the bugs in my scripts of layer sample pareparing code

Hi All:

Right now i am doing some simulation based on the following: (i am doing the same job as Nima Goudarzi mentioned)
As a part of a trixal test with my own implemented model in YADE, I need to compact my sample in the vertical direction to reach to a target void ratio. Dimensions of the sample are 3.5*3.5mm*7.1mm and it will be confined in six frictionless walls. The method of compaction is UCM and the sample will be compacted in 5 layers. As I am going to produce 100000 particles (based on a PSD), I may assume that each layer has 2000 spheres in it. Here is the sequence of compacting:
1- First layer is deposited and then compacted to a target void ratio of 0.73.
2- After depositing the second layer on top of the first layer, both layers will be compacted to reach a target void ratio of 0.71.
3- After depositing the third layer on top of the second layer, all three layers will be compacted to reach a target void ratio of 0.69.
4- After depositing the fourth layer on top of the third layer, all four layers will be compacted to reach a target void ratio of 0.67.
5- After depositing the fifth layer on top of the fourth layer, all five layers will be compacted to reach a target void ratio of 0.65.
This 0.65 is the target void ratio for the whole assembly.

the following is the code:

# -*- coding: utf-8 -*-
############################################
### DEFINING VARIABLES AND MATERIALS ###
############################################

# The following 5 lines will be used later for batch execution
nRead=readParamsFromTable(
 num_spheres=2000,# number of spheres
 compFricDegree = 30, # contact friction during the confining phase
 key='_triax_base_', # put simulation's name here
 unknownOk=True
)
############################################
from yade.params import table
a = [1,2,3,4,5]
b = [1]
c = [5]
psdSizes,psdCumm=[.1,.13,.16,.19,.22,.26,.31],[0.,0.01,0.05,0.25,.6,.92,1.]
for t in a:
 num_spheres=table.num_spheres*t# number of spheres
 key=table.key

 compFricDegree = table.compFricDegree # initial contact friction during the confining phase (will be decreased during the REFD compaction process)
 finalFricDegree = 30 # contact friction during the deviatoric loading
 rate=-0.02 # loading rate (strain rate)
 damp=0.7 # damping coefficient
 stabilityThreshold=0.01 # we test unbalancedForce against this value in different loops
 young=100000000 # contact stiffness

 mn,mx=Vector3(0,0,(7.1/5)*(t-1)),Vector3(3.5,3.5,(7.1/5)*t) # corners of the initial packing
 targetPorosity = (0.73-0.02*(t-1))/(1+0.73-0.02*(t-1)) #the porosity we want for the packing (just for testing)

 ## create materials for spheres and plates
 O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres')) #material for the spheres
 O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls')) #material for the wall

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

 while t > b:
  O.bodies.erase(4) #delect the rigid plate in the bottom

 ## use a SpherePack object to generate a random loose particles packing
 sp=pack.SpherePack()
 sp.makeCloud(mn,mx,-1,num_spheres,psdSizes=psdSizes,psdCumm=psdCumm)

 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.

 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.
 ## 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)

 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()]
 ),

 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()

 ####################################################
 ### APPLYING Z direction PRESSURE for porosity ##
 ####################################################

 #the value of (isotropic) confining stress defines the target stress to be applied in Z directions
 triax.goal2=-50000
 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(-50000/3-triax.meanStress)/(50000/3)<0.001:
    break

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

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

 ### We will reach a prescribed value of porosity with the REFD algorithm

 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 = 0.85*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)

 while t < c:
 O.bodies.erase(5) #delect the wall in the positive direction of Z
 O.save('compactedState'+key+'.yade.gz')
 print (targetPorosity)
 print "### Compacted state saved ###"

O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp])

#########################################################
### APPLYING CONFINING PRESSURE for triaxial test ####
#########################################################

#the value of (isotropic) confining stress defines the target stress to be applied in all three directions
triax.goal1=triax.goal2=triax.goal3=-5000

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(-5000-triax.meanStress)/5000<0.001:
    break
O.save('confinedState'+key+'.yade.gz')
print "### Isotropic 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 #mask = x*1 + y*2 + z*4, when x and z, 101
##now goal2 is the target strain rate
triax.goal2=rate
## we define the lateral stresses during the test, here the same 50kPa as for the initial confinement.
triax.goal1=-50000
triax.goal3=-50000

##we can change damping here.
newton.damping=0.7

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

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

### 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],

      sinPhi=(-triax.stress(triax.wall_right_id)[0]+triax.stress(triax.wall_front_id)[2])/(-triax.stress(triax.wall_right_id)[0]-triax.stress(triax.wall_front_id)[2]),

      #deviatoric=s11-s33,

      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')

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')}

#plot.plots={'i':('s11','s22','s33'),'i':('e11','e22','e33')}
#plot.plots={'e22':('(s11-s33)/(s11+s33)',),}
plot.plots={'e22':('sinPhi',),}

### the traditional triaxial curves would be more like this:

##plot.plots={'e22':('s11','s22','s33',None,'ev')}

## 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('results'+key)

##or even generate a script for gnuplot. Open another terminal and type "gnuplot plotScriptKEY.gnuplot:

plot.saveGnuplot('plotScript'+key)

The major problem is when the code finished the first loop, it will stop at the part of reaching target porosity. The following simulation cannot go through. However, i cannot find the reason. if anyone can point out the bug part, please reply me! Thank you so much and sorry for taking your time!

Regards,
Ting