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[Nicholas Ng <question677829@xxxxxxxxxxxxxxxxxxxxx>]

New question #677829 on Yade:
https://answers.launchpad.net/yade/+question/677829

Hi Yade developers & users,

I'm a beginner in Yade who just tried this DEM code about 1 month ago.  The version of Yade I installed is 2018.02b version.  I am currently trying to learn the python codes from tutorial example of "periodic triaxial test" obtained from Yade website.  However, when I try to run the script for periodic triaxial test tutorial example, the following error message pop up:

==================================================================================================
FATAL /build/yade-fDuCoe/yade-2018.02b/pkg/common/InsertionSortCollider.cpp:495 spatialOverlapPeri: Body #930 spans over half of the cell size 0.167286 (axis=2, see flag allowBiggerThanPeriod)


FATAL /build/yade-fDuCoe/yade-2018.02b/core/ThreadRunner.cpp:30 run: Exception occured: 
/build/yade-fDuCoe/yade-2018.02b/pkg/common/InsertionSortCollider.cpp: Body larger than half of the cell size encountered.
=====================================================================================================

I hope someone can advise me how to solve this problem.  


Thanks in advance,
Nicholas

***** the script for periodic triaxial test in tutorial example is as follow:
=============================================================================================

# encoding: utf-8

# periodic triaxial test simulation
#
# The initial packing is either
#
# 1. random cloud with uniform distribution, or
# 2. cloud with specified granulometry (radii and percentages), or
# 3. cloud of clumps, i.e. rigid aggregates of several particles
#
# The triaxial consists of 2 stages:
#
# 1. isotropic compaction, until sigmaIso is reached in all directions;
#    this stage is ended by calling compactionFinished() 
# 2. constant-strain deformation along the z-axis, while maintaining 
#    constant stress (sigmaIso) laterally; this stage is ended by calling
#    triaxFinished()
# 
# Controlling of strain and stresses is performed via PeriTriaxController,
# of which parameters determine type of control and also stability
# condition (maxUnbalanced) so that the packing is considered stabilized
# and the stage is done.
#

sigmaIso=-1e5

#import matplotlib
#matplotlib.use('Agg')

# generate loose packing
from yade import pack, qt, plot

O.periodic=True
sp=pack.SpherePack()
if 0:
   ## uniform distribution
   sp.makeCloud((0,0,0),(2,2,2),rMean=.1,rRelFuzz=.3,periodic=True)
else:
   ## create packing from clumps
   # configuration of one clump
   c1=pack.SpherePack([((0,0,0),.03333),((.03,0,0),.017),((0,.03,0),.017)])
   # make cloud using the configuration c1 (there could c2, c3, ...; selection between them would be random)
   sp.makeClumpCloud((0,0,0),(2,2,2),[c1],periodic=True,num=500)

# setup periodic boundary, insert the packing
sp.toSimulation()

O.engines=[
   ForceResetter(),
   InsertionSortCollider([Bo1_Sphere_Aabb()]),
   InteractionLoop(
      [Ig2_Sphere_Sphere_ScGeom()],
      [Ip2_FrictMat_FrictMat_FrictPhys()],
      [Law2_ScGeom_FrictPhys_CundallStrack()]
   ),
   PeriTriaxController(label='triax',
      # specify target values and whether they are strains or stresses
      goal=(sigmaIso,sigmaIso,sigmaIso),stressMask=7,
      # type of servo-control
      dynCell=True,maxStrainRate=(10,10,10),
      # wait until the unbalanced force goes below this value
      maxUnbalanced=.1,relStressTol=1e-3,
      # call this function when goal is reached and the packing is stable
      doneHook='compactionFinished()'
   ),
   NewtonIntegrator(damping=.2),
   PyRunner(command='addPlotData()',iterPeriod=100),
]
O.dt=.5*PWaveTimeStep()

def addPlotData():
   plot.addData(unbalanced=unbalancedForce(),i=O.iter,
      sxx=triax.stress[0],syy=triax.stress[1],szz=triax.stress[2],
      exx=triax.strain[0],eyy=triax.strain[1],ezz=triax.strain[2],
      # save all available energy data
      Etot=O.energy.total(),**O.energy
   )

# enable energy tracking in the code
O.trackEnergy=True

# define what to plot
plot.plots={'i':('unbalanced',),'i ':('sxx','syy','szz'),' i':('exx','eyy','ezz'),
   # energy plot
   ' i ':(O.energy.keys,None,'Etot'),
}
# show the plot
plot.plot()

def compactionFinished():
   # set the current cell configuration to be the reference one
   O.cell.trsf=Matrix3.Identity
   # change control type: keep constant confinement in x,y, 20% compression in z
   triax.goal=(sigmaIso,sigmaIso,-.2)
   triax.stressMask=3
   # allow faster deformation along x,y to better maintain stresses
   triax.maxStrainRate=(1.,1.,.1)
   # next time, call triaxFinished instead of compactionFinished
   triax.doneHook='triaxFinished()'
   # do not wait for stabilization before calling triaxFinished
   triax.maxUnbalanced=10

def triaxFinished():
   print 'Finished'
   O.pause()

========================================================================================



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