Polyhedrons escaping the shear box walls during deposition

Asked by Ali HAIDAR on 2020-05-17

Hello,

I am trying to perform the direct shear test using polyhedrons but, I am facing a problem which is that during deposition process which is the first step , several polyhedrons are escaping out of the box one after another.
The box is formed of facets where I tried to increase their stiffness or decrease the time step to solve the problem but it still exists.
Note that the whole shear test procedure was done also using spherical particles and it worked perfectly.
This problem is not allowing the pack to finish the deposition and reach equilibrium so that I can continue the shear test methodology.

Thank you in advance for your advises and help,

Best Regards,
Ali HAIDAR

Question information

Language:
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Status:
Answered
For:
Yade Edit question
Assignee:
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Last query:
2020-05-18
Last reply:
2020-05-18
Jan Stránský (honzik) said : #1

Hello,

please provide a MWE [1].

> I tried to increase their stiffness

please provide values. increase 2x? 10x? 1000x? 1e12x?

cheers
Jan

[1] https://www.yade-dem.org/wiki/Howtoask

Ali HAIDAR (alihaidar976) said : #2

Hi,

Thank you for your reply.
Kindly find attached the script and the zip file of the polyhedrons I am importing into my simulation.
Regarding the stiffness, I used an initial value of young’s modules of 1E10 Pa and then tried 1E50 and 1E100 but, the problem was the same.
After a long wait, the polyhedrons are escaping one after another before the end of deposition.

Thank you in advance,
Ali HAIDAR

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

From: Jan Stránský<mailto:<email address hidden>>
Sent: Sunday, May 17, 2020 11:45 PM
To: <email address hidden><mailto:<email address hidden>>
Subject: Re: [Question #690777]: Polyhedrons escaping the shear box walls during deposition

Your question #690777 on Yade changed:
https://answers.launchpad.net/yade/+question/690777

    Status: Open => Needs information

Jan Stránský requested more information:
Hello,

please provide a MWE [1].

> I tried to increase their stiffness

please provide values. increase 2x? 10x? 1000x? 1e12x?

cheers
Jan

[1] https://www.yade-dem.org/wiki/Howtoask

--
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this email or enter your reply at the following page:
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Jan Stránský (honzik) said : #3

Hello,
you cannot attach files here. Also please read [1], section "Please, no external links!"
cheers
Jan

Ali HAIDAR (alihaidar976) said : #4

Hello,
Sorry about the link.
The script is the following:
But it needs the polyhedrons files I am using to run.
Thank you

from yade import plot,polyhedra_utils
import pickle

with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion1", "rb") as fp:
  v1 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion2", "rb") as fp:
  v2 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion3", "rb") as fp:
  v3 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion4", "rb") as fp:
  v4 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion5", "rb") as fp:
  v5 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion6", "rb") as fp:
  v6 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion7", "rb") as fp:
  v7 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion8", "rb") as fp:
  v8 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion9", "rb") as fp:
  v9 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion10", "rb") as fp:
  v10 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion11", "rb") as fp:
  v11 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion12", "rb") as fp:
  v12 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion13", "rb") as fp:
  v13 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion14", "rb") as fp:
  v14 = pickle.load(fp)
with open("/home/alihaidar/Desktop/data/Fusion/pickle_reducedvertices/tolerance=20mm/20-preducedfusion15", "rb") as fp:
  v15 = pickle.load(fp)

m = PolyhedraMat()
m.density = 2607 #kg/m^3
m.frictionAngle = 0.3 #rad
#m.young = 1E10 #Pa
#m.poisson = 20000/1E6
m2= PolyhedraMat()
m2.frictionAngle = 0.3 #rad
m2.young = 1E100
x=.3
y=.3
z=.2
a=b=0.04
i=0
while a<=(x-0.05):
  while b<=(y-0.05):
    O.bodies.append([
                     polyhedra_utils.polyhedra(material=m,v=v1),
                     polyhedra_utils.polyhedra(material=m,v=v2),
                     polyhedra_utils.polyhedra(material=m,v=v3),
                     polyhedra_utils.polyhedra(material=m,v=v4),
                     polyhedra_utils.polyhedra(material=m,v=v5),
                     polyhedra_utils.polyhedra(material=m,v=v6),
                     polyhedra_utils.polyhedra(material=m,v=v7),
                     polyhedra_utils.polyhedra(material=m,v=v8),
                     polyhedra_utils.polyhedra(material=m,v=v9),
                     polyhedra_utils.polyhedra(material=m,v=v10),
                     polyhedra_utils.polyhedra(material=m,v=v11),
                     polyhedra_utils.polyhedra(material=m,v=v12),
                     polyhedra_utils.polyhedra(material=m,v=v13),
                     polyhedra_utils.polyhedra(material=m,v=v14),
                     polyhedra_utils.polyhedra(material=m,v=v15),
      ]
     )
    if i==0 or i==5 or i==13 or i==10:
      O.bodies[-1].state.pos=(a,b,.04-z)
      O.bodies[-2].state.pos=(a,b,.12-z)
      O.bodies[-3].state.pos=(a,b,.2-z)
      O.bodies[-4].state.pos=(a,b,.28-z)
      O.bodies[-5].state.pos=(a,b,.36-z)
      O.bodies[-6].state.pos=(a,b,.44-z)
      O.bodies[-7].state.pos=(a,b,.52-z)
      O.bodies[-8].state.pos=(a,b,.6-z)
      O.bodies[-9].state.pos=(a,b,.68-z)
      O.bodies[-10].state.pos=(a,b,.76-z)
      O.bodies[-11].state.pos=(a,b,.84-z)
      O.bodies[-12].state.pos=(a,b,.92-z)
      O.bodies[-13].state.pos=(a,b,1-z)
      O.bodies[-14].state.pos=(a,b,1.08-z)
      O.bodies[-15].state.pos=(a,b,1.16-z)
    if i==1 or i==6 or i==12 or i==8:
      O.bodies[-15].state.pos=(a,b,.04-z)
      O.bodies[-14].state.pos=(a,b,.12-z)
      O.bodies[-13].state.pos=(a,b,.2-z)
      O.bodies[-12].state.pos=(a,b,.28-z)
      O.bodies[-11].state.pos=(a,b,.36-z)
      O.bodies[-10].state.pos=(a,b,.44-z)
      O.bodies[-9].state.pos=(a,b,.52-z)
      O.bodies[-8].state.pos=(a,b,.6-z)
      O.bodies[-7].state.pos=(a,b,.68-z)
      O.bodies[-6].state.pos=(a,b,.76-z)
      O.bodies[-5].state.pos=(a,b,.84-z)
      O.bodies[-4].state.pos=(a,b,.92-z)
      O.bodies[-3].state.pos=(a,b,1-z)
      O.bodies[-2].state.pos=(a,b,1.08-z)
      O.bodies[-1].state.pos=(a,b,1.16-z)
    if i==4 or i==15 or i==11 or i==9:
      O.bodies[-12].state.pos=(a,b,.04-z)
      O.bodies[-3].state.pos=(a,b,.12-z)
      O.bodies[-9].state.pos=(a,b,.2-z)
      O.bodies[-5].state.pos=(a,b,.28-z)
      O.bodies[-10].state.pos=(a,b,.36-z)
      O.bodies[-15].state.pos=(a,b,.44-z)
      O.bodies[-4].state.pos=(a,b,.52-z)
      O.bodies[-1].state.pos=(a,b,.6-z)
      O.bodies[-6].state.pos=(a,b,.68-z)
      O.bodies[-8].state.pos=(a,b,.76-z)
      O.bodies[-2].state.pos=(a,b,.84-z)
      O.bodies[-7].state.pos=(a,b,.92-z)
      O.bodies[-11].state.pos=(a,b,1-z)
      O.bodies[-14].state.pos=(a,b,1.08-z)
      O.bodies[-13].state.pos=(a,b,1.16-z)
    if i==3 or i==7 or i==2 or i==14:
      O.bodies[-13].state.pos=(a,b,.04-z)
      O.bodies[-14].state.pos=(a,b,.12-z)
      O.bodies[-11].state.pos=(a,b,.2-z)
      O.bodies[-7].state.pos=(a,b,.28-z)
      O.bodies[-2].state.pos=(a,b,.36-z)
      O.bodies[-8].state.pos=(a,b,.44-z)
      O.bodies[-6].state.pos=(a,b,.52-z)
      O.bodies[-1].state.pos=(a,b,.6-z)
      O.bodies[-4].state.pos=(a,b,.68-z)
      O.bodies[-15].state.pos=(a,b,.76-z)
      O.bodies[-10].state.pos=(a,b,.84-z)
      O.bodies[-5].state.pos=(a,b,.92-z)
      O.bodies[-9].state.pos=(a,b,1-z)
      O.bodies[-3].state.pos=(a,b,1.08-z)
      O.bodies[-12].state.pos=(a,b,1.16-z)
    b=b+0.07
    i=i+1
  a=a+0.07
  b=0.04

f1=utils.facet([(0,0,0),(0,0,z),(x,0,0)],material=m2)
f2=utils.facet([(x,0,z),(0,0,z),(x,0,0)],material=m2)
f3=utils.facet([(x,0,z),(x,y,z),(x,0,0)],material=m2)
f4=utils.facet([(x,y,0),(x,y,z),(x,0,0)],material=m2)
f5=utils.facet([(x,y,0),(x,y,z),(0,y,z)],material=m2)
f6=utils.facet([(x,y,0),(0,y,0),(0,y,z)],material=m2)
f7=utils.facet([(0,0,0),(0,y,0),(0,y,z)],material=m2)
f8=utils.facet([(0,0,0),(0,0,z),(0,y,z)],material=m2)
f9=utils.facet([(0,0,0),(0,-.5*y,0),(x,-.5*y,0)],material=m2)
f10=utils.facet([(0,0,0),(x,-.5*y,0),(x,0,0)],material=m2)
f11=utils.facet([(0,0,z),(0,0,5*z),(x,0,z)],material=m2)
f12=utils.facet([(x,0,5*z),(0,0,5*z),(x,0,z)],material=m2)
f13=utils.facet([(x,0,5*z),(x,y,5*z),(x,0,z)],material=m2)
f14=utils.facet([(x,y,z),(x,y,5*z),(x,0,z)],material=m2)
f15=utils.facet([(x,y,z),(x,y,5*z),(0,y,5*z)],material=m2)
f16=utils.facet([(x,y,z),(0,y,z),(0,y,5*z)],material=m2)
f17=utils.facet([(0,0,z),(0,y,z),(0,y,5*z)],material=m2)
f18=utils.facet([(0,0,z),(0,0,5*z),(0,y,5*z)],material=m2)
O.bodies.append([f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f11,f12,f13,f14,f15,f16,f17,f18])
f19=utils.facet([(0,y,0),(0,1.5*y,0),(x,y,0)],fixed=True,material=m2)
f20=utils.facet([(x,y,0),(x,1.5*y,0),(0,1.5*y,0)],fixed=True,material=m2)
f=0
t=0
n=0
A=.3*.3
V=0.1
F=-13500
O.bodies.append([
  utils.facet([(0,0,0),(0,0,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(0,0,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(x,y,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,y,0),(x,y,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,y,0),(x,y,-z),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(x,y,0),(0,y,0),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(0,0,0),(0,y,0),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(0,0,0),(0,0,-z),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(0,0,-z),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(x,y,-z),(0,y,-z)],material=m2,fixed=True),f19,f20
        ])

O.engines=[
 ForceResetter(),
 InsertionSortCollider([Bo1_Polyhedra_Aabb(),Bo1_Facet_Aabb(),Bo1_Wall_Aabb()],verletDist=0.1),
 InteractionLoop(
   [Ig2_Polyhedra_Polyhedra_PolyhedraGeom(),Ig2_Facet_Polyhedra_PolyhedraGeom(),Ig2_Wall_Polyhedra_PolyhedraGeom()],
   [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()],
   [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()]
         ),
 NewtonIntegrator(gravity=(0,0,-9.81),damping=0.5),
 PyRunner(command='checkUnbalanced()',realPeriod=2,label='checker'),
   ]

O.dt=.05*polyhedra_utils.PWaveTimeStep()

def checkUnbalanced():

  if O.iter<100000: return
  if unbalancedForce()>.2: return
  m.frictionAngle=.5
  m2.frictionAngle=.5
  for i in O.interactions: i.phys.tangensOfFrictionAngle=tan(.5)
  O.bodies.append(wall(max([b.state.pos[2]+0.05 for b in O.bodies if isinstance(b.shape,Polyhedra)]),axis=2,sense=-1,material=m2))
  global plate
  plate=O.bodies[-1]
  plate.state.blockedDOFs='xyXYZ'
  plate.state.mass=.1
  O.forces.setPermF(plate.id,(0,0,F))
  checker.command='pos()'
def pos():
  global l
  l=plate.state.pos[2]
  checker.command='shear()'

def shear():
  f1.state.vel=(0,V,0)
  f2.state.vel=(0,V,0)
  f3.state.vel=(0,V,0)
  f4.state.vel=(0,V,0)
  f5.state.vel=(0,V,0)
  f6.state.vel=(0,V,0)
  f7.state.vel=(0,V,0)
  f8.state.vel=(0,V,0)
  f9.state.vel=(0,V,0)
  f10.state.vel=(0,V,0)
  f11.state.vel=(0,V,0)
  f12.state.vel=(0,V,0)
  f13.state.vel=(0,V,0)
  f14.state.vel=(0,V,0)
  f15.state.vel=(0,V,0)
  f16.state.vel=(0,V,0)
  f17.state.vel=(0,V,0)
  f18.state.vel=(0,V,0)
  O.engines=O.engines+[PyRunner(command='addData()',iterPeriod=100)]
def addData():

  f=-sum(O.forces.f(b.id)[1] for b in [f1,f2,f3,f4,f5,f6,f7,f8,plate,f19,f20])
  A=(.3*(.3-V*O.dt*O.iter))
  t=f/A/1000
  print('Shear force',f,'Contact Area',A,'shear stress',t,'KPa')
  n=(O.forces.f(plate.id)[2]+F)/(.3*.3)/1000
  print('normal stress',n,'KPa')
  d=f1.state.pos[1]
  d2=(plate.state.pos[2]-l)
  plot.addData(Shear_displacement=d,Normal_disp=d2,Shear_Stress=t,Normal_Stress=n,i=O.iter)

plot.plots={'Shear_displacement':('Shear_Stress'),'Shear_displacement ':('Normal_Stress'),'Shear_displacement ':'Normal_disp'}

plot.plot()
yade.qt.View()
O.run()
O.saveTmp()

Jérôme Duriez (jduriez) said : #5

For the record, the user-input stiffnesses (so-called "PolyhedraMat.young") here are not in Pa: https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys

Jan Stránský (honzik) said : #6

Thanks, but please do some more improvements :-)

we prefer (= it is much more likely that you will get the answer) a code in the form of MWE [1], where M stands for minimal. In this case, where the problem is about gravity deposition, all the stuff concerning shear (e.g. shear() function), is irrelevant.
I think that checkUnbalanced() and plotting stuff is not important either.

> But it needs the polyhedrons files I am using to run.

seems like 15 arrays of Vector3, should be possible to provide in the form "v1=[...]", or?

Just a **personal** note, do you have a special need to save the data using pickle module? I refer "human readable" formats (plain text, json, xml, ...) unless the file size really matters..

cheers
Jan

Ali HAIDAR (alihaidar976) said : #7

Can I put a google drive link for the pickle files I am using ?
And if not, how do you want me to share them with you ?
I am using pickle module because I found it simple and efficient and the files size is really small.
I am reducing the vertices number of the polyhedrons and saving several cases.
So, I found it simpler.

Jan Stránský (honzik) said : #8

> Can I put a google drive link for the pickle files I am using ?

preferably not ([1], section "Please, no external links!")

> how do you want me to share them with you ?

as I wrote, e.g. as a code in the form
v1 = [(1,2,3),(3,4,5),...]
(polyhedron vertices is just a list of Vector3/tuple, so it should be no problem)
(also concerning M in MWE, you may try if a specific shape has influence or not - if you have the same issue with "default" polyhedrons)

cheers
Jan

[1] https://www.yade-dem.org/wiki/Howtoask

Ali HAIDAR (alihaidar976) said : #9

The 15 lists of vertices are the following:

v1=[[-0.05773000046610832, 0.010489999316632748, 0.006389999762177467],
 [-0.05770999938249588, 0.01027000043541193, 0.006389999762177467],
 [-0.05761000141501427, 0.009290000423789024, 0.006169999949634075],
 [-0.057429999113082886, 0.008369999937713146, 0.005739999935030937],
 [-0.056770000606775284, 0.007219999562948942, 0.004780000075697899],
 [-0.05624999850988388, 0.00558000011369586, 0.007260000333189964],
 [-0.055240001529455185, 0.004360000137239695, 0.008679999969899654],
 [-0.05339000001549721, 0.002959999954327941, 0.016700001433491707],
 [-0.05065999925136566, 0.019290000200271606, 0.014569999650120735],
 [-0.04575999826192856, 0.0017399999778717756, 0.005520000122487545],
 [-0.04270000010728836, 0.021229999139904976, 0.030489999800920486],
 [-0.04106999933719635, 0.020409999415278435, 0.03171999752521515],
 [-0.04024999961256981, 0.03294999897480011, -0.0012400000123307109],
 [-0.03942999988794327, 0.0341699980199337, 0.00018000000272877514],
 [-0.03870999813079834, 0.03425999730825424, -0.0017900000093504786],
 [-0.03779999911785126, 0.034040000289678574, 0.0016499999910593033],
 [-0.03638000041246414, 0.02920999936759472, -0.009750000201165676],
 [-0.034630000591278076, 0.021389998495578766, -0.012539999559521675],
 [-0.03256000205874443, 0.029570000246167183, -0.013609999790787697],
 [-0.030489999800920486, 0.0012199999764561653, -0.009810000658035278],
 [-0.02962000109255314, -0.00839999970048666, 0.027979999780654907],
 [-0.029179999604821205, 0.017649998888373375, 0.03627000004053116],
 [-0.028529999777674675, -0.010999999940395355, 0.026760000735521317],
 [-0.02809000015258789, 0.01092000026255846, 0.03824000060558319],
 [-0.027549998834729195, -0.0004199999966658652, -0.008880000561475754],
 [-0.02677999995648861, -0.012189999222755432, 0.02579999901354313],
 [-0.025909999385476112, -0.0012199999764561653, -0.010180000215768814],
 [-0.02426999993622303, -0.012590000405907631, 0.020899999886751175],
 [-0.02078000083565712, 0.032930001616477966, -0.02457999996840954],
 [-0.01915000006556511, -0.004889999981969595, -0.007790000177919865],
 [-0.01860000006854534, 0.03294999897480011, -0.026599999517202377],
 [-0.017190000042319298, -0.00015999999595806003, -0.02271999977529049],
 [-0.016530001536011696, 0.03613999858498573, -0.02752000093460083],
 [-0.015550000593066216, -0.0012400000123307109, -0.022830000147223473],
 [-0.01285999920219183, 0.03579000011086464, -0.0284000001847744],
 [-0.012390000745654106, 0.02847999893128872, 0.022110000252723694],
 [-0.01206000056117773, 0.029079999774694443, 0.019370000809431076],
 [-0.010970000177621841, 0.027139998972415924, 0.02296999841928482],
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v10=[[-0.05626999959349632, -0.010979999788105488, 0.047029998153448105],
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v11=[[-0.1279599964618683, 0.01939000003039837, -0.09086000174283981],
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v12=[[-0.1637599915266037, -0.0008899999666027725, -0.03258000314235687],
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 [0.13283999264240265, -0.04453999921679497, -0.041259996592998505],
 [0.1341100037097931, -0.03979000076651573, -0.031139999628067017],
 [0.13596999645233154, -0.04041999951004982, -0.029889998957514763],
 [0.13782000541687012, -0.06619999557733536, -0.015650000423192978],
 [0.13875000178813934, -0.03950999677181244, -0.03440999984741211],
 [0.1410599946975708, -0.06712000072002411, -0.01843000017106533],
 [0.1440799981355667, -0.04268999770283699, -0.03808000311255455]]

v14=[[-0.0492900013923645, 0.05581999942660332, -0.07337000221014023],
 [-0.04927000030875206, 0.055650003254413605, -0.07319999486207962],
 [-0.04904999956488609, 0.05480000004172325, -0.07440000027418137],
 [-0.04822999984025955, 0.053770001977682114, -0.0728600025177002],
 [-0.04749000072479248, 0.05753999948501587, -0.07727999985218048],
 [-0.046459998935461044, 0.049320001155138016, -0.07089000195264816],
 [-0.04456999897956848, 0.056849997490644455, -0.08041000366210938],
 [-0.04165999963879585, 0.058729998767375946, -0.0831800028681755],
 [-0.03756000101566315, 0.06328000128269196, -0.0773099958896637],
 [-0.035669997334480286, 0.0334399975836277, -0.06532000005245209],
 [-0.03328000009059906, 0.03099999949336052, -0.06560999900102615],
 [-0.03208000212907791, 0.03220000118017197, -0.061799999326467514],
 [-0.030709998682141304, 0.026440000161528587, -0.06378000229597092],
 [-0.029170000925660133, 0.034939996898174286, -0.059209998697042465],
 [-0.028179999440908432, 0.0649000033736229, -0.052650000900030136],
 [-0.026770001277327538, 0.06933999806642532, -0.05762000009417534],
 [-0.025909999385476112, 0.06980000436306, -0.05608000233769417],
 [-0.024540001526474953, 0.06658000499010086, -0.05110999941825867],
 [-0.02305999957025051, 0.06917999684810638, -0.04906000196933746],
 [-0.02095000073313713, 0.07002999633550644, -0.04772000014781952],
 [-0.018209999427199364, 0.0672600045800209, -0.04665999859571457],
 [-0.015809999778866768, 0.004739999771118164, -0.06430000066757202],
 [-0.015300000086426735, 0.044349998235702515, -0.08559999614953995],
 [-0.015130000188946724, 0.044679999351501465, -0.08620999753475189],
 [-0.014439999125897884, 0.005319999996572733, -0.06566999852657318],
 [-0.013240000233054161, 0.006000000052154064, -0.06794999539852142],
 [-0.012729999609291553, 0.04583999887108803, -0.08741000294685364],
 [-0.011869999580085278, -0.00041000000783242285, -0.06532000005245209],
 [-0.010850000195205212, 0.0031700001563876867, -0.07011999934911728],
 [-0.009479999542236328, 0.0032599999103695154, -0.06127000227570534],
 [-0.008960000239312649, 0.05274000018835068, -0.08048000186681747],
 [-0.007420000154525042, 0.04521000012755394, -0.08312999457120895],
 [-0.005710000172257423, 0.056849997490644455, -0.07575999945402145],
 [-0.005369999911636114, 0.036090001463890076, -0.047520000487565994],
 [-0.004170000087469816, 0.03294000029563904, -0.04699999839067459],
 [-0.003829999826848507, 0.03435000032186508, -0.046150002628564835],
 [-0.0031400001607835293, 0.08466000109910965, -0.0317700020968914],
 [-0.002630000002682209, 0.08524999767541885, -0.030910000205039978],
 [-0.001769999973475933, 0.08337000012397766, -0.02645999938249588],
 [-0.0009200000204145908, 0.08669999986886978, -0.03552999719977379],
 [0.00011000000085914508, 0.08157999813556671, -0.025600001215934753],
 [0.0011399999493733048, 0.08854000270366669, -0.04033000022172928],
 [0.002680000150576234, 0.0899600014090538, -0.03913000226020813],
 [0.002849999815225601, 0.04316999763250351, -0.03759000077843666],
 [0.004559999797493219, 0.0486300028860569, -0.031540002673864365],
 [0.005590000189840794, 0.03545000031590462, -0.04465999826788902],
 [0.006099999882280827, 0.04213999956846237, -0.04906000196933746],
 [0.008670000359416008, 0.060099996626377106, -0.05984000116586685],
 [0.010300000198185444, 0.06300999969244003, -0.05728000029921532],
 [0.011239999905228615, 0.053599998354911804, -0.02483000047504902],
 [0.01448999997228384, 0.050360001623630524, -0.02662999927997589],
 [0.018769999966025352, 0.056609999388456345, -0.02457999996840954]]

v15=[[-0.01834000088274479, -0.03125, 0.03870999813079834],
 [-0.018319999799132347, -0.035360001027584076, 0.04828999936580658],
 [-0.018290000036358833, -0.034299999475479126, 0.05164000019431114],
 [-0.018229998648166656, -0.030649999156594276, 0.03638000041246414],
 [-0.017819998785853386, -0.03474999964237213, 0.04343000054359436],
 [-0.017319999635219574, -0.0361500009894371, 0.049970000982284546],
 [-0.016440000385046005, -0.029120000079274178, 0.02442000061273575],
 [-0.01534000039100647, -0.029430000111460686, 0.020510001108050346],
 [-0.013359999284148216, -0.02882000058889389, 0.016979999840259552],
 [-0.011390000581741333, -0.031449999660253525, 0.05863000079989433],
 [-0.009560000151395798, -0.017260000109672546, 0.023739999160170555],
 [-0.007130000274628401, -0.012959999963641167, 0.02563999965786934],
 [-0.00484999967738986, -0.025779999792575836, 0.015949999913573265],
 [-0.003329999977722764, -0.013989999890327454, 0.06532000005245209],
 [-0.002420000033453107, -0.013880000449717045, 0.06639000028371811],
 [-0.0016499999910593033, -0.013770000077784061, 0.06683999300003052],
 [-0.0007399999885819852, -0.0036600001621991396, 0.029589999467134476],
 [-0.00013000000035390258, -0.0009899999713525176, 0.017810000106692314],
 [0.0013899999903514981, -0.00798999983817339, 0.061970002949237823],
 [0.0024500000290572643, 0.0023499999660998583, 0.033240001648664474],
 [0.0035200000274926424, -0.003909999970346689, 0.06015000119805336],
 [0.004429999738931656, 0.006530000362545252, 0.023809999227523804],
 [0.006099999882280827, 0.010609999299049377, 0.03353999927639961],
 [0.007929999381303787, 0.0017399999778717756, 0.07005999982357025],
 [0.00914000067859888, 0.008129999972879887, 0.06366999447345734],
 [0.010359999723732471, 0.018639998510479927, 0.029589999467134476],
 [0.010660000145435333, -0.03993000090122223, 0.03505999967455864],
 [0.011270000599324703, -0.03988000005483627, 0.03294000029563904],
 [0.01218000054359436, -0.03869999945163727, 0.03821000084280968],
 [0.012640000320971012, -0.03766999766230583, 0.040389999747276306],
 [0.014159999787807465, -0.0372299998998642, 0.039319999516010284],
 [0.01613999903202057, -0.033069998025894165, 0.045099999755620956],
 [0.017659999430179596, 0.02662999927997589, 0.03750000149011612],
 [0.01827000081539154, 0.028690000995993614, 0.030049998313188553],
 [0.019179999828338623, 0.02718999981880188, 0.04220999777317047],
 [0.020239999517798424, 0.02476000040769577, 0.06244000047445297],
 [0.02085000090301037, 0.03202999755740166, 0.0218299999833107],
 [0.022370001301169395, 0.02273000031709671, 0.06695999950170517],
 [0.02449999935925007, 0.026990000158548355, 0.062300000339746475],
 [0.026329999789595604, 0.016189999878406525, 0.06993000209331512],
 [0.027540000155568123, 0.035349998623132706, 0.028870001435279846],
 [0.02785000018775463, -0.015060000121593475, 0.02412000112235546],
 [0.028149999678134918, -0.013770000077784061, 0.023969998583197594],
 [0.028909999877214432, -0.011789999902248383, 0.023799998685717583],
 [0.029969999566674232, -0.014069999568164349, 0.024979999288916588],
 [0.03179999813437462, -0.007079999893903732, 0.024399999529123306],
 [0.033740002661943436, -0.005400000140070915, 0.024879999458789825],
 [0.035419996827840805, -0.0038800002075731754, 0.030959999188780785],
 [0.03650999814271927, -0.004399999976158142, 0.05787000060081482],
 [0.03787999972701073, -0.0028199998196214437, 0.06244000047445297],
 [0.03985999897122383, -0.0022799998987466097, 0.062130000442266464],
 [0.042899999767541885, -0.0003499999875202775, 0.06304000318050385],
 [0.04395999759435654, 0.04195000231266022, 0.03886999934911728],
 [0.04593999683856964, 0.011630000546574593, 0.048580002039670944],
 [0.04684999957680702, 0.03894999995827675, 0.038259997963905334],
 [0.047609999775886536, 0.031849998980760574, 0.0392099991440773]]

Jan Stránský (honzik) said : #10

Thanks. Now please try to make your script a MWE - reproducing your problem, but with all unused/unnecessary/irrelevant code removed.
cheers
Jan

Ali HAIDAR (alihaidar976) said : #11

The MWE is the following:
Thank you

from yade import plot,polyhedra_utils

m = PolyhedraMat()
m.density = 2607 #kg/m^3
m.frictionAngle = 0.05 #rad
#m.young = 1E10 #Pa
#m.poisson = 20000/1E6
m2= PolyhedraMat()
m2.frictionAngle = 0.3 #rad
m2.young = 1E300
x=.3
y=.3
z=.2
a=b=0.04
i=0
while a<=(x-0.05):
  while b<=(y-0.05):
    O.bodies.append([
                     polyhedra_utils.polyhedra(material=m,v=v1),
                     polyhedra_utils.polyhedra(material=m,v=v2),
                     polyhedra_utils.polyhedra(material=m,v=v3),
                     polyhedra_utils.polyhedra(material=m,v=v4),
                     polyhedra_utils.polyhedra(material=m,v=v5),
                     polyhedra_utils.polyhedra(material=m,v=v6),
                     polyhedra_utils.polyhedra(material=m,v=v7),
                     polyhedra_utils.polyhedra(material=m,v=v8),
                     polyhedra_utils.polyhedra(material=m,v=v9),
                     polyhedra_utils.polyhedra(material=m,v=v10),
                     polyhedra_utils.polyhedra(material=m,v=v11),
                     polyhedra_utils.polyhedra(material=m,v=v12),
                     polyhedra_utils.polyhedra(material=m,v=v13),
                     polyhedra_utils.polyhedra(material=m,v=v14),
                     polyhedra_utils.polyhedra(material=m,v=v15),
      ]
     )
    if i==0 or i==5 or i==13 or i==10:
      O.bodies[-1].state.pos=(a,b,.04-z)
      O.bodies[-2].state.pos=(a,b,.12-z)
      O.bodies[-3].state.pos=(a,b,.2-z)
      O.bodies[-4].state.pos=(a,b,.28-z)
      O.bodies[-5].state.pos=(a,b,.36-z)
      O.bodies[-6].state.pos=(a,b,.44-z)
      O.bodies[-7].state.pos=(a,b,.52-z)
      O.bodies[-8].state.pos=(a,b,.6-z)
      O.bodies[-9].state.pos=(a,b,.68-z)
      O.bodies[-10].state.pos=(a,b,.76-z)
      O.bodies[-11].state.pos=(a,b,.84-z)
      O.bodies[-12].state.pos=(a,b,.92-z)
      O.bodies[-13].state.pos=(a,b,1-z)
      O.bodies[-14].state.pos=(a,b,1.08-z)
      O.bodies[-15].state.pos=(a,b,1.16-z)
    if i==1 or i==6 or i==12 or i==8:
      O.bodies[-15].state.pos=(a,b,.04-z)
      O.bodies[-14].state.pos=(a,b,.12-z)
      O.bodies[-13].state.pos=(a,b,.2-z)
      O.bodies[-12].state.pos=(a,b,.28-z)
      O.bodies[-11].state.pos=(a,b,.36-z)
      O.bodies[-10].state.pos=(a,b,.44-z)
      O.bodies[-9].state.pos=(a,b,.52-z)
      O.bodies[-8].state.pos=(a,b,.6-z)
      O.bodies[-7].state.pos=(a,b,.68-z)
      O.bodies[-6].state.pos=(a,b,.76-z)
      O.bodies[-5].state.pos=(a,b,.84-z)
      O.bodies[-4].state.pos=(a,b,.92-z)
      O.bodies[-3].state.pos=(a,b,1-z)
      O.bodies[-2].state.pos=(a,b,1.08-z)
      O.bodies[-1].state.pos=(a,b,1.16-z)
    if i==4 or i==15 or i==11 or i==9:
      O.bodies[-12].state.pos=(a,b,.04-z)
      O.bodies[-3].state.pos=(a,b,.12-z)
      O.bodies[-9].state.pos=(a,b,.2-z)
      O.bodies[-5].state.pos=(a,b,.28-z)
      O.bodies[-10].state.pos=(a,b,.36-z)
      O.bodies[-15].state.pos=(a,b,.44-z)
      O.bodies[-4].state.pos=(a,b,.52-z)
      O.bodies[-1].state.pos=(a,b,.6-z)
      O.bodies[-6].state.pos=(a,b,.68-z)
      O.bodies[-8].state.pos=(a,b,.76-z)
      O.bodies[-2].state.pos=(a,b,.84-z)
      O.bodies[-7].state.pos=(a,b,.92-z)
      O.bodies[-11].state.pos=(a,b,1-z)
      O.bodies[-14].state.pos=(a,b,1.08-z)
      O.bodies[-13].state.pos=(a,b,1.16-z)
    if i==3 or i==7 or i==2 or i==14:
      O.bodies[-13].state.pos=(a,b,.04-z)
      O.bodies[-14].state.pos=(a,b,.12-z)
      O.bodies[-11].state.pos=(a,b,.2-z)
      O.bodies[-7].state.pos=(a,b,.28-z)
      O.bodies[-2].state.pos=(a,b,.36-z)
      O.bodies[-8].state.pos=(a,b,.44-z)
      O.bodies[-6].state.pos=(a,b,.52-z)
      O.bodies[-1].state.pos=(a,b,.6-z)
      O.bodies[-4].state.pos=(a,b,.68-z)
      O.bodies[-15].state.pos=(a,b,.76-z)
      O.bodies[-10].state.pos=(a,b,.84-z)
      O.bodies[-5].state.pos=(a,b,.92-z)
      O.bodies[-9].state.pos=(a,b,1-z)
      O.bodies[-3].state.pos=(a,b,1.08-z)
      O.bodies[-12].state.pos=(a,b,1.16-z)
    b=b+0.07
    i=i+1
  a=a+0.07
  b=0.04

f1=utils.facet([(0,0,0),(0,0,z),(x,0,0)],material=m2)
f2=utils.facet([(x,0,z),(0,0,z),(x,0,0)],material=m2)
f3=utils.facet([(x,0,z),(x,y,z),(x,0,0)],material=m2)
f4=utils.facet([(x,y,0),(x,y,z),(x,0,0)],material=m2)
f5=utils.facet([(x,y,0),(x,y,z),(0,y,z)],material=m2)
f6=utils.facet([(x,y,0),(0,y,0),(0,y,z)],material=m2)
f7=utils.facet([(0,0,0),(0,y,0),(0,y,z)],material=m2)
f8=utils.facet([(0,0,0),(0,0,z),(0,y,z)],material=m2)
f9=utils.facet([(0,0,0),(0,-.5*y,0),(x,-.5*y,0)],material=m2)
f10=utils.facet([(0,0,0),(x,-.5*y,0),(x,0,0)],material=m2)
f11=utils.facet([(0,0,z),(0,0,5*z),(x,0,z)],material=m2)
f12=utils.facet([(x,0,5*z),(0,0,5*z),(x,0,z)],material=m2)
f13=utils.facet([(x,0,5*z),(x,y,5*z),(x,0,z)],material=m2)
f14=utils.facet([(x,y,z),(x,y,5*z),(x,0,z)],material=m2)
f15=utils.facet([(x,y,z),(x,y,5*z),(0,y,5*z)],material=m2)
f16=utils.facet([(x,y,z),(0,y,z),(0,y,5*z)],material=m2)
f17=utils.facet([(0,0,z),(0,y,z),(0,y,5*z)],material=m2)
f18=utils.facet([(0,0,z),(0,0,5*z),(0,y,5*z)],material=m2)
O.bodies.append([f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f11,f12,f13,f14,f15,f16,f17,f18])
f19=utils.facet([(0,y,0),(0,1.5*y,0),(x,y,0)],fixed=True,material=m2)
f20=utils.facet([(x,y,0),(x,1.5*y,0),(0,1.5*y,0)],fixed=True,material=m2)
f=0
t=0
n=0
A=.3*.3
V=0.1
F=-13500
O.bodies.append([
  utils.facet([(0,0,0),(0,0,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(0,0,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(x,y,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,y,0),(x,y,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,y,0),(x,y,-z),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(x,y,0),(0,y,0),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(0,0,0),(0,y,0),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(0,0,0),(0,0,-z),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(0,0,-z),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(x,y,-z),(0,y,-z)],material=m2,fixed=True),f19,f20
        ])

O.engines=[
 ForceResetter(),
 InsertionSortCollider([Bo1_Polyhedra_Aabb(),Bo1_Facet_Aabb(),Bo1_Wall_Aabb()],verletDist=0.1),
 InteractionLoop(
   [Ig2_Polyhedra_Polyhedra_PolyhedraGeom(),Ig2_Facet_Polyhedra_PolyhedraGeom(),Ig2_Wall_Polyhedra_PolyhedraGeom()],
   [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()],
   [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()]
         ),
 NewtonIntegrator(gravity=(0,0,-9.81),damping=0.5),
 PyRunner(command='checkUnbalanced()',realPeriod=2,label='checker'),
   ]

O.dt=.05*polyhedra_utils.PWaveTimeStep()

yade.qt.View()
O.run()
O.saveTmp()

Jan Stránský (honzik) said : #12

Thanks

> PyRunner(command='checkUnbalanced()',realPeriod=2,label='checker'),

I am getting "NameError: name 'checkUnbalanced' is not defined"
in MWE, W stands for working, please next time check that the MWE is working and does not produce errors.. (now it is trivial to fix)
Also check that the MWE actually reproduce your problem. I suppose you did not check it (?) and it is possible that the problem was in the deleted code..

cheers
Jan

Ali HAIDAR (alihaidar976) said : #13

I am really sorry.
This one will work for sure after defining the list of vertices.
The problem is that after waiting for the polyhedrons to deposit, several polyhedrons will start escaping out of the box.
It needs time to inspect the problem since the deposition process is a little bit long.

from yade import plot,polyhedra_utils

m = PolyhedraMat()
m.density = 2607 #kg/m^3
m.frictionAngle = 0.05 #rad
#m.young = 1E10 #Pa
#m.poisson = 20000/1E6
m2= PolyhedraMat()
m2.frictionAngle = 0.3 #rad
m2.young = 1E300
x=.3
y=.3
z=.2
a=b=0.04
i=0
while a<=(x-0.05):
  while b<=(y-0.05):
    O.bodies.append([
                     polyhedra_utils.polyhedra(material=m,v=v1),
                     polyhedra_utils.polyhedra(material=m,v=v2),
                     polyhedra_utils.polyhedra(material=m,v=v3),
                     polyhedra_utils.polyhedra(material=m,v=v4),
                     polyhedra_utils.polyhedra(material=m,v=v5),
                     polyhedra_utils.polyhedra(material=m,v=v6),
                     polyhedra_utils.polyhedra(material=m,v=v7),
                     polyhedra_utils.polyhedra(material=m,v=v8),
                     polyhedra_utils.polyhedra(material=m,v=v9),
                     polyhedra_utils.polyhedra(material=m,v=v10),
                     polyhedra_utils.polyhedra(material=m,v=v11),
                     polyhedra_utils.polyhedra(material=m,v=v12),
                     polyhedra_utils.polyhedra(material=m,v=v13),
                     polyhedra_utils.polyhedra(material=m,v=v14),
                     polyhedra_utils.polyhedra(material=m,v=v15),
      ]
     )
    if i==0 or i==5 or i==13 or i==10:
      O.bodies[-1].state.pos=(a,b,.04-z)
      O.bodies[-2].state.pos=(a,b,.12-z)
      O.bodies[-3].state.pos=(a,b,.2-z)
      O.bodies[-4].state.pos=(a,b,.28-z)
      O.bodies[-5].state.pos=(a,b,.36-z)
      O.bodies[-6].state.pos=(a,b,.44-z)
      O.bodies[-7].state.pos=(a,b,.52-z)
      O.bodies[-8].state.pos=(a,b,.6-z)
      O.bodies[-9].state.pos=(a,b,.68-z)
      O.bodies[-10].state.pos=(a,b,.76-z)
      O.bodies[-11].state.pos=(a,b,.84-z)
      O.bodies[-12].state.pos=(a,b,.92-z)
      O.bodies[-13].state.pos=(a,b,1-z)
      O.bodies[-14].state.pos=(a,b,1.08-z)
      O.bodies[-15].state.pos=(a,b,1.16-z)
    if i==1 or i==6 or i==12 or i==8:
      O.bodies[-15].state.pos=(a,b,.04-z)
      O.bodies[-14].state.pos=(a,b,.12-z)
      O.bodies[-13].state.pos=(a,b,.2-z)
      O.bodies[-12].state.pos=(a,b,.28-z)
      O.bodies[-11].state.pos=(a,b,.36-z)
      O.bodies[-10].state.pos=(a,b,.44-z)
      O.bodies[-9].state.pos=(a,b,.52-z)
      O.bodies[-8].state.pos=(a,b,.6-z)
      O.bodies[-7].state.pos=(a,b,.68-z)
      O.bodies[-6].state.pos=(a,b,.76-z)
      O.bodies[-5].state.pos=(a,b,.84-z)
      O.bodies[-4].state.pos=(a,b,.92-z)
      O.bodies[-3].state.pos=(a,b,1-z)
      O.bodies[-2].state.pos=(a,b,1.08-z)
      O.bodies[-1].state.pos=(a,b,1.16-z)
    if i==4 or i==15 or i==11 or i==9:
      O.bodies[-12].state.pos=(a,b,.04-z)
      O.bodies[-3].state.pos=(a,b,.12-z)
      O.bodies[-9].state.pos=(a,b,.2-z)
      O.bodies[-5].state.pos=(a,b,.28-z)
      O.bodies[-10].state.pos=(a,b,.36-z)
      O.bodies[-15].state.pos=(a,b,.44-z)
      O.bodies[-4].state.pos=(a,b,.52-z)
      O.bodies[-1].state.pos=(a,b,.6-z)
      O.bodies[-6].state.pos=(a,b,.68-z)
      O.bodies[-8].state.pos=(a,b,.76-z)
      O.bodies[-2].state.pos=(a,b,.84-z)
      O.bodies[-7].state.pos=(a,b,.92-z)
      O.bodies[-11].state.pos=(a,b,1-z)
      O.bodies[-14].state.pos=(a,b,1.08-z)
      O.bodies[-13].state.pos=(a,b,1.16-z)
    if i==3 or i==7 or i==2 or i==14:
      O.bodies[-13].state.pos=(a,b,.04-z)
      O.bodies[-14].state.pos=(a,b,.12-z)
      O.bodies[-11].state.pos=(a,b,.2-z)
      O.bodies[-7].state.pos=(a,b,.28-z)
      O.bodies[-2].state.pos=(a,b,.36-z)
      O.bodies[-8].state.pos=(a,b,.44-z)
      O.bodies[-6].state.pos=(a,b,.52-z)
      O.bodies[-1].state.pos=(a,b,.6-z)
      O.bodies[-4].state.pos=(a,b,.68-z)
      O.bodies[-15].state.pos=(a,b,.76-z)
      O.bodies[-10].state.pos=(a,b,.84-z)
      O.bodies[-5].state.pos=(a,b,.92-z)
      O.bodies[-9].state.pos=(a,b,1-z)
      O.bodies[-3].state.pos=(a,b,1.08-z)
      O.bodies[-12].state.pos=(a,b,1.16-z)
    b=b+0.07
    i=i+1
  a=a+0.07
  b=0.04

f1=utils.facet([(0,0,0),(0,0,z),(x,0,0)],material=m2)
f2=utils.facet([(x,0,z),(0,0,z),(x,0,0)],material=m2)
f3=utils.facet([(x,0,z),(x,y,z),(x,0,0)],material=m2)
f4=utils.facet([(x,y,0),(x,y,z),(x,0,0)],material=m2)
f5=utils.facet([(x,y,0),(x,y,z),(0,y,z)],material=m2)
f6=utils.facet([(x,y,0),(0,y,0),(0,y,z)],material=m2)
f7=utils.facet([(0,0,0),(0,y,0),(0,y,z)],material=m2)
f8=utils.facet([(0,0,0),(0,0,z),(0,y,z)],material=m2)
f9=utils.facet([(0,0,0),(0,-.5*y,0),(x,-.5*y,0)],material=m2)
f10=utils.facet([(0,0,0),(x,-.5*y,0),(x,0,0)],material=m2)
f11=utils.facet([(0,0,z),(0,0,5*z),(x,0,z)],material=m2)
f12=utils.facet([(x,0,5*z),(0,0,5*z),(x,0,z)],material=m2)
f13=utils.facet([(x,0,5*z),(x,y,5*z),(x,0,z)],material=m2)
f14=utils.facet([(x,y,z),(x,y,5*z),(x,0,z)],material=m2)
f15=utils.facet([(x,y,z),(x,y,5*z),(0,y,5*z)],material=m2)
f16=utils.facet([(x,y,z),(0,y,z),(0,y,5*z)],material=m2)
f17=utils.facet([(0,0,z),(0,y,z),(0,y,5*z)],material=m2)
f18=utils.facet([(0,0,z),(0,0,5*z),(0,y,5*z)],material=m2)
O.bodies.append([f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f11,f12,f13,f14,f15,f16,f17,f18])
f19=utils.facet([(0,y,0),(0,1.5*y,0),(x,y,0)],fixed=True,material=m2)
f20=utils.facet([(x,y,0),(x,1.5*y,0),(0,1.5*y,0)],fixed=True,material=m2)
f=0
t=0
n=0
A=.3*.3
V=0.1
F=-13500
O.bodies.append([
  utils.facet([(0,0,0),(0,0,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(0,0,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(x,y,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,y,0),(x,y,-z),(x,0,0)],material=m2,fixed=True),
  utils.facet([(x,y,0),(x,y,-z),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(x,y,0),(0,y,0),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(0,0,0),(0,y,0),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(0,0,0),(0,0,-z),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(0,0,-z),(0,y,-z)],material=m2,fixed=True),
  utils.facet([(x,0,-z),(x,y,-z),(0,y,-z)],material=m2,fixed=True),f19,f20
        ])

O.engines=[
 ForceResetter(),
 InsertionSortCollider([Bo1_Polyhedra_Aabb(),Bo1_Facet_Aabb(),Bo1_Wall_Aabb()],verletDist=0.1),
 InteractionLoop(
   [Ig2_Polyhedra_Polyhedra_PolyhedraGeom(),Ig2_Facet_Polyhedra_PolyhedraGeom(),Ig2_Wall_Polyhedra_PolyhedraGeom()],
   [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()],
   [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()]
         ),
 NewtonIntegrator(gravity=(0,0,-9.81),damping=0.5),
   ]

O.dt=.05*polyhedra_utils.PWaveTimeStep()

yade.qt.View()
O.run()
O.saveTmp()

Jan Stránský (honzik) said : #14

> I am really sorry.

no problem for the first question

> It needs time ... since the deposition process is a little bit long.

yes, I noticed :-D
currently I do not have capacity myself to run it so long (need my computer for other tasks)..

Try to use walls instead of facets if possible, might help. I am not sure how the contact is evaluated at the connection of two facets.
Also defining the boundary as thin polyhedrons with very high stiffness might improve the problem..

cheers
Jan

Can you help with this problem?

Provide an answer of your own, or ask Ali HAIDAR for more information if necessary.

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