Segmentation fault (core dumped) when I am using clump in Tiaxial test

Asked by Alireza Sadeghi

Hello,

I use Yadedaily on ubuntu 18 and 20. I want to simulate a triaxial test. When I use clump instead of spherical particles, I received this error:
Segmentation fault (core dumped)
I don't know how to fix it. I was wondering if you could help me. An example of my script is:

from yade import utils, plot
from yade import pack, qt
from datetime import datetime
import math
import pylab
import sys
from numpy import *

qtr=qt.Renderer()
qtr.bgColor=(1,1,1)

#==============================================================
#================= define the materials =======================
#==============================================================

O.materials.append(CohFrictMat(normalCohesion= 1e20, shearCohesion= 1e20, isCohesive= True, young=6.81e8, density=1377.5, poisson=0.3, frictionAngle= 0.31, fragile=False, label='aggregate-48'))

O.materials.append(CohFrictMat(normalCohesion= 1e20, shearCohesion= 1e20, isCohesive= False, young=2e11,
density=0, poisson=0.3, frictionAngle= 0, fragile=False, label='wall-frictionless'))

#===============================================================
#=================== define walls ============================
#===============================================================

walls=aabbWalls([(0,0,0),(4e-2,4e-2,4e-2)],thickness=0.001,oversizeFactor=1.5,material='wall-frictionless')
wallIds=O.bodies.append(walls)

#===============================================================
#===================clump shape=================================
#===============================================================

radz1=[0.355155e-3,0.505113e-3,0.397713e-3,0.465286e-3,0.484395e-3,0.394534e-3,0.493151e-3,0.487328e-3,0.613619e-3,0.413455e-3]
poz1= [[1.13418e-3,-0.703895e-3,-1.20338e-3],[-0.390408e-3,0.476061e-3,-0.150612e-3],[-0.556545e-3,0.451341e-3,1.1495e-3],[-0.633942e-3,0.498253e-3,0.348231e-3],[0.0256934e-3,0.388855e-3,-0.733445e-3],[-0.218563e-3,0.504478e-3,1.54117e-3],[-0.319601e-3,0.104778e-3,0.742895e-3],[0.650678e-3,-0.76675e-3,-0.289908e-3],[0.0113115e-3,-0.207684e-3,0.00255944e-3],[0.594902e-3,-0.301473e-3,-0.878654e-3]]
template1= []
template1.append(clumpTemplate(relRadii=radz1,relPositions=poz1))

#===============================================================
#=================== define packing ============================
#===============================================================

coke=((1.875e-3,100),(1.875e-3,100),(1.875e-3,100))

nums=['t','t','t']

temps=[template1,template1,template1]

mats=['aggregate-48','aggregate-48','aggregate-48']

tolerance=[(0.4752e-3),(0.4752e-3),(0.4752e-3)]

for i in range(len(nums)):
    nums[i]=pack.SpherePack()
    nums[i].makeCloud((0.005,0.005,0.005),(0.035,0.035,0.035),rMean=coke[i][0],rRelFuzz=tolerance[i],num=coke[i][1])
    O.bodies.append([utils.sphere(c,r,material=mats[i]) for c,r in nums[i]])
    O.bodies.replaceByClumps(temps[i],[1.0],discretization=5)

#===============================================================
#=================== define Engine =============================
#===============================================================

O.engines=[
 ForceResetter(),
 InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb(),Bo1_Facet_Aabb()]),
 InteractionLoop([Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Box_Sphere_ScGeom6D(),Ig2_Facet_Sphere_ScGeom6D()],
 [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys()],
 [Law2_ScGeom_FrictPhys_CundallStrack(),Law2_ScGeom6D_CohFrictPhys_CohesionMoment()]
 ),
 TriaxialStateRecorder(iterPeriod=10000,file='WallStresses'),
 NewtonIntegrator(damping=0.4,gravity=[0,0,-9.81]),
 PyRunner(iterPeriod=10000,command='addPlotData()'),
]

O.dt=5e-7

def addPlotData():
   plot.addData(exx=-triax.strain[0], eyy=-triax.strain[1], ezz=-triax.strain[2], ev=(triax.strain[0]+triax.strain[1]+triax.strain[2]), sxx=-triax.stress(triax.wall_right_id)[0], syy=-triax.stress(triax.wall_top_id)[1], szz=-triax.stress(triax.wall_front_id)[2], q=-(triax.stress(triax.wall_front_id)[2]-triax.stress(triax.wall_right_id)[0]), p=triax.meanStress, R=triax.stress(triax.wall_front_id)[2]/sigmaIso, por=triax.porosity, i=O.iter,**O.energy,total=O.energy.total()),

#=================================================================
#================= APPLYING CONFINING PRESSURE ================
#=================================================================
sigmaIso=-1e5
triax=TriaxialStressController(
 maxMultiplier=1.000,
 finalMaxMultiplier=1.000,
 thickness = 0,
 stressMask = 7,
 internalCompaction=False,
 max_vel=1,
)

O.engines=O.engines+[triax]

triax.goal1=sigmaIso
triax.goal2=sigmaIso
triax.goal3=sigmaIso
triax.wall_back_activated=True

while 1:
 O.run(100, True)
 unb=unbalancedForce()
 meanS=(triax.stress(triax.wall_right_id)[0]+triax.stress(triax.wall_top_id)[1]+triax.stress(triax.wall_front_id)[2])/3
 print('mean Stress:',triax.meanStress,'porosity:', triax.porosity,'Unbalancing:',unb)
 if triax.porosity<0.63 and abs(sigmaIso-triax.meanStress)/abs(sigmaIso)<0.01:
  print('Isotropic strain1:',-triax.strain[0], 'Isotropic strain 2:',-triax.strain[1], 'Isotropic strain 3:', -triax.strain[2])
  break
  print('### Isotropic state saved ###')

triax.depth0 = triax.depth
triax.height0 = triax.height
triax.width0 = triax.width
O.save('RVE3000-sizeDis3-solid-Iso5e4-Rate005-Isopart.yade')

#====================================================================
#===================== DEVIATORIC LOADING =======================
#====================================================================

triax.stressMask = 3
triax.goal1 = sigmaIso
triax.goal2 = sigmaIso
triax.goal3 = -0.05
triax.max_vel = 0.05

O.trackEnergy=True
O.saveTmp()

#====================================================================
#==================== Micro Strain ===========================
#====================================================================

TW=TesselationWrapper()
TW.triangulate()
TW.computeVolumes()
TW.volume(10)
TW.setState(0)
step=0
while 1:
 step +=1
 O.run(10000,True)
 print('Dev strain1:',-triax.strain[0], 'Dev strain 2:',-triax.strain[1], 'Dev strain 3:', -triax.strain[2])
 TW.setState(1)
 TW.defToVtk("strain_"+str(step)+".vtk")
 if abs(triax.strain[2]) > 0.5:
  print(O.iter)
  print('time is ', O.time)
  print('porosity:',triax.porosity)
  print('strain 1:',-triax.strain[0], 'strain 2:',-triax.strain[1], 'strain 3:',-triax.strain[2])
  O.save('RVE3000-sizeDis3-solid-Iso5e4-Rate005-Devpart.yade')
  plot.saveDataTxt('RVE3000-sizeDis3-solid-Iso5e4-Rate005-Devpart.txt')
  break
  O.pause()

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