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[Question #694148]: why my particles don`t show in paraview?

To: yade-users@xxxxxxxxxxxxxxxxxxx
From: Mahdeyeh <question694148@xxxxxxxxxxxxxxxxxxxxx>
Date: Mon, 23 Nov 2020 14:20:50 -0000
Reply-to: question694148@xxxxxxxxxxxxxxxxxxxxx
Sender: bounces@xxxxxxxxxxxxx
New question #694148 on Yade:
https://answers.launchpad.net/yade/+question/694148

Hello 
when I check model in paraview, just I see facets and there aren`t clumps or particles. why? 

here is codes:

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
from yade import qt
import numpy as np
from numpy import *
from yade import export as expt

# Materials type:

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

Bound = FrictMat()
Bound.density = 2870 #kg/m^3 
Bound.young = 60e10 #Pa 
Bound.poisson = 0.2
Bound.frictionAngle = radians(55.12) #rad

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

#O.materials.append(Dolomite)

SphCordns=np.genfromtxt('ring.txt',names=True,dtype=None)
ListSph=[]
LayNo=SphCordns[0][4]
for b in SphCordns:
    if LayNo!=b[4]:
        LayNo=b[4]
        O.bodies.appendClumped(ListSph)
        ListSph=[]
    ListSph.append(sphere([b[0],b[1],b[2]], radius=b[3], color=(0.1,0.5,0.2),material=Dolomite))


SphCordns=np.genfromtxt('waste.txt',names=True,dtype=None)
ListSph=[]
LayNo=SphCordns[0][4]
for b in SphCordns:
    if LayNo!=b[4]:
        LayNo=b[4]
        O.bodies.appendClumped(ListSph)
        ListSph=[]
    ListSph.append(sphere([b[0],b[1],b[2]], radius=b[3], color=(0.8,0.9,0.9),material=Shale))


v1=((-2.4993,-0.01,2),(-2,-0.01,2),(-2.4993,-0.01,-2))
v2=((-2,-0.01,2),(-2,-0.01,-2),(-2.4993,-0.01,-2))
v3=((-1.99,-0.01,2),(-1.99,-0.01,-2),(-1,-0.01,2))
v4=((-1,-0.01,2),(-1,-0.01,-2),(-1.99,-0.01,-2))
v5=((-0.99,-0.01,2),(-0.99,-0.01,-2),(1,-0.01,2))
v6=((1,-0.01,2),(1,-0.01,-2),(-0.99,-0.01,-2))
v7=((1.01,-0.01,2),(1.01,-0.01,-2),(2,-0.01,2))
v8=((2,-0.01,2),(2,-0.01,-2),(1.01,-0.01,-2))
v9=((2.01,-0.01,2),(2.01,-0.01,-2),(3,-0.01,2))
v10=((3,-0.01,2),(3,-0.01,-2),(2.01,-0.01,-2))
v11=((3.01,-0.01,2),(3.01,-0.01,-2),(4.58,-0.01,2))
v12=((4.58,-0.01,2),(4.58,-0.01,-2),(3.01,-0.01,-2))
v13=((4.7,0.0059,2),(5.3,0.93,2),(4.7,0.0059,-2))
v14=((5.3,0.93,2),(5.3,0.93,-2),(4.7,0.0059,-2))
v15=((5.3,0.94,2),(5.3,0.94,-2),(6.47,2.57,2))
v16=((6.47,2.57,2),(6.47,2.57,-2),(5.3,0.94,-2))
v17=((6.47,2.58,2),(6.47,2.58,-2),(6.85,3.01,2))
v18=((6.85,3.01,2),(6.85,3.01,-2),(6.47,2.58,-2))
v19=((6.85,3.0162,2),(6.851,4,2),(6.85,3.0162,-2))
v20=((6.85,3.0162,-2),(6.851,4,-2),(6.851,4,2))
v21=((6.851,4.0079,2),(7.08,5.6,2),(6.851,4.0079,-2))
v22=((7.08,5.6,2),(7.08,5.6,-2),(6.851,4.0079,-2))
v23=((7.08,5.61,2),(7.08,5.61,-2),(7.35,7.01,2))
v24=((7.35,7.01,2),(7.35,7.01,-2),(7.08,5.61,-2))
v25=((7.35,7.02,2),(7.35,7.02,-2),(7.59,8.51,2))
v26=((7.59,8.51,2),(7.59,8.51,-2),(7.35,7.02,-2))
v27=((7.59,8.52,2),(7.59,8.52,-2),(7.85,10,2))
v28=((7.85,10,2),(7.85,10,-2),(7.59,8.52,-2))
v29=((7.85,10.01,2),(7.85,10.01,-2),(8.19,12,2))
v30=((8.19,12,2),(8.19,12,-2),(7.85,10.01,-2))
v31=((8.19,12.01,2),(8.19,12.01,-2),(8.55,14,2))
v32=((8.55,14,2),(8.55,14,-2),(8.19,12,-2))
v33=((8.55,14.01,2),(8.55,14.01,-2),(8.8,15.5,2))
v34=((8.8,15.5,2),(8.8,15.5,-2),(8.55,14.01,-2))
v35=((8.8,15.51,2),(8.8,15.51,-2),(9.1,16.9981,2))
v36=((9.1,16.9981,2),(9.1,16.9981,-2),(8.8,15.51,-2))
v37=((9.1,17.0187,2),(9.15,19,2),(9.1,17.087,-2))
v38=((9.15,19,2),(9.15,19,-2),(9.1,17.0187,-2))
v39=((9.15,19.01,2),(9.15,19.01,-2),(9.25,20.9992,2))
v40=((9.25,20.9992,2),(9.25,20.9992,-2),(9.15,19.01,-2))
v41=((9.29,21.1,2),(9.29,21.1,-2),(9.38,22.7,2))
v42=((9.38,22.7,2),(9.38,22.7,-2),(9.29,21.1,-2))
v43=((9.38,22.73,2),(9.38,22.73,-2),(9.40,25.3,2))
v44=((9.4,25.3,2),(9.4,25.3,-2),(9.38,22.73,-2))
v45=((5.45,25.3,2),(5.45,25.3,-2),(5.32,22.5,2))
v46=((5.32,22.5,2),(5.32,22.5,-2),(5.45,25.3,-2))
v47=((5.32,22.4,2),(5.32,22.4,-2),(5.32,20,2))
v48=((5.32,20,2),(5.32,20,-2),(5.32,22.4,-2))
v49=((5.32,19.96,2),(5.32,19.96,-2),(5.82,19.96,2))
v50=((5.82,19.96,2),(5.82,19.96,-2),(5.32,19.96,-2))
v51=((5.82,19.94,2),(5.82,19.94,-2),(5.57,18.5,2))
v52=((5.57,18.5,2),(5.57,18.5,-2),(5.82,19.94,-2))
v53=((5.53,18.45,2),(5.53,18.45,-2),(5.3,17.2,2))
v54=((5.3,17.2,2),(5.3,17.2,-2),(5.53,18.45,-2))
v55=((5.3,17.15,2),(5.3,17.15,-2),(5.1,16,2))
v56=((5.1,16,2),(5.1,16,-2),(5.3,17.15,-2))
v57=((5.1,15.98,2),(5.1,15.98,-2),(4.88,15,2))
v58=((4.88,15,2),(4.88,15,-2),(5.1,15.98,-2))
v59=((4.9,14.98,2),(4.9,14.98,-2),(4.77,14.3,2))
v60=((4.77,14.3,2),(4.77,14.3,-2),(4.9,14.98,-2))
v61=((4.77,14.27,2),(4.77,14.27,-2),(4.64,13.5,2))
v62=((4.64,13.5,2),(4.64,13.5,-2),(4.77,14.27,-2))
v63=((4.64,13.47,2),(4.64,13.47,-2),(4.54,13,2))
v64=((4.54,13,2),(4.54,13,-2),(4.64,13.47,-2))
v65=((4.54,12.98,2),(4.54,12.98,-2),(4.39,12.2,2))
v66=((4.39,12.2,2),(4.39,12.2,-2),(4.54,12.98,-2))
v67=((4.39,12.18,2),(4.39,12.18,-2),(4.24,11.4,2))
v68=((4.24,11.4,2),(4.24,11.4,-2),(4.39,12.18,-2))
v69=((4.24,11.38,2),(4.24,11.38,-2),(4.1,10.55,2))
v70=((4.1,10.55,2),(4.1,10.55,-2),(4.24,11.38,-2))
v71=((4.1,10.53,2),(4.1,10.53,-2),(4,9.97,2))
v72=((4,9.97,2),(4,9.97,-2),(4.1,10.53,-2))
v73=((4,9.94,2),(4,9.94,-2),(3.87,9,2))
v74=((3.87,9,2),(3.87,9,-2),(4,9.94,-2))
v75=((3.87,8.99,2),(3.87,8.99,-2),(3.69,8,2))
v76=((3.69,8,2),(3.69,8,-2),(3.87,8.99,-2))
v77=((3.69,7.99,2),(3.69,7.99,-2),(3.51,7,2))
v78=((3.51,7,2),(3.51,7,-2),(3.69,7.99,-2))
v79=((3.51,6.99,2),(3.51,6.99,-2),(3.34,5.99,2))
v80=((3.34,5.99,2),(3.34,5.99,-2),(3.51,6.99,-2))
v81=((3.34,5.98,2),(3.34,5.98,-2),(3.16,4.98,2))
v82=((3.16,4.98,2),(3.16,4.98,-2),(3.34,5.98,-2))
v83=((3.16,4.97,2),(3.16,4.97,-2),(2.95,4.0001,2))
v84=((2.95,4.0001,2),(2.95,4.0001,-2),(3.16,4.97,-2))
v85=((0,4,2),(0,4,-2),(2.9,3.9,2))
v86=((0,4,-2),(2.9,3.9,2),(2.9,3.9,-2))

O.bodies.append(utils.facet(v1,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v2,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v3,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v4,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v5,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v6,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v7,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v8,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v9,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v10,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v11,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v12,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v13,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v14,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v15,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v16,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v17,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v18,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v19,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v20,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v21,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v22,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v23,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v24,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v25,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v26,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v27,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v28,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v29,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v30,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v31,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v32,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v33,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v34,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v35,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v36,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v37,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v38,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v39,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v40,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v41,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v42,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v43,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v44,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v45,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v46,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v47,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v48,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v49,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v50,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v51,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v52,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v53,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v54,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v55,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v56,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v57,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v58,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v59,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v60,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v61,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v62,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v63,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v64,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v65,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v66,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v67,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v68,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v69,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v70,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v71,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v72,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v73,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v74,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v75,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v76,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v77,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v78,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v79,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v80,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v81,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v82,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v83,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v84,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v85,color=(1,0,1), material=Bound))
O.bodies.append(utils.facet(v86,color=(1,0,1), material=Bound))


for b in O.bodies:
    if b.material is Dolomite or b.material is Shale:
        b.state.blockedDOFs='zXY'
        b.state.angMom[2]=0
        b.state.angVel[2]=0
        b.state.vel[2]=0



O.engines=[
   ForceResetter(),
   InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()],verletDist=0.001),
   InteractionLoop(
      [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], 
      [Ip2_FrictMat_FrictMat_FrictPhys()], 
      [Law2_ScGeom_FrictPhys_CundallStrack()]   
   ),
   NewtonIntegrator(gravity=(0,-9.81,0),damping=0.2),
]

utils.calm()
O.dt=10e-6
O.run(1000,True)
O.run()

os.mkdir(O.tags['id'])   
O.engines=O.engines+[PyRunner(iterPeriod=10000,command='VTKview()',label="VTKview")]         
ClumpVtkData = expt.VTKExporter(O.tags['id']+'/'+'clumpData')          
def VTKview():
    ClumpVtkData.exportSpheres(ids='all', what={('color','b.shape.color')})
    ClumpVtkData.exportFacets(ids='all', what={('color','b.shape.color')})



thanks a lot 

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