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[Xue lihua <question681569@xxxxxxxxxxxxxxxxxxxxx>]

New question #681569 on Yade:
https://answers.launchpad.net/yade/+question/681569

Hello everyone:
  the following is my script:
  
******************************
from yade import pack,utils,plot

from yade import utils

matP = FrictMat()
matP.density=2500#kg/m^3
matP.young = 3e9
matP.poisson = 0.21 
matP.frictionAngle = 0.65

matW = FrictMat()
matW.density = 1950#kg/m^3 
matW.young = 1.2e9
matW.poisson = 0.33 
matW.frictionAngle = 0.23

O.materials.append(matP)
O.materials.append(matW)

#cylinder in triaxial
#cyl=yade.geom.facetCylinder((0,0,0),radius=15,height=60,orientation=Quaternion((0,0,1),0),wallMask=7)  # test this code singlely
#O.bodies.append(cyl)
#O.bodies.erase()

#wall1=utils.wall(0,axis=2,sense=1,material=matW)
#wall2=utils.wall(0,axis=2,sense=1,material=matW)
#O.bodies.append(wall1)

#pred=pack.inCylinder((0,0,0),(0,0,60),15)#theunitoflengthiscm
#sp=SpherePack()
#sp=pack.randomDensePack(pred,radius=6,rRelFuzz=3)
#spheres=sp.toSimulation(color=(0,1,1),material=matP)
#former context is concern about how to build the model in cylinder,have some question.

wall1=utils.wall(0,axis=2,sense=1,material=matW)
wall2=utils.wall(0.15,axis=0,sense=-1,material=matW)
wall3=utils.wall(-0.15,axis=0,sense=1,material=matW)
wall4=utils.wall(-0.15,axis=1,sense=1,material=matW)
wall5=utils.wall(0.15,axis=1,sense=-1,material=matW)

O.bodies.append((wall1,wall2,wall3,wall4,wall5))

#pre=pack.inAlignedBox((-0.15,-0.15,0),(0.15,0.15,0.60));
#spheres=pack.randomDensePack(pre,radius=6,rRelFuzz=2.5,material=matP); # in chapter 3, packing algorithms
#O.bodies.append([sphere(c, r) for c, r in spheres]); #id=-1 is the last particle in box.

sp=pack.SpherePack()
sp.makeCloud((-0.15,-0.15,0),(0.15,0.15,0.60),rMean=0.02,rRelFuzz=.006,periodic=True)
sp.toSimulation()

#pre=pack.inAlignedBox((-15,-15,0),(15,15,60));
#spheres=pack.randomDensePack(pre,radius=6,rRelFuzz=2.5,material=matP); # in chapter 3, packing algorithms
#O.bodies.append([sphere(c, r) for c, r in spheres]); #id=-1 is the last particle in box.

sp=pack.SpherePack()
sp.makeCloud((-0.15,-0.15,0),(0.15,0.15,0.60),rMean=0.02,rRelFuzz=.006,periodic=True)
sp.toSimulation()

lpm=O.bodies[-1].id
O.bodies[lpm].state.blockerDOFs='xyzXYZ'
global inipos# global var, attention
inipos=O.bodies[lpm].state.pos[2]
O.bodies.erase(lpm)
wall6= utils.wall(inipos-0.02,axis=2,sense=-1,material=matW)
O.bodies.append(wall6);
lpm=O.bodies[-1].id;
inipos=O.bodies[lpm].state.pos[2];

from yade import timing
yade.timing.reset() #Zero all timing data

O.engines=[
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Wall_Aabb()]),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom(), Ig2_Wall_Sphere_ScGeom()],
		[Ip2_FrictMat_FrictMat_FrictPhys()],
		[Law2_ScGeom_FrictPhys_CundallStrack()]
	),
	NewtonIntegrator(damping=0.3, label='newton'),
	PyRunner(command='Step()',iterPeriod=1,label='step'),
	PyRunner(command='Save()',iterPeriod=50)
]

def Step():
	from yade import utils, plot
	global stepnum, inipos, deltpos, n
	lpm=O.bodies[-1].id
	platepos=O.bodies[lpm].state.pos[2]
	plateforce=O.forces.f(lpm)[2]
	O.bodies[lpm].state.blockedDOFs='xyzXYZ'
	O.bodies[lpm].state.vel=(0,0,-0.005)
	platepos2=inipos-platepos
	wallx1pos=O.bodies[1].state.pos[0]
	wallx2pos=O.bodies[2].state.pos[0]
	wally1pos=O.bodies[3].state.pos[1]
	wally2pos=O.bodies[4].state.pos[1]
	areaplate=platepos*(wallx1pos-wallx2pos)
	wallx1force=O.forces.f(1)[0]
	wallx2force=O.forces.f(2)[0]
	wally1force=O.forces.f(3)[1]
	wally2force=O.forces.f(4)[1]
	fmw=[abs(wallx1force)+abs(wallx2force)+abs(wally1force)+abs(wally2force)]/(4*areaplate)
	G=(0.5*areaplate)/(matW.young*10*0.0005)
	wav=G*(fmw-500)
	O.bodies[1].state.vel[0]=-wav#可能有错误，正负号
	O.bodies[2].state.vel[0]=wav
	O.bodies[3].state.vel[1]=-wav
	O.bodies[4].state.vel[1]=wav
	delvol=(wallx2pos-wallx1pos)*(wally2pos-wally1pos)*platepos-0.09*inipos#体积变化量
	plot.addData(Pf=plateforce,Pp=platepos2,Pps=platepos2,Pv=delvol,Cof=fmw,**O.energy)
	plot.saveDataTxt('Triaxial-ballast.txt.bz2',vars=('Pp','Pf','Pv','Cof'))
	if stepnum==1:
		O.bodies[lpm].state.vel=(0,0,-0.005) 
		if plateforce< 4500: return 
		stepnum=stepnum+1
	elif stepnum==2:
		O.bodies[lpm].state.blockedDOFs='xyzXYZ'
		delconf=abs(fwm-500)
		if abs > 100: return
		export.Spheres('/tmp/Triaxial-pre.dat')
		print "wall6pos=%.5f"%(platepos)
		O.pause()

def Save():
	global n
	O.save('Compression'+str(n)+'.yade.gz')
	n=n+1

#plot.plots={'Pp':('Pf',),'Pps':('Pv',)}
plot.plots={'Pp':('Pf',)}
plot.plot()
#plot.saveDataTxt('Compression.txt.bz2',vars('Pp','Pf'))
from yade import qt
O.dt = 0.0005
V = qt.View()
V.screenSize = (550,450)
V.sceneRadius = 20
V.eyePosition = (0.7,0.5,0.1)
V.upVector = (0,0,1)
V.lookAt = (0.15,0.15,0.1)
O.run()
****************************************************** 
  
However, when i tested it in yadedaily it showed some problems in below:
   FATAL /data/trunk/pkg/common/InsertionSortCollider.cpp:495 spatialOverlapPeri: Body #0 spans over half of the cell size 0.3 (axis=0, see flag allowBiggerThanPeriod)
FATAL /data/trunk/core/ThreadRunner.cpp:30 run: Exception occured: 
/data/trunk/pkg/common/InsertionSortCollider.cpp: Body larger than half of the cell size encountered.

 Besides that, i found that the walls in lateral are different from what i designed in line 35-41 after i added particles in the model.
 So, i would be greatful if you can help me find out  the causes of these problems.
 Thanks a lot!

 xue


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