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[Bruno Chareyre <1663899@xxxxxxxxxxxxxxxxxx>]

Hi, I realize that there are plenty differences between your script and the example script, depsite your statement that it is similar to the original.
Please be more accurate on which change caused the crash, and provide us with a way to pinpoint it (e.g. triggering the crash or not by changing just one line).
Bruno

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https://bugs.launchpad.net/bugs/1663899

Title:
  SetCohesionNow & setCohesionOnNewContacts /triaxial test

Status in Yade:
  New

Bug description:
  Hello all,

  can I turn on setCohesionNow, setCohesionOnNewContacts in triaxial
  test as well? if yes, why I set these parameters the porosity &
  friction does not change and I face with below error? while without
  these consideration code works.

   "Friction: 33.25 porosity: 1.0python: malloc.c:3720: _int_malloc: Assertion `(unsigned long) (size) >= (unsigned long) (nb)' failed.
  Aborted (core dumped)"

  the triaxial script is not different from the original one, I just
  copy it here if you need to know about the inputs.

  Thanks,
  Seti

  from yade import pack,plot

  ############################################
  ### DEFINING VARIABLES AND MATERIALS ###
  ############################################

  # The following 5 lines will be used later for batch execution
  nRead=readParamsFromTable(
   num_spheres=1000,# number of spheres
   compFricDegree =35, # contact friction during the confining phase
   key='_triax_base_', # put you simulation's name here
   unknownOk=True
  )
  from yade.params import table

  num_spheres=table.num_spheres# number of spheres
  key=table.key
  targetPorosity = 0.42 #the porosity we want for the packing
  compFricDegree = table.compFricDegree # initial contact friction during the confining phase (will be decreased during the REFD compaction process)
  finalFricDegree = 35# contact friction during the deviatoric loading
  rate=-0.005 # loading rate (strain rate)
  damp=0.3 # damping coefficient
  stabilityThreshold=0.01 # we test unbalancedForce against this value in different loops (see below)
  young=100e6# contact stiffness
  mn,mx=Vector3(0,0,0),Vector3(0.09,0.18,0.09) # corners of the initial packing

  ## create materials for spheres and plates
  O.materials.append(CohFrictMat(alphaKr=0.5,young=young,poisson=0.09,frictionAngle=radians(33.5),normalCohesion=7.5e3,shearCohesion=2.25e3,momentRotationLaw=True,etaRoll=0.001,density=2600,isCohesive=True,label='spheres'))
  O.materials.append(CohFrictMat(young=young,poisson=0,frictionAngle=radians(0),density=0,label='walls'))

  ## create walls around the packing
  walls=aabbWalls([mn,mx],thickness=0,material='walls')
  wallIds=O.bodies.append(walls)

  ## use a SpherePack object to generate a random loose particles packing
  sp=pack.SpherePack()

  clumps=False #turn this true for the same example with clumps
  if clumps:
   ## approximate mean rad of the futur dense packing for latter use
   volume = (mx[0]-mn[0])*(mx[1]-mn[1])*(mx[2]-mn[2])
   mean_rad = pow(0.09*volume/num_spheres,0.3333)
   ## define a unique clump type (we could have many, see clumpCloud documentation)
   c1=pack.SpherePack([((-0.2*mean_rad,0,0),0.5*mean_rad),((0.2*mean_rad,0,0),0.5*mean_rad)])
   ## generate positions and input them in the simulation
   sp.makeClumpCloud(mn,mx,[c1],periodic=False)
   sp.toSimulation(material='spheres')
   O.bodies.updateClumpProperties()#get more accurate clump masses/volumes/inertia
  else:
   sp.makeCloud(mn,mx,-1,0,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same
   #sp.makeCloud(mn,mx,0.066,num_spheres) #"seed" make the "random" generation always the same
   O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp])
   #or alternatively (higher level function doing exactly the same):
   #sp.toSimulation(material='spheres')

  ############################
  ### DEFINING ENGINES ###
  ############################

  triax=TriaxialStressController(
   ## TriaxialStressController will be used to control stress and strain. It controls particles size and plates positions.
   ## this control of boundary conditions was used for instance in http://dx.doi.org/10.1016/j.ijengsci.2008.07.002
   maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
   finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
   thickness = 0,
   ## switch stress/strain control using a bitmask. What is a bitmask, huh?!
   ## Say x=1 if stess is controlled on x, else x=0. Same for for y and z, which are 1 or 0.
   ## Then an integer uniquely defining the combination of all these tests is: mask = x*1 + y*2 + z*4
   ## to put it differently, the mask is the integer whose binary representation is xyz, i.e.
   ## "100" (1) means "x", "110" (3) means "x and y", "111" (7) means "x and y and z", etc.
   stressMask = 7,
   internalCompaction=True, # If true the confining pressure is generated by growing particles
  )

  newton=NewtonIntegrator(damping=damp)
  ########################################
  #Modified engine
  ##################################
  O.engines=[
          ForceResetter(),
          InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
          InteractionLoop(
                  [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
                  [Ip2_FrictMat_FrictMat_FrictPhys (),Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow = True, setCohesionOnNewContacts = True,label="cohesiveIp")],
                  [Law2_ScGeom_FrictPhys_CundallStrack(),Law2_ScGeom_CohFrictPhys_CohesionMoment(
     useIncrementalForm=True, #useIncrementalForm is turned on as we want plasticity on the contact moments
     always_use_moment_law=False, #if we want "rolling" friction even if the contact is not cohesive (or cohesion is broken), we will have to turn this true somewhere
     label='cohesiveLaw')]
          ),
          ## We will use the global stiffness of each body to determine an optimal timestep (see https://yade-dem.org/w/images/1/1b/Chareyre&Villard2005_licensed.pdf)
          GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
          triax,
          TriaxialStateRecorder(iterPeriod=100,file='150,damp0.8,rate 0.005,NEW50,alphaKr=0.5,young=100e6,poisson=0.09,frictionAngle=radians(50),normalCohesion=7.5e10,shearCohesion=2.25e10,etaRoll=0.025,density=2600,wall35,'+key),
          newton
  ]
  ##########################################################
  #O.engines=[
   #ForceResetter(),
   #InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
   #InteractionLoop(
    #[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
    #[Ip2_FrictMat_FrictMat_FrictPhys()],
    #[Law2_ScGeom_FrictPhys_CundallStrack()]
   #),
   ## We will use the global stiffness of each body to determine an optimal timestep (see https://yade-dem.org/w/images/1/1b/Chareyre&Villard2005_licensed.pdf)
   #GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
   #triax,
   #TriaxialStateRecorder(iterPeriod=100,file='WallStresses'+table.key),
   #newton
  #]
  #############################
  #Display spheres with 2 colors for seeing rotations better
  Gl1_Sphere.stripes=0
  if nRead==0: yade.qt.Controller(), yade.qt.View()

  ## UNCOMMENT THE FOLLOWING SECTIONS ONE BY ONE
  ## DEPENDING ON YOUR EDITOR, IT COULD BE DONE
  ## BY SELECTING THE CODE BLOCKS BETWEEN THE SUBTITLES
  ## AND PRESSING CTRL+SHIFT+D
  #if nRead==0: yade.qt.Controller(), yade.qt.View()
  print 'Number of elements: ', len(O.bodies)
  print 'Box Volume: ', triax.boxVolume
  #######################################
  ### APPLYING CONFINING PRESSURE ###
  #######################################

  #the value of (isotropic) confining stress defines the target stress to be applied in all three directions
  triax.goal1=triax.goal2=triax.goal3=-150000

  #while 1:
    #O.run(1000, True)
    ##the global unbalanced force on dynamic bodies, thus excluding boundaries, which are not at equilibrium
    #unb=unbalancedForce()
    #print 'unbalanced force:',unb,' mean stress: ',triax.meanStress
    #if unb<stabilityThreshold and abs(-10000-triax.meanStress)/10000<0.001:
      #break

  #O.save('confinedState'+key+'.yade.gz')
  #print "### Isotropic state saved ###"

  ###################################################
  ### REACHING A SPECIFIED POROSITY PRECISELY ###
  ###################################################

  ### We will reach a prescribed value of porosity with the REFD algorithm
  ### (see http://dx.doi.org/10.2516/ogst/2012032 and
  ### http://www.geosyntheticssociety.org/Resources/Archive/GI/src/V9I2/GI-V9-N2-Paper1.pdf)

  import sys #this is only for the flush() below
  while triax.porosity>targetPorosity:
   ## we decrease friction value and apply it to all the bodies and contacts
   compFricDegree = 0.95*compFricDegree
   setContactFriction(radians(compFricDegree))
   print "\r Friction: ",compFricDegree," porosity:",triax.porosity,
   sys.stdout.flush()
   ## while we run steps, triax will tend to grow particles as the packing
   ## keeps shrinking as a consequence of decreasing friction. Consequently
   ## porosity will decrease
   O.run(500,1)

  O.save('compactedStateBEL20,young=63.9e8'+key+'.yade.gz')
  print "### Compacted state saved ###"

  ##############################
  ### DEVIATORIC LOADING ###
  ##############################

  ##We move to deviatoric loading, let us turn internal compaction off to keep particles sizes constant
  triax.internalCompaction=False

  ## Change contact friction (remember that decreasing it would generate instantaneous instabilities)
  setContactFriction(radians(finalFricDegree))

  ##set stress control on x and z, we will impose strain rate on y
  triax.stressMask = 5
  ##now goal2 is the target strain rate
  triax.goal2=rate
  ## we define the lateral stresses during the test, here the same 10kPa as for the initial confinement.
  triax.goal1=-150000
  triax.goal3=-150000

  ##we can change damping here. What is the effect in your opinion?
  newton.damping=0.1

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