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[Question #700596]: negative volume for an ordinary pore (temp warning, should still be safe)

 

New question #700596 on Yade:
https://answers.launchpad.net/yade/+question/700596

Hello,
When I run my script,the prompt as shown in the title appears.
Actually,I search the forum and found [1] [2].But I see different solutions in these two links, which makes me very confused.
In [1],the solution is to use DFNFlowEngine instead of FlowEngine.In [2],the solution is to reduce the time step.
These are obviously two completely different solutions, and I don't know which one applies to me.
Following is my script:
---------------------------------------------
from yade import pack, ymport, plot, utils, export, timing
from builtins import range 
import numpy as np
#from __future__ import print_function
import sys

rate=-0.01
damp=0.4
stabilityThreshold=0.001
key='_triax_base_'
young=20e9
name='JCFPM_triax'
#targetPorosity=0.43
compFricDegree=30
poisson=0.1

mn,mx=Vector3(0,0,0),Vector3(0.05,0.05,0.05)
O.materials.append(JCFpmMat(type=1,density=2640,young=young,poisson=poisson,tensileStrength=15e6,cohesion=30e6,frictionAngle=radians(60),label='sphere'))
O.materials.append(JCFpmMat(type=1,frictionAngle=0,density=0,label='wall'))

walls=aabbWalls([mn,mx],thickness=0,material='wall')
wallIds=O.bodies.append(walls)

O.bodies.append(ymport.text('packing-JCFPM.spheres',scale=1,shift=Vector3(0,0,0),material='sphere',color=(0.6,0.5,0.15)))

triax=TriaxialStressController(
	maxMultiplier=1.+4e8/young, 
	finalMaxMultiplier=1.+4e7/young, 
	thickness = 0,
	stressMask = 7,
	internalCompaction=True, 
)
newton=NewtonIntegrator(damping=damp)
O.timingEnabled=True


def recorder():
	yade.plot.addData(
	i=O.iter,
	e11=-triax.strain[0],e22=-triax.strain[1],e33=-triax.strain[2],
	s11=-triax.stress(triax.wall_right_id)[0],#0+边界id为right
	s22=-triax.stress(triax.wall_top_id)[1],#1+边界id为top
	s33=-triax.stress(triax.wall_front_id)[2],#2+边界id为front
	P=triax.porosity,
	#meanS=-triax.meanStress[2]
	ev=triax.volumetricStrain,
	numberTc=interactionLaw.nbTensCracks,
	numberSc=interactionLaw.nbShearCracks,
	unb=unbalancedForce()
)
	plot.saveDataTxt('triax_JCFPM_HM_Wy=10.0Mpa,Sy=2.0MPa')

def stop_condition():
	if abs(triax.strain[2]) > 0.01:
		O.pause()
		presentcohesive_count = 0
		for i in O.interactions:
        		if hasattr(i.phys, 'isCohesive'):
            			if i.phys.isCohesive == 1:
                			presentcohesive_count+=1
		print('the number of cohesive bond now is:',presentcohesive_count)

O.engines=[
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=1.3,label='is2aabb'),Bo1_Box_Aabb()]),
	InteractionLoop(
		[Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=1.3,label='ss2sc'),Ig2_Box_Sphere_ScGeom()],
		[Ip2_JCFpmMat_JCFpmMat_JCFpmPhys()],
		[Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(recordCracks=True,Key='triax_JCFPM_HM',label='interactionLaw')]
	),
	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
	triax,
	#TriaxialStateRecorder(iterPeriod=100,file='WallStresses'+key),
	FlowEngine(dead=1,label='flow'),
	PyRunner(iterPeriod=int(1000),initRun=True,command='recorder()',label='data',dead=0),
	PyRunner(iterPeriod=1000,command='stop_condition()',dead=0),
	newton,
]

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

triax.goal1=triax.goal2=triax.goal3=-10e6
yade.timing.reset()
while 1:
	O.run(1000,1)
	unb=unbalancedForce()
	print('unbalanced force:',unb,'mean stres:',triax.meanStress)
	if unb<stabilityThreshold and abs(-10000000-triax.meanStress)/10000000<0.001:
		break
yade.timing.stats()
cohesiveCount = 0
for i in O.interactions:
 if hasattr(i.phys, 'isCohesive'):
              if i.phys.isCohesive == True:
                     cohesiveCount+=1
print('the origin total number of cohesive bond is:',cohesiveCount)


yade.timing.reset()
flow.dead=0
#flow.defTolerance=0.3
flow.debug=False
flow.fluidBulkModulus=2.2e9
flow.permeabilityFactor=-1e-5
flow.decoupleForces =  False
flow.meshUpdateInterval=100
flow.useSolver=4
flow.viscosity=0.001
flow.bndCondIsPressure=[0,0,0,0,1,1]
flow.bndCondValue=[0,0,0,0,0,2e6]

triax.internalCompaction=False
flow.emulateAction()
triax.stressMask=3
triax.goal1=-1e7
triax.goal2=-1e7
triax.goal3=rate

plot.plots={'e33':('s33',None,'unb'),'i':('numberTc','numberSc',None,'s33')}
plot.plot(subPlots=False)
O.run()
-----------------------------------------------------------
By the way,should this prompt be regarded as a warning or an error?In other words, will this prompt cause my simulation to run incorrectly (because my script didn't stop running).

Best wishes!

[1]https://answers.launchpad.net/yade/+question/690716
[2]https://answers.launchpad.net/yade/+question/670765

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