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[Ziyu Wang <question702373@xxxxxxxxxxxxxxxxxxxxx>]

New question #702373 on Yade:
https://answers.launchpad.net/yade/+question/702373

Hi,
I'm trying to simulate the fluid-solid coupling of a cylinder and use flow.saveVtk() to save .vtk file to view relevant data in paraview.
However,when I open the .vtk files in paraview 5.9.1,I got the following error prompt:

###
Generic Warning: In /builds/gitlab-kitware-sciviz-ci/build/superbuild/paraview/src/VTK/IO/Legacy/vtkDataReader.cxx, line 1506
Error reading ascii data. Possible mismatch of datasize with declaration.
###

I do not know what happened..,thanks for help!

###my code###
from yade import pack, ymport, plot, utils, export, timing
import numpy as np
import sys
damp=0.4
young=66.2e9
name='JCFPM_triax'
poisson=0.522
name='cylinder'
preStress=-30e6
strainRate = -0.1
OUT=str(preStress)+'_JCFPM_triax'
r1=0.002
r2=0.01
nw=24
nh=15
rParticle=0.000731723
bcCoeff = 5
width = 0.025
height = 0.05

allx,ally,allz,r=np.genfromtxt('packing-cylinder.spheres', unpack=True)
mnx=min(allx)*1.01 #same as aabbExtrema, get the xyz of the lowest corner, multiply by factor to reduce it to let the wall surround all the spheres.
mny=min(ally)*1.01
mnz=min(allz)*0.99
mxx=max(allx)*1.01 #same as aabbExtrema, get the xyz of the top corner, multiply by factor to increase it to let the wall surround all the spheres.
mxy=max(ally)*1.01
mxz=max(allz)*1.01
Sy=2e6

O.materials.append(JCFpmMat(type=1,density=2640,young=young,poisson=poisson,tensileStrength=8e6,cohesion=40e6,frictionAngle=radians(25),label='sphere'))
O.materials.append(JCFpmMat(type=1,label='wall1',young=young,poisson=poisson,frictionAngle=radians(25)))
O.materials.append(JCFpmMat(type=1,frictionAngle=0,density=0,label='wall2'))

mn,mx=Vector3(mnx,mny,mnz),Vector3(mxx,mxy,mxz)
walls=aabbWalls([mn,mx],thickness=0,material='wall2')
wallIds=O.bodies.append(walls)

bottom,top=Vector3(0,0,0),Vector3(0,0,0.05)
sp=pack.SpherePack()
pred=pack.inCylinder(bottom,top,radius)
sp=pack.randomDensePack(pred,radius=0.0005,rRelFuzz=0,returnSpherePack=True,memoizeDb='/tmp/triax.sqlite')
spheres=sp.toSimulation(color=(0.9,0.8,0.6),material='sphere')

bot = [O.bodies[s] for s in spheres if O.bodies[s].state.pos[2]<rParticle*bcCoeff]
top = [O.bodies[s] for s in spheres if O.bodies[s].state.pos[2]>height-rParticle*bcCoeff]
vel = strainRate*(height-rParticle*2*bcCoeff)
for s in bot:
 s.shape.color = (1,0,0)
 s.state.blockedDOFs = 'xyzXYZ'
 #s.state.vel = (0,0,-vel)
for s in top:
 s.shape.color = Vector3(0,1,0)
 s.state.blockedDOFs = 'xyzXYZ'
 s.state.vel = (0,0,vel)

facets = []
rCyl2 = .5*width / cos(pi/float(nw))
for r in range(nw):
 for h in range(nh):
  v1 = Vector3( rCyl2*cos(2*pi*(r+0)/float(nw)), rCyl2*sin(2*pi*(r+0)/float(nw)), height*(h+0)/float(nh) )
  v2 = Vector3( rCyl2*cos(2*pi*(r+1)/float(nw)), rCyl2*sin(2*pi*(r+1)/float(nw)), height*(h+0)/float(nh) )
  v3 = Vector3( rCyl2*cos(2*pi*(r+1)/float(nw)), rCyl2*sin(2*pi*(r+1)/float(nw)), height*(h+1)/float(nh) )
  v4 = Vector3( rCyl2*cos(2*pi*(r+0)/float(nw)), rCyl2*sin(2*pi*(r+0)/float(nw)), height*(h+1)/float(nh) )
  f1 = facet((v1,v2,v3),color=(0,0,1),material='wall1')
  f2 = facet((v1,v3,v4),color=(0,0,1),material='wall1')
  facets.extend((f1,f2))

O.bodies.append(facets)
mass = O.bodies[7].state.mass
for f in facets:
 f.state.mass = mass
 f.state.blockedDOFs = 'XYZz'

def addForces():
 for f in facets:
  n = f.shape.normal
  a = f.shape.area
  O.forces.addF(f.id,preStress*a*n)
O.dt=.5*utils.PWaveTimeStep()
newton=NewtonIntegrator(damping=damp)
O.engines=[
 ForceResetter(),
 InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=1.5,label='is2aabb'),Bo1_Facet_Aabb(),Bo1_Box_Aabb()]),
 InteractionLoop(
  [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=1.5,label='ss2sc'),Ig2_Facet_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
  [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys()],
  [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(recordCracks=True,Key=OUT+'_Crack',label='interactionLaw')]
 ),
 PyRunner(iterPeriod=1,command="addForces()"),
 FlowEngine(dead=1,label="flow"),
 newton,
 PyRunner(command='plotAddData()',iterPeriod=10),
 PyRunner(iterPeriod=2000,command='flow.saveVtk(withBoundaries=1)'),
]

def plotAddData():
 perme = permeability()
 f1 = sum(O.forces.f(b.id)[2] for b in top)
 f2 = sum(O.forces.f(b.id)[2] for b in bot)
 f = .5*(f2-f1)
 s = f/(pi*.25*width*width)
 e = (top[0].state.displ()[2] - bot[0].state.displ()[2]) / (height-rParticle*2*bcCoeff)
 plot.addData(
  i = O.iter,
  s = -s,
  e = -e,
  tc = interactionLaw.nbTensCracks,
  sc = interactionLaw.nbShearCracks,
  permeab = perme
 )
 plot.saveDataTxt(OUT)
O.step()
ss2sc.interactionDetectionFactor=-1
is2aabb.aabbEnlargeFactor=-1

flow.debug=False
flow.permeabilityMap = False
flow.fluidBulkModulus=2.2e9
flow.useSolver=4
flow.permeabilityFactor=1
flow.viscosity= 0.001
flow.decoupleForces = False
flow.boundaryUseMaxMin=[0,0,0,0,0,0]
flow.bndCondIsPressure=[1,1,1,1,1,1]
flow.bndCondValue=[0,0,0,0,0,Sy]
flow.dead=0
flow.emulateAction()


plot.plots = { 'e':('s',), 'elateral':('s'),}
plot.plot()
O.run()
###

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