Clumping positioning and bursting

I create clumping with total of 8 layers, but for layer 2, 4, 6, and 8 the x axis and y axis will be move by 0.002. It would result in rhombohedral shape. However, the sphere is suppose to be within the cylinder range and once I press start the sphere would directly burst. In addition, I have try to set color but it doesn't work.

### Here is my code ###

import random
import math
from yade import geom, pack, utils, plot, ymport, export
import numpy as np

# Define cylinder with funnel parameters
center = (0, 0, 0)
diameter = 0.102
height = 0.18

# create cylindrical body with radius 0.102 m and height 0.064 m
cylinder = geom.facetCylinder(center=center, radius=diameter/2, height=height, segmentsNumber=80, wallMask=6)

# add cylinder to simulation
O.bodies.append(cylinder)

# plate properties
clump_plate = CohFrictMat(density = 7500, label = 'clump_plate')

# add properties
O.materials.append(clump_plate)

bodyList = []
zi = 0.1
radius = 0.00221
clumpLimit = diameter - 0.005
num_layers = 8
z_offset_increment = 0.00128

for layer in range(num_layers):
    z_offset = layer * z_offset_increment # Adjust the z-coordinate based on the layer

    for xi in range(-50, 51, 4):
        xi = xi / 1000
        for yi in range(-50, 51, 4):
            yi = yi / 1000

        # Check if the sphere is within the clump limit
            if abs(xi) <= clumpLimit and abs(yi) <= clumpLimit:
                # Move spheres in layers 2, 4, 6, and 8 in x and y axes by 2mm
                if layer in [2, 4, 6, 8]:
                    xi += 0.002
                    yi += 0.002
                sphere_obj = sphere([xi, yi, zi + z_offset], radius)
                # Assign material properties to the sphere
                sphere_obj.material = clump_plate
                bodyList.append(O.bodies.append(sphere_obj))