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[Seti <question451417@xxxxxxxxxxxxxxxxxxxxx>]

New question #451417 on Yade:
https://answers.launchpad.net/yade/+question/451417

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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