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[Katia Boschi <question695827@xxxxxxxxxxxxxxxxxxxxx>]

New question #695827 on Yade:
https://answers.launchpad.net/yade/+question/695827

Dear All,

I have tried to run the following code (simple shear test upon a saturated granular sample under constant pressure conditions):


from yade import pack,qt,utils,ymport
from yade import export
from yade import timing
from yade import plot
from builtins import range
import numpy
import time
from math import *

O.load('prova.xml')

num_spheres=5000
young=750.e6
finalFricDegree = 0.35
graindensity=2600.0
poisson=0.17
en=0.9
sigmaIso=-150.e3
radiusR=0.001/2.
D50=radiusR*2.0

#O.materials.append(FrictViscoMat(young=young,poisson=poisson,frictionAngle=compFricDegree,density=graindensity,betan=0.0336,label='spheres'))

triax=PeriTriaxController(
	dynCell=True,
	mass=0.2,
	goal=[sigmaIso,sigmaIso,sigmaIso],
	stressMask=7,
	maxStrainRate=[0.0001,0.0001,0.0001],
	label='triax')

newton=NewtonIntegrator(damping=0.1)

O.engines=[
	ForceResetter(),
	InsertionSortCollider([Bo1_Sphere_Aabb()]),
	InteractionLoop(
        	[Ig2_Sphere_Sphere_ScGeom()],
        	[Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys()],
        	[Law2_ScGeom_FrictViscoPhys_CundallStrackVisco(traceEnergy=True)]
	),
	PeriodicFlowEngine(dead=1,label="flow"),
	GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.5),
	triax,
	newton
]

while 1:
	O.run(1000, True)
	unb=unbalancedForce()
	if unb<0.00001:
		break

triax.dead=0
flow.dead=0

flow.pressureForce=True
flow.viscousShear=True
flow.viscousNormalBodyStress=True
flow.viscousShearBodyStress=True
flow.normalLubrication=True
flow.shearLubrication=True

flow.defTolerance=0.1
flow.meshUpdateInterval=200
flow.useSolver=3
flow.permeabilityFactor=1
flow.viscosity=0.001
flow.bndCondIsPressure=[0,0,0,0,1,1]
flow.bndCondValue=[0,0,0,0,0,0]
GlobalStiffnessTimeStepper.dead=True
O.dt=min(0.5*PWaveTimeStep(),0.5*1./1200.*pi/flow.viscosity*graindensity*(D50/2.)**2)
O.dynDt=False
    
O.run(10,1)

while 1:
	O.run(5000, True)
	unb=unbalancedForce()
	if unb<0.0001:
		if O.cell.velGrad[0,1]<0.01:
			O.cell.velGrad=O.cell.velGrad+Matrix3(0,0.001,0, 0,0,0, 0,0,0)
			O.dt=min(0.5*PWaveTimeStep(),0.5*1./1200.*pi/flow.viscosity*graindensity*(D50/2.)**2)
		if O.cell.velGrad[0,1]>0.01:
			break

with "prova.xml" a dry granular sample properly generated in a periodic cell.

Even if I switch off both the PeriTriaxialController and the cell strain rate imposition, after some cycles, the following error appears:

CHOLMOD warning: matrix not positive definite. file: ../Supernodal/t_cholmod_super_numeric.c line: 911
something went wrong in Cholesky factorization, use LDLt as fallback this time1

Would you mind helping me with this error? 


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