Simple shear with oedometric loading

Hi, I am new to yade. plz help me removing the following error.

My problem description- It is basically a simple shear problem. Firstly isometric compression is done to prepare the sample by compacting. Periodic boundary conditions were used. Then a plate in the form of wall is applied at the top and normal loading is applied by velocity gradient tensor. After it reaches the defined value then shear is applied by distorting the cell. I know i am doing some mistake but unable to catch it up. please help me in finding the same. Script is attacted.

Error- python3.10: ./pkg/common/InsertionSortCollider.cpp:779: bool yade::InsertionSortCollider::spatialOverlapPeri(yade::Body::id_t, yade::Body::id_t, yade::Scene*, yade::Vector3i&) const: Assertion `maxima[3 * id2 + axis] - minima[3 * id2 + axis] < .99 * dim' failed.
Aborted (core dumped)

Script-

# setup the periodic boundary
from __future__ import print_function
O.periodic = True
O.cell.hSize = Matrix3(2, 0, 0, 0, 2, 0, 0, 0, 2)

# CREATION OF PARTICLES
from yade import pack, qt

#Define Material- E=7*e8, poisson=0.25, friction angle=31 degree(0.541 radians), density=2650kg/m^3
O.materials.append(FrictMat(young=7e8,poisson=.25,frictionAngle=.541, density=2650, label="soil"))

# create cloud of spheres and insert them into the simulation
# we give corners, mean radius, radius variation, material
sp = pack.SpherePack()
sp.makeCloud((0, 0, 0), (2, 2, 2), periodic=True, rMean=0.05, rRelFuzz=0.2, seed=10)
# insert the packing into the simulation
sp.toSimulation(material="soil")

# create "dense" packing by setting friction to zero initially
O.materials[0].frictionAngle = 0

# simulation loop (will be run at every step)
O.engines = [
        ForceResetter(),
        InsertionSortCollider([Bo1_Sphere_Aabb(), Bo1_Wall_Aabb()]),
        InteractionLoop(
                # interaction loop
                [Ig2_Sphere_Sphere_ScGeom(), Ig2_Wall_Sphere_ScGeom()],
                [Ip2_FrictMat_FrictMat_MindlinPhys()],
                [Law2_ScGeom_MindlinPhys_Mindlin()]
        ),
        NewtonIntegrator(damping=.4),
        PyRunner(command='checkStress()', iterPeriod=100, label='checker')
]
O.dt = .7 * PWaveTimeStep()

# prescribe isotropic normal deformation (constant strain rate)
O.cell.velGrad = Matrix3(-.1, 0, 0, 0, -.1, 0, 0, 0, -.1)
qt.View()

# when to stop the isotropic compression
limitMeanStress = -1000

#Regenerating the friction
O.materials[0].frictionAngle = .54

def checkStress():
 # stress tensor as the sum of normal and shear contributions
 # Matrix3.Zero is the intial value for sum(...)
 stress = getStress().trace()/3.
 print('Stress at', O.iter, '=', stress)
 # if mean stress is below (bigger in absolute value) limitMeanStress, start shearing
 if stress < limitMeanStress:
  O.bodies.append(wall(max([b.state.pos[2] + b.shape.radius for b in O.bodies if isinstance(b.shape, Sphere)]), axis=2, sense=-1))
  global plate
         plate = O.bodies[-1] # the last particles is the plate
  # plate moves downwards by giving velocity gradient
  plate.state.vel = (0, 0, -.1)
  checker.command='stopplate()'

#Apply oedometric compression by applying velocity over a plate/wall

def stopplate():
 force= O.forces.f(plate.id)[2]
 print('Force on plate=', force)
 # if the force on plate exceeds maximum load, start unloading
 if O.forces.f(plate.id)[2]> 1e5:
  plate.state.vel = (0, 0, 0)
  print('Plate stops and Distortion is applied at 0.1 strain rate')
  #Apply Distorsion
  O.cell.velGrad = Matrix3(0, 0, .1, 0, 0, 0, 0, 0, 0)
  checker.command = 'checkDistorsion()'

def checkDistorsion():
 # if the distorsion value is >.5, exit; otherwise do nothing
 if abs(O.cell.trsf[0, 2]) > .5:
  O.pause()
  print('Distortion of cell exceeds 0.5')

Gl1_Sphere.stripes = True
O.saveTmp()

NOTE: Error mainly comes after isometric compression

Thank you in advance.