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[enki <question701731@xxxxxxxxxxxxxxxxxxxxx>]

Question #701731 on Yade changed:
https://answers.launchpad.net/yade/+question/701731

Description changed to:
Hi all,

I'm working on my cylinder particle case, however, when I start running
my script below, the cylinder particles are segmented and the whole
cylinder particle extends over time. I do not know why...

Additionally, the script points out a ValueError: cannot convert float
Nan to integer

After I create the walls via aabbWalls(), only 3 walls are shown in the
3D view, why is it not showing all 6 walls?

Finally, I checked my script and there is no code to create the yellow
box shown in the 3D view... So, why the 3D view show this yellow Box?

May someone have experience for this error?

### Scripts ###

from __future__ import print_function
from yade.gridpfacet import *
from yade import pack, plot,qt
import gts, os.path, locale

from numpy import arange

O.periodic=True


#### Parameters ####

# radius of cylinder
cyl_R=0.1
# length of cylinder
cyl_L=0.2
# friction angle
phi=30.0
# Young's modulus
E=1e6


idSteel=O.materials.append(FrictMat(young=210e9,poisson=.25,frictionAngle=.8,density=7.85e3,label='steel'))
# wallMask=31 >> +/-x, +/-y, -z
#O.bodies.append(geom.facetBox((0,0,0),(2.5,2.5,1),wallMask=63,material="steel" ))

## create walls 
walls=aabbWalls([(0,0,0),(5,5,2)],thickness=0.0,material='steel')
wallIds=O.bodies.append(walls)

### periodic boundary for facetBox ###

#O.cell.setBox(2.5,20.0,20.0)

### set the velocity for facet ###

#for id in range(6):
#    b = O.bodies[id]
#    b.state.vel = (0,0,0.5)



### create materials ###

# gridConnections material

gridConMat= O.materials.append(CohFrictMat(young=E, poisson=0.5,
density=1500, frictionAngle=radians(phi), normalCohesion=1e10,
shearCohesion=1e10, momentRotationLaw=True, label='gcMat'))

# general interactions

cylMat= O.materials.append(FrictMat(young=E, poisson=0.5, density=1500,
frictionAngle=radians(phi), label='cMat'))

### create particles/packing: cylinders ###

nodesIds=[]
cylIds=[]

dx=0.5
dy=0.5
nx=5
ny=5
nz=1
dz=0


for i in range(0,nx):
	x=0+i*dx
	for j in range(0,ny):
		y=0+j*dy
		for k in range(0,nz):
			z=0+k*dz
			cylinder((x,y+cyl_L,z),(x,y,z),radius=cyl_R,nodesIds=nodesIds,cylIds=cylIds,
color=[1,0,0],fixed=False,intMaterial='gcMat',extMaterial='cMat')

#O.bodies.appendClumped()

move = TranslationEngine(translationAxis=[0,0,1],velocity=0.1,ids=[0,1])


### Engines ###

O.engines = [
	ForceResetter(),
        InsertionSortCollider([Bo1_GridConnection_Aabb(),Bo1_PFacet_Aabb(), Bo1_Wall_Aabb()]),
        InteractionLoop([
			Ig2_GridNode_GridNode_GridNodeGeom6D(),
                 	Ig2_GridConnection_GridConnection_GridCoGridCoGeom(),
			Ig2_Wall_Sphere_ScGeom(),
			Ig2_Sphere_Sphere_ScGeom(),
			Ig2_Sphere_GridConnection_ScGridCoGeom(),
			Ig2_GridConnection_PFacet_ScGeom(),
                ],
                [
# internal cylinder physics 
         		Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=False),
# physics for external interactions, i.e., cylinder-cylinder 
                        Ip2_FrictMat_FrictMat_FrictPhys()   
                ],
                [
                        Law2_ScGeom6D_CohFrictPhys_CohesionMoment(),     # contact law for "internal" cylinder forces
                        Law2_GridCoGridCoGeom_FrictPhys_CundallStrack(),  # contact law for cylinder-cylinder interaction
			Law2_ScGeom_FrictPhys_CundallStrack(),
			Law2_ScGridCoGeom_FrictPhys_CundallStrack()              
		 ]
        ),
	GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.5),
        NewtonIntegrator(gravity=(0., 0., -9.81), damping=0.5, label='newton'),
	move
	#TranslationEngine(translationAxis=[1,0,0],velocity=0.5,ids=[0,1,2,3,4,5])
	#PyRunner(iterPeriod=1e-3,command="")
]
 	
O.dt=0.5*PWaveTimeStep()

### Define Functions ###


#### For viewing ####
qt.View()

#### Allows to reload the simulation ####
O.saveTmp()

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