, label='wall'))



O.materials.append(CohFrictMat(normalCohesion= 1e1, shearCohesion= 1e1, 
isCohesive= False, young=1.82e7, 
density=1523.6, poisson=0.3, frictionAngle= 0.28, fragile=True, label='agg'))


#-----------------------------packing-----------------------------------

O.periodic=True
O.cell.refSize=(3,3,3)


O.bodies.append(
      
pack.regularOrtho(pack.inAlignedBox((0.1,1,1),(2.9,2,2)),material='agg',radius=.05,gap=1e-5,color=(0,0,1)))


qtr=qt.Renderer()
qtr.bgColor=(1,1,1)


#-----------------------------engines-------------------------------------

O.engines=[
   ForceResetter(),
   
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()],allowBiggerThanPeriod=1),
   InteractionLoop(
      [Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Box_Sphere_ScGeom6D()],
      [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True, 
setCohesionOnNewContacts=True)],
      
[Law2_ScGeom6D_CohFrictPhys_CohesionMoment(),Law2_ScGeom_FrictPhys_CundallStrack()]
   ),
   NewtonIntegrator(damping=.4)]


O.dt=1e-5
#------------------------------------------------------------------------



box1 = 
O.bodies.append(box((1.5,1.5,1.9),(3.0,0.5,0.01),fixed=True,wire=False,material='wall'))
box2 = 
O.bodies.append(box((1.5,1.5,1.0),(3.0,0.5,0.01),fixed=True,wire=False,material='wall'))

box3 = 
O.bodies.append(box((1.5,0.95,1.5),(1.5,0.01,0.5),fixed=True,wire=False,material='wall'))
box4 = 
O.bodies.append(box((1.5,2.00,1.5),(1.5,0.01,0.5),fixed=True,wire=True,material='wall'))


O.bodies[box1].state.vel=(1,0,-1)
O.bodies[box2].state.vel=(-1,0,1)


 

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