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[Son Pham Thai <question681336@xxxxxxxxxxxxxxxxxxxxx>]

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


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