Re: [Yade-users] [Question #691874]: batch-table
Question #691874 on Yade changed: https://answers.launchpad.net/yade/+question/691874 Status: Open => Answered Jan Stránský proposed the following answer: Hello, please provide also the content of the table and which OS and Yade version you are using > #0 (damping=.6) FAILED (exit status 34304), duration 00:00:13, log 1batch.py.damping=.6.log FAILED means that there was some problem. Have a look at "1batch.py.damping=.6.log" file to see the problem (basically it is redirected output of the Yade run) 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 #691808]: Mesoscale modeling in YADE
Question #691808 on Yade changed: https://answers.launchpad.net/yade/+question/691808 Faqih Maarif posted a new comment: Dear Jan, Thank you very much for your explanation and solution. I will try it. For macroscale to mesoscale particle, I would like to discuss later. Regards, Faqih -- 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 #691808]: Mesoscale modeling in YADE
Question #691808 on Yade changed: https://answers.launchpad.net/yade/+question/691808 Status: Answered => Solved Faqih Maarif 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 #691874]: batch-table
Question #691874 on Yade changed: https://answers.launchpad.net/yade/+question/691874 Status: Answered => Open Lei Hang is still having a problem: Hello, Sorry, I don't know the meaning of 'OS'. I f it means operation system, the OS is Linux. The Yade version is 2020.01a. There is a "Fatal Python error" in the "1batch.py.damping=.6.log" file . But I don't understand this error and don't know how to deal with this error. The content of the table and the "1batch.py.damping=.6.log" file are as follows, The content of the table: # damping .6 .4 .2 # The "1batch.py.damping=.6.log" file: # Welcome to Yade 2020.01a Using python version: 3.8.2 (default, Apr 27 2020, 15:53:34) [GCC 9.3.0] Warning: no X rendering available (see https://bbs.archlinux.org/viewtopic.php?id=13189) XMLRPC info provider on http://localhost:21000 TCP python prompt on localhost:9000, auth cookie `assduk' Running script 1batch.py /usr/lib/x86_64-linux-gnu/yade/py/yade/plot.py:444: MatplotlibDeprecationWarning: The 'verts' kwarg was deprecated in Matplotlib 3.0 and will be removed in 3.2. Use 'marker' instead. scatter=pylab.scatter(scatterPt[0] if not math.isnan(scatterPt[0]) else 0,scatterPt[1] if not math.isnan(scatterPt[1]) else 0,s=scatterSize,color=line.get_color(),**scatterMarkerKw) No handles with labels found to put in legend. yade.plot: creating fake plot, since there are no y-data yet Fatal Python error: This thread state must be current when releasing Python runtime state: finalizing (tstate=0x15783b0) Current thread 0x7f83e1660700 (most recent call first): File "/usr/lib/python3.8/bz2.py", line 125 in close File "/usr/lib/x86_64-linux-gnu/yade/py/yade/plot.py", line 664 in saveDataTxt File "1batch.py", line 37 in checkUnbalanced File "", line 1 in Thread 0x7f83e43d4700 (most recent call first): File "/usr/lib/python3.8/selectors.py", line 415 in select File "/usr/lib/python3.8/socketserver.py", line 232 in serve_forever Thread 0x7f83e4bd5700 (most recent call first): File "/usr/lib/python3.8/selectors.py", line 415 in select File "/usr/lib/python3.8/socketserver.py", line 232 in serve_forever Thread 0x7f83f9e50740 (most recent call first): File "/usr/lib/python3.8/_weakrefset.py", line 38 in _remove Aborted (core dumped) === JOB SUMMARY id : damping=.6 status : 34304 (FAILED) duration: 00:00:13 command : YADE_BATCH=params.txt:2 DISPLAY= /usr/bin/yade --threads=1 --nice=10 -x 1batch.py> 1batch.py.damping=.6.log 2>&1 started : Wed Jul 15 09:02:36 2020 finished: Wed Jul 15 09:02:49 2020 # Many thanks -- 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 #691808]: Mesoscale modeling in YADE
Question #691808 on Yade changed: https://answers.launchpad.net/yade/+question/691808 Jan Stránský posted a new comment: I also think Luc Scholtes did some work on this topic, but currently I cannot find it.. Just to note, there is really many options and approaches, this is just one of them. 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 #691874]: batch-table
Question #691874 on Yade changed: https://answers.launchpad.net/yade/+question/691874 Status: Open => Answered Jan Stránský proposed the following answer: yes, OS is operating system. Linux is too general, what is meant is distribution (Debian, Ubuntu) and version (e.g. Ubuntu 18.04) > File "/usr/lib/x86_64-linux-gnu/yade/py/yade/plot.py", line 664 in saveDataTxt > File "1batch.py", line 37 in checkUnbalanced as the error says, the problem is on line 37, something about plot.saveDataTxt > plot.saveDataTxt(O.tags['d.id']+'.data.bz2') This worked for me: ### ... def checkUnbalanced(): if unbalancedForce()<.05: O.pause() ... O.run() waitIfBatch() plot.saveDataTxt(O.tags['d.id']+'.data.bz2') ### The problem is O.pause with O.wait (or waitIfBatch). When O.pause() is called, the waiting is released. The only other (probably very quick) Python command is O.saveTmp(). This very quick command is executed and the script finishes, no matter that saving is in progress (it is called from C++ in another thread). In the modified version, after waiting there are still Python commands (plot.saveDataTxt) to be processed and the script finishes after it is executed. 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 #691874]: batch-table
Question #691874 on Yade changed:
https://answers.launchpad.net/yade/+question/691874
Status: Answered => Open
Lei Hang is still having a problem:
Thank you Jan,
The OS information is(Linux version 5.4.0-37-generic
(buildd@lcy01-amd64-001) (gcc version 9.3.0 (Ubuntu 9.3.0-10ubuntu2))
#41-Ubuntu SMP Wed Jun 3 18:57:02 UTC 2020)
The method you provided solved my problem. But when I conduct the below script,
why it can run normally? The position of
"plot.saveDataTxt(O.tags['d.id']+'.data.bz2')" fllows the "O.pause()". It is
not changed to behind the "waitIfBatch()".
The script:
#
readParamsFromTable(damping=.2)
from yade.params import table
from yade import pack, plot
O.bodies.append(geom.facetBox((.5,.5,.5),(.5,.5,.5),wallMask=31))
# create empty sphere packing
# sphere packing is not equivalent to particles in simulation, it contains only
the pure geometry
sp=pack.SpherePack()
# generate randomly spheres with uniform radius distribution
sp.makeCloud((0,0,0),(1,1,1),rMean=.05,rRelFuzz=.5)
# add the sphere pack to the simulation
sp.toSimulation()
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=(0,0,-9.81),damping=table.damping),
# call the checkUnbalanced function (defined below) every 2 seconds
PyRunner(command='checkUnbalanced()',realPeriod=2),
# call the addPlotData function every 200 steps
PyRunner(command='addPlotData()',iterPeriod=100)
]
O.dt=.5*PWaveTimeStep()
# enable energy tracking; any simulation parts supporting it
# can create and update arbitrary energy types, which can be
# accessed as O.energy['energyName'] subsequently
O.trackEnergy=True
# if the unbalanced forces goes below .05, the packing
# is considered stabilized, therefore we stop collected
# data history and stop
def checkUnbalanced():
if unbalancedForce()<.05:
O.pause()
plot.saveDataTxt(O.tags['d.id']+'.data.bz2')
# plot.saveGnuplot('bbb') is also possible
# collect history of data which will be plotted
def addPlotData():
# each item is given a names, by which it can be the unsed in plot.plots
# the **O.energy converts dictionary-like O.energy to plot.addData
arguments
plot.addData(i=O.iter,unbalanced=unbalancedForce(),**O.energy)
# define how to plot data: 'i' (step number) on the x-axis, unbalanced force
# on the left y-axis, all energies on the right y-axis
# (O.energy.keys is function which will be called to get all defined energies)
# None separates left and right y-axis
plot.plots={'i':('unbalanced',None,O.energy.keys)}
# show the plot on the screen, and update while the simulation runs
plot.plot()
O.run() # run forever, until stopped by checkUnbalancedForce()
waitIfBatch()
O.saveTmp()
#
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Re: [Yade-users] [Question #691829]: Filterpack predicate definition issue
Question #691829 on Yade changed:
https://answers.launchpad.net/yade/+question/691829
Status: Answered => Open
Yuxuan Wang is still having a problem:
Hi Jan,
Thank you for the suggestions and they worked quite well for me upon
implementation. I saw a significant reduction of particles going from the
compressed pack to the filtered pack.
There is only one thing that I'm still confused about now: I was not
able to see any of the particles after "assembly.toSimulation()" in the
simulation view, even though I could output their locations. Would you
mind giving me a hand on that again?
Thanks again!
Best,
Yuxuan
-
#!/usr/bin/python
# -*- coding: utf-8 -*-
#modifications from trial 10: incorporating Jan's advice on filterpack.
from __future__ import print_function
import matplotlib; matplotlib.rc('axes',grid=True)
import pylab
from yade import pack, plot, qt
from yade import export
### DEFINING VARIABLES AND MATERIALS ###
#geometry definition
Ri,Rs,Ro=6.5,8.5,10.5
H=3.5
p=H/2
k=0.01
Hs=H*k
hs=Hs/2
Rx=2*Ro
Hx=2*H
c1=geom.facetCylinder(center=(0,0,p),radius=Ro, height=H, segmentsNumber=20,
wallMask=6)
c2=geom.facetCylinder(center=(0,0,hs),radius=Rs, height=Hs, segmentsNumber=20,
wallMask=7)
c3=geom.facetCylinder(center=(0,0,p),radius=Ri, height=H, segmentsNumber=20,
wallMask=7)
nRead=readParamsFromTable(
num_spheres=5000,
compFricDegree = 30,
unknownOk=True
)
from yade.params import table
num_spheres=table.num_spheres
compFricDegree = table.compFricDegree
damp=0.2
young=5e6 # contact stiffness
mn,mx=Vector3(-12,-12,-12),Vector3(12,12,12) # corners of the initial packing
## create materials for spheres and plates
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'))
## create walls around the packing
walls=aabbWalls([mn,mx],thickness=0,material='walls')
wallIds=O.bodies.append(walls)
## use a SpherePack object to generate a psd loose particles packing
global sp
sp=pack.SpherePack()
sp.makeCloud(mn,mx,num=1000,psdSizes=[0.399,0.4,0.799,0.8],psdCumm=[0,0.5,0.5,1])
sp.toSimulation(material='spheres')
### DEFINING ENGINES ###
triax=TriaxialStressController(
thickness = 0,
stressMask = 7,
internalCompaction=False,
label='controller'
)
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()]
),
PyRunner(command='stop()',iterPeriod=1,label='checker'),
GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
triax,
newton
]
#Display spheres with 2 colors for seeing rotations better
Gl1_Sphere.stripes=0
if nRead==0: yade.qt.Controller(), yade.qt.View()
###
### APPLYING CONFINING PRESSURE ###
###
triax.goal1=triax.goal2=triax.goal3=-100
def stop():
if O.iter<100:return
else:
controller.dead=True
for wall in walls:
wall.state.vel = Vector3.Zero
for b in O.bodies:
b.state.vel = Vector3.Zero
sp.fromSimulation() # update sp from original loose pack to compressed dense
pack
checker.command='gravityDeposition()'
def gravityDeposition():
if O.iter==101:
pred=pack.inCylinder((0,0,0),(0,0,H),Ro)-pack.inCylinder((0,0,0),(0,0,Hs),Rs)-pack.inCylinder((0,0,0),(0,0,H),Ri)
assembly=pack.filterSpherePack(pred,sp,True)
O.bodies.clear() #delete compressed pack sp
print(len(O.bodies))
assembly.toSimulation()
print(len(O.bodies))
for b in O.bodies:print(b.id,b.state.pos,b.shape.radius)
else:
print ('done')
O.pause()
#...connect to next steps in simulation
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Re: [Yade-users] [Question #691828]: Deactivate triaxial stress controller
Question #691828 on Yade changed: https://answers.launchpad.net/yade/+question/691828 Status: Answered => Solved Yuxuan Wang 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
[Yade-users] [Question #691885]: thermo-hydro-mechanical modeling
New question #691885 on Yade: https://answers.launchpad.net/yade/+question/691885 I’m interested in the THM modeling by Yade and was wondering if someone could post a version of codes used for this paper [1]. And also, can we do THM with any kind of body in Yade like box elements, walls, or clumps? Thanks Zoheir [1] R. Caulk, B. Chareyre, 2019. An open framework for the simulation of coupled Thermo-Hydro-Mechanical processes in Discrete Element Systems. https://www.researchgate.net/publication/335272631_An_open_framework_for_the_simulation_of_coupled_Thermo-Hydro-Mechanical_processes_in_Discrete_Element_Systems -- 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
