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[Mahdeyeh <question684492@xxxxxxxxxxxxxxxxxxxxx>]

Question #684492 on Yade changed:
https://answers.launchpad.net/yade/+question/684492

Description changed to:
Hi there

I drew my whole polygons in Autocad (2D) and exported the vertices of them (of AutoCad) as text for using in YADE and creating polyhedra. I did that because I want pack of many polyhedrons with very small void and certain shape and size.  
Here is my code:


import numpy as np
from numpy import *

RawVer=np.genfromtxt('polyline.txt',names=True,dtype=None)
# ListVer is list of all the vertices of all the polygons
Ver=()
ListVer=[]
for b in RawVer:
    if b[0]=='*LWPOLYLINE':
        ListVer.append(Ver)
        Ver=()
        continue
    Cordn=b[0]
    Cordn=np.fromstring(Cordn, sep=',')
    Cordn=tuple(Cordn.tolist())
    Cordn1=Cordn+(0.1,)   # add z vertex to coordinates 
    Cordn2=Cordn+(0.3,)   # add z vertex to coordinates
    if not Cordn1 in Ver:
        Ver=Ver+(Cordn1,Cordn2)
ListVer.append(Ver)


from yade import plot, polyhedra_utils


Dolomite = PolyhedraMat()
Dolomite.density = 2870 
Dolomite.young = 24.36e9  
Dolomite.poisson = 0.2
Dolomite.frictionAngle = radians(55.12) 


for ii in ListVer:
    O.bodies.append(polyhedra_utils.polyhedra(Dolomite,v=ii,fixed=True, color=(1,0.5,1), mask=3))


for b in O.bodies:
    b.state.blockedDOFs='zXYZ'


O.engines=[
   ForceResetter(),
   InsertionSortCollider([Bo1_Polyhedra_Aabb(),]),
   InteractionLoop(
      [Ig2_Polyhedra_Polyhedra_PolyhedraGeom(),], 
      [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], 
      [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()]   
   ),
   NewtonIntegrator(damping=0.6,gravity=(0,-9.81,0)),
]


O.engines=O.engines+[PyRunner(iterPeriod=20,command='calm()',label="calmRunner")]  

O.dt=10e-6

O.run(50000,True)
print(O.dt)


After run script, when  I see graphical interface, particles are not near each other and they have moved far from each other. If I decrease young module, particles will be near each other same as initial model in AutoCad.
But I don`t want to decrease young module. I thought this distance and exploding between particles is because of overlapping of polyhedra vertices and then with Offset in AUTOCAD I moved polygons vertices so they hadn`t overlapping any more but the problem didn`t solve.

I should mention; after this step, I should allow particles move down under gravity. 
Now please help me Why the particles move and aren`t near each other?
How I should fix this problem

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