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[Leonard <question685054@xxxxxxxxxxxxxxxxxxxxx>]

Question #685054 on Yade changed:
https://answers.launchpad.net/yade/+question/685054

Description changed to:
Hi,
I'm trying to generate a set of spheres which are arranged along a spherical surface based on Fibonacci algorithm (see MWE), these spheres generally have no physical contact with each other. However, after run one step (or more), some of them have interactions but there is no physical overlap for these balls. Here is the MWE, the problematic balls are shown in red color.
##################
from yade import pack, plot
import math
import numpy as np
import random
from random import gauss

numBalls=500
Gl1_Sphere.quality=3
O.engines=[
    ForceResetter(),
    InsertionSortCollider([Bo1_Sphere_Aabb()]),
    InteractionLoop(
        [Ig2_Sphere_Sphere_ScGeom()],
        [Ip2_FrictMat_FrictMat_FrictPhys()],
        [Law2_ScGeom_FrictPhys_CundallStrack()]
    ),
    NewtonIntegrator(damping=0.4),
]

rnd = random.random() * numBalls
offset = 2. / numBalls
increment = math.pi * (3. - math.sqrt(5.))
ballsList=[]
for i in range(numBalls):
    y = ((i * offset) - 1) + (offset / 2);
    r = math.sqrt(1 - pow(y, 2))

    phi = ((i + rnd) % numBalls) * increment

    x = math.cos(phi) * r
    z = math.sin(phi) * r
    Center =1.05 * np.array([x, y, z])
    ballsList.append(
        O.bodies.append(sphere((Center[0], Center[1], Center[2]), radius=0.05, color=[1, 1, 1])))

O.step()
OverlapBalls=set()
def findOverlapBalls():
    for i in ballsList:
        for j in ballsList:
            if i>=j:
                continue
            else:
                if O.interactions.has(i,j):
                    OverlapBalls.add(i)
findOverlapBalls()
print 'There are',len(OverlapBalls),'balls which have interactions'

def changeColor():
    for i in OverlapBalls:
        O.bodies[i].shape.color=[1,0,0]

changeColor()
###############
My Yade version is 2018.02b on Ubuntu 18.04.
So, why these balls with no contact but have interactions?

Thanks
Leonard

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