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[Question #671006]: Too many pore throats have been adjusted

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New question #671006 on Yade:
https://answers.launchpad.net/yade/+question/671006

Hi,

I am working on the coupling of DEM and PFV. When I use the function of 'actinoTPF()' of UnsaturatedEngine, the program crash and show the following information:
-----------------------------------------------------------------------------------------------------------
WARNING! rmin>rmax. rmin=0.176802 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.176802 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.19667 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.202432 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.202432 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.19667 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.234851 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.232155 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.232155 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.234851 ,rmax=1e-10

Welcome to the two-phase flow Engine
by T.Sweijen, B.Chareyre and S.M.Hassanizadeh
For contact: T.Sweijen@uu.nlWARNING! rmin>rmax. rmin=0.176802 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.176802 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.19667 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.202432 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.202432 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.19667 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.234851 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.232155 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.232155 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.234851 ,rmax=1e-10

Error! Too many pore throats have been adjusted, more than 10%. Simulation is stopped2865 tot:7332
Error! Too many pore throats have been adjusted, more than 10%. Simulation is stopped1816 tot:7332
Error! Too many pore throats have been adjusted, more than 10%. Simulation is stopped1691 tot:7332
Error! Too many pore throats have been adjusted, more than 10%. Simulation is stopped1689 tot:7332
Error! Too many pore throats have been adjusted, more than 10%. Simulation is stopped1689 tot:7332Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-99.1101 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-83.1875 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-73.6424 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-120.595 132.556Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-91.3727 102.514Error, saturation from Pc(S) curve is not correct: 1.35569 -1 log:-6.98179 -5.15 pw=-435.509 435.105Error, saturation from Pc(S) curve is not correct: 1.35569 -1 log:-6.98179 -5.15 pw=-435.509 435.105
entry saturation error!1.10401 517 0.0256674 0.0126551
Simulation is terminated because of an error in entry saturation!Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-83.5472 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-59.7782 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-59.7782 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-95.4429 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-87.9524 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-64.482 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-75.6826 102.514Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-91.8705 132.556Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-89.2921 102.514Error, saturation from Pc(S) curve is not correct: 1.17045 -1 log:-4.53153 -3.8716 pw=-284.131 281.073Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-114.795 132.556Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-60.4799 102.514Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-107.287 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-110.389 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-107.287 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-79.699 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-79.699 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-88.9439 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-88.9439 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-93.9523 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-110.389 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-120.595 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 -1 log:nan -35.4098 pw=-121.624 132.556Error, saturation from Pc(S) curve is not correct: 1.10874 -1 log:-8.54795 -7.7096 pw=-245.342 245.295Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-78.2814 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-69.6981 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 -1 log:nan -39.1871 pw=-64.482 102.514
Boundary and initial conditions are set for: Primary Drainage
Water pressure at: -2000 and air pressure at: 0 InitialPC: 2000Error, saturation from Pc(S) curve is not correct: -0.0750167 1 log:nan -39.1871 pw=-91.3727 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 1 log:nan -39.1871 pw=-83.5472 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 1 log:nan -39.1871 pw=-59.7782 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 1 log:nan -39.1871 pw=-64.482 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 1 log:nan -39.1871 pw=-60.4799 102.514Error, saturation from Pc(S) curve is not correct: -0.0750167 1 log:nan -39.1871 pw=-78.2814 102.514Error, saturation from Pc(S) curve is not correct: -0.031019 44 log:nan -35.4098 pw=-99.1101 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 44 log:nan -35.4098 pw=-83.1875 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 44 log:nan -35.4098 pw=-73.6424 132.556Error, saturation from Pc(S) curve is not correct: -0.031019 4Segmentation fault (core dumped)
-------------------------------------------------------------------------------------------

Actually, even though I haven't use 'actionTPF()', the following warning appears:
------------------------------------------------------------------------------
WARNING! rmin>rmax. rmin=0.171706 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.190537 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.190537 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.188082 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.171706 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.188082 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.190463 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.21136 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.191666 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.206474 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.206474 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.191666 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.21136 ,rmax=1e-10
WARNING! rmin>rmax. rmin=0.190463 ,rmax=1e-10
---------------------------------------------------------------------------------

If I try 'unsat.invasion()' instead of 'unsat.actionTPF()', the program didn't crash.

Can anyone give me some suggestion about what 'rmin' and 'rmax' is and what wrong with the function 'actionTPF()'[1]? Thanks a lot.

[1]https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.UnsaturatedEngine.actionTPF

I'm running Yade 2018.02b, Ubuntu 18.04.

My code is shown as follow:
==============================================================
from yade import pack,qt,plot

key=1

num_spheres=1000# number of spheres
young=1e6
compFricDegree = 3 # initial contact friction during the confining phase
finalFricDegree = 30 # contact friction during the deviatoric loading
mn,mx=Vector3(0,0,0),Vector3(2,2,6) # corners of the initial packing

O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)

sp=pack.SpherePack()
sp.makeCloud(mn,mx,rMean=0.3,rRelFuzz=0,num=50,periodic=False)
sp.makeCloud(mn,mx,rMean=0.03,rRelFuzz=0,num=1000,periodic=False)
sp.toSimulation(material='spheres')

triax=TriaxialStressController(
	thickness = 0,
	stressMask = 7,
	max_vel = 0.005,
	internalCompaction=0, # If true the confining pressure is generated by growing particles
#    wall_bottom_activated=False
)

newton=NewtonIntegrator(damping=0.2)

#flow1=FlowEngine(dead=1,label="flow")

O.engines=[
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
		[Ip2_FrictMat_FrictMat_FrictPhys()],
		[Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop"
	),
	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
	triax,
	newton,
]

triax.goal1=triax.goal2=triax.goal3=-10000

while 1:
  O.run(1000,1)
  unb=unbalancedForce()
  if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001:
    break

setContactFriction(radians(finalFricDegree))
O.run(1000,1)

## ______________   Oedometer section   _________________

unsat=UnsaturatedEngine()

unsat.bndCondIsPressure=[0,0,0,0,1,1]
unsat.bndCondValue=[0,0,0,0,10,0]
unsat.isPhaseTrapped=True #the W-phase can be disconnected from its reservoir
unsat.initialization()
unsat.surfaceTension = 10

unsat.actionTPF()
============================================================================




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