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[Mahdeyeh <question686446@xxxxxxxxxxxxxxxxxxxxx>]

Question #686446 on Yade changed:
https://answers.launchpad.net/yade/+question/686446

    Status: Needs information => Open

Mahdeyeh gave more information on the question:
Here is my code:


from yade import export,polyhedra_utils
import os
from yade import plot
import math
from yade import utils
import pylab
import matplotlib; matplotlib.rc('axes',grid=True)
from matplotlib import pyplot
import numpy as np
from numpy import *



RawVer=np.genfromtxt('ri.txt',names=True,dtype=None)
# ListVer is list of all the vertices of ring`s 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+(0.2,)   # add z vertex to coordinates
    if not Cordn1 in Ver:
        Ver=Ver+(Cordn1,Cordn2)
ListVer.append(Ver)

RawVer1=np.genfromtxt('boundary.txt',names=True,dtype=None)
# ListVer is list of all the vertices of boundary`s polygons
Ver1=()
ListVer1=[]
for b in RawVer1:
    if b[0]=='*LWPOLYLINE':
        ListVer1.append(Ver1)
        Ver1=()
        continue
    Cordn=b[0]
    Cordn=np.fromstring(Cordn, sep=',')
    Cordn=tuple(Cordn.tolist())
    Cordn1=Cordn+(-2,)   # add z vertex to coordinates 
    Cordn2=Cordn+(2,)   # add z vertex to coordinates
    if not Cordn1 in Ver1:
        Ver1=Ver1+(Cordn1,Cordn2)
ListVer1.append(Ver1)

RawVer2=np.genfromtxt('wa.txt',names=True,dtype=None)
# ListVer is list of all the vertices of caved waste rock`s polygons
Ver2=()
ListVer2=[]
for b in RawVer2:
    if b[0]=='*LWPOLYLINE':
        ListVer2.append(Ver2)
        Ver2=()
        continue
    Cordn=b[0]
    Cordn=np.fromstring(Cordn, sep=',')
    Cordn=tuple(Cordn.tolist())
    Cordn1=Cordn+(0.1,)   # add z vertex to coordinates 
    Cordn2=Cordn+(0.2,)   # add z vertex to coordinates
    if not Cordn1 in Ver2:
        Ver2=Ver2+(Cordn1,Cordn2)
ListVer2.append(Ver2)


Dolomite = PolyhedraMat()
Dolomite.density = 2870 #kg/m^3 
Dolomite.young = 24.36e9 #Pa 
Dolomite.poisson = 0.2
Dolomite.frictionAngle = radians(55.12) #rad

Shale = PolyhedraMat()
Shale.density = 2750 #kg/m^3 
Shale.young = 6e9 #Pa 
Shale.poisson = 0.23
Shale.frictionAngle = radians(42) #rad

for ii in ListVer:
    O.bodies.append(polyhedra_utils.polyhedra(Dolomite,v=ii,fixed=False, color=(0.1,0.5,0.2), mask=3))

for iii in ListVer1:
    O.bodies.append(polyhedra_utils.polyhedra(Dolomite,v=iii,fixed=True, color=(1,0,1), mask=4))

for iiii in ListVer2:
    O.bodies.append(polyhedra_utils.polyhedra(Shale,v=iiii,fixed=False, color=(0.9,0.81,0.45), mask=5))



O.bodies.erase(12)   


 

def checkUnbalanced():   
    print "iter %d , unbalanced forces %f"%(O.iter, utils.unbalancedForce())  # %[(keyname)][flags][width][.precision]typecode : String Formatting

O.engines=[
   ForceResetter(),
   InsertionSortCollider([Bo1_Polyhedra_Aabb(),]), # We can set collider's verletDist to a fraction of the polyhedra minimum size, since it determines how much is each body enlarged to avoid collision detection at every step.
   InteractionLoop(
      [Ig2_Polyhedra_Polyhedra_PolyhedraGeom(),], 
      [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], # collision "physics"
      [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()]   # contact law -- apply forces
   ),
   NewtonIntegrator(gravity=(0,-9.81,0),damping=0.2),
]

O.engines=O.engines+[PyRunner(iterPeriod=20,command='calm()',label="calmRunner")]  #  because we need to calm only on the first few steps in our model.
O.engines=O.engines+[PyRunner(command='checkUnbalanced()',iterPeriod=1000,label="checker")]  # call our function defined above 1000 cycles


polyhedra_utils.SizeRatio()    # save sizes of polyhedra into file

export.textPolyhedra('poly.txt')   # Save polyhedra into a text file,
id, number of vertices and number of surfaces, particleVelocity and ...
.


clrOre=[0.1,0.5,0.2]
clrWaste=[0.9,0.81,0.45]


def positions():
    for b in O.bodies:
        if b.shape.color==clrOre:
            print "%.9f  , %.9f , %.9f "%(b.state.pos[0],b.state.pos[1],b.state.pos[2])
            time1=O.time
        
            Positions=open("Positions time x y z.txt","a")
            Positions.write(repr(time1)+'	'+repr(b.state.pos[0])+'	'+repr(b.state.pos[1])+'	'+repr(b.state.pos[2])+'	'"\n")
            Positions.close() 
            

O.engines=O.engines+[PyRunner(command='positions()',realPeriod=0.5,label="flow")]
# call our function defined above every 60 seconds


O.dt=10e-6


iii=0
while iii<50:
    O.run(1000,True)
    iii+=1


O.save('test1.bz2')
O.saveTmp('test1')

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