Image and erase
Hi,
How can I erase "walls" and the "plate" once my simulation is done (after o.pause). I also would like take a image of my simulation after o.pause.
Here is my code:
#!/usr/bin/env python
#encoding: ascii
# Testing of the Deformation Enginge with Luding Contact Law
# Modified Oedometric Test
# The reference paper [Haustein2017]
from __future__ import print_function
from yade import utils, plot, timing
from yade import pack
import pandas as pd
o = Omega()
# Physical parameters
fr = 0.3
rho = 2000
Diameter = 16.5e-3
r1 = Diameter
r2 = Diameter
k1 = 1005.0
kp = 10.0*k1
kc = k1 * 0.0
ks = k1 * 0.1
DeltaPMax = Diameter/3.0
Chi1 = 0.34
o.dt = 1.0e-5
particleMass = 4.0/3.0*
Vi1 = math.sqrt(
PhiF1 = DeltaPMax*
#******
# Add material
mat1 = O.materials.
# Spheres for compression
sp=pack.
sp.makeCloud(
cyl = pack.inCylinder
sp = pack.filterSphe
sp.toSimulation
##No of particles
count = 0
for b in O.bodies:
if isinstance(b.shape, Sphere):
count +=1
#######
walls=O.
df = pd.DataFrame(
df.to_csv(
from csv import writer
def append_
# Open file in append mode
with open(file_name, 'a+', newline='') as write_obj:
# Create a writer object from csv module
csv_writer = writer(write_obj)
# Add contents of list as last row in the csv file
# Add engines
o.engines = [
ForceResetter(),
InsertionSort
InteractionLoop(
[Ig2_
Ig2_
Ig2_
[Ip2_
[Law2_
),
NewtonIntegra
#VTKRecorder(
PyRunner(
DeformControl
]
def checkForce():
# at the very start, unbalanced force can be low as there is only few
# contacts, but it does not mean the packing is stable
if O.iter < 20000:
return
# the rest will be run only if unbalanced is < .1 (stabilized packing)
timing.reset()
if unbalancedForce() > 0.3:
return
# add plate at upper box side
highSphere = 0.0
for b in O.bodies:
if highSphere < b.state.pos[2] and isinstance(b.shape, Sphere):
else:
pass
O.bodies.
# without this line, the plate variable would only exist inside this
# function
global plate
plate = O.bodies[-1] # the last particles is the plate
# Wall objects are "fixed" by default, i.e. not subject to forces
# prescribing a velocity will therefore make it move at constant velocity
# (downwards)
plate.state.vel = (0, 0, -.1)
# start plotting the data now, it was not interesting before
O.engines = O.engines + [PyRunner(
# next time, do not call this function anymore, but the next one
# (unloadPlate) instead
fCheck.command = 'unloadPlate()'
def unloadPlate():
# if the force on plate exceeds maximum load, start unloading
# if abs(O.forces.
if abs(O.forces.
# next time, do not call this function anymore, but the next one
# (stopUnloading) instead
def stopUnloading():
if abs(O.forces.
# O.tags can be used to retrieve unique identifiers of the simulation
# if running in batch, subsequent simulation would overwrite each other's output files otherwise
# d (or description) is simulation description (composed of parameter values)
# while the id is composed of time and process number
# plot.saveDataTx
O.pause()
#Want Erase wall and plate
#Take snap of my simualation
D=Diameter
for i in range (0,len(
def addPlotData():
if not isinstance(
return
Fz = O.forces.
plot.addData(
Fz=Fz,
i=O.iter
)
def defVisualizer():
with open("data.
for b in O.bodies:
if isinstance(b.shape, Sphere):
O.timingEnabled
O.run(1, True)
plot.plots=
plot.plot()
Question information
- Language:
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- Status:
- Answered
- For:
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- Last reply:
Revision history for this message
|
#1 |
Hello,
you have 2 problems in one question. Next time, please create separate question for separate problem [1]
> How can I erase "walls" and the "plate" once my simulation is done (after o.pause).
Depends on what "walls" and "plate" are and how to indentify them w.r.t. other bodies. In general O.bodies.erase [2] is probably what you want. You can use it in different ways:
O.bodies.erase(id) # if you know the ID
O.bodies.
for b in O.bodies:
if isinstance(
> I also would like take a image of my simulation after o.pause.
Several options, too, depending on actual needs
- create screenshot manually
- use SnapshotEngine to create the screenshot
- export data and create image externally (e.g. using Paraview)
Cheers
Jan
[1] https:/
[2] https:/
Revision history for this message
|
#2 |
Hi Jan,
Thank you for reply, sorry for asking two questions. I thought both of them were on the same code.
When I add the o.bodies.erase, I am getting error message "Segmentation fault (core dumped)".
Snapshot engine works only during the iteration, and does not take image after o.pause.
Best,
Mithu
Revision history for this message
|
#3 |
> When I add the o.bodies.erase, I am getting error message "Segmentation fault (core dumped)".
please provide the code causing this.
> Snapshot engine works only during the iteration, and does not take image after o.pause.
not necessarily, something like
###
e = SnapshotEngine(...) # create a SnapshotEngine instance
e() # call the instance
###
could/should work
cheers
Jan
Revision history for this message
|
#4 |
Hi Jan,
The snapshotengine does not work, getting erro message saying 'SnapshotEngine' is not defined.
Here is my code:
#!/usr/bin/env python
#encoding: ascii
# Modefied Oedometric Test for particle deformation under const. volume
# The reference paper [Haustein2017]
from __future__ import print_function
from yade import utils, plot, timing
from yade import pack
o = Omega()
# Physical parameters
fr = 0.3
rho = 2000
tc = 0.002
en = 0.7
et = 0.7
Diameter = 16.5e-3 # R
#******
o.dt = 1.0e-5 # Timestep
#******
# Add material
mat1 = O.materials.
# Spheres for compression
sp=pack.
sp.makeCloud(
sp.toSimulation()
#######
cylinder=
geom.
)
# Add engines
o.engines = [
ForceResetter(),
InsertionSort
InteractionLoop(
[Ig2_
Ig2_
Ig2_
[Ip2_
[Law2_
),
NewtonIntegra
#VTKRecorder(
PyRunner(
DeformControl
]
def checkForce():
# at the very start, unbalanced force can be low as there is only few
# contacts, but it does not mean the packing is stable
if O.iter < 20000:
return
# the rest will be run only if unbalanced is < 1.0 (stabilized packing)
timing.reset()
if unbalancedForce() > 0.2:
return
highSphere=0.0
for b in O.bodies:
if highSphere < b.state.pos[2] and isinstance(b.shape, Sphere):
else:
pass
# add plate at upper box side
O.bodies.
# without this line, the plate variable would only exist inside this
# function
global plate
plate = O.bodies[-1] # the last particles is the plate
# Wall objects are "fixed" by default, i.e. not subject to forces
# prescribing a velocity will therefore make it move at constant velocity
# (downwards)
plate.state.vel = (0, 0, -0.1)
# start plotting the data now, it was not interesting before
O.engines = O.engines + [PyRunner(
# next time, do not call this function anymore, but the next one
# (unloadPlate) instead
fCheck.command = 'unloadPlate()'
def unloadPlate():
# if the force on plate exceeds maximum load, start unloading
# if abs(O.forces.
# if plate.state.pos[2] < (-4*Diameter+
if abs(O.forces.
# next time, do not call this function anymore, but the next one
# (stopUnloading) instead
def stopUnloading():
if abs(O.forces.
# O.tags can be used to retrieve unique identifiers of the simulation
# if running in batch, subsequent simulation would overwrite each other's output files otherwise
# d (or description) is simulation description (composed of parameter values)
# while the id is composed of time and process number
# plot.saveDataTx
O.pause()
for b in O.bodies:
if isinstance(
for j in cylinder: O.bodies.erase(j)
def addPlotData():
if not isinstance(
return
Fz = O.forces.
plot.addData(
Fz=Fz,
i=O.iter
)
O.timingEnabled
O.run(1, True)
plot.plots=
plot.plot()
Revision history for this message
|
#5 |
SnapshotEngine should work, don't know why. also qt.SnapshotEngine cannot be found.. I think it is a topic for separate question :-)
concerning segmentation fault, it is probably somewhere, where the code expects a body, but it is deleted at the time.
Please run
catchsegv yade script.py
(where "yade" and "script.py" are the executable and the file you are using)
and provide the output
cheers
Jan
Revision history for this message
|
#6 |
Note: if you want to just "not show" (instead of "delete") you can also use this:
In [2]: rr=yade.
In [3]: rr.hideBody?
Docstring:
hideBody( (OpenGLRenderer
Hide body from id (see :yref:`
Regards
Bruno
Revision history for this message
|
#7 |
Hi Jan,
Here is my output from running with catchsegv:
Segmentation fault (core dumped)
*** Segmentation fault
Register dump:
RAX: 0000000000000000 RBX: 00000000000016a1 RCX: 0000000000000007
RDX: 00007feaa81371c0 RSI: 0000000000016a10 RDI: 000000000143add0
RBP: 00007feaa87bac00 R8 : 0000000000000006 R9 : 00007feb66f400c0
R10: 0000000000000000 R11: 0000000000000246 R12: 000000000143add0
R13: 0000000000000030 R14: 0000000003928bd0 R15: 00007feb66f47200
RSP: 00007feaafffea90
RIP: 00007feb6444a173 EFLAGS: 00010202
CS: 0033 FS: 0000 GS: 0000
Trap: 0000000e Error: 00000004 OldMask: 00000000 CR2: 00000038
FPUCW: 0000037f FPUSW: 00000020 TAG: 00007feb
RIP: 68b40b56 RDP: 00000000
ST(0) ffff 8000000000000000 ST(1) 0000 0000000000000000
ST(2) 0000 0000000000000000 ST(3) 0000 0000000000000000
ST(4) ffff 8000000000000000 ST(5) 0000 0000000000000000
ST(6) ffff 8000000000000000 ST(7) 8000 8000000000000000
mxcsr: 1fa5
XMM0: 000000000000000
XMM2: 000000000000000
XMM4: 000000000000000
XMM6: 000000000000000
XMM8: 000000000000000
XMM10: 000000000000000
XMM12: 000000000000000
XMM14: 000000000000000
Backtrace:
/home/mithu/
/home/mithu/
/home/mithu/
/home/mithu/
/home/mithu/
/home/mithu/
/home/mithu/
/lib/x86_
/lib/x86_
/lib/x86_
Memory map:
00400000-00423000 r--p 00000000 08:05 2098035 /usr/bin/python3.8
00423000-006b7000 r-xp 00023000 08:05 2098035 /usr/bin/python3.8
006b7000-008f3000 r--p 002b7000 08:05 2098035 /usr/bin/python3.8
008f4000-008f5000 r--p 004f3000 08:05 2098035 /usr/bin/python3.8
008f5000-0093c000 rw-p 004f4000 08:05 2098035 /usr/bin/python3.8
0093c000-0095f000 rw-p 00000000 00:00 0
010b2000-06dd0000 rw-p 00000000 00:00 0 [heap]
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#8 |
> Backtrace:
> /home/mithu/
This is the problem, inside DeformControl:
b ... body container (like O.bodies in Python)
i ... some index
b[i] ... i-th body. But after O.bodies.erase b[i] it is possibly nullptr (None in Python). The null-ity is not checked (but it should be to work with O.bodies.erase)
b[i]-> ... some operation with the body. But if the body is erased, b[i] is nullptr and it ends with segmentation fault.
If you want it to be fixed, you can:
- fix it yourself
- report an issue on gitlab (referencing this question)
Similar questions (O.bodies.erase and then segmentation fault) arises from time to time, with always the same reason - some piece of Yade C++ code not considering the possibility of erased bodies, maybe the topic deserves a FAQ.
Cheers
Jan
[3] https:/
[4] https:/
Revision history for this message
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#9 |
Hi Jan,
Thank you, what do I need to do to fix it? And how can I report it to gitlab?
For my code I did not use ViscoeleasticPM, I used LudingPM.
Thanks,
Mithu
Revision history for this message
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#10 |
Just one thing, when I am running the command in the terminal is erase my walls. It only crashes when I add it in my script.
Revision history for this message
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#11 |
> what do I need to do to fix it?
> And how can I report it to gitlab?
- fix in source code: add checking if b[i] is nullptr and if yes, implement different behavior
- gitlab issue (and wait until some developer fix it and publish the fix): [5] (or [6] -> Issues -> New issue)
> For my code I did not use ViscoeleasticPM, I used LudingPM.
> O.engines = [ ..., DeformControl(
As explained, the problem is in DeformControl.
Placement of that class source code in "ViscoelasticPM
> when I am running the command in the terminal is erase my walls. It only crashes when I add it in my script.
More information is needed to solve this problem.
This behavior should be independent of terminal/script. Of course assuming you do the same thing in terminal and script.
Since in your provided script, the erase is "deep" inside PyRunner and checkers, I suspect that "running the command in the terminal" might simply do something different than "added it in the script".
Cheers
Jan
[5] https:/
[6] https:/
Revision history for this message
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#12 |
Is #6 not enough to avoid the issue? I understand what you want is to produce an image without the wall, isn't it?
Bruno
Can you help with this problem?
Provide an answer of your own, or ask Mithushan Soundaranathan for more information if necessary.