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[Rahul R <question701028@xxxxxxxxxxxxxxxxxxxxx>]

Question #701028 on Yade changed:
https://answers.launchpad.net/yade/+question/701028

    Status: Needs information => Open

Rahul R gave more information on the question:
Hi Jan,
Sorry for the delayed reply. Your solution of positioning the cylinder pack
correctly worked, but the membrane is not applying confining stress to the
pack. It shows some error in the terminal saying:

<FATAL ERROR> ThreadRunner:35 void yade::ThreadRunner::run(): Exception
occured:
PyRunner error.

COMMAND: 'stopIfDamaged()'

ERROR:
max() arg is an empty sequence

STACK TRACE:
Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "Triax.py", line 119, in stopIfDamaged
    extremum = max(abs(s) for s in plot.data['s'])

ValueError: max() arg is an empty sequence

Why does this happen? This is the updated code:

# -*- encoding=utf-8 -*-
from __future__ import print_function
################################################################################
#
# Triaxial test. Axial strain rate is prescribed and transverse prestress.
# Test is possible on prism or cylinder
# An independent c++ engine may be created from this script in the future.
#
################################################################################
from builtins import range
from yade import ymport, plot
from yade import pack, plot
import os

# default parameters or from table
readParamsFromTable(noTableOk=True,
# material parameters
young = 10e7,
poisson = .3,
frictionAngle = 0.15,
sigmaT = 1.5e6,

# prestress
preStress = -3e6,
# axial strain rate
strainRate = -100,

# assamlby parameters
rParticle = 0.0005,
width = 5,
height = 9.85,
bcCoeff = 5,

# facets division
nw = 48,
nh = 30,

# output specifications
fileName = 'test',
exportDir = '/tmp',
runGnuplot = False,
runInGui = True,
)
from yade.params.table import *

# materials
sphereMat =
O.materials.append(CohFrictMat(young=young,poisson=poisson,frictionAngle=frictionAngle,alphaKr=0.25,alphaKtw=0,etaRoll=0.005,etaTwist=0,normalCohesion=5e6,shearCohesion=5e6,momentRotationLaw=True,density=2530))

frictMat = O.materials.append(FrictMat(
young=young,poisson=poisson,frictionAngle=frictionAngle
))

# spheres
sp= ymport.textExt('DensepackRD70-80',format='x_y_z_r',shift=
Vector3(-27,-27,-51), scale=1.0, material=sphereMat)
spheres = O.bodies.append(sp)


# bottom and top of specimen. Will have prescribed velocity
bot = [O.bodies[s] for s in spheres if
O.bodies[s].state.pos[2]<rParticle*bcCoeff]
top = [O.bodies[s] for s in spheres if
O.bodies[s].state.pos[2]>height-rParticle*bcCoeff]
vel = strainRate*(height-rParticle*2*bcCoeff)
top_limit = 0
top_id = 0
for s in bot:
s.shape.color = (1,0,0)
s.state.blockedDOFs = 'xyzXYZ'
s.state.vel = (0,0,-vel)
for s in top:
s.shape.color = Vector3(0,1,0)
s.state.blockedDOFs = 'xyzXYZ'
s.state.vel = (0,0,vel)

# facets
facets = []
rCyl2 = .5*width / cos(pi/float(nw))
for r in range(nw):
for h in range(nh):
v1 = Vector3( rCyl2*cos(2*pi*(r+0)/float(nw)),
rCyl2*sin(2*pi*(r+0)/float(nw)), height*(h+0)/float(nh) )
v2 = Vector3( rCyl2*cos(2*pi*(r+1)/float(nw)),
rCyl2*sin(2*pi*(r+1)/float(nw)), height*(h+0)/float(nh) )
v3 = Vector3( rCyl2*cos(2*pi*(r+1)/float(nw)),
rCyl2*sin(2*pi*(r+1)/float(nw)), height*(h+1)/float(nh) )
v4 = Vector3( rCyl2*cos(2*pi*(r+0)/float(nw)),
rCyl2*sin(2*pi*(r+0)/float(nw)), height*(h+1)/float(nh) )
f1 = facet((v1,v2,v3),color=(0,0,1),material=frictMat)
f2 = facet((v1,v3,v4),color=(0,0,1),material=frictMat)
facets.extend((f1,f2))

O.bodies.append(facets)
mass = O.bodies[0].state.mass
for f in facets:
f.state.mass = mass
f.state.blockedDOFs = 'XYZz'

# plots
plot.plots = { 'e':('s',), }
def plotAddData():
f1 = sum(O.forces.f(b.id)[2] for b in top)
f2 = sum(O.forces.f(b.id)[2] for b in bot)
f = .5*(f2-f1)
s = f/(pi*.25*width*width)
e = (top[0].state.displ()[2] - bot[0].state.displ()[2]) /
(height-rParticle*2*bcCoeff)
plot.addData(
i = O.iter,
s = s,
e = e,
)

# apply prestress to facets
def addForces():
for f in facets:
n = f.shape.normal
a = f.shape.area
O.forces.addF(f.id,preStress*a*n)

# stop condition and exit of the simulation
def stopIfDamaged(maxEps=5e-3):
extremum = max(abs(s) for s in plot.data['s'])
s = abs(plot.data['s'][-1])
e = abs(plot.data['e'][-1])
if O.iter < 1000 or s > .5*extremum and e < maxEps:
return
f = os.path.join(exportDir,fileName)
print('gnuplot',plot.saveGnuplot(f,term='png'))
if runGnuplot:
import subprocess
os.chdir(exportDir)
subprocess.Popen(['gnuplot',f+'.gnuplot']).wait()
print('Simulation finished')
O.pause()
#sys.exit(0) # results in some threading exception

O.dt=.5*utils.PWaveTimeStep()
enlargeFactor=1.5
O.engines=[
ForceResetter(),
InsertionSortCollider([
Bo1_Sphere_Aabb(aabbEnlargeFactor=enlargeFactor,label='bo1s'),
Bo1_Facet_Aabb()
]),
InteractionLoop(
[
Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=enlargeFactor,label='ss2d3dg'),
Ig2_Facet_Sphere_ScGeom(),
],
[
Ip2_CpmMat_CpmMat_CpmPhys(cohesiveThresholdIter=O.iter+5),
Ip2_FrictMat_CpmMat_FrictPhys(),
Ip2_FrictMat_FrictMat_FrictPhys(),
],
[
Law2_ScGeom_CpmPhys_Cpm(),
Law2_ScGeom_FrictPhys_CundallStrack(),
],
),
PyRunner(iterPeriod=1,command="addForces()"),
NewtonIntegrator(damping=.3),
CpmStateUpdater(iterPeriod=50,label='cpmStateUpdater'),
PyRunner(command='plotAddData()',iterPeriod=100),
PyRunner(iterPeriod=50,command='stopIfDamaged()'),
]

# run one step
O.step()

# reset interaction detection enlargement
bo1s.aabbEnlargeFactor=ss2d3dg.interactionDetectionFactor=1.0

# initialize auto-updated plot
if runInGui:
plot.plot()
try:
from yade import qt
renderer=qt.Renderer()
# uncomment following line to exagerate displacement
#renderer.dispScale=(100,100,100)
except:
pass

# run
O.run()

> What are the stop conditions? what number of iteration run it?
The second code I shared is just for gravity deposition. It does not
contain the code for applying compression and extensions to the pack. I did
compression and extension cycles manually in the terminal after gravity
deposition. Each time a cycle is completed, I check if the porosity of the
pack reaches a constant value. If it does, I repeat the cycle again until
the porosity reaches the desired value. So there are no stop conditions in
the code.


On Tue, 22 Mar 2022 at 22:05, Jan Stránský <
question701028@xxxxxxxxxxxxxxxxxxxxx> wrote:

> Your question #701028 on Yade changed:
> https://answers.launchpad.net/yade/+question/701028
>
>     Status: Open => Needs information
>
> Jan Stránský requested more information:
> > I tried scaling the packing, but that doesn't seem to eliminate the
> issue.
>
> if the issue is that the cylinder is not positioned correctly, then the
> solution is to position it correctly :-)
>
> > I've shared the coordinates file in the mail.
>
> launchpad questions does not work well with mail.. you can put it here
> directly,
>
> > Here is the code I used to create the sample:
>
> what are the stop conditions? what number of iterations to run it?
>
> Cheers
> Jan
>
> --
> To answer this request for more information, you can either reply to
> this email or enter your reply at the following page:
> https://answers.launchpad.net/yade/+question/701028
>
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>

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