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[Bruno Chareyre <1009257@xxxxxxxxxxxxxxxxxx>]

Fixed in https://bugs.launchpad.net/yade/+bug/1009257
The clump part of the script still needs some tuning.

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https://bugs.launchpad.net/bugs/1009257

Title:
  Periodic triaxial test example in chapter 2 does not work

Status in Yet Another Dynamic Engine:
  Fix Released

Bug description:
  Hello,
  Periodic triaxial test examplein chapter 2 (Tutorial) does not work.

  ------------when I use yade 0.70 it gives the message as fllow:
  yade.plot: creating new line for kinetic
  yade.plot: creating new line for elastPotential
  yade.plot: creating new line for nonviscDamp
  yade.plot: creating new line for velGradWork
  yade.plot: creating new line for plastDissip
  FATAL /build/buildd/yade-0.70.0/core/ThreadRunner.cpp:31 run: Exception occured:
  Body #270 has velocity==NaN!

  ------------when I use yade 0.80 it gives the message as fllow:(Yade 0.80.0+1+9~precise1, from 2012-05-04
  )

  Yade [1]: FATAL /build/buildd/yade-stable-0.80.0+1+9~precise1/core/ThreadRunner.cpp:31 run: Exception occured:
  PeriTriaxController run on aperiodic simulation.
  yade.plot: creating new line for kinetic
  yade.plot: creating new line for nonviscDamp

  the scripts is in 2.6.6 Periodic triaxial test in yade document , for
  easy, list as fllowing:

  ----------------------------------begin
  # 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
  sp=pack.SpherePack()
  if 0:
     ## uniform distribution
     sp.makeCloud((0,0,0),(2,2,2),rMean=.1,rRelFuzz=.3,periodic=True)
  elif 0:
     ## per-fraction distribution
     ## passing: cummulative percentage
     sp.particleSD2(radii=[.09,.1,.2],passing=[40,80,100],periodic=True,numSph=1000)
  else:
     ## create packing from clumps
     # configuration of one clump
     c1=pack.SpherePack([((0,0,0),.1),((.15,0,0),.05),((0,.1,0),.05)])
     # 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)

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

  O.engines=[
     ForceResetter(),
     InsertionSortCollider([Bo1_Sphere_Aabb()]),
     InteractionLoop(
        [Ig2_Sphere_Sphere_L3Geom()],
        [Ip2_FrictMat_FrictMat_FrictPhys()],
        [Law2_L3Geom_FrictPhys_ElPerfPl()]
     ),
     NewtonIntegrator(damping=.6),
     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=(.1,.1,.1),
        # 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()'
     ),
     PyRunner(command='addPlotData()',iterPeriod=100),
  ]
  O.dt=.5*utils.PWaveTimeStep()

  def addPlotData():
     plot.addData(unbalanced=utils.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,-.3)
     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()

  -------------------------------------------------------end

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