New question #697642 on Yade:
https://answers.launchpad.net/yade/+question/697642
After deleting some particles, I encountered a lot of problems in the
PeriodicFlowEngine. Such as:
(1) GS did not converge in 20k iterations (maybe because the reference pressure
is 0?);
(2) segmentation fault (core dumped);
(3) Periodicity is broken;
(4) 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
For errors (3) and (4), I have solved it by changing the value of
PeriodicFlowEngine.duplicateThreshold and the PeriodicFlowEngine.useSolver.
For errors (1) and (2), I spent a lot of time and tried a lot, but I still
can't solve them. Please help me!
I have searched for the answers about the PeriodicFlowEngine. I concluded that
since there is no boundary condition for periodic boundary conditions, the
PeriodicFlowEngine does not need to set boundary conditions，that is, it does
not need to set the bndCondIsPressure, bndCondValue, boundaryUseMaxMin. As I
want to achieve a similar simulation like the paper " A discrete numerical
model involving partial fluid-solid coupling to describe suffusion effects in
soils "[1], In short, it is to achieve the fluid flow from top to bottom under
a certain pressure gradient, and no fluid flows out from the side, and some
particles are removed during the calculation. So I just need to apply a
macroscopic pressure gradient by flow.gradP=Vector3(0, i,0), where i is the
macroscopic pressure gradient. Is that right?
The errors (1) and (2) still exist, this is my simplified code:
##______________ 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=0
flow.permeabilityFactor=1
flow.viscosity=10
flow.gradP=Vector3(0,1,0)
flow.duplicateThreshold=0.3
flow.updateTriangulation=True
O.run(1,1)
csdList=flow.getConstrictionsFull()
print(len(O.bodies),len(csdList),'finished')
flow.dead=1
print(O.bodies[10].shape.radius)
for i in range(10,90):
O.bodies.erase(i)
print(len(O.bodies))
O.run(1000,True)
flow.dead=0
flow.defTolerance=-1
flow.meshUpdateInterval=-1
flow.useSolver=0
flow.permeabilityFactor=1
flow.viscosity=10
flow.gradP=Vector3(0,1,0)
flow.duplicateThreshold=0.3
flow.updateTriangulation=True
O.run(3,1)
csdList1=flow.getConstrictionsFull()
print(len(csdList1))
[1]https://www.sciencedirect.com/science/article/pii/S0266352X17303087
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