Some particles pop out of facets

Thanks to Jean, I was able to come this far.

I am doing an analysis on a direct(simple) shear test.
I have created a program like below.

Why do "some" of the particles exit from the top of the facet when the plate is used to compress the particles?

Is there a solution to this problem?

##############################################
from __future__ import print_function
from yade import pack,plot,polyhedra_utils,geom
from yade import export,qt
from yade.gridpfacet import *
import math
import numpy as np
import os

###############################################
#parameter　(パラメーター　in japanese)
###############################################

frictangle = np.radians(25)#45do
density = 3400.0
young = 3e8
gravity = (0.0, 0.0, 0)
velocity_cyl=2.5
velocity_cyl_idsCyl2=2.5
velocity_cyl_Box=2.5

###############################################
#Create sphere (モデルの作成 in japanese)
###############################################

mat_sp = CohFrictMat(alphaKr=.2,alphaKtw=.2,young = young, poisson = 0.35,frictionAngle=(frictangle),density=density)
O.materials.append(mat_sp)

pred=pack.inCylinder(centerBottom=(0,0,0.0),centerTop=(0,0,.02),radius=.03)
sp0=pack.randomDensePack(pred,spheresInCell=3000,radius=0.0004)
O.bodies.append(sp0)

###############################################
#Boundary creation
###############################################

idsCyl1 = O.bodies.append(geom.facetCylinder((0, 0, 0.0075), radius=.03, height=.015, segmentsNumber=30, wallMask=6))

idsCyl2 = O.bodies.append(geom.facetCylinder((0, 0, 0.015), radius=.03, height=.01, segmentsNumber=30, wallMask=5))

#idsCyl3 = O.bodies.append(geom.facetCylinder((0, 0, .0225), radius=0.10, height=.005, segmentsNumber=100, wallMask=2))

radius1 = .03
radius2 = .15

fixBoxIds=[]
moveBoxIds=[]

upper_plate=box((0,0,-0.001),(0.06,0.06,0.001))
upper_plateID=O.bodies.append(upper_plate)
O.bodies[upper_plateID].state.blockedDOFs = 'xyXY' #xy:xyの方向角の固定、XY：XY変位の固定
upper_plate=box((0,0,-0.001),(0.06,0.06,0.001))
upper_plateID=O.bodies.append(upper_plate)
O.bodies[upper_plateID].state.blockedDOFs = 'xyXY' #xy:xyの方向角の固定、XY：XY変位の固定

#O.forces.addF(upper_plateID,(0,0,50e3),permanent=True)
O.forces.setPermF(upper_plateID,(0,0,100e3))

for i in range(0,365,5):
 r = math.radians(i)
 x1 = radius1 * math.cos(r)
 y1 = radius1 * math.sin(r)
 x2 = radius2 * math.cos(r-math.radians(5))
 y2 = radius2 * math.sin(r-math.radians(5))
 x3 = radius2 * math.cos(r+math.radians(5))
 y3 = radius2 * math.sin(r+math.radians(5))

 x4 = radius1 * math.cos(r-math.radians(5))
 y4 = radius1 * math.sin(r-math.radians(5))
 x5 = radius1 * math.cos(r+math.radians(5))
 y5 = radius1 * math.sin(r+math.radians(5))
 x6 = radius2 * math.cos(r)
 y6 = radius2 * math.sin(r)

 fixBoxIds.append(O.bodies.append(facet([(x1,y1,.015),(x2,y2,.015),(x3,y3,.015)])))
 fixBoxIds.append(O.bodies.append(facet([(x4,y4,.015),(x5,y5,.015),(x6,y6,.015)])))
 moveBoxIds.append(O.bodies.append(facet([(x1,y1,.015),(x2,y2,.015),(x3,y3,.015)])))
 moveBoxIds.append(O.bodies.append(facet([(x4,y4,.015),(x5,y5,.015),(x6,y6,.015)])))

###############################################
#engines　（制御　in japanese）
###############################################

O.engines = [
        ForceResetter(),
        InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),Bo1_Box_Aabb()]),
        InteractionLoop(
                # interaction loop
                [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
                [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys()],
                [Law2_ScGeom6D_CohFrictPhys_CohesionMoment(always_use_moment_law=True),Law2_ScGeom_FrictPhys_CundallStrack()]
        ),
        NewtonIntegrator(),
        ###TranslationEngine(translationAxis=[0,0,1],velocity=-1,ids=idsCyl3),
        ##TranslationEngine(translationAxis=[1,0,0],velocity=velocity_cyl_idsCyl2,ids=idsCyl2),
        ##TranslationEngine(translationAxis=[1,0,0],velocity=velocity_cyl_Box,ids=moveBoxIds),
        #TranslationEngine(ids=idsCyl2,label="translation"),
 #TranslationEngine(ids=moveBoxIds,label="translation2"),
        #PyRunner(iterPeriod=1,command="setTranslation()"),
        #PyRunner(iterPeriod=1,command="setTranslation2()"),
        PyRunner(command='checkStress()', iterPeriod=10),
        PyRunner(command='plotPlotData()',iterPeriod=1),
        #PyRunner(command='checkStressNO()', iterPeriod=10),
]

###############################################
#Definition of distortion
###############################################
def checkStress1():
 if O.bodies[idsCyl2[0]].state.displ()[0] > 0.015:
  O.pause()

def checkStress2():
 if O.bodies[idsCyl2[0]].state.displ()[0] > 0.015 and O.bodies[idsCyl2[0]].state.displ()[1] > 0 :
  O.pause()

###############################################
#Circle Control（円の制御 in japanese）
###############################################
def setTranslation():
    x = O.bodies[idsCyl2[0]].state.displ()[0]
    y = O.bodies[idsCyl2[0]].state.displ()[1]
    angle = atan2(y,x)
    a = Vector3(-sin(angle),cos(angle),0)
    v = 50
    translation.translationAxis = a
    translation.velocity = v

def setTranslation2():
    x = O.bodies[idsCyl2[0]].state.displ()[0]
    y = O.bodies[idsCyl2[0]].state.displ()[1]
    angle = atan2(y,x)
    a = Vector3(-sin(angle),cos(angle),0)
    v = 50
    translation2.translationAxis = a
    translation2.velocity = v

###############################################
#output（出力 in japanese）
###############################################

sp_num = len([b for b in O.bodies if isinstance(b.shape, Sphere)]) # 粒子の総数をカウント
print("number of spheres = ",sp_num)

def checkStress():
 cylDisplacement_x = O.bodies[idsCyl2[0]].state.displ()[0]
 cylDisplacement_y = O.bodies[idsCyl2[0]].state.displ()[1]
 print('{:1.04f}'.format(cylDisplacement_x)," ", '{:1.04f}'.format(cylDisplacement_y))

O.dt=0.5*PWaveTimeStep()
def plotPlotData():
 pipe_force_x = sum([O.forces.f(i)[0] for i in idsCyl2])
 pipe_force_y = sum([O.forces.f(i)[1] for i in idsCyl2])
 cylDisplacementx = O.bodies[idsCyl2[0]].state.displ()[0]
 cylDisplacementy = O.bodies[idsCyl2[0]].state.displ()[1]
 cylDisplacementz = O.bodies[idsCyl2[0]].state.displ()[2]
 Dz=upper_plate.state.displ()[2]
 plot.addData(
 i=O.iter,
 disp=O.time*velocity_cyl,
 force_x=pipe_force_x,
 force_y=pipe_force_y,
 Dz=Dz,
 cylDisplacementx=cylDisplacementx,
 cylDisplacementy=cylDisplacementy,
 cylDisplacementz=cylDisplacementz,
 )
 plot.saveDataTxt('pipe_force.out',vars=('disp','force_x','force_y',
      'Dz',
      'cylDisplacementx','cylDisplacementx','cylDisplacementx'
      ))

plot.plots={
 'disp':('force_x','force_y'),
 'i':('Dz'),
 'cylDisplacementx':('cylDisplacementy',)
 }
plot.plot()

#plot.saveDataTxt(O.tags['id'] + '.txt')