Re: [Yade-users] [Question #692392]: i.geom.penetrationDepth = nan after load yade.gz file
Question #692392 on Yade changed: https://answers.launchpad.net/yade/+question/692392 Leonard posted a new comment: Great, thanks Bruno! Cheers Leonard -- 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 #692392]: i.geom.penetrationDepth = nan after load yade.gz file
Question #692392 on Yade changed: https://answers.launchpad.net/yade/+question/692392 Chareyre posted a new comment: @Leonard The rationale for not saving/loading Un is that it is always unambiguously deduced from positions and sizes. We try to store only independent variables, not derived variables. What you report is not actually a problem, or it is only a problem of the way you output penetrationDepth. Insert a PyRunner to print Un, after NewtonIntegrator. The apparent issue will disappear. B On Thu, 20 Aug 2020 at 17:48, Bruno Chareyre wrote: > > (I did not really get your comment :-) > > I was pointing the fact that the notion of "value of X at iteration N" is > vague in the first place, since X can change at any point within one > time-loop. > Virtually you could insert multiple O.save() or any form of snapshot > within an iteration, interleaved with the usual engines, and you would get > different numbers in each of them depending on their relative positions in > the sequence of engines. > The above save/load issue is nearly the same thing I would say. > B > -- 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 #692392]: i.geom.penetrationDepth = nan after load yade.gz file
Question #692392 on Yade changed: https://answers.launchpad.net/yade/+question/692392 Chareyre posted a new comment: > (I did not really get your comment :-) I was pointing the fact that the notion of "value of X at iteration N" is vague in the first place, since X can change at any point within one time-loop. Virtually you could insert multiple O.save() or any form of snapshot within an iteration, interleaved with the usual engines, and you would get different numbers in each of them depending on their relative positions in the sequence of engines. The above save/load issue is nearly the same thing I would say. B -- 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 #692392]: i.geom.penetrationDepth = nan after load yade.gz file
Question #692392 on Yade changed: https://answers.launchpad.net/yade/+question/692392 Leonard 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
Re: [Yade-users] [Question #692392]: i.geom.penetrationDepth = nan after load yade.gz file
Question #692392 on Yade changed: https://answers.launchpad.net/yade/+question/692392 Status: Answered => Solved Leonard confirmed that the question is solved: Thanks Jan and Bruno for your comments, I tried a few more times in different ways (e.g., set O.dt=0 or not in both scripts) and still can't find the "exact state (i.e., the same penetrationDepth)'' between script1 and script2. What Jan explained make sense. It is good that I can use O.step() to re-gain the penetrationDepth after loading the sample. I will check further and hope this one additional step will not affect the final results compared to the case which doesn't involve this O.step. Thanks Leonard -- 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 #692392]: i.geom.penetrationDepth = nan after load yade.gz file
Question #692392 on Yade changed: https://answers.launchpad.net/yade/+question/692392 Jan Stránský posted a new comment: @Bruno: more like: re-running after reload is equivalent to continuing with simulation (further step(s)) in the original simulation. I.e. the values are intrinsically different that the saved state (I did not really get your comment :-) cheers Jan -- 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 #692392]: i.geom.penetrationDepth = nan after load yade.gz file
Question #692392 on Yade changed: https://answers.launchpad.net/yade/+question/692392 Chareyre proposed the following answer: Hi Jan, > After one simulation step (one execution of O.interactionLoop engines) you have "old" penetrationDepth even the particle position are "new". >From this insightful comment is it ok to conclude that re-running after reload will give same result as with no save/load (I guess so), since interaction loop will update wrt new positions before computing forces? If so the issue is nearly the same as "if I put penetrationDepth recorder before/after interactionLoop I get different values at iteration N". Cheers B -- 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 #692392]: i.geom.penetrationDepth = nan after load yade.gz file
Question #692392 on Yade changed: https://answers.launchpad.net/yade/+question/692392 Status: Open => Answered Jan Stránský proposed the following answer: These are limitations of the (explicit? not sure) discrete model, where the values in one time step may differ in "actual" time 1) have a look at the O.interactionLoop. Ig2 (where penetrationDepth is computed) is before NewtonIntegrator (where the position are updated). After one simulation step (one execution of O.interactionLoop engines) you have "old" penetrationDepth even the particle position are "new". 2) is very similar. After script1, you already have "new" positons, from which penetrationDepth in script2 is computed, but if you just print penetrationDepth in script1, you are getting "old" values. You would have to set O.dt=0 also for the last step in script1 to get the same values in both script1 and script2 cheers Jan -- 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 #692392]: i.geom.penetrationDepth = nan after load yade.gz file
Question #692392 on Yade changed:
https://answers.launchpad.net/yade/+question/692392
Status: Answered => Open
Leonard is still having a problem:
Hi Jan,
Many thanks for your reply.
With your suggestion, I got the i.geom.penetrationDepth=someValue. It is
really good compared to Nan before.
However, I found another two problems that I'd like to discuss:
(1) In the Script2(i.e., loading sample). No matter I set O.dt=0 or not, the
i.geom.penetrationDepth (for a certain interaction) is the same. You may see it
by skipping O.dt=0 in Script2 below.
(2) At the end of Script1 (i.e., making sample), I record a penetrationDepth of
a certain interaction, for example
O.interactions[2154,3930].geom.penetrationDepth=1.54203739497e-06.
And when I go to Script2, I check the penetrationDepth of that interaction ,
the value I got in Script2 is slightly different with Script1 (i.e.,
O.interactions[2154,3930].geom.penetrationDepth=1.5419131404164482e-06). which
means that the state has changed although it is slight.
You may reproduce the problem using the following MWE (Script1 and
Script2) below if you are interested. (if O.interactions[2154,3930]
isn't existed, You may need to select a new one from script1):
##Script 1###
from __future__ import division
from yade import pack, plot
num_spheres=7000#
targetPorosity = 0.45
compFricDegree = 30
finalFricDegree = 18
rate=-0.01
damp=0.6
stabilityThreshold=0.001
young=2e8
confinement=100e3
mn,mx=Vector3(0,0,0),Vector3(0.07,0.14,0.07)
MatWall=O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
MatSand =
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
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='spheres') for center,rad in sp])
triax=TriaxialStressController(
maxMultiplier=1.+3e7/young,
finalMaxMultiplier=1.+16e4/young,
thickness = 0,
stressMask = 7,
internalCompaction=True,
)
newton=NewtonIntegrator(damping=damp)
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Box_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()],
[Law2_ScGeom_FrictPhys_CundallStrack()]
),
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
triax,
TriaxialStateRecorder(iterPeriod=100,file='WallStresses'),
newton,
]
Gl1_Sphere.stripes=0
triax.goal1=triax.goal2=triax.goal3=-confinement
while 1:
O.run(1000, True)
#the global unbalanced force on dynamic bodies, thus excluding boundaries,
which are not at equilibrium
unb=unbalancedForce()
print 'unbF:',unb,' meanStress:
',-triax.meanStress,'top:',-triax.stress(triax.wall_top_id)[1]
if unbtargetPorosity:
compFricDegree = 0.95*compFricDegree
setContactFriction(radians(compFricDegree))
print "\r Friction: ",compFricDegree," porosity:",triax.porosity,
sys.stdout.flush()
O.run(500,1)
O.save('sample.yade.gz')
print "### Compacted state saved ###"
for i in O.interactions:
print i.id1,i.id2,i.geom.penetrationDepth
##Script 2###
from __future__ import division
from yade import pack, plot
O.load('sample.yade.gz')
confinement=100e3
triax=TriaxialStressController(
thickness = 0,
stressMask = 5,
internalCompaction=False,
)
newton=NewtonIntegrator(damping=0.4)
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Box_Sphere_ScGeom()],
[Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(),
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),
triax,
TriaxialStateRecorder(iterPeriod=1000,file='WallStresses'),
newton,
]
triax.goal2=-1
triax.goal1=-confinement
triax.goal3=-confinement
print "penetrationDepth:", O.interactions[2154,3930].geom.penetrationDepth
print "O.dt:", O.dt
# O.dt=0 #(or skip this step for my question 1)
O.step()
print "penetrationDepth:", O.interactions[2154,3930].geom.penetrationDepth
#
Do you have any ideas about this?
Thanks
Leonard
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Re: [Yade-users] [Question #692392]: i.geom.penetrationDepth = nan after load yade.gz file
Question #692392 on Yade changed: https://answers.launchpad.net/yade/+question/692392 Status: Open => Answered Jan Stránský proposed the following answer: Hello, i.geom (assuming it is ScGeom instance) has penetrationDepth attribute, but is is marked as noSave [1], which "avoids serialization of the attribute" [2] (section 'attrs' -> 'Attribute flags') If you run O.step (possibly with O.dt=0 not to affect the state of the simulation), they should be computed. cheers Jan [1] https://gitlab.com/yade-dev/trunk/-/blob/master/pkg/dem/ScGeom.hpp#L104 [2] https://yade-dem.org/doc/prog.html#yade-class-base-doc-macro-family -- 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 #692392]: i.geom.penetrationDepth = nan after load yade.gz file
New question #692392 on Yade:
https://answers.launchpad.net/yade/+question/692392
Hi,
I am working on the sample preparation for triaxial compression test, there are
two steps: (1st) making sample and save it, (2nd) load the sample. However,
when I load the sample in step2, I found that all the penetractionDepth
(i.geom.penetrationDepth) become nan, while they should have a small value in
fact. Here is the MWE (modified from Bruno's script) which can produce the
problem.
### Script1(sample generation)
from __future__ import division
from yade import pack, plot
num_spheres=7000#
targetPorosity = 0.45
compFricDegree = 30
finalFricDegree = 18
rate=-0.01
damp=0.6
stabilityThreshold=0.001
young=2e8
confinement=100e3
mn,mx=Vector3(0,0,0),Vector3(0.07,0.14,0.07)
MatWall=O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls'))
MatSand =
O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres'))
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='spheres') for center,rad in sp])
triax=TriaxialStressController(
maxMultiplier=1.+3e7/young,
finalMaxMultiplier=1.+16e4/young,
thickness = 0,
stressMask = 7,
internalCompaction=True,
)
newton=NewtonIntegrator(damping=damp)
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Box_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()],
[Law2_ScGeom_FrictPhys_CundallStrack()]
),
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
triax,
TriaxialStateRecorder(iterPeriod=100,file='WallStresses'),
newton,
]
Gl1_Sphere.stripes=0
triax.goal1=triax.goal2=triax.goal3=-confinement
while 1:
O.run(1000, True)
#the global unbalanced force on dynamic bodies, thus excluding boundaries,
which are not at equilibrium
unb=unbalancedForce()
print 'unbF:',unb,' meanStress:
',-triax.meanStress,'top:',-triax.stress(triax.wall_top_id)[1]
if unbtargetPorosity:
compFricDegree = 0.95*compFricDegree
setContactFriction(radians(compFricDegree))
print "\r Friction: ",compFricDegree," porosity:",triax.porosity,
sys.stdout.flush()
O.run(500,1)
O.save('sample.yade.gz')
print "###Compacted state saved ###"
for i in O.interactions:
print i.geom.penetrationDepth
Script2(loading sample and checking penetrationDepth)
O.load('sample.yade.gz')
for i in O.interactions:
print i.geom.penetrationDepth
Do you have any ideas for this problem?
Thanks
Leonard
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