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. _______________________________________________ Mailing list: https://launchpad.net/~yade-users Post to : [email protected] Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
