Re: [Yade-users] [Question #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed: https://answers.launchpad.net/yade/+question/701438 Status: Open => Answered Bruno Chareyre proposed the following answer: Hi, I guess you want to simulate elastic waves or something, but as I was reading phase 2 I did not see anything special exerted on the boundaries. If you analyze velocities in a situation of static equilibrium, what you get is just some random noise. It is not deeply surprizing that random noise depends on timestep (and, basically, on anything else). Did I miss something? Bruno -- 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 #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed: https://answers.launchpad.net/yade/+question/701438 Aoxi Zhang posted a new comment: Hi Karol, Sorry for not making it clear. I mean the damping is changing properly, but the problem is not solved and I still need help on it. Thanks, Aoxi -- 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 #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed: https://answers.launchpad.net/yade/+question/701438 Karol Brzezinski posted a new comment: Hi Zhang, Do you mean 'work well', so the damping is changing properly, but you still need help or work well and the problem is solved? Cheers, Karol -- 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 #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed: https://answers.launchpad.net/yade/+question/701438 Aoxi Zhang posted a new comment: Hi Karol, I have (1) updated the way of setting daping in phase2.py, now it works well, (2) changed iterPeriod=1 to virtPeriod = RunTimeLength/1000 as you suggested. Thanks, Aoxi -- 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 #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed: https://answers.launchpad.net/yade/+question/701438 Karol Brzezinski posted a new comment: Just a comment regarding changing the damping. I loaded the save from phase1, and inspected damping in the following way > O.engines[5].damping Output is 0.6, which confirms that damping didn't change during the simulation at all. Also, please note that you set damping in function stopStressRelaxation. After setting damping there as >newton.damping = 0 it changes as expected (please inspect the save file after this). Unfortunately, it doesn't answer your question. Also, I think that saving data every iteration may cause some efficiency issues (in phase 2). Instead, I propose the same time interval for all the cases (virtPeriod = RunTimeLength/1000). Cheers, Karol -- 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 #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed: https://answers.launchpad.net/yade/+question/701438 Status: Answered => Open Aoxi Zhang is still having a problem: Hi, I'd like also use labels for engines. But sometimes I found that using label cannot successfully control the engine. For instance, in phase2.py: O.engines[3].dead=True## turn of GlobalStiffnessTimeStepper # TimeStepper.dead=True## Note, use label cannot successfully close time stepper In above codes, I want to close GlobalStiffnessTimeStepper, if I use TimeStepper.dead=True, it doesn't work. Thereby, I use O.engines[3].dead=True to turn of GlobalStiffnessTimeStepper. I don't know why. Regarding the original question, I use newton.damping=0.9 and/or NewtonIntegrator.damping=0.9 to set the damping. The problem is still there :( Any ideas or comments are welcome. Best, Aoxi -- 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 #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed:
https://answers.launchpad.net/yade/+question/701438
Jan Stránský posted a new comment:
@Karol: I was surprised, too, but it does works also this way :-D
It seems that somehow using class directly passes the argument to some
instances.
Maybe something about how boost.python and YADE macros deals with it?
Anyway, I would not call it the best practice..
### MWE
newton1 = NewtonIntegrator()
print("1",newton1.damping) # 0.2
newton1.damping = 0.3
print("1",newton1.damping) # 0.3
NewtonIntegrator.damping = 0.4
print("1",newton1.damping) # 0.4 (!)
newton2 = NewtonIntegrator
print("1",newton1.damping) # 0.4
print("2",newton2.damping) # 0.4
NewtonIntegrator.damping = 0.5
print("1",newton1.damping) # 0.5 (!)
print("2",newton2.damping) # 0.5 (!)
newton1.damping = 0.6
newton2.damping = 0.7
print("1",newton1.damping) # 0.6
print("2",newton2.damping) # 0.7
NewtonIntegrator.damping = 0.8
print("1",newton1.damping) # 0.6 (!)
print("2",newton2.damping) # 0.8 (!)
###
Cheers
Jan
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Re: [Yade-users] [Question #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed: https://answers.launchpad.net/yade/+question/701438 Status: Open => Answered Karol Brzezinski proposed the following answer: Hi, I didn't run your code yet, but I am looking at the example. Are you sure that you modify the damping by > NewtonIntegrator.damping=0.9 earlier you created an instance called 'newton', so maybe it should be rather >newton.damping=0.9 I prefer using labels for engines. Cheers, Karol -- 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 #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed:
https://answers.launchpad.net/yade/+question/701438
Aoxi Zhang gave more information on the question:
Hi Jan,
Thanks for your comments.
>> it is not small enough to neglect the effect of its value.
I further tested on other smaller dt values, e.g. 1e-10, but it has the
same problem.
>> You are examining a few "random" particle's velocities in a
simulation with "many" particles. Such DEM simulation is "chaotic".
That is a good point. I updated phase2.py (attached below) by monitoring
a layer of sands, thereby more sands are monitored. But I still got this
problem.
updated phase2.py in which more sands are monitored###
from __future__ import division
from yade import pack, plot
import math
import numpy as np
import random
import pickle
from yade import ymport,export
utils.readParamsFromTable(dt=1e-7)
from yade.params import table
finalFricDegree=19
O.load('sample_generatedFromPhase1_afterRelax.yade.gz')
RunTimeLength=3e-4 # how long for the time of data recording
Odt=table.dt
O.dt=Odt
O.engines[3].dead=True## turn of GlobalStiffnessTimeStepper
# TimeStepper.dead=True## Note, use label cannot successfully close time stepper
StopRelaxation.dead=True## turn of StopRelaxation in previous phase
NewtonIntegrator.damping=0.0
# monitoredSand=[1000,2001,3002,4003,5004]
monitoredSand=[]
def getMonitoredSand():
halfHeigh=aabbDim()[1]/2
for i in O.bodies:
if isinstance(i.shape, Sphere):
if halfHeighhttps://launchpad.net/~yade-users
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Re: [Yade-users] [Question #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed:
https://answers.launchpad.net/yade/+question/701438
Status: Answered => Open
Aoxi Zhang is still having a problem:
Hi Karol and Jan,
Thanks for your feedback!
Below are the scripts of the MWE:
phase1.py
from __future__ import division
from yade import pack, plot
import math
import numpy as np
import random
from random import gauss
import timeit
import pickle
num_spheres=5000
targetPorosity = 0.405
compFricDegree = 30
finalFricDegree = 19
rate=-0.01
damp=0.6
stabilityThreshold=0.001
confinement=100e3
mn,mx=Vector3(0,0,0),Vector3(0.07,0.14,0.07)
MatWall=O.materials.append(FrictMat(young=2e9,poisson=0.3,frictionAngle=0,density=0,label='walls'))
MatSand =
O.materials.append(CohFrictMat(isCohesive=True,young=2e8,alphaKr=0.15,alphaKtw=0.15,\
poisson=0.3,frictionAngle=radians(30),etaRoll=0.15,etaTwist=0.15,\
density=2650.0,normalCohesion=0, shearCohesion=0,\
momentRotationLaw=True,label='sand'))
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
sp=pack.SpherePack()
sp.makeCloud(mn,mx,-1,0.3,num_spheres,False, 0.95,seed=1)
O.bodies.append([sphere(center,rad,material='sand') for center,rad in sp])
Gl1_Sphere.quality=3
newton=NewtonIntegrator(damping=damp)
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Box_Sphere_ScGeom()],
[Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(label="Ip2Coh"),
Ip2_FrictMat_FrictMat_FrictPhys()],
[Law2_ScGeom6D_CohFrictPhys_CohesionMoment(useIncrementalForm=True,always_use_moment_law=True),Law2_ScGeom_FrictPhys_CundallStrack()]
),
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8,label="TimeStepper"),
TriaxialStressController(
maxMultiplier=1.4,
finalMaxMultiplier=1.004,
thickness = 0,
stressMask = 7,
internalCompaction=True,
label='triax'),
newton,
]
Gl1_Sphere.stripes=0
triax.goal1=triax.goal2=triax.goal3=-confinement
while 1:
O.run(1000, True)
unb=unbalancedForce()
print 'unbF:',unb,' meanStress:
',-triax.meanStress,'top:',-triax.stress(triax.wall_top_id)[1]
if unb0.0001:
compFricDegree = 0.95*compFricDegree
setContactFriction(radians(compFricDegree))
print "\r Friction: ",compFricDegree," porosity:",triax.porosity,
sys.stdout.flush()
O.run(500,1)
print "### state 2 Reach target porosity completed ###"
print "### state 3 - click run to start stress relaxation ###"
setContactFriction(radians(finalFricDegree))
NewtonIntegrator.damping=0.9
O.engines=O.engines+[PyRunner(command='stopStressRelaxation()',
iterPeriod=1,label="StopRelaxation")]
for i in range(6):
O.bodies[i].state.vel = Vector3(0,0,0)
O.bodies[i].state.blockedDOFs='xyzXYZ'
triax.dead=True
def stopStressRelaxation():
print('unb',unbalancedForce())
if unbalancedForce()<1e-7:
O.pause()
NewtonIntegrator.damping=0.0#newton.damping=0
print "stress relaxation finished, damping has been set as 0"
print "Please go to phase2"
O.save('sample_generatedFromPhase1_afterRelax.yade.gz')
#
# phase2.py#
from __future__ import division
from yade import pack, plot
import math
import numpy as np
import random
import pickle
from yade import ymport,export
utils.readParamsFromTable(dt=1e-7)
from yade.params import table
finalFricDegree=19
O.load('sample_generatedFromPhase1_afterRelax.yade.gz')
RunTimeLength=3e-4 # how long for the time of data recording
Odt=table.dt
O.dt=Odt
O.engines[3].dead=True## turn of GlobalStiffnessTimeStepper
# TimeStepper.dead=True## Note, use label cannot successfully close time stepper
StopRelaxation.dead=True## turn of StopRelaxation in previous phase
NewtonIntegrator.damping=0.0
monitoredSand=[1000,2001,3002,4003,5004]
def avgVel(idList):
vel=0.0
avg=0.0
for i in idList:
vel+=O.bodies[i].state.vel[1]
avg=vel/len(idList)
return avg
print("O.dt=",O.dt)
O.engines=O.engines+[PyRunner(command='outputData()',
iterPeriod=1,label="outputData")]
O.engines=O.engines+[PyRunner(command='stopSimulation()',
iterPeriod=1,label="stopSimu")]
def stopSimulation():
print ('Running, O.time,',O.time)
if O.time > RunTimeLength:
O.pause()
print ('Running finished, O.realtime,',O.realtime)
def outputData():
f = open("ResultsOfPhase2_dt{}.txt
Re: [Yade-users] [Question #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed: https://answers.launchpad.net/yade/+question/701438 Status: Needs information => Answered Jan Stránský proposed the following answer: Hello, please read [3], section "Please, no external links!". MWE can be put directly in the question (assuming satisfying M=minimal condition). > even dt is small enough compared to the dt obtained from PWaveTimeStep() > If I understood correctly, when dt is small enough, different dt should not > affect the results. Do you have any ideas about it? Straightforward answer could be that it is not small enough to neglect the effect of its value But, more importantly: You are examining a few "random" particle's velocities in a simulation with "many" particles. Such DEM simulation is "chaotic", i.e. a small change in input may lead to big changes for such quantities like velocity or position of one individual particle. You can try running exactly the same simulation (same O.dt, same initial configuration, everything the same) in parallel, let's say with "-j 4" option and you should get different result for each run [4]. So what you are experiencing with different velocities is the feature of DEM and its computer solution. So you should be interested in some "overall" quantities, like average velocity of some band or region of particles Concerning premature exit, I have no idea. The log files of those simulations does not contain the line "Running finished". But it has status: 0 (OK) result. So it must have been stopped somehow differently than by stopSimulation() function.. Cheers Jan [3] https://www.yade-dem.org/wiki/Howtoask [4] https://yade-dem.org/doc/formulation.html#result-indeterminism -- 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 #701438]: Why particle velocity varies with time step
Question #701438 on Yade changed: https://answers.launchpad.net/yade/+question/701438 Status: Open => Needs information Karol Brzezinski requested more information: Hi, Could you just just paste your code? Please find enclosed some good reasons provided for such a practice [1]. Best wishes, KB [1] https://www.yade-dem.org/wiki/Howtoask PS I know that it is a little bit ironic that I am providing link saying why you shouldn't incorporate links in your posts. But mostly refers to external file repositories :) -- 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 #701438]: Why particle velocity varies with time step
New question #701438 on Yade: https://answers.launchpad.net/yade/+question/701438 Hi, I was trying to simulate a bender element test using DEM, and I'd like to ask that why the evolution of particle velocity varies with time step, even dt is small enough compared to the dt obtained from PWaveTimeStep(). The attached MWE can illustrate my question, the MWE consists of 3 scripts, which can be found from [1]. (1) phase1.py is for sample generation and stress relaxation, it takes around 7 minutes if you want to reproduce the results. The idea is: firstly having a sample according to Bruno's example[2], then closing triax engine and increasing damping to quickly reduce unb. phase1 stops when unb reaches a small value (e.g.,1e-7). (2) phase2.py is the test under different dt, if you want to reproduce the resutls, you may use yade-batch phase2_batchParam.txt phase2.py, it takes around 8 minutes in general. The idea of this test is: firstly load the sample generated from phase1, then turn damping to 0, close time stepper, select some particles whose velocity will be recorded. phase2 will terminate when the time reaches 3e-4. (3) phase3.py is for plotting the results to get a figure which compared the results under different dt. You can directly find it in the attached files. The MWE above leads to two questions: (a) When I run phase2 in batch mode, not all simulations terminate when the time reaches 3e-4. Some of them terminated in advance. This can be seen from the figure. (b) As you can see from the figure, different dt leads to different velocity of the same group of particles. If I understood correctly, when dt is small enough, different dt should not affect the results. Do you have any ideas about it? Thank you very much! Aoxi [1]https://we.tl/t-B5s6rc6dRP [2]https://gitlab.com/yade-dev/trunk/blob/master/examples/triax-tutorial/script-session1.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
