New question #681336 on Yade: https://answers.launchpad.net/yade/+question/681336
Hi YADE community, I want to generate a pore network by using regular triangulation method implemented in YADE. The following properties are given: 1. Radius and center coordinate of solid particle 2. Cylindrical wall (facet) 3. The material properties of the solid particle and cylindrical wall When I run initialization(), I got the error: python: /usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:408: Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, 1>::operator[](Eigen::Index) [with Derived = Eigen::Matrix<double, 3, 1>; Eigen::DenseCoeffsBase<Derived, 1>::Scalar = double; Eigen::Index = long int]: Assertion `index >= 0 && index < size()' failed. SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-sQh1QT/tmp-0' GNU gdb (Ubuntu 7.7.1-0ubuntu5~14.04.3) 7.7.1 Copyright (C) 2014 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-linux-gnu". Type "show configuration" for configuration details. For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>. Find the GDB manual and other documentation resources online at: <http://www.gnu.org/software/gdb/documentation/>. For help, type "help". Type "apropos word" to search for commands related to "word". Could not attach to process. If your uid matches the uid of the target process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try again as the root user. For more details, see /etc/sysctl.d/10-ptrace.conf /tmp/yade-sQh1QT/tmp-0:1: Error in sourced command file: ptrace: Operation not permitted. (gdb) quit Aborted (core dumped) # ------------------------------------------------------------ # A mini script to reproduce the above error: # ------------------------------------------------------------ # # encoding: utf-8 finalFricDegree = 30 damping0=0.4 young0= 30e9 poisson0= 0.2 density0 = 2530 tensileStrength = 40e5 shearStrength = 40e6 compFricDegree = 1 youngDrying= 30e9 poissonDrying= 0.2 densityDrying = 2530*1e3 surfaceTension= 0.07274 ##################################### ### setup the material properties ### ##################################### O.materials.append(CohFrictMat(young=young0,poisson=poisson0,density=density0,frictionAngle=radians(compFricDegree), normalCohesion=tensileStrength, shearCohesion=shearStrength, momentRotationLaw=True,label='CohSpheres')) O.materials.append(FrictMat(young=young0,poisson=poisson0,frictionAngle=0,density=0,label='frictionlessWalls')) O.materials.append(FrictMat(young=youngDrying,poisson=poissonDrying,frictionAngle=radians(finalFricDegree),density=densityDrying,label='frictionSphere')) ################################################## ### --- reloading the sphere and wall data --- ### ################################################## import numpy as np #-----------------------------------# ### the spheres ### of main network # #-----------------------------------# particleInMainNetworkRad= [ 0.000859884 , 0.000861149 , 0.000842029 , 0.00085647 ] particleInMainNetworkPos=[( 0.00317429 , 0.00550978 , 0.004819 ), ( 0.00531241 , 0.00159537 , 0.000953932 ), ( 0.00144734 , 0.00667752 , 0.00547688 ), ( 0.00521373 , 0.00203944 , 0.00291114 )] for i in range(len(particleInMainNetworkRad)): O.bodies.append([utils.sphere(center=particleInMainNetworkPos[i],radius=particleInMainNetworkRad[i],material='CohSpheres')]) #----------------------------------# ### the walls ### cylinder facet ### #----------------------------------# ### --- generate the cylindrical wall --- ### centerCylinder=(0.004095328, 0.0041199985, 0.0023) radiusCylinder=0.00418 heightCylinder=0.0085 segmentsNumberCylinder=5 # number of edges on the cylinder surface (>=5) oriCylinder=Quaternion((1,0,0),0) wallMaskCylinder=5 kwMeshes={'color':[1,0,0],'wire':True,'dynamic':False,'material':"frictionlessWalls"} # COLOR = red O.bodies.append(geom.facetCylinder(centerCylinder, radius=radiusCylinder, height=heightCylinder, orientation=oriCylinder, segmentsNumber=segmentsNumberCylinder, wallMask=wallMaskCylinder, **kwMeshes)) #---------------------# ### Engine setup ### # #---------------------# gravityVector = (0.0,0,-9.81) damping0=0.4 newton=NewtonIntegrator(damping=damping0, gravity=gravityVector) unsat=UnsaturatedEngine(dead=1,label="unsat") globals()['unsat'] = unsat O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Box_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys(),Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=True, label="cohesiveIp")], [Law2_ScGeom_FrictPhys_CundallStrack(),Law2_ScGeom6D_CohFrictPhys_CohesionMoment( useIncrementalForm=True, always_use_moment_law=False, label='cohesiveLaw')] ), GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=1,timestepSafetyCoefficient=0.5), newton, ] O.dt=.5*PWaveTimeStep() ################################ ## Drying simulation ### ################################ from numpy import * #set boundary conditions unsat.bndCondIsPressure=[0,0,0,1,0,0] unsat.bndCondValue=[0,0,0,0,0,0] unsat.isPhaseTrapped=True # the W-phase can be disconnected from its reservoir unsat.isInvadeBoundary=True # if False, the NW-phase can not invade the side pores unsat.drainageFirst=True ### "If true, activate drainage first (initial saturated), then imbibition; if false, activate imbibition first (initial unsaturated), then drainage. unsat.isDrainageActivated=True unsat.isImbibitionActivated=False unsat.computeForceActivated=True unsat.initialization() # Regular triangulation, pore network generation, and initializeReservoirs() (set pore saturation for boundingCells[2] as W-reservoir and boundingCells[3] as NW-reservoir ) # ----------------------------------------------------------------- # Looking forward to your help! Thanks and best regards, Son Pham -- 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 : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp