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[Luc Scholtès <lscholtes63@xxxxxxxxx>]

"Also, my curves do not match yours exactly (they are close though),
why?"

-> Probably because I ran these with the option to delete the contact as
soon as it fails in shear (JCFPM.cpp line 249: option 2: delete contact
if in tension). That's not the issue here.

"is it possible that the interaction between two particles gets
"neverErased" (i.e. shearForce = normalForce = FnMax=FsMax = 0), but
then the particles later regain contact and "want" to interact
frictionally?"

-> As suggested Bruno, I tend to think so... My first guess was that it
is due to the interaction range: when the same particles come into
contact after failure, interaction range is different for erased contact
than for "neverErased" contact (the neverErased contacts keeps record of
the initial equilibrium distance which corresponds to the centre to
centre distance at t=0 while the erased one initializes it to the
default value which is the sum of the 2 radii). I tried to run the
simulation with the default interaction range (bonds created for strict
geometric contact) and the discrepancy tends to reduce (but it still
exists). I am working on the 2 sphere examples but I am also wondering:

Can we have 2 interactions (in the interaction container") which
concerns the same particles pair? For instance could we have, at the
same time, a "non erased / broken /frictional" and a "new / frictional"
interaction between the 2 same particles?

"What we really need is to keep interactions alive until a condition is
met. What about erasing (i.e. returning false) beyond a certain
distance?"

-> we need to keep record of the crack aperture for the computation of
the local permeability. Ideally, we need this during the whole duration
of the simulation.

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https://bugs.launchpad.net/bugs/1790167

Title:
  JCFPM: "neverErase" modifies the simulated behavior while it should
  not

Status in Yade:
  New

Bug description:
  I noticed that running the exact same simulation (with same initial
  packing) gives different behaviors (stress-strain response in, e.g., a
  compression test) when neverErase is True or False. Given the purpose
  of neverErase (keep record of broken contacts, primarily for DFNFlow),
  it should not. The difference can be more or less important depending
  on the situation but it always exists. I could not figure out the
  cause of this yet but it seems that it comes from the treatment of
  broken contacts (obviously).

  Here is a simulation (uniaxial compression) that illustrates the
  problem. Running the same script using the exact same sample (to make
  sure the error does not come from a difference in the packings used)
  with either neverErase=True or neverErase=False produces 2 stress-
  strain curves which deviate at some point during the simulation. I
  made sure that the error is only due to neverErase by running the same
  simulations several times. The curves obtained with neverErase=True
  are always identical, as the curves obtained with neverErase=False.
  For those who would be interested, I also attach a packing  and the
  python script to plot the curves (below the simulation script).

  
  ### yade script ###

  
  from yade import ymport, pack, plot                                 

  #### material definition
  def sphereMat(): return JCFpmMat(type=1,density=3000,young=1e9,poisson=0.2,tensileStrength=1e6,cohesion=10e6,frictionAngle=radians(30))

  ##### create the specimen
  #L=0.10
  #D=0.05
  #pred=pack.inCylinder((0,0,0),(0,0,L),D/2.)
  #O.bodies.append(pack.regularHexa(pred,radius=D/20.,gap=0.,material=sphereMat)) 
  #O.bodies.append(pack.randomDensePack(pred,radius=D/20.,rRelFuzz=0.4,spheresInCell=1000,memoizeDb='/tmp/gts-triax-packings.sqlite',returnSpherePack=False,color=(0.9,0.8,0.6),material=sphereMat))

  #### import the specimen
  O.bodies.append(ymport.text('121_3k.spheres',scale=1.,shift=Vector3(0,0,0),material=sphereMat))

  #### help define boundary conditions (see utils.uniaxialTestFeatures)
  bb=utils.uniaxialTestFeatures()
  negIds,posIds,longerAxis,crossSectionArea=bb['negIds'],bb['posIds'],bb['axis'],bb['area']

  ################# DEM loop + ENGINES DEFINED HERE

  O.engines=[
   ForceResetter(),
          InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=1.2,label='Saabb')]),
   InteractionLoop(
    [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=1.2,label='SSgeom')],
    [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1,label='interactionPhys')],
    [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(neverErase=False,label='interactionLaw')]
   ),
   UniaxialStrainer(strainRate=-0.01,axis=longerAxis,asymmetry=0,posIds=posIds,negIds=negIds,crossSectionArea=crossSectionArea,blockDisplacements=1,blockRotations=1,setSpeeds=0,stopStrain=0.1,dead=1,label='strainer'),
   GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=10,timestepSafetyCoefficient=0.8,defaultDt=utils.PWaveTimeStep()),
   NewtonIntegrator(damping=0.4,label='newton'),
   PyRunner(iterPeriod=int(100),initRun=True,command='recorder()',label='data'),
  ]

  ################# RECORDER DEFINED HERE

  def recorder():
      yade.plot.addData({'i':O.iter,
                         'eps':strainer.strain,
                         'sigma':strainer.avgStress,
                         'tc':interactionLaw.nbTensCracks,
                         'sc':interactionLaw.nbShearCracks,
                         'te':interactionLaw.totalTensCracksE,
                         'se':interactionLaw.totalShearCracksE,
                         'unbF':utils.unbalancedForce()})
      plot.saveDataTxt('compressionTest_1')

  ################# PREPROCESSING

  #### manage interaction detection factor during the first timestep and then set default interaction range
  O.step();
  ### initializes the interaction detection factor
  SSgeom.interactionDetectionFactor=-1.
  Saabb.aabbEnlargeFactor=-1.

  ################# SIMULATION REALLY STARTS HERE
  strainer.dead=0
  O.run(50000)


  ### python script ###

  
  # -*- coding: utf-8 -*-
  from pylab import *

  ### processing function
  def store(var,textFile):
      data=loadtxt(textFile,skiprows=1)
      it=[]
      e=[]
      s=[]
      tc=[]
      sc=[]
      uf=[]
      for i in range(0,len(data)):
        it.append(float(data[i,1]))
        e.append(-float(data[i,0]))
        s.append(-float(data[i,4]))
        tc.append(float(data[i,5]))
        sc.append(float(data[i,2]))
        uf.append(float(data[i,7]))
      var.append(it)
      var.append(e)
      var.append(s)
      var.append(tc)
      var.append(sc)
      var.append(uf)
     
  ### data input
  dataFile1='compressionTest'
  a1=[]
  store(a1,dataFile1)

  dataFile2='compressionTest_neverErase'
  a2=[]
  store(a2,dataFile2)

  rcParams.update({'legend.numpoints':1,'font.size':20,'axes.labelsize':28,'xtick.major.pad':10,'ytick.major.pad':10,'legend.fontsize':18})

  figure(1,figsize=(10,10))
  xlabel(r'$\epsilon_1$ [millistrain]')
  #axis(xmax=0.1)
  plot([x*1e3 for x in a1[1]],[x/1e6 for x in a1[2]],'-k',linewidth=2)
  plot([x*1e3 for x in a2[1]],[x/1e6 for x in a2[2]],'-r',linewidth=2)
  ylabel(r'$\sigma_1$ [MPa]')
  axis(ymin=0)
  #savefig(dataFile1+'_qVSeps.eps',dpi=1000,format='eps',transparent=False)

  ### show
  show()

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