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[Alireza Sadeghi <question694158@xxxxxxxxxxxxxxxxxxxxx>]

New question #694158 on Yade:
https://answers.launchpad.net/yade/+question/694158

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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