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New question #693071 on Yade:
https://answers.launchpad.net/yade/+question/693071

hi

I encounter this problem "ValueError: cannot convert float NaN to integer" when running my script about "2D triax"…i get that "There should be a warning if mass = 0.0 and fixed = False ..." just dont know how to correct it, below is my code.

#############################################################################

from yade.gridpfacet import *
from yade import pack, plot
from random import random
import numpy as np
from numpy import *
import math

#parameters
rParticle = 0.14e-3#diameter0.28
rRelFuzz=.0005
mi,ma = (0.,0.,0.),(1000e-3,0,250e-3)
#nCyls,nSphs = 8000,28216
frictionAngleSph=30
frictionAngleCyl=30

#meterials########
O.materials.append(FrictMat(young=4.0e6,poisson=.3,frictionAngle=20,density=910e+6,label='sphcylMat'))
O.materials.append(FrictMat(young=4.0e6,poisson=.3,frictionAngle=26,density=910e+6,label='cylinderMat'))
O.materials.append(FrictMat(young=4.0e6,poisson=.15,frictionAngle=30,density=2630e+6,label='sphereMat'))
O.materials.append(FrictMat(young=4.0e6,poisson=.15,frictionAngle=0,density=0,label='walls'))

## create walls around the packing
walls=aabbWalls([(0,-0.5,0),(1000e-3,0.5,250e-3)],thickness=0,material='walls')
wallIds=O.bodies.append(walls)

##sphere
sp = yade.pack.SpherePack()
sp.makeCloud(mi,ma,porosity=0.7/1.7,psdSizes=[.00014,0.00016,0.00022,.0003,.00035],psdCumm=[0.,0.1,0.3,0.6,1.],num=35000)
#psdSizes=[0.01,0.0125,0.015,0.018,0.02,0.023,0.025,0.027,0.029,0.03],psdCumm=[0,0.05,0.15,0.38,0.54,0.77,0.9,0.97,0.99,1]) # makeCloud for spheres
spheres=sp.toSimulation(color=(0,0.5,0.7),material='sphereMat')
print "cheers"

for i in O.bodies:
 i.state.blockedDOFs="yXZ"
 i.shape.color=(0.,0.5,0.7)

num=0
vol=0
mass=0
area=0
for b in O.bodies:
 if isinstance(b.shape,Sphere):
     r=b.shape.radius
     x=b.state.pos[0]
     y=b.state.pos[1]
     z=b.state.pos[2]
     ID=b.id
     num+=1
     #vol+=4./3.*np.pi*r**3
     mass+=2.63*4./3.*np.pi*r**3
   area+=np.pi*r**2
print 'num,mass,voidRatio =',num,mass,((1000e-3*250e-3)-area)/area

length=6e-3
rfiber=0.023e-3/2
fibre_mass=np.pi*(rfiber)**2*length*0.91
Xw=0.5*1e-2 # fiber content
numFiber=Xw*mass/fibre_mass
print "the numer of fibres =",int(numFiber)

Ne=int(length/(0.28e-3/2))
print 'Ne=',Ne
nodesIds=[]
cylIds=[]
numFibre=0
#target_num=int(numFiber)
target_num=1200
deleted_sphere=0

####fiberfilewrite
fiberwr=open('fibers.txt','w')
cylNodes=[]

for n in range(2000):
 if numFibre<target_num:

  random.seed()
  l_x=random.uniform(0,1000e-3)
  l_z=random.uniform(0,250e-3)
  x0=l_x
  z0=l_z

  u1 = random.random()
  u2 = random.random()*pi
  u3 = random.random()*pi
  a = sqrt(1-u1)
  b = sqrt(u1)
  t=((a*cos(u2))**2+(b*sin(u3))**2)**0.5
  cosphi=a*cos(u2)/t
  sinphi=b*sin(u3)/t

  hx=length*cosphi
  hz=length*sinphi

  x1=x0+hx
  y1=0
  z1=z0+hz

  if 0<x1<1000e-3 and 0<z1<250e-3 and 0<x0<1000e-3 and 0<z0<250e-3:
   if len(cylNodes)<=1:
    fiberwr.write(str(numFibre)+'\t'+str(x0)+'\t'+str(0)+'\t'+str(z0)+'\t'+str(x1)+'\t'+str(0)+'\t'+str(z1)+'\n')
    cylNodes.append([x0,z0,x1,z1])
    numFibre+=1
    vertices=[]
    for i in range(0, Ne+1):
     px=float(i)*hx/float(Ne)+x0; py=0; pz=float(i)*hz/float(Ne)+z0;
     vertices.append([px,py,pz])
    cylinderConnection(vertices,0.023e-3/2,nodesIds,cylIds,color=[0.5,0.5,0],highlight=False,intMaterial='cylinderMat',extMaterial='fMat')
    print "+1"
   else:
    valid=True
    #print len(cylNodes)
    for c in cylNodes:
     #if(max(c[0],c[2])>=min(x0,x1)
     #and max(x0,x1)>=min(c[0],c[2])
     #and max(c[1],c[3])>=min(z0,z1)
     #and max(z0,z1)>=min(c[1],c[3])):
     x12=(x1-x0)
     z12=(z1-z0)
     x13=(c[0]-x0)
     z13=(c[1]-z0)
     x14=(c[2]-x0)
     z14=(c[3]-z0)
     cross1=x12*z13-x13*z12
     cross2=x12*z14-x14*z12
     x34=c[2]-c[0]
     z34=c[3]-c[1]
     x23=c[0]-x1
     z23=c[1]-z1
     x24=c[2]-x1
     z24=c[3]-z1
     cross3=x34*z23-x23*z34
     cross4=x34*z24-x24*z34
     if(cross1*cross2<=0
     and cross3*cross4<=0):
      valid=False
      print "next"
      break
    if valid:
     fiberwr.write(str(numFibre)+'\t'+str(x0)+'\t'+str(0)+'\t'+str(z0)+'\t'+str(x1)+'\t'+str(0)+'\t'+str(z1)+'\n')
     cylNodes.append([x0,z0,x1,z1])
     numFibre+=1
     #print "++1"
     vertices=[]
     for i in range(0, Ne+1):
      px=float(i)*hx/float(Ne)+x0; py=0; pz=float(i)*hz/float(Ne)+z0;
      vertices.append([px,py,pz])
     cylinderConnection(vertices,0.023e-3/2,nodesIds,cylIds,color=[0.5,0.5,0],highlight=False,intMaterial='cylinderMat',extMaterial='fMat')

   ###spherefileWrite
   ##################################################################
   sphwr=open('spheres.txt','w')
   for b in O.bodies:
    if isinstance(b.shape,Sphere):
         r=b.shape.radius
     if r>0.012e-3:
          x=b.state.pos[0]
         y=b.state.pos[1]
          z=b.state.pos[2]
      ID=b.id
      k=(z1-z0)/(x1-x0)
      #kx-z+z0-kx0=0
      A=k
      B=-1
      C=z0-k*x0
      #if (A*x+B*z+C)/(A^2+B^2)^0.5<=(0.14e-3+0.023e-3/2):
      if abs(k*x-1*z+C)/(k**2+1)**0.5<=(r+0.0115e-3):
       O.bodies.erase(b.id)
       deleted_sphere+=1
      #else:
      sphwr.write(str(ID)+'\t'+str(x)+'\t'+str(y)+'\t'+str(z)+'\t'+str(r)+'\n')
   sphwr.close()
   ##################################################################
fiberwr.close()
print 'numFibre , deleted_sphere =',numFibre, deleted_sphere

triax=TriaxialStressController(
 ## TriaxialStressController will be used to control stress and strain. It controls particles size and plates positions.
 ## this control of boundary conditions was used for instance in http://dx.doi.org/10.1016/j.ijengsci.2008.07.002
 # maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth)
 # finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth)
 thickness = 0,
 ## switch stress/strain control using a bitmask. What is a bitmask, huh?!
 ## Say x=1 if stess is controlled on x, mask = x*1 + y*2 + z*4
 ## "100" (1) means "x", "110" (3) means "x and y", "111" (7) means "x and y and z", etc.
 stressMask = 2,
 goal1=-0.9,
 goal2=0,
 goal3=-0.9,
 internalCompaction=False # If true the confining pressure is generated by growing particles
)

O.engines=[
 ForceResetter(),
 InsertionSortCollider([
  Bo1_Box_Aabb(),
  Bo1_Sphere_Aabb(),
  Bo1_GridConnection_Aabb(),
 ]),
 InteractionLoop([
  Ig2_Sphere_Sphere_ScGeom(),
  Ig2_Box_Sphere_ScGeom(),
  Ig2_GridNode_GridNode_GridNodeGeom6D(),
  Ig2_Sphere_GridConnection_ScGridCoGeom(),
  Ig2_GridConnection_GridConnection_GridCoGridCoGeom()
 ],
 [
  Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=False), # internal cylinder physics
  Ip2_FrictMat_FrictMat_FrictPhys() # physics for external interactions, i.e., cylinder-cylinder, sphere-sphere, cylinder-sphere
 ],
 [
  Law2_ScGeom_FrictPhys_CundallStrack(), # contact law for sphere-sphere
  Law2_ScGridCoGeom_FrictPhys_CundallStrack(), # contact law for cylinder-sphere
  Law2_ScGeom6D_CohFrictPhys_CohesionMoment(), # contact law for "internal" cylinder forces
  Law2_GridCoGridCoGeom_FrictPhys_CundallStrack() # contact law for cylinder-cylinder interaction
 ]
 ),
 GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.1,label='ts'),
 #triax,
 #TriaxialStateRecorder(iterPeriod=100,file='WallStresses'+table.key),
 NewtonIntegrator(gravity=(0,0,10),damping=0.1,label='newton'),
]

#######################################
### APPLYING CONFINING PRESSURE ###
#######################################

#the value of (isotropic) confining stress defines the target stress to be applied in all three directions
triax.goal1=triax.goal3=-10000
triax.goal2=0

Gl1_Sphere.stripes=1
yade.qt.Controller(), yade.qt.View()

print triax.porosity

###########################################################################

it is mainly about generating spheres and cylinders(fibers) then delete objects if they interact each other."ValueError: cannot convert float NaN to integer" occurs when i click the run button. thanks so much if anyone can help!!!!!!!!

xxxe

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