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[Bug 1663899] Re: etCohesionNow & setCohesionOnNewContacts /triaxial test

 

** Description changed:

  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.
+  "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
+  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
+  ## 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')
+  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
+  ## 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
+         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
+  #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.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)
+  ## 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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https://bugs.launchpad.net/bugs/1663899

Title:
  etCohesionNow & 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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References