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[Luis Barbosa <question695873@xxxxxxxxxxxxxxxxxxxxx>]

Question #695873 on Yade changed:
https://answers.launchpad.net/yade/+question/695873

    Status: Answered => Open

Luis Barbosa is still having a problem:
Thank you all.
When I run the code [1], getCellBarycenter giving some strange values (coordinates totally outside my sample):

For instance, these values 125107.48 or -125097.48:
True 0.01797170859509369 Vector3(125107.4828372159245,1.62543863864436311,3.652322448466255977)
True 0.011656083836606964 Vector3(9.624066355278376506,1.530915196593882976,4.766563274628489388)
True 0.020528870575860336 Vector3(7.413446355544288657,-125097.4827497912484,7.885475000566313675)
True 0.01815466910920833 Vector3(125106.2605586981226,-125096.2810642897675,6.157849618659231083)

is it some mistake in the usage?

[1]
import matplotlib; matplotlib.rc('axes',grid=True)
from yade import pack
import pylab
from numpy import *

utils.readParamsFromTable(seed=1,compFricDegree = 15.0)
from yade.params import table

seed=table.seed
#num_spheres=table.num_spheres# number of spheres
compFricDegree = table.compFricDegree # initial contact friction during the confining phase (will be decreased during the REFD compaction process),num_spheres=1000
confiningS=-1e5

## creat a packing with a specific particle side distribution (PSD)
#psdSizes,psdCumm=[.599,0.6,0.849,0.85,1.0,1.40],[0.,0.35,0.35,0.70,.70,1.] psdSizes=psdSizes,psdCumm=psdCumm,distributeMass=True,
sp=pack.SpherePack()
sp1=pack.SpherePack()
mn,mx=Vector3(0,0,0),Vector3(10,2,10)
mnn,mxx=Vector3(0,2,0),Vector3(10,10,10)
mnc,mxc=Vector3(0,0,0),Vector3(10,10,10)
sp.makeCloud(minCorner=mn,maxCorner=mx,rMean=0.15,seed=seed)
sp1.makeCloud(minCorner=mnn,maxCorner=mxx,rMean=0.4,seed=seed)

## create material #0, which will be used as default
O.materials.append(FrictMat(young=15e7,poisson=.4,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
O.materials.append(FrictMat(young=15e7,poisson=.4,frictionAngle=radians(compFricDegree),density=2600,label='spheres1'))
O.materials.append(FrictMat(young=15e7,poisson=.4,frictionAngle=0,density=0,label='frictionless'))

## create walls around the packing
walls=aabbWalls((mnc,mxc),thickness=0,material='frictionless')
wallIds=O.bodies.append(walls)

O.bodies.append([utils.sphere(center,rad,material='spheres') for center,rad in sp])
O.bodies.append([utils.sphere(center,rad,material='spheres1') for center,rad in sp1])

triax=TriaxialStressController(
	internalCompaction=True,
	goal1=confiningS,
	goal2=confiningS,
	goal3=confiningS,
	max_vel=10,
	label="triax"
)

newton=NewtonIntegrator(damping=0.4)

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,
#	VTKRecorder(iterPeriod=100,recorders=['all'],fileName="/home/user/Área de Trabalho/PVF/vtk/Spheres"),
	newton
]

while 1:
  O.run(1000,True)
  unb=unbalancedForce()
  if unb<0.01 and abs(triax.goal1-triax.meanStress)/abs(triax.goal1)<0.001:
    break

#############################
##   REACH NEW EQU. STATE ###
#############################
finalFricDegree = 30 # contact friction during the 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))

while 1:
  O.run(1000,True)
  unb=unbalancedForce()
  if unb<0.001 and abs(triax.goal1-triax.meanStress)/abs(triax.goal1)<0.001:
    break  

triax.depth0=triax.depth
triax.height0=triax.height
triax.width0=triax.width
O.save('1kPacking.yade') #save the packing, which can be reloaded later.

O.run(1000,True)
ei0=-triax.strain[0];ei1=-triax.strain[1];ei2=-triax.strain[2]
si0=-triax.stress(0)[0];si1=-triax.stress(2)[1];si2=-triax.stress(4)[2]

from yade import plot
O.engines=O.engines+[PyRunner(iterPeriod=20,command='history()',dead=1,label='recorder')]

def history():
	plot.addData(e11=-triax.strain[0]-ei0, e22=-triax.strain[1]-ei1, e33=-triax.strain[2]-ei2,
		s11=-triax.stress(0)[0]-si0,
		s22=-triax.stress(2)[1]-si1,
		s33=-triax.stress(4)[2]-si2,
		pc=-unsat.bndCondValue[2],
		sw=unsat.getSaturation(False),
		i=O.iter
		)

plot.plots={'pc':('sw',None,'e22')}
plot.plot()

#######################################################
##     Drainage Test under oedometer conditions     ###
#######################################################
##oedometer conditions
triax.stressMask=2
triax.goal1=triax.goal3=0
goalTop=triax.stress(3)[1]
triax.goal2=goalTop
triax.wall_bottom_activated=0
recorder.dead=0

##Instantiate a two-phase engine
unsat=TwoPhaseFlowEngine()
meanDiameter=(O.bodies[-1].shape.radius + O.bodies[6].shape.radius) / 2.

##set boundary conditions, the drainage is controlled by decreasing W-phase pressure and keeping NW-phase pressure constant
unsat.bndCondIsPressure=[0,0,1,1,0,0]
unsat.bndCondValue=[0,0,-1e8,0,0,0]
unsat.isPhaseTrapped=True #the W-phase can be disconnected from its reservoir
unsat.initialization()
unsat.surfaceTension = 10

#start invasion, the data of normalized pc-sw-strain will be written into pcSwStrain.txt
f1=open('Cells1.txt',"w")
f5=open('SwPc.txt',"w")
for pg in arange(1.0e-5,15.0,0.1):
  #increase gaz pressure at the top boundary
  unsat.bndCondValue=[0,0,(-1.0)*pg*unsat.surfaceTension/meanDiameter,0,0,0]
  #compute the evolution of interfaces
  unsat.invasion()
  #save the phases distribution in vtk format, to be displayed by paraview
#  unsat.savePhaseVtk("/home/user/Área de Trabalho/PVF/vtk/Pressurefield")
  #compute and apply the capillary forces on each particle
  unsat.computeCapillaryForce()
  for b in O.bodies:
    O.forces.setPermF(b.id, unsat.fluidForce(b.id))

  if pg==0.60001:
    cels=unsat.nCells()
    celsW1 = [0.0]*cels
    celsV1 = [0.0]*cels
    celsBar1 = [0.0]*cels
    for ii in range(cels):
      celsW1=unsat.getCellIsWRes(ii)
      celsV1=unsat.getCellVolume(ii)
      celsBar1=unsat.getCellBarycenter(ii)
      f1.write(str(celsW1)+" "+str(celsV1)+" "+str(celsBar1)+"\n")
    f1.close()

  #reac
  while 1:
    O.run(1000,True)
    unb=unbalancedForce()
    if unb<0.001:
      break
  f5.write(str(pg)+" "+str(unsat.getSaturation(False))+" "+str(triax.strain[1]-ei1)+"\n")
f5.close()

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