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[SayedHessam <question676382@xxxxxxxxxxxxxxxxxxxxx>]

Question #676382 on Yade changed:
https://answers.launchpad.net/yade/+question/676382

SayedHessam posted a new comment:
Dear Bruno,

I tried to run a triaxial simulation based on the JCFpmMat with a simple
script but still is not working properly.

Please find here in my script:


from yade import pack,plot
from yade import export, ymport
import random
from yade import utils
import numpy as np

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

# The following 5 lines will be used later for batch execution
nRead=readParamsFromTable(
 num_spheres=1000,# number of spheres
 compFricDegree =30, # contact friction during the confining phase
 key='_TriaxJ2_', # 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 = 0.5 #the porosity we want for the packing
frictionAngle = 30# contact friction during the deviatoric loading
finalFricDegree = 30
rate=-0.02 # loading rate (strain rate)
damp=0.1 # Newton damping 
stabilityThreshold=0.01 # we test unbalancedForce against this value in different loops (see below)
iterper=1000
young=4.5e5# contact stiffness
poisson=0.25
cohesion=20e6
tensileStrength = 7e6
density = 1950
intRadius= 1


mn,mx=Vector3(0,0,0),Vector3(.1,.1,.1) # corners of the initial packing


O.materials.append(JCFpmMat(young=young, cohesion=cohesion,
density=density, frictionAngle=radians(frictionAngle),
tensileStrength=tensileStrength, poisson=poisson,label='spheres'))

#frictionless walls
O.materials.append(FrictMat(young=80e9,poisson=.45,frictionAngle=radians(frictionAngle),density=7000,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()


###########################
## 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,
 stressMask = 7,
 internalCompaction=False, # If true the confining pressure is generated by growing particles
)

newton=NewtonIntegrator(damping=damp, gravity=[0,0,0])
########################################
#Modified engine
##################################
O.engines=[
        ForceResetter(),
        InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=intRadius),Bo1_Box_Aabb()]),
        InteractionLoop(
                [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intRadius),Ig2_Box_Sphere_ScGeom()],
                [Ip2_FrictMat_FrictMat_FrictPhys(),Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1, label='jcf')],
  #[Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,label="cohesiveIp")],
                [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=True,label='interactionLaw', recordCracks=True),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=True, #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=0.05),
        triax,
		#VTKRecorder(iterPeriod=100,initRun=True,fileName='VTKFiles/'+'-',recorders=['all']),
        TriaxialStateRecorder(iterPeriod=100,file='Wall stress,'+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

###################################################
### 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)


while triax.porosity>targetPorosity:
 ## we decrease friction value and apply it to all the bodies and contacts
 frictionAngle = 0.95*frictionAngle
 setContactFriction(radians(frictionAngle))
 print "\r Friction: ",frictionAngle," 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('compactedStateJ2'+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

###########
##############

##Save temporary state in live memory. This state will be reloaded from the interface with the "reload" button.
O.saveTmp()

#####################################################
### Example of how to record and plot data ###
#####################################################

#from yade import plot

### a function saving variables
def history():
   plot.addData(e11=-triax.strain[0], e22=-triax.strain[1], e33=-triax.strain[2],
        ev=-triax.strain[0]-triax.strain[1]-triax.strain[2],
      s11=-triax.stress(triax.wall_right_id)[0],
      s22=-triax.stress(triax.wall_top_id)[1],
      s33=-triax.stress(triax.wall_front_id)[2],
      i=O.iter)

if 1:
  ## include a periodic engine calling that function in the simulation loop
  O.engines=O.engines[0:5]+[PyRunner(iterPeriod=20,command='history()',label='recorder')]+O.engines[5:7]
  ##O.engines.insert(4,PyRunner(iterPeriod=20,command='history()',label='recorder'))
else:
  ## With the line above, we are recording some variables twice. We could in fact replace the previous
  ## TriaxialRecorder
  ## by our periodic engine. Uncomment the following line:
  O.engines[4]=PyRunner(iterPeriod=20,command='history()',label='recorder')

  #NOTE, that after replacing some overlaps may occur.
#So after replacing calm() function may be helpful:
#if 0:
	#print '\nPlease wait a minute ...\n'
	#O.engines=O.engines+[PyRunner(iterPeriod=10000,command='calm()',label='calmRunner')]
	#O.run(1000000,True)
	#calmRunner.dead=True
	
O.run(100,True)

### declare what is to plot. "None" is for separating y and y2 axis
#plot.plots={'i':('e11','e22','e33',None,'s11','s22','s33')}
### the traditional triaxial curves would be more like this:
#plot.plots={'e22':('s11','s22','s33',None,'ev')}
plot.plots={'e22':('s11','s22')}

## display on the screen (doesn't work on VMware image it seems)
plot.plot()

##### PLAY THE SIMULATION HERE WITH "PLAY" BUTTON OR WITH THE COMMAND
O.run(N) #####

## In that case we can still save the data to a text file at the the end of the simulation, with:
plot.saveDataTxt('resultsJ2'+key)
##or even generate a script for gnuplot. Open another terminal and type "gnuplot plotScriptKEY.gnuplot:
plot.saveGnuplot('plotScriptJ2'+key)
rr=yade.qt.Renderer()
rr.shape=True
rr.intrPhys=False


Regards
Hessam

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