[Yade-users] [Question #698498]: How to use cellRepeat
New question #698498 on Yade:
https://answers.launchpad.net/yade/+question/698498
Hi,
I'd like to ask how to use cellRepeat[1] function to stack several copies of a
cell along one direction. One illustration can be found in Fig. 3 in [2].
I use the following MWE (from[3]) to make a sample in a cell, the MWE pauses
after the sample reaches the target isotropic state. I'd like to reproduce
several of the cell at that state, and stack them together along one direction,
but I didn't make it after some attempts. Here is the MWE, it may take around
50 seconds for running.
MWE begins ###
from __future__ import print_function
sigmaIso = -100e3
from yade import pack, qt, plot
mn,mx=Vector3(0,0,0),Vector3(0.07,0.14,0.07)
O.periodic = True
O.cell.setBox(.07,.14,.07)
sp = pack.SpherePack()
sp.makeCloud(mn,mx,-1,0.,num=7000, periodic=True)
sp.toSimulation()
O.engines = [
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb()]),
InteractionLoop([Ig2_Sphere_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()]),
PeriTriaxController(
label='triax',
goal=(sigmaIso, sigmaIso, sigmaIso),
stressMask=7,
dynCell=True,
maxStrainRate=(10, 10, 10),
maxUnbalanced=.1,
relStressTol=1e-3,
doneHook='compactionFinished()'
),
NewtonIntegrator(damping=.2),
]
O.dt = .5 * PWaveTimeStep()
O.trackEnergy = True
def compactionFinished():
print('stage1
finished','sxx',triax.stress[0],'syy',triax.stress[1],'szz',triax.stress[2])
O.cell.trsf=Matrix3.Identity
triax.goal = (sigmaIso, -0.1, sigmaIso)
triax.stressMask = 5
triax.maxStrainRate = (1., 0.5, 1.)
triax.maxUnbalanced = 10
O.pause()
# here I want to repeat the current cell
def triaxFinished():
print('Finished')
O.pause()
MWE finish ###
Thanks very much!
Leonard
[1]https://yade-dev.gitlab.io/trunk/yade.pack.html?highlight=cell#yade._packSpheres.SpherePack.cellRepeat
[2]Cheng, Hongyang, Stefan Luding, Kuniyasu Saitoh, and Vanessa Magnanimo.
"Elastic wave propagation in dry granular media: effects of probing
characteristics and stress history." International journal of solids and
structures 187 (2020): 85-99.
[3]https://gitlab.com/yade-dev/trunk/blob/master/doc/sphinx/tutorial/06-periodic-triaxial-test.py
--
You received this question notification because your team yade-users is
an answer contact for Yade.
___
Mailing list: https://launchpad.net/~yade-users
Post to : yade-users@lists.launchpad.net
Unsubscribe : https://launchpad.net/~yade-users
More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #698493]: Spheres overlap in periodic simulations
Question #698493 on Yade changed: https://answers.launchpad.net/yade/+question/698493 Description changed to: Hello, I am currently performing a simulation of an inclined flume that goes across the X-axis with periodic walls on the sides(Y-axis). This runs without any major concern mainly thanks to the help provided on this website to many other users. However, when it comes to doing the post- processing, I have noticed that when a sphere crosses the periodic border the following thing occurs: The sphere's Y-axis(width) coordinates do not restart despite being now on the opposite side of the flume. Instead, they keep increasing "out of the flume". This is not a big concern since this can be easily adjusted on the post-processing and I'm aware this could be useful in other scenarios. Nevertheless, When the sphere crosses the periodic border, it seems that no contact is considered against those particles that did not cross the periodic boundary(or did it more than once). This is observed after manually calculating each contact overlap. When doing this, spheres on the same "coordinates" do have normal overlaps but those who are not on the same boundary have a huge range of overlap(up to one radius) as if no interaction occurs. Based on this I am curious if this could be a bug or if I am missing any contact law that would allow contact between particles that are not on the same "coordinates". Finally, I have attached a few code lines regarding the engines used and how I add the spheres. If any additional information is required, or if there are any suggestions(or ideas), I'd be delighted to read about it. Best, Andrés Additional information: How spheres are added: (This is not really relevant, just to emphasize that I add spheres through O.bodies.append(utils.sphere()) command. for i in np.arange(4*d,lr,2*d): for j in np.arange(d+hr,5*hr,2*d): for k in np.arange(-wc/2+3*d,wc/2-3*d,2*d): O.bodies.append(utils.sphere((i,k,j),radius=float(random.randint(int(10*(d-disp)),int(10*(d+disp/10,material=sphereMat)) Engines: O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()],allowBiggerThanPeriod=True), InteractionLoop( # handle sphere+sphere and box+sphere collisions [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()]), NewtonIntegrator(gravity=(g*sin(slope),0,-g*cos(slope)), damping=0), #add gravity VTKRecorder(fileName=addrec+'3d-'+str(zeta)+'-vtk-',recorders=['all'],iterPeriod=it), ] -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #697783]: BoxFactory for creating spheres on periodic conditions
Question #697783 on Yade changed: https://answers.launchpad.net/yade/+question/697783 Andres Escobar posted a new comment: Hi Jérôme, I did finally work on a function that performs the same task without any problems, thanks for your help with letting me know the source of the problem! Finally, I apologize for my late reply since I did read this earlier but I was convinced I had answered. Best, Andrés -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #698493]: Spheres overlap in periodic simulations
New question #698493 on Yade: https://answers.launchpad.net/yade/+question/698493 Hello, I am currently performing a simulation of an inclined flume that goes across the X-axis with periodic walls on the sides(Y-axis). This runs without any major concern mainly thanks to the help provided on this website to many other users. However, when it comes to doing the post-processing, I have noticed that when a sphere crosses the periodic border the following thing occurs: The sphere's Y-axis(width) coordinates do not restart despite being now on the opposite side of the flume. Instead, they keep increasing "out of the flume". This is not a big concern since this can be easily adjusted on the post-processing and I'm aware this could be useful in other scenarios. Nevertheless, When the sphere crosses the periodic border, it seems that no contact is detected against those particles that did not cross the periodic boundary(or did it more than once). This is observed after manually calculating each contact overlap. When doing this, spheres on the same "coordinates" do have normal overlaps but those who are not on the same boundary have a huge range of overlap(up to one radius) as if no interaction occurs. Based on this I am curious if this could be a bug or if I am missing any contact law that would allow contact between particles that are not on the same "coordinates". Finally, I have attached a few code lines regarding the engines used and how I add the spheres. If any additional information is required, or if there are any suggestions(or ideas), I'd be delighted to read about it. Best, Andrés Additional information: How spheres are added: (This is not really relevant, just to emphasize that I add spheres through O.bodies.append(utils.sphere()) command. for i in np.arange(4*d,lr,2*d): for j in np.arange(d+hr,5*hr,2*d): for k in np.arange(-wc/2+3*d,wc/2-3*d,2*d): O.bodies.append(utils.sphere((i,k,j),radius=float(random.randint(int(10*(d-disp)),int(10*(d+disp/10,material=sphereMat)) Engines: O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()],allowBiggerThanPeriod=True), InteractionLoop( # handle sphere+sphere and box+sphere collisions [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()]), NewtonIntegrator(gravity=(g*sin(slope),0,-g*cos(slope)), damping=0), #add gravity VTKRecorder(fileName=addrec+'3d-'+str(zeta)+'-vtk-',recorders=['all'],iterPeriod=it), ] -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
[Yade-users] [Question #698487]: Change boundary condition from rigid wall to periodic boundary
New question #698487 on Yade:
https://answers.launchpad.net/yade/+question/698487
Hi,
I'd like to ask is it possible that change model boundary from rigid wall to
periodic boundary? My attempt is as follow:
I use script1 (from Bruno [1]) to generate a sample with rigid wall boundary,
note that I set periodic=True in makeCloud. And then I save the sample as
sample.yade.gz.
Then I import the sample.yade.gz into script2 (from periodic-triax example[2]),
and I remove the rigid walls and give it a periodic boundary.
However, I failed in switching the boundary. The sample exploded immediately
after one O.step() forward. I am not sure whether it is impossible to switch
the boundary or I have not found out the correct way. Thereby, I'd like to ask
for you advice for that:
-Is it possible that change model boundary from rigid wall to periodic boundary
after I generate a sample under the condition of rigid wall?
-The reason why I want to switch the boundary is that using the example code[1]
(which is rigid wall) is easy to make a sample with target confining presure
and porosity by using radii expansion methods (by setting
internalCompaction=True), but it seems that there is no radii expansion method
for periodic engine. Which makes it uneasy for using only periodic engine to
generate target sample. Do you have any idea about how to integrate [1] and
[2], specifically, making sample by using [1] and carrying out triaxial loading
by using periodic engine as [2]?
Below are the MWE:
script1 begin##Around 15 second for running ##
from yade import pack, plot
nRead=readParamsFromTable(
num_spheres=1000,
compFricDegree = 30,
key='_triax_base_',
unknownOk=True
)
from yade.params import table
num_spheres=table.num_spheres
key=table.key
targetPorosity = 0.43
compFricDegree = table.compFricDegree
finalFricDegree = 30
rate=-0.02
damp=0.2
stabilityThreshold=0.01
young=5e6
mn,mx=Vector3(0,0,0),Vector3(0.7,0.7,1.4)
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
sp=pack.SpherePack()
sp.makeCloud(mn,mx,-1,0.,num_spheres,periodic=True,porosity=0.95,seed=1)
O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp])
Gl1_Sphere.quality=3
### DEFINING ENGINES ###
triax=TriaxialStressController(
maxMultiplier=1.+2e4/young,
finalMaxMultiplier=1.+2e3/young,
thickness = 0,
stressMask = 7,
internalCompaction=True,## please change True to False here to look at what I
say
)
newton=NewtonIntegrator(damping=damp)
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()],
[Law2_ScGeom_FrictPhys_CundallStrack()]
),
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
triax,
newton
]
Gl1_Sphere.stripes=0
if nRead==0: yade.qt.Controller(), yade.qt.View()
### APPLYING CONFINING PRESSURE ###
triax.goal1=triax.goal2=triax.goal3=-1
while 1:
O.run(1000, True)
unb=unbalancedForce()
print 'unbalanced force:',unb,' mean stress: ',triax.meanStress
if unbtargetPorosity:
# we decrease friction value and apply it to all the bodies and contacts
compFricDegree = 0.95*compFricDegree
setContactFriction(radians(compFricDegree))
print "\r Friction: ",compFricDegree," porosity:",triax.porosity,
sys.stdout.flush()
O.run(500,1)
print "### Compacted state saved ###"
O.save('sample.yade.gz')
script1 done##
script2 begin
from __future__ import print_function
sigmaIso = -10e3
from yade import pack, qt, plot
O.load('sample.yade.gz')
for i in range(6):
O.bodies.erase(i)
O.periodic = True
O.cell.setBox(0.7,0.7,1.4)
sp = pack.SpherePack()
sp.fromSimulation()
sp.toSimulation()
O.engines = [
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb()]),
InteractionLoop([Ig2_Sphere_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()]),
PeriTriaxController(
label='triax',
# specify target values and whether they are strains or stresses
goal=(sigmaIso, sigmaIso, sigmaIso),
stressMask=7,
# type of servo-control
dynCell=True,
maxStrainRate=(10, 10, 10),
# wait until the unbalanced force goes below this value
maxUnbalanced=.1,
relStressTol=1e-3,
# call this function when goal is reached and the packing is
stable
doneHook='compactionFinished()'
),
NewtonIntegrator(damping=.2),
# PyRunner(command='addPlotDat
Re: [Yade-users] [Question #698377]: How to correct the strain
Question #698377 on Yade changed: https://answers.launchpad.net/yade/+question/698377 Jan Stránský posted a new comment: Please try to mark "the best answers" according to the relation to the original problem, not necessarily the last one. According to the OP description, Robert's answer #1 is the answer. My post #4 was reaction to your post #3, which actually should be a separate question according to [1] Cheers Jan [1] https://www.yade-dem.org/wiki/Howtoask -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
Re: [Yade-users] [Question #698377]: How to correct the strain
Question #698377 on Yade changed: https://answers.launchpad.net/yade/+question/698377 Status: Answered => Solved Zhicheng Gao confirmed that the question is solved: Thanks Jan Stránský, that solved my question. -- You received this question notification because your team yade-users is an answer contact for Yade. ___ Mailing list: https://launchpad.net/~yade-users Post to : yade-users@lists.launchpad.net Unsubscribe : https://launchpad.net/~yade-users More help : https://help.launchpad.net/ListHelp
