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[Son Pham Thai <question679445@xxxxxxxxxxxxxxxxxxxxx>]

Question #679445 on Yade changed:
https://answers.launchpad.net/yade/+question/679445

    Status: Needs information => Open

Son Pham Thai gave more information on the question:
Hi,

thanks for the response!

The new crash log I got is:

python: /usr/include/boost/smart_ptr/shared_ptr.hpp:646: typename
boost::detail::sp_dereference<T>::type boost::shared_ptr<T>::operator*()
const [with T = BodyContainer; typename
boost::detail::sp_dereference<T>::type = BodyContainer&]: Assertion `px
!= 0' failed.

SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-
FSueZ2/tmp-0'

GNU gdb (Ubuntu 7.7.1-0ubuntu5~14.04.3) 7.7.1


Copyright (C) 2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
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There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
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Type "show configuration" for configuration details.
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<http://www.gnu.org/software/gdb/bugs/>.
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Could not attach to process.  If your uid matches the uid of the target
process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
again as the root user.  For more details, see /etc/sysctl.d/10-ptrace.conf
/tmp/yade-FSueZ2/tmp-0:1: Error in sourced command file:
ptrace: Operation not permitted.
(gdb) 


To reproduce the above crash, pls try run these 2 following scripts (in
2 different terminals)

##########################
### --- Mini working scripts 1:   --- ###
##########################

# encoding: utf-8
### INPUT for Material ###
young0= 30e9
poisson0= 0.2
density0 = 2530
compFricDegree=15

### PARAMETERs of particle packing ###
mn=Vector3(0.,0.,0.)
mx=Vector3(.4e-2,.6e-2,.4e-2)
rMean0=4e-4
rRelFuzz0=5./100
porosity0=0.4
distributeMass0=True
seed0=1

### INPUT for mechanical loading ###
maxVel0=5e-7
confiningS= -2.725e5

### defining MATERIALs ###
O.materials.append(FrictMat(young=young0,poisson=poisson0,frictionAngle=radians(compFricDegree), density=density0, label='spheres'))
O.materials.append(FrictMat(young=young0,poisson=poisson0,frictionAngle=0,density=0,label='frictionlessWalls'))

### creating the boundary walls ###
walls=aabbWalls((mn,mx),thickness=0,material='frictionlessWalls')
wallIds=O.bodies.append(walls)

### generating spheres ###
sp=pack.SpherePack()
sp.makeCloud(minCorner=mn,maxCorner=mx,rMean=rMean0,rRelFuzz=rRelFuzz0,porosity=porosity0,distributeMass=distributeMass0,seed=seed0) # POLY
O.bodies.append([utils.sphere(center,rad,material='spheres') for center,rad in sp])

### mechanical loading #### To confer a solid-like nature to the packing

triax=TriaxialStressController(
 internalCompaction=True,
 goal1=confiningS,
 goal2=confiningS,
 goal3=confiningS,
 max_vel=maxVel0,
 label="triax"
)

triax.maxMultiplier=1.+5e-6
triax.finalMaxMultiplier=1.+1e-7

newton=NewtonIntegrator(damping=.4, gravity=(0.0,-9.81,0.0))

O.engines=[
 ForceResetter(),
 InsertionSortCollider([Bo1_Sphere_Aabb(label='aabb'),Bo1_Box_Aabb()]),
 InteractionLoop(
  [Ig2_Sphere_Sphere_ScGeom6D(label='Ig2ssGeom'),Ig2_Box_Sphere_ScGeom()],
  [Ip2_FrictMat_FrictMat_FrictPhys(),Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=True, label="cohesiveIp")],
  [Law2_ScGeom_FrictPhys_CundallStrack(),Law2_ScGeom6D_CohFrictPhys_CohesionMoment(
   useIncrementalForm=True, always_use_moment_law=False, label='cohesiveLaw')]
 ),
 GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.5),
 triax,
 newton
]

### --- 1st stage, particle growing while boundary walls are fixed --
###

NumDEMRun1=100000
while 1:

 O.run(NumDEMRun1,True)
 unb=unbalancedForce()

 if unb<0.01 and abs(triax.goal1-triax.meanStress)/abs(triax.goal1)<0.001:
  break

### --- 2nd stage, particle sizes are fixed while boundary walls move
very slowly -- ###

finalFricDegree = 30 # contact friction during the deviatoric loading
triax.internalCompaction=False
setContactFriction(radians(finalFricDegree))

NumDEMRun2=50000

while 1:

 O.run(NumDEMRun2 ,True)
 unb=unbalancedForce()

 if unb<0.001 and abs(triax.goal1-triax.meanStress)/abs(triax.goal1)<0.001:
  break

import os.path
initStateFilename="savedPacking" +".yade.gz"
savedState = os.path.exists(initStateFilename)
O.save(initStateFilename)

##########################
### --- Mini working scripts 2:   --- ###
##########################

# encoding: utf-8

import os.path
initStateFilename='savedPacking.yade.gz' 
O.load(initStateFilename)

compFricDegree = 1 
young0= 30e9
poisson0= 0.2
density0 = 2530
tensileStrength = 40e5
shearStrength = 40e6

### setup the material properties, first, Cohesion material
O.materials.append(CohFrictMat(young=young0,poisson=poisson0,density=density0,frictionAngle=radians(compFricDegree), normalCohesion=tensileStrength, shearCohesion=shearStrength, momentRotationLaw=True,label='CohFrictspheres'))

### --- change material of the spheres to create cohesive bond between
particles --- ###

pairs = [(i.id1,i.id2) for i in O.interactions]
for b in O.bodies:
 if not isinstance(b.shape,Box):
  b.mat = O.materials[2]
  ### [0] is Friction spheres, [1] is frictionlessWalls, [2] is the newly added CohFrict sphere

O.interactions.clear()
for id1,id2 in pairs: utils.createInteraction(id1,id2) ### The crash occurs here, detected by uncommenting line by line

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