Small density sphere in micron size makes segment fault (core dumped)

Hello,

thanks for the code. I have tried the script for a while without any problem. Please provide more info:
- At which iteration the problem occur?
- is the SnapshotEngine and VTKRecorder needed to reproduce the problem? If no, please remove them to make the script a true MWE [1]
- please use a 'seed' parameter to sp.makeCloud

thanks
Jan

[1] https://yade-dem.org/wiki/Howtoask

Hi, Jan. Yes, you are right. I have tried the above code and no segment fault occurred. Then I add some lines which i thought were unimportant in the past and the problems happened at about 341300 iteration. As you suggested, i leave the snap and VTK code out. Also, to make the crash easy to happen, i amplify the density by a small factor as 1e3.
The following is the code,

from yade import geom,pack
import math
from yade import qt
import os

#os.system('rm -rf plt;mkdir ./plt/')
#os.system('rm -rf out;mkdir ./out/')

# PhysicalParameters
muS = 0.57735 # Friction coefficient (30 degree)
muLB = 0.0001 # Friction coefficient
muF = 0.17632 # Friction coefficient (10 degree)
FricAngleS = math.atan(muS)
FricAngleLB = math.atan(muLB)
FricAngleF = math.atan(muF)

### mass amplification factor ###
masscof = 1e3

# PhysicalParameters
matSph = CohFrictMat(
 density = 7990*masscof,
 young = 193e9,
 poisson = 0.3,
 frictionAngle = FricAngleS,
 momentRotationLaw = True)
SMat = O.materials.append(matSph)

# create empty sphere packing
sp = pack.SpherePack()
# generate spheres1 with a certain diameter distribution
sp.makeCloud((0,0,0.35e-3), (1.0e-3,1.0e-3,1.4e-3), psdSizes=[0.012e-3,0.0186e-3,0.0312e-3,0.0484e-3,0.053e-3], psdCumm=[0,0.1,0.5,0.9,1.0])
# add the sphere pack to the simulation
sp.toSimulation(material=SMat)

# create rectangular box1(Left) from facets
O.bodies.append(geom.facetBox((0.5e-3,0.5e-3,0.5e-3),(0.5e-3,0.5e-3,0.5e-3), wallMask=31, material=SMat))
Cylinder1IDs=O.bodies.append(geom.facetBox((0.5e-3,0.5e-3,0.15e-3),(0.5e-3,0.5e-3,0.2e-3), wallMask=63, color=(0,1,0), wire=False, material=SMat))

################## add these lines, problem happens #####################
################## add these lines, problem happens #####################

def changeValues():

# Standstill for stabilization
   if O.time < 0.2:
       O.engines = O.engines + [
               TranslationEngine(dead=False, translationAxis= [0,0,1], velocity=0.0, ids=Cylinder1IDs)
   ]
       # Vibrate Piston1
   elif 0.2 <= O.time < 0.4:
       O.engines = O.engines + [
               HarmonicMotionEngine(A=(0.0,0.0,1.5e-5), f=(0.0,0.0,3600/60.0), ids=Cylinder1IDs)
   ]
# Vibrate Stop
   elif 0.4 <= O.time < 0.5129:
       O.engines = O.engines + [
               HarmonicMotionEngine(A=(0.0,0.0,0.0), f=(0.0,0.0,0.0), ids=Cylinder1IDs)
   ]

   O.dt = 0.85*utils.PWaveTimeStep()

################## add these lines, problem happens #####################
################## add these lines, problem happens #####################

def print_ite():
    print("ite is %d" % O.iter)

O.engines=[
 ForceResetter(),
 InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),
 InteractionLoop(
       # handle sphere+sphere and facet+sphere collisions
         [Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Facet_Sphere_ScGeom6D()],
         [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys()],
          [Law2_ScGeom6D_CohFrictPhys_CohesionMoment()]
    ),
 NewtonIntegrator(damping=0.75, exactAsphericalRot=True, gravity=(0,0,-9.81)),
     PyRunner(iterPeriod=100,command='changeValues()'),
    PyRunner(iterPeriod=100,command='print_ite()'),
# qt.SnapshotEngine(fileBase="./plt/",iterPeriod=200,label='snapshot'),
# VTKRecorder(iterPeriod=200, recorders=['spheres','colors'], fileName='./out/'),
]

#show geometry:
qtr = qt.Renderer()
qtr.bgColor = [1,1,1]
qt.Controller()
v = qt.View()
#v.center()
v.axes=False
v.viewDir=Vector3(0,1,0)
v.eyePosition=Vector3(1.8e-3,-5.2e-3,1.0e-3)

O.run()

Sorry to add the ubuntu and yade version used.
The ubuntu is Ubuntu 18.04.1 LTS, and the yade is 2018.02b.
Much thanks.

Thanks. Jan. The adapted code runs well. I think the problem is the increasing length of O.engines.

Thanks Jan Stránský, that solved my question.