facet disappear when modifying examples/concrete/triax.py

Hi,everyone!

Due to the actual demand, the triaxial compression of rock I conducted was based on the cylinder shape and the simulation of triaxial compression under different confining pressures is successfully carried out.However,when I try to add flowengine to try fluid-solid coupling, an error occurs.(My code is attached at the end)

According to my purpose, I applied 30MPa confining pressure and 2MPa osmotic pressure. However, the stress-strain curve I obtained was close to the uniaxial compression result. When I opened the Show 3D interface, I found that the facet added in the script disappeared.(Maybe the cause of uniaxial compression results I guess?)

Thanks for help!

My code as follows:
######################
from yade import pack, ymport, plot, utils, export, timing
import numpy as np
import sys

young=66.2e9
name='JCFPM_triax'
compFricDegree=30
poisson=0.522
name='cylinder'
preStress=-30e6
strainRate = -0.1
OUT=str(preStress)+'_JCFPM_triax'
r1=0.005
r2=0.008

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
mny=min(ally)*1.01
mnz=min(allz)*0.99
mxx=max(allx)*1.01
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)
radius=0.0125
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(material='sphere',color=(0.9,0.8,0.6))

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[0].state.mass
for f in facets:
 f.state.mass = mass
 f.state.blockedDOFs = 'XYZz'

def lateral():
 elatTot=0.0
 nTot=0
 for b in O.bodies:
  x=b.state.refPos[0]
  y=b.state.refPos[1]
  d=sqrt(pow(x,2)+pow(y,2))
  if d > r1 and d < r2:
   b.shape.color=(0.6,0.5,0.15)
   xnew=b.state.pos[0]
   ynew=b.state.pos[1]
   dnew=sqrt(pow(xnew,2)+pow(ynew,2))
   elat=(dnew-d)/d
   elatTot+=elat
   nTot+=1
 elat_avg=elatTot/nTot
 return elat_avg

def addForces():
 for f in facets:
  n = f.shape.normal
  a = f.shape.area
  O.forces.addF(f.id,preStress*a*n)

def stopIfDamaged(maxEps=0.001):
 extremum = max(abs(s) for s in plot.data['s'])
 s = abs(plot.data['s'][-1])
 e = abs(plot.data['e'][-1])
 if O.iter < 1000 or e < maxEps:
  return
 if abs(s)/abs(extremum) < 0.5 :
  print('Simulation finished')
  presentcohesive_count = 0
  for i in O.interactions:
          if hasattr(i.phys, 'isCohesive'):
               if i.phys.isCohesive == True:
                   presentcohesive_count+=1
  print('the number of cohesive bond now is:',presentcohesive_count)
  print('Max stress and strain:',extremum,e)
  O.pause()

O.dt=.5*utils.PWaveTimeStep()
newton=NewtonIntegrator(damping=damp)

O.engines=[
 ForceResetter(),
 InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=1.5,label='is2aabb'),Bo1_Facet_Aabb()]),
 InteractionLoop(
  [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=1.5,label='ss2sc'),Ig2_Facet_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",multithread=False),
 newton,
 PyRunner(command='plotAddData()',iterPeriod=10),
 PyRunner(iterPeriod=20,command='stopIfDamaged()'),
]

def plotAddData():
 elat_avg=lateral()
 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(
  elateral = elat_avg,
  i = O.iter,
  s = -s,
  e = -e,
  tc = interactionLaw.nbTensCracks,
  sc = interactionLaw.nbShearCracks,
  flux1=flow.getBoundaryFlux(4),
  flux2=flow.getBoundaryFlux(5),
 )
 plot.saveDataTxt(OUT)

O.step()
ss2sc.interactionDetectionFactor=-1
is2aabb.aabbEnlargeFactor=-1

flow.debug=False
flow.permeabilityMap = False
flow.meshUpdateInterval=-1
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.bndCondIsTemperature=[0,0,0,0,0,0]
flow.thermalEngine=False
flow.thermalBndCondValue=[0,0,0,0,0,0]

flow.dead=0
flow.emulateAction()

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