New question #697779 on Yade:
https://answers.launchpad.net/yade/+question/697779
Hi,
I use the PeriodicFlowEngine to simulate the erosion, I get such warning:
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
Segmentation fault (core dumped)
I am looking forward to your help ? Thanks a lot !
My code is shown as follow:
##______________ First section, generate sample_________
from __future__ import print_function
from yade import pack, qt, plot
from math import *
nRead=readParamsFromTable(
## model parameters
num_spheres=100,
targetPorosity= .4,
confiningPressure=-100000,
## material parameters
compFricDegree=15,#contact friction during the confining phase
finalFricDegree=30,#contact friction during the deviatoric loading
young=2e8,
poisson=.2,
density=2600,
alphaKr=7.5,
alphaKtw=0,
competaRoll=.22,
finaletaRoll=.22,
etaTwist=0,
normalCohesion=0,
shearCohesion=0,
## fluid parameters
fluidDensity=1000,
dynamicViscosity=.001,
## control parameters
damp=0,
stabilityThreshold=.001,
## output specifications
filename='suffusion',
unknowOk=True
)
from yade.params.table import *
O.periodic=True
O.cell.hSize=Matrix3(1,0,0, 0,1,0, 0,0,1)
# create materials for spheres
#shear strength is the sum of friction and adhesion, so the
momentRotationLaw=True
O.materials.append(CohFrictMat(alphaKr=alphaKr,alphaKtw=alphaKtw,density=density,etaRoll=competaRoll,etaTwist=etaTwist,frictionAngle=radians(compFricDegree),momentRotationLaw=True,normalCohesion=normalCohesion,poisson=poisson,shearCohesion=shearCohesion,young=young,label='spheres'))
# generate particles packing
sp=pack.SpherePack()
sp.makeCloud((0,0,0),(1,1,1),-1,0.3333,num_spheres,False, 0.95,seed=1)
sp.toSimulation(material='spheres')
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom6D()],
[Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(label='contact',setCohesionNow=False,setCohesionOnNewContacts=False)],
[Law2_ScGeom6D_CohFrictPhys_CohesionMoment(useIncrementalForm=True,always_use_moment_law=True)],
),
PeriodicFlowEngine(dead=1,label="flow"),#introduced as a dead engine
for the moment, see 2nd section
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
PeriTriaxController(label='triax',
# specify target values and whether they are strains or stresses
goal=(confiningPressure,confiningPressure,confiningPressure),
stressMask=7,
# type of servo-control, the strain rate isn't determined, it
shloud check the unbalanced force
dynCell=True,maxStrainRate=(10,10,10),
# wait until the unbalanced force goes below this value
maxUnbalanced=stabilityThreshold,relStressTol=1e-3,
doneHook='compactionFinished()'
),
NewtonIntegrator(damping=0)
]
import sys
def compactionFinished():
# after sample preparation, save the state
O.save('compactedState'+filename+'.yade.gz')
print('Compacted state saved', 'porosity', porosity())
# next time, called python command
triax.doneHook=''
O.pause()
O.run()
O.wait()
#B. Activate flow engine
flow.dead=0
flow.defTolerance=-1
flow.meshUpdateInterval=-1
flow.useSolver=3
flow.permeabilityFactor=1
flow.viscosity=10
flow.gradP=Vector3(0,1,0)
flow.duplicateThreshold=0.3
flow.updateTriangulation=True
O.run(2,1)
csdList=flow.getConstrictionsFull()
print(len(O.bodies),len(csdList),'finished')
flow.dead=1
print(O.bodies[10].shape.radius)
for i in range(10,80):
O.bodies.erase(i)
print(len(O.bodies))
O.run(1000,True)
O.engines=O.engines[0:3]+O.engines[4:]
O.step()
O.step()
O.engines=O.engines[0:3]+[PeriodicFlowEngine(dead=0,label="flow")]+O.engines[3:]
flow.defTolerance=-1
flow.meshUpdateInterval=-1
flow.useSolver=3
flow.permeabilityFactor=1
flow.viscosity=10
flow.gradP=Vector3(0,1,0)
flow.duplicateThreshold=0.3
flow.updateTriangulation=True
O.run(2,1)
csdList1=flow.getConstrictionsFull()
print(len(csdList1))
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