[Yade-users] [Question #665440]: how can make a path for yade to load python files
New question #665440 on Yade: https://answers.launchpad.net/yade/+question/665440 Hello, I am new user of YADE. I can't load any python files in the yade. when I write the file (for example: yade Hello.py) it shows me an error like this: Welcome to Yade 2016-05-04.git-040f642 TCP python prompt on localhost:9000, auth cookie `uaydks' XMLRPC info provider on http://localhost:21000 Running script Hello.py Traceback (most recent call last): File "/usr/bin/yade", line 182, in runScript execfile(script,globals()) IOError: [Errno 2] No such file or directory: 'Hello.py' [[ ^L clears screen, ^U kills line. F12 controller, F11 3d view (use h-key for showing help), F10 both, F9 generator, F8 plot. ]] Could you please help me?I don't know what should I do :( Thanks a lot -- 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 #665387]: Compile error JointedCohesiveFrictionalPM
Question #665387 on Yade changed: https://answers.launchpad.net/yade/+question/665387 Status: Open => Answered Robert Caulk proposed the following answer: Hello William, Which linux distribution are you running? Which compiler are you using (gcc --version)? As Bruno mentions on yade-dev, your most recent build passes the buildbot [1] - so it may be a local problem. (I think Bruno's message [2] was not posted here as intended. He suggests you join yade-dev list serv [3] and send compiler questions there). Although it seems unlikely - is it possible this has something to do with this unusual merge of master with itself [4]? Is that a merge into your local repository? Perhaps you are you working off a read-only clone? Do you have duplicated commits on your local machine? I can't quite figure out what is going on there, the "merge" seems to simply add commits that are already committed to the repository. Cheers, Robert [1]https://yade-dem.org/buildbot/builders/yade-full/builds/4507 [2]https://lists.launchpad.net/yade-dev/msg13755.html [3]https://launchpad.net/~yade-dev [4]https://github.com/yade/trunk/commit/921bb17079fea51385fe620526f9bc48c055918e -- 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 #665379]: penetrationDepth calculation
Question #665379 on Yade changed: https://answers.launchpad.net/yade/+question/665379 Status: Open => Solved Andrea Puglisi confirmed that the question is solved: A, I've understood my error! The overlap contained in penetrationDepth is the one computed for the force, which corresponds to positions at the previous step! Sorry to make you lose your precious time and thanks for help anyway! -- 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 #665405]: Parallelism inconsistency
Question #665405 on Yade changed: https://answers.launchpad.net/yade/+question/665405 Bruno Chareyre posted a new comment: Hi, I would say this is not a misfeature that one wants to avoid. Instead it is an opportunity to assess indeterminism, which is in most cases inherent to the underlying physics. Re-ordering the bodies (i.e renumbering) while keeping everything else the same would give similar fluctuations in single thread yet I don't think anyone would claim that one numbering is better than another. The single thread result is like selecting one numbering and sticking to it, while parallel runs are like renumbering randomly each time. If the fluctuations are about 100% it is an interesting indication that the physical problem could be somehow ill-posed. Like asking in which direction a sphere will fall if you put it right on the top of a needle. Regards 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 #665379]: penetrationDepth calculation
Question #665379 on Yade changed:
https://answers.launchpad.net/yade/+question/665379
Status: Answered => Open
Andrea Puglisi is still having a problem:
Thanks Jan and Bruno. From Jan'answer I understand that the variable
shift2 should not be a problem in my example (I have no periodicity, it
is just a collision between two spheres). From Bruno's answer I learn
that there is something wrong in my script where I measure both the
quantity overlap=2*r-(x2-x1) (I have x2>x1) and the quantity
interaction.geom.penetrationDepth and they do not coincide.
My script is the following. The graph of the two quantity penetrationDepth vs.
overlap can be found at this shared link
https://drive.google.com/file/d/1r6YWwbg56jIN3EGB4RzoBRGHgHyHAhir/view?usp=sharing
#!/usr/bin/python
# -*- coding: utf-8 -*-
from yade import pack,ymport,export,geom,bodiesHandling,qt,plot
import math
rad = 0.00774
f=open("forces.dat" , "w")
def forces():
x1 = O.bodies[0].state.pos[0]
v1 = O.bodies[0].state.vel[0]
v2 = O.bodies[1].state.vel[0]
x2 = O.bodies[1].state.pos[0]
ov = 2*rad-(x2-x1)
intrs = O.bodies[0].intrs()
if (len(intrs)):
nfx = intrs[0].phys.normalForce[0]
nfy = intrs[0].phys.normalForce[1]
nfz = intrs[0].phys.normalForce[2]
sfx = intrs[0].phys.shearForce[0]
sfy = intrs[0].phys.shearForce[1]
sfz = intrs[0].phys.normalForce[2]
dep = intrs[0].geom.penetrationDepth
else:
nfx = nfy = nfz = sfx = sfy = sfz = dep = 0
f.write ("%6d %12.8f %12.8f %12.8f %12.8f %9.6f %9.6f %9.6f %9.6f %9.6f
%9.6f %12.8f\n" % (O.iter,O.time,ov,v1,v2,nfx,nfy,nfz,sfx,sfy,sfz,dep))
f.flush()
O.materials.append(FrictMat(young=0.1e9,poisson=.22,frictionAngle=0,density=2300,label='glass'))
Sph_1 = O.bodies.append([sphere([0,0,0], radius=rad, material = "glass")])
Sph_2 = O.bodies.append([sphere([0.1,0,0], radius=rad, material = "glass")])
O.bodies[1].state.vel = Vector3(-0.3,0,0)
O.bodies[0].state.vel = Vector3(0.3,0,0)
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),
],label='collider'),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_MindlinPhys()],
[Law2_ScGeom_MindlinPhys_Mindlin()],
),
NewtonIntegrator(damping=0.0,exactAsphericalRot=True,gravity=(0,0,0)),
PyRunner(command='forces()', iterPeriod=1),
]
O.dt=PWaveTimeStep()
try:
from yade import qt
qt.Controller()
qt.View()
except ImportError: pass
O.saveTmp()
O.timingEnabled=True
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Re: [Yade-users] [Question #665385]: Clumping the big number of grains
Question #665385 on Yade changed: https://answers.launchpad.net/yade/+question/665385 Status: Open => Answered Bruno Chareyre proposed the following answer: Hi, O.bodies.appendClumped() takes a list of bodies as input regardless of the number of bodies in the list. What is the problem with large clumps? 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 #665379]: penetrationDepth calculation
Question #665379 on Yade changed: https://answers.launchpad.net/yade/+question/665379 Bruno Chareyre proposed the following answer: Hi, It does correspond to x1-x2-2*r. Cheers 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 #665361]: Cylindrical Specimens for Triaxial modelling
Question #665361 on Yade changed: https://answers.launchpad.net/yade/+question/665361 Status: Open => Answered Bruno Chareyre proposed the following answer: Hi, there is still no easy method to simulate a cylindrical boundary presently. Simulate a different specimen shape is inconsequential in most cases fortunately, besides the fact that it does not "look like" the lab specimens. 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 #665293]: Issues with implementation of Law2_ScGeom_CapillaryPhys_Capillarity
Question #665293 on Yade changed: https://answers.launchpad.net/yade/+question/665293 Status: Open => Answered Bruno Chareyre proposed the following answer: The normalized capillary pressure Pc*D/σ (D: particle size, σ surface tension) is approximately 10 at air entry [1]. It suggests a lower bound which you can use as a reference value to scale pressure wrt. particle size and surface tension. Not sure this is what you are asking though. Bruno [1] https://www.sciencedirect.com/science/article/pii/S0045782516307216 -- 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 #665405]: Parallelism inconsistency
Question #665405 on Yade changed: https://answers.launchpad.net/yade/+question/665405 JOHN gave more information on the question: And now my new simulation is ~100% different. Reading the source i got the feeling that such large fluctuations are not normal -- 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 #665379]: penetrationDepth calculation
Question #665379 on Yade changed: https://answers.launchpad.net/yade/+question/665379 Status: Open => Answered Jan Stránský proposed the following answer: Hello Andrea, shift2 is used for periodic contact detection, have a look at [1]. See [2] for the meaning of Interaction::cellDist. cheers Jan [1] https://github.com/yade/trunk/blob/master/pkg/common/InteractionLoop.cpp#L113 [2] https://yade-dem.org/doc/formulation.html#collision-detection-in-periodic-cell -- 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 #665405]: Parallelism inconsistency
Question #665405 on Yade changed: https://answers.launchpad.net/yade/+question/665405 Status: Open => Needs information Jan Stránský requested more information: Hi John, in general it depends very much on the problem and how you measure fluctuation. I am afraid there is no way to decrease the effect with current implementation.. Can you please post your example (ideally in the minimal form)? thanks 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 #662529]: References for randomDensePack
Question #662529 on Yade changed: https://answers.launchpad.net/yade/+question/662529 Jan Stránský posted a new comment: Thanks guys for tips 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 #662529]: References for randomDensePack
Question #662529 on Yade changed: https://answers.launchpad.net/yade/+question/662529 Status: Answered => Solved Jan Stránský confirmed that the question is solved: Thanks Robert Caulk, 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 #665405]: Parallelism inconsistency
Question #665405 on Yade changed: https://answers.launchpad.net/yade/+question/665405 JOHN 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 #665405]: Parallelism inconsistency
Question #665405 on Yade changed: https://answers.launchpad.net/yade/+question/665405 Status: Needs information => Solved JOHN confirmed that the question is solved: Hi, thanks again. My example is unfortunately not easily given in minimal form. The simulation itself just creates a hexagonal packing, imports an stl, substracts spheres that are in or partially in the walls and runs with the following engine O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( # handle sphere+sphere and facet+sphere collisions [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(gravity=(0,-9.81,0),damping=0.4, label='newtonInt'), the tricky part is an outside function that calculates rotations which is not easily given in minimal form -- 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 #665405]: Parallelism inconsistency
Question #665405 on Yade changed: https://answers.launchpad.net/yade/+question/665405 Status: Answered => Open JOHN is still having a problem: Hi Jan, thanks for the info! That makes sense. Though it seems like there is no way around it, is it possible to decrease that effect? I am now seeing up to ~15% difference in some simulations Thanks again cheers John -- 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 #665341]: iterations in c++
Question #665341 on Yade changed: https://answers.launchpad.net/yade/+question/665341 Status: Open => Solved JOHN confirmed that the question is solved: nevermind, i compiled the yade trunk myself and i was able to link with the correct hpp files -- 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 #665405]: Parallelism inconsistency
Question #665405 on Yade changed: https://answers.launchpad.net/yade/+question/665405 Status: Open => Answered Jan Stránský proposed the following answer: Hi John, yes, this is a known issue, see [1] cheers Jan [1] 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
[Yade-users] [Question #665405]: Parallelism inconsistency
New question #665405 on Yade: https://answers.launchpad.net/yade/+question/665405 Good evening, I recently tried yade in parallel. To test it, i created a scene and then loaded it with various thread numbers. With 1 thread the data was consistently the same (positions times till the end etc) with more, there were differences. The particles werent that many at the beginning (1330) but the message saying WARN /build/yade-KKgSmd/yade-1.20.0/pkg/common/InsertionSortCollider.cpp:80 insertionSortParallel: Parallel insertion: only 2 thread(s) used. The number of bodies is probably too small for allowing more threads, or the geometry is flat. The contact detection should succeed but not all available threads are used. didnt appear for 2 threads(oviously), which also produced differences One thing is that the number of particles decreases with the simulation time. I cant think however why the results would vary for 2 threads anyway (openmp is safer than mpi) Is this a known issue? Any suggestions? Thank you very much in advance John -- 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
