yade-users team mailing list archive

[Luis Barbosa <question698313@xxxxxxxxxxxxxxxxxxxxx>]

New question #698313 on Yade:
https://answers.launchpad.net/yade/+question/698313

Dear all,

I am facing an error of segmentation fault with this script.
Not sure if it is hardware limitation or if it is related to tessellation issue, since this packing is very peculiar.

I have checked similar questions but couldn't find a way out.

Do you have an idea of size ration between particle diameter and aggregate diameter.

Cheers,


# encoding: utf-8
# This script demonstrates a simple case of drainage simulation using the "2PFV" two-phase model implemented in UnsaturatedEngine.
# The script was used to generate the result and supplementary material (video) of [1]. The only difference is the problem size (40k particles in the paper vs. 1k (default) in this version)
# [1] Yuan, C., & Chareyre, B. (2017). A pore-scale method for hydromechanical coupling in deformable granular media. Computer Methods in Applied Mechanics and Engineering, 318, 1066-1079. (http://www.sciencedirect.com/science/article/pii/S0045782516307216)
from yade import plot
from yade import ymport
from yade import bodiesHandling
from yade import export
from yade import utils

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

utils.readParamsFromTable(seed=1,compFricDegree = 10.0)
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=-1e6

## 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(0.004,0.0005,0.004)
mnn,mxx=Vector3(0,0,0),Vector3(0.006,0.006,0.006)
mnc,mxc=Vector3(0,0,0),Vector3(0.006,0.006,0.006)
#Coating
sp.makeCloud(minCorner=mn,maxCorner=mx,rMean=0.00005,seed=seed)
#Matrix
sp1.makeCloud(minCorner=mnn,maxCorner=mxx,rMean=0.0004,seed=seed)

O.materials.append(JCFpmMat(type=1,young=70e6,poisson=0.3,frictionAngle=radians(compFricDegree),density=2600,tensileStrength=100e6,cohesion=100e6,jointNormalStiffness=0,jointShearStiffness=0,jointCohesion=100e6,jointFrictionAngle=radians(0),jointDilationAngle=0.0,label='coating'))
O.materials.append(JCFpmMat(type=1,young=50e5,poisson=0.3,frictionAngle=radians(compFricDegree),density=2600,tensileStrength=100e5,cohesion=100e5,jointNormalStiffness=0,jointShearStiffness=0,jointCohesion=100e5,jointFrictionAngle=radians(0),jointDilationAngle=0.0,label='matrix'))
O.materials.append(JCFpmMat(type=1,young=50e5,poisson=0.3,frictionAngle=radians(0),density=2600,tensileStrength=0,cohesion=0,jointNormalStiffness=0,jointShearStiffness=0,jointCohesion=0,jointFrictionAngle=radians(0),jointDilationAngle=0.0,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='coating') for center,rad in sp])
#for center,rad in sp:
#	print (center,rad)
#O.bodies.append([utils.sphere(center,rad,material='matrix') for center,rad in sp1])
#O.bodies.append([utils.sphere(center,rad,material='spheres') for center,rad in sp2])

for p in sp1:
	a=p[0]
#	print (a)
	f1=O.bodies.append(ymport.textExt("aggcoating.txt", format='x_y_z_r', shift=a-Vector3(0,0,0.0004), scale=1.0,material='matrix',color=(0,1,1)))

triax=TriaxialStressController(
#	wall_back_activated=True,
#	wall_bottom_activated=True,
#	wall_front_activated=True,
#	wall_left_activated=True,
#	wall_right_activated=True,
#	wall_top_activated=True,
	internalCompaction=True,
	goal1=confiningS,
	goal2=confiningS,
	goal3=confiningS,
	max_vel=5,
	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_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=-1)],
		[Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=False)]
#		[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=2000,recorders=['all','cracks'],fileName="/home/user/Área de Trabalho/Paper_Biopore/SandBox_Laser/Video/Videotest"),
	newton
]

O.dt=0.08*PWaveTimeStep()
O.dynDt=False

while 1:
  O.run(1000,True)
  unb=unbalancedForce()
#  print(triax.meanStress)
  if unb<0.01 and abs(triax.goal1-triax.meanStress)/abs(triax.goal1)<0.01:
    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<0.01 and abs(triax.goal1-triax.meanStress)/abs(triax.goal1)<0.01:
    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=100,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]
#print(goalTop)
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 = 0.0728

#start invasion, the data of normalized pc-sw-strain will be written into pcSwStrain.txt
f1=open('Cells1.txt',"w")
f2=open('Cells2.txt',"w")
f3=open('Cells3.txt',"w")
f4=open('Cells4.txt',"w")
f5=open('SwPc.txt',"w")
for pg in arange(1.0e-5,2.5,0.1):
  #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/Paper_Biopore/SandBox_Laser/Video/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)
      celsBar1=unsat.getCellCenter(ii)
      f1.write(str(celsW1)+" "+str(celsV1)+" "+str(celsBar1)+"\n")
    f1.close()

  if pg==2.30001:
    cels2=unsat.nCells()
    celsW2 = [0.0]*cels2
    celsV2 = [0.0]*cels2
    celsBar2 = [0.0]*cels2
    for jj in range(cels2):
      celsW2=unsat.getCellIsWRes(jj)
      celsV2=unsat.getCellVolume(jj)
      celsBar2=unsat.getCellCenter(jj)
      f2.write(str(celsW2)+" "+str(celsV2)+" "+str(celsBar2)+"\n")
    f2.close()

  if pg==3.10001:
    cels3=unsat.nCells()
    celsW3 = [0.0]*cels3
    celsV3 = [0.0]*cels3
    celsBar3 = [0.0]*cels3
    for gg in range(cels3):
      celsW3=unsat.getCellIsWRes(gg)
      celsV3=unsat.getCellVolume(gg)
      celsBar3=unsat.getCellCenter(gg)
      f3.write(str(celsW3)+" "+str(celsV3)+" "+str(celsBar3)+"\n")
    f3.close()

  if pg==9.90001:
    cels4=unsat.nCells()
    celsW4 = [0.0]*cels4
    celsV4 = [0.0]*cels4
    celsBar4 = [0.0]*cels4
    for hh in range(cels4):
      celsW4=unsat.getCellIsWRes(hh)
      celsV4=unsat.getCellVolume(hh)
      celsBar4=unsat.getCellCenter(hh)
      f4.write(str(celsW4)+" "+str(celsV4)+" "+str(celsBar4)+"\n")
    f4.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()


-- 
You received this question notification because your team yade-users is
an answer contact for Yade.