Re: [Yade-users] [Question #707197]: Undrained triaxial (NOT CONSTANT VOLUME)

[Bruno Chareyre]

Question #707197 on Yade changed:
https://answers.launchpad.net/yade/+question/707197

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
The issue doesn't seem to be closed. So, no, you don't have to close it.
I don't have time to inspect any new script now, though. General lesson: please 
make sure you post working scripts.
B.

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Re: [Yade-users] [Question #707183]: High unbalanced force ratio

[Bruno Chareyre]

Question #707183 on Yade changed:
https://answers.launchpad.net/yade/+question/707183

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,

> "I don't know why the high unbalanced force ratio happened and exists
without any trend toward reduction."

The initial state is simply out of equilibrium apparently. I suppose
there is a trend toward reduction (hence settlement) but maybe to slow
for you to realize - that's more a question about computation time.

Cheers

Bruno

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Re: [Yade-users] [Question #707148]: Cylindrical triaxial test using Pfacet

[Bruno Chareyre]

Question #707148 on Yade changed:
https://answers.launchpad.net/yade/+question/707148

Bruno Chareyre proposed the following answer:
Hi,

> "My problem is that I just finished the part about generating flexible
membranes using Pfacet and don't know what to do next."

I did not read all the details but if you are at this step I suppose "what to 
do next" is to assign forces to the nodes of the membranes to reflect external 
pressure. It certainly needs to account for some area and local orientation.
I never tried such thing myself so I'm not 100% sure what to expect. It should 
work but it probably needs to update the external forces after large 
deformations.

Cheers
Bruno

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Re: [Yade-users] [Question #707019]: plot.plot() issue...unexpected keyword argument 'verts'

[Bruno Chareyre]

Question #707019 on Yade changed:
https://answers.launchpad.net/yade/+question/707019

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi, in general using "pip install" is the best way to break a debian 
distribution. What you get is not systematic but unsurprising.
Just don't use pip. You want to "apt install".

In fact, I wonder what happens when you "pip install matplotlib" since
after installing yade matplotlib is _already_ installed.

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Re: [Yade-users] [Question #706740]: Excess pore-water pressure in triaxial test

[Bruno Chareyre]

Question #706740 on Yade changed:
https://answers.launchpad.net/yade/+question/706740

Bruno Chareyre proposed the following answer:
I doubt vtkRecorder was the problem given this line (related to solving a 
linear system):
CHOLMOD error: invalid xtype. file: ../Cholesky/cholmod_analyze.c line: 431

More likely, the problem appears randomly, and it is the annoying part.

> How should i deal with it?

By "passing the actual volume"? ;)
If the contacts on the boundaries are sufficiently stiff it probably makes a 
very small difference.

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Re: [Yade-users] [Question #706740]: Excess pore-water pressure in triaxial test

[Bruno Chareyre]

Question #706740 on Yade changed:
https://answers.launchpad.net/yade/+question/706740

Bruno Chareyre proposed the following answer:
Thanks. We have the same versions... hard to tell why it doesn't give the same 
behavior on two computers and very difficult to debug.
Do you get the same error always? Or are there cases when it runs 
longer/differently?
What if you try multiple times with "yade -j3 test.py"?

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Re: [Yade-users] [Question #706740]: Excess pore-water pressure in triaxial test

[Bruno Chareyre]

Question #706740 on Yade changed:
https://answers.launchpad.net/yade/+question/706740

Bruno Chareyre proposed the following answer:
Try yadedaily?

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Re: [Yade-users] [Question #706740]: Excess pore-water pressure in triaxial test

[Bruno Chareyre]

Question #706740 on Yade changed:
https://answers.launchpad.net/yade/+question/706740

Bruno Chareyre proposed the following answer:
2018...
Apparently something has been improved since then.
I suggest using a newer version.

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Re: [Yade-users] [Question #706740]: Excess pore-water pressure in triaxial test

[Bruno Chareyre]

Question #706740 on Yade changed:
https://answers.launchpad.net/yade/+question/706740

Bruno Chareyre requested more information:
I cannot reproduce your problem with current yadedaily 
(20230525-7264~94b01fd~focal1).
Which version are you using?

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Re: [Yade-users] [Question #706740]: Excess pore-water pressure in triaxial test

[Bruno Chareyre]

Question #706740 on Yade changed:
https://answers.launchpad.net/yade/+question/706740

Bruno Chareyre proposed the following answer:
Initially, I thought your script was crashing in undrained conditions. I thus 
conjectured that it could come from uninitialized pressure.
But in fact the script does not crash. Pressure is simply initialized at zero. 
There is no problem.

Imposing pressure in one point would not only initialize, it would
continuously impose pressure (at least if you just uncomment the
corresponding line, that's what would happen).

> In undrained experiment usually the pore pressure is rising during
deviatoric

That is another question. It depends on many things. Let's stick to the
numerical model and let's see if it is self-consistent
before considering experiments. The main question at this step: is
pressure change consistent with the volume change?

> Now I tried with comprssible fluid and receive this

I suppose you meant "incompressible"? This one won't solve: the pressure
of an incompressible fluid is unknown if no pressure is imposed
somewhere (in other words, the matrix is singular).

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Re: [Yade-users] [Question #706740]: Excess pore-water pressure in triaxial test

[Bruno Chareyre]

Question #706740 on Yade changed:
https://answers.launchpad.net/yade/+question/706740

Bruno Chareyre proposed the following answer:
>  I imposed pressure (flow.imposePressure)

No, you don't. In the script this line is commented out. If you were
imposing pressure it would be a "drained" test.

> volumetric strain should not change during undrained condition

If the fluid is compressible there is nothing to prevent volume changes,
as long as you don't force a constant volume (and you don't, because you
have mixed stress/displacement conditions on the walls).

> i could not see pore pressure built up

Not sure what you mean. I run your script and I see a plot with changes
in the value of "p".

Yuri is correct in #13: flow.fluidBulkModulus=0.1 is really not
water but I don't mind that at this point, it is a value and it gives a
response in truly undrained (not "constant volume") conditions.

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Re: [Yade-users] [Question #706740]: Excess pore-water pressure in triaxial test

[Bruno Chareyre]

Question #706740 on Yade changed:
https://answers.launchpad.net/yade/+question/706740

Bruno Chareyre proposed the following answer:
Hi,
I checked the script and I did not see a problem.
There is a pressure response by the fluid when loading is applied.
Did you expect something different? How?

There is indeed this annoying warning (but "should still be safe") ,
I'll remove it from source code. You can ignore it.

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Re: [Yade-users] [Question #706740]: Excess pore-water pressure in triaxial test

[Bruno Chareyre]

Question #706740 on Yade changed:
https://answers.launchpad.net/yade/+question/706740

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi Fedor,

Mathematically it should be possible to solve for pressure when the fluid is 
compressible (else it is ill-posed), but it requires that at least the initial 
value of pressure is defined. I don't think I've tried that before.
Do you have a (non-)working example?
Regards
Bruno

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Re: [Yade-users] [Question #706573]: Troble with porosity calculation

[Bruno Chareyre]

Question #706573 on Yade changed:
https://answers.launchpad.net/yade/+question/706573

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hello,

Most likely this equation is erroneous:
 new_volume_cylinder = math.pi * (0.051)**2 * top

In fact I don't see "0.051" anywhere else in the script.
Regards
Bruno

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Re: [Yade-users] [Question #706571]: Problem with using rolling resistance in ViscElCap physics

[Bruno Chareyre]

Question #706571 on Yade changed:
https://answers.launchpad.net/yade/+question/706571

Status: Open => Needs information

Bruno Chareyre requested more information:
Hi, could you detail the differences between a working version (before "When I 
add mR to my script") and a non working version?
Are you only changing the values of some parameters or are you also changing 
the functors?
Bruno

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Re: [Yade-users] [Question #706569]: Dynamic Triaxial test

[Bruno Chareyre]

Question #706569 on Yade changed:
https://answers.launchpad.net/yade/+question/706569

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi, 
You can use "goal" and "stressMask" [1] to impose stress in some direction.
If you can do that then you can also change goal at runtime using any function 
of time. I don't think it needs anything else.
Regards
Bruno

[1] https://yade-
dem.org/doc/yade.wrapper.html?highlight=peritriax#yade.wrapper.PeriTriaxController

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Re: [Yade-users] [Question #706553]: About simulating constant volume condition in a triaxial test

[Bruno Chareyre]

Question #706553 on Yade changed:
https://answers.launchpad.net/yade/+question/706553

Bruno Chareyre posted a new comment:
Hi,
I think strain damping could give a null volumetric rate in this case. It's 
consistent with the fact that even with 0.99 ev is still (somehow) small.

The algorithm implies an exponential convergence to the goal rates, 
approximately like this:  
  rate += (goal-rate)*(1-damping) (a discrete form of d(rate)/dt = - 
a*(goal-rate))[1].
If I'm not wrong, it leads to proportional increases of the rates in the 
different directions, and so the trace of the strain rate tensor should be 
always zero.

In this reasoning I'm assuming that all strains start from zero, though. If you 
start the constant volume stage from a state where the velocities are not zero 
(which is the case if you impose stresses for instance), then there can be 
small offsets of the different components during the convergence. 
If that is the cause of the small volume changes, there could be multiple 
solutions, e.g.
- assign goals=0 and run a few iterations, then shear
- assign velocities=0 directly (wall.state.vel=(0,0,0)), then shear

Another option is to simply set set strainDamping=0, and implement your
own ramp in the script, possibly reproducing [1] or with a different
equation, changing the goals incrementally (this is to reduce elastic
waves mainly).

Bruno

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Re: [Yade-users] [Question #706218]: Microstrain for an assembly of clumps in direct shear test

[Bruno Chareyre]

Question #706218 on Yade changed:
https://answers.launchpad.net/yade/+question/706218

Bruno Chareyre posted a new comment:
Hi,
I confirm that clumps are not supported in this case. In fact, it should work 
if the clumped spheres are not overlapping too much, but in the general case it 
won't.
Jan suggests a good workaround in #3.

Note:  a newer function [1] will let you switch from 
> Matrix3(*[TW.deformation(b.id,i,j) for i in range(0,3) for j in range(0,3)])
to
> TW.deformationTensor(b.id)

since the first is obviously a pain.


[1] 
https://gitlab.com/yade-dev/trunk/-/merge_requests/943/diffs#4571c09191fb63b1bdb53a5ad573e72677b1892b_176_177
Should be reflected in yadedaily very soon.

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Re: [Yade-users] [Question #706072]: Simple shear with oedometric loading

[Bruno Chareyre]

Question #706072 on Yade changed:
https://answers.launchpad.net/yade/+question/706072

Status: Open => Needs information

Bruno Chareyre requested more information:
Could you show a script where walls do not follow the prescribed
velocity gradient?

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Re: [Yade-users] [Question #706100]: Torque values too low

[Bruno Chareyre]

Question #706100 on Yade changed:
https://answers.launchpad.net/yade/+question/706100

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,

> Is this normal DEM behavior?

I don't know what "normal DEM behavior" is, so I would say "no".

The reason may be that the actual rubber particles interact in ways which you 
did not account correctly (inappropriate selection of contact model, or 
inappropriate model parameters).
It is difficult to say more without knowing the physical system in details and 
without knowing how you simulated it.
Bruno

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Re: [Yade-users] [Question #706072]: Simple shear with oedometric loading

[Bruno Chareyre]

Question #706072 on Yade changed:
https://answers.launchpad.net/yade/+question/706072

Bruno Chareyre proposed the following answer:
Hi,
In fact, allowBiggerThanPeriod=True is perfectly fine, and it is designed 
exactly for this case where large plates are used as boundary conditions.

You need to make sure that the height of the period is larger than the
gap between the plates since what you want basically is to suppress
periodic interactions in the corresponding direction.

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Re: [Yade-users] [Question #705955]: MindlinDeresiewitz Contact Law Issue

[Bruno Chareyre]

Question #705955 on Yade changed:
https://answers.launchpad.net/yade/+question/705955

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,

> Has the contact law been tested before?

I am not quite sure.
Maybe Chiara Modenese used mainly one of the different versions in here PhD 
although she implemented all of them. So it is not extremely surprising if they 
have different levels of maturity.

Maybe you found a bug.

What's surprising is that contact detection is not so much dependent of
the Law2 functors. If you could reduce the example script to a simpler
case it would help finding out if it is really a detection problem, as
you suspect, or something else. I mean: reduce the number of PyRunners,
impose velocity instead of exerted force, and show that a contact should
exist after (let's say) 10 iterations.

In any case, I strongly recommend that you go through code-inspection
and, at least, basic verifications of the results if using that functor
(of course, that's if at least something is computed...).

Bruno

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Re: [Yade-users] [Question #705913]: how to run yade on multiple nodes using openmpi

[Bruno Chareyre]

Question #705913 on Yade changed:
https://answers.launchpad.net/yade/+question/705913

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
Your problems seem very platform dependent.
I have been working in a couple different contexts and I have never seen a need 
for the flag " --allow-run-as-root".

I would suggest you try running simple parallel jobs. 
"hostname" is a good start but it is excessively simple. Try running a python 
script for instance, then if it works try an example script from the mpi4py 
module (i.e. an actual parallel job), then only if the previous two work it 
could be that yade's implementation has an issue on you specific system (in 
this case please report here). 

Bruno

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Re: [Yade-users] [Question #705760]: How to get the runtime or CPU time?

[Bruno Chareyre]

Question #705760 on Yade changed:
https://answers.launchpad.net/yade/+question/705760

Bruno Chareyre proposed the following answer:
Python's time.time() is enough in many cases, as long as you don't need
per-engine data or nano-second accuracy.

t1 = time.time()
O.run(...)
realTime = time.time() - t1

yade.timing is convenient if you want more granularity in the timings
(you probably forgot 'from yade import timing'). You can also introduce
your own checkpoints in the source code which will be reflected in the
output of yade.timing.stats().

Bruno

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Re: [Yade-users] [Question #705740]: GlobalStiffnessTimestepper gives dt of 0.0 when the saved file is restored

[Bruno Chareyre]

Question #705740 on Yade changed:
https://answers.launchpad.net/yade/+question/705740

Status: Open => Answered

Bruno Chareyre proposed the following answer:
I was not questioning why you use multiple scripts to produce results, this is 
your business (although none of the reasons you list are applicable see [1,2], 
there are better solutions). The point is that it is better to avoid multiple 
scripts at least when asking questions, namely because nobody wants to go 
through 3 scripts to try and understand your problem.
And, in fact, by trying to provide a unique script for this question you would 
have find that reloading wasn't the cause of your problem, at all.
The only problem is to unblock the DOFs of bodies with null mass (facets).
Bruno

[1]  According to https://www.yade-dem.org/wiki/Howtoask: "If the input of one 
script is the output of another script, then both scripts should be merged into 
one. That is: avoid sending multiple scripts just like you avoid sending input 
files to a script. If needed, the method to save and reload in one single 
script is illustrated here [2]." 
[2] 
https://gitlab.com/yade-dev/trunk/-/blob/3e9a209234b7f23241d5f4bdef1b586056e97582/examples/simple-scene/save-then-reload.py

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Re: [Yade-users] [Question #705150]: Yade-OpenFOAM coupling

[Bruno Chareyre]

Question #705150 on Yade changed:
https://answers.launchpad.net/yade/+question/705150

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
"yadeimport" used to be a symlink to the yade executable, created locally by 
the user.
If you run, let's say, the "yadedaily" package, then the executable "yadedaily" 
is a python script (or "module"), but python will not import it because there 
is no ".py" postfix.
The solution is "ln -s yadedaily yadeimport.py".
If you run  a stable version, "ln -s yade yadeimport.py".
A compiled version: "ln -s yade-myversion yadeimport.py".
Etc.

I hope it helps.

Bruno

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Re: [Yade-users] [Question #705740]: GlobalStiffnessTimestepper gives dt of 0.0 when the saved file is restored

[Bruno Chareyre]

Question #705740 on Yade changed:
https://answers.launchpad.net/yade/+question/705740

Status: Needs information => Answered

Bruno Chareyre proposed the following answer:
Something rings a bell:

O.bodies[-1].state.blockedDOFs='xyXYZ'

Does body "-1" have a mass, at least?...
I'm unsure save/load needs to be in the picture. That's why we ask to not send 
multiple scripts, it raises false issues in many cases. 
Just load+run, nothing else, and see if the 0 timestep happens?

Do you really need to keep "z" unblocked? Blocking everything would
probably fix the problem.

Bruno

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Re: [Yade-users] [Question #705740]: GlobalStiffnessTimestepper gives dt of 0.0 when the saved file is restored

[Bruno Chareyre]

Question #705740 on Yade changed:
https://answers.launchpad.net/yade/+question/705740

Status: Open => Needs information

Bruno Chareyre requested more information:
Hello,
Could you please try an concatenate the files as much as possible (ideally just 
one file)? or find a way to reproduce the zero timestep which wouldn't require 
us to go through 3 scripts?
Bruno

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Re: [Yade-users] [Question #704306]: DFN-Thermal Engine Link

[Bruno Chareyre]

Question #704306 on Yade changed:
https://answers.launchpad.net/yade/+question/704306

Bruno Chareyre posted a new comment:
Dear Ahmad, it is very difficult to answer without seeing an actual code.
You should push code/scripts to some branch.

One thing I can explain is that ThermalEngine will not select DFNFlowEngine, 
and then flow remains undefined (and segfault).
It is because of this condition: "if (e->getClassName() == "FlowEngine")".
The class name of DFNFlowEngine is not FlowEngine, so it is not selected.
A "or" in the condition could help.

Bruno

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Re: [Yade-users] [Question #704434]: Pfacet in periodic boundary conditions

[Bruno Chareyre]

Question #704434 on Yade changed:
https://answers.launchpad.net/yade/+question/704434

Status: Open => Answered

Bruno Chareyre proposed the following answer:
For the uniaxial periodicity, I think yes, what you do is correct.

The hollowness is really not a problem. If you know the mass you can
just assign it: plate.phys.mass = whatever.

I hope it helps.

Bruno

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Re: [Yade-users] [Question #704434]: Pfacet in periodic boundary conditions

[Bruno Chareyre]

Question #704434 on Yade changed:
https://answers.launchpad.net/yade/+question/704434

Status: Open => Needs information

Bruno Chareyre requested more information:
Hello, I don't understand the problem very well.
What is x,y,z? Is there gravity (which axis?)?
Why do you care about the plate being hollow? Isn't it a rigid object described 
by it's external shape?
Regards
Bruno

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Re: [Yade-users] [Question #704389]: Problem with OpenMP

[Bruno Chareyre]

Question #704389 on Yade changed:
https://answers.launchpad.net/yade/+question/704389

Bruno Chareyre proposed the following answer:
Hello Roxana,
I have no real knowledge of how LiqControl works but maybe it's taking most of 
the time, and if it is not parallelized it would explain.
I see you enabled timing, would you paste the output of "timing.stats()" after 
many iterations? It would tell.
Bruno

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Re: [Yade-users] [Question #704035]: O.save/O.load problem

[Bruno Chareyre]

Question #704035 on Yade changed:
https://answers.launchpad.net/yade/+question/704035

Bruno Chareyre proposed the following answer:
Hi,
I reported the bug [1]. It sounds like an initialization problem that could be 
solved by inspecting how the YADE_CLASS_... macro is used.

[1] https://gitlab.com/yade-dev/trunk/-/issues/292

Bruno

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Re: [Yade-users] [Question #703901]: whats the difference between “GlobalStiffnessTimeStepper”and "O.dt"

[Bruno Chareyre]

Question #703901 on Yade changed:
https://answers.launchpad.net/yade/+question/703901

Bruno Chareyre posted a new comment:
Hi,
> I am confused coz I tried these two ways and they are different in my 
> simulation

They are derived with slightly different logics and so they have no
reason to be exactly the same. Usually they should be of the same order.

More generally I would give a response even stronger that Jan's: if GSTS
gives a certain O.dt with timestepSafetyCoefficient=0.8, then the
maximum O.dt you can theoretically use is 1.25 times greater (1/0.8). If
you exceed that it will not just "affect the stability". In most cases
it will go completely wrong (division by zero, NaN and such things) and
at some point it will segfault.

Better experiment with 4000 particles first, it will be easier to
understand what happens.

Also note that there is an example rotating drum using MPI parallelization: 
https://gitlab.com/yade-dev/trunk/-/blob/master/examples/DEM2020Benchmark/Case2_rotating_drum_mpi.py

Cheers
Bruno

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Re: [Yade-users] [Question #703707]: Water pressure

[Bruno Chareyre]

Question #703707 on Yade changed:
https://answers.launchpad.net/yade/+question/703707

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,

> I assume 2PFV does not appropriate for this aim.

Correct. For one-phase flow based on the PFV method the engine is
FlowEngine [1].

Regards

Bruno

[1] https://yade-
dem.org/doc/yade.wrapper.html?highlight=flowengine#yade.wrapper.FlowEngine

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Re: [Yade-users] [Question #703681]: Yade with RedHat / AlmaLinu

[Bruno Chareyre]

Question #703681 on Yade changed:
https://answers.launchpad.net/yade/+question/703681

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,

> 'VTKRecorder', 'TwoPhaseFlowEngine' is not defined.

Apparently, you disabled them at compile time.
Please post the output of cmake command if you are not sure.

On HPC, best option is to use system images if  Singularity is
available.

Bruno

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Re: [Yade-users] [Question #703498]: Young's modulus or the effect of the wall on the test

[Bruno Chareyre]

Question #703498 on Yade changed:
https://answers.launchpad.net/yade/+question/703498

Bruno Chareyre proposed the following answer:
Hi,
Without knowing anything of your problem. My first guess is that even a 
symmetric distribution of positions will result in non-symmetric results, 
provided that the number of particles "N" is large enough. That's due to 
chaotic behavior.
It may approach symmetry asymptotically if it's averaged on many different 
realizations, or if N tends to infinity.

If you want to force symmetric results you can simply simulate only one
half of the problem...

Bruno

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Re: [Yade-users] [Question #703504]: Compilation and Running on HPC cluster -Centos 7

[Bruno Chareyre]

Question #703504 on Yade changed:
https://answers.launchpad.net/yade/+question/703504

Bruno Chareyre posted a new comment:
Hi,
In your situation, I would first check if the host HPC has Singularity (maybe) 
or Docker (unlikely) available.
If so, you don't need to compile. Just run a virtual machine.

ENABLE_OAR is unrelated to the problem, and it is not a requirement even
for submitting OAR jobs.

Neither is https://yade-dem.org/doc/mpy.html supposed to provide any
guidance on the issue at hand.

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Re: [Yade-users] [Question #703489]: Lower corner and upper corner of the box in TriaxialStressController

[Bruno Chareyre]

Question #703489 on Yade changed:
https://answers.launchpad.net/yade/+question/703489

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
You can indeed use the  wall_XXX_id's to retrieve the boxes and take their 
positions.
If thickness is 0 their positions will be the position of the boundary (else 
remove half the thickness).

"coordinate 2-" refers to the side bounded by a certain box: x-, x+, y-, y+, 
z-, z+ (replace the letters with axis 1,2,3).
Regards
Bruno

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Re: [Yade-users] [Question #703284]: If the PeriodicFlowEngine can simulate the oedometer test

[Bruno Chareyre]

Question #703284 on Yade changed:
https://answers.launchpad.net/yade/+question/703284

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Q1. " could the setting of pressure be applied by flow.imposePressure()?"
Yes, it could.

Q2. Yes.

Q3. Take the average of the pressure in all pores?

Q4. It is very unclear what it is since a consolidating volume is never 
homogeneous (first problem), and the stress definition at the microscale is 
assuming a system of forces in equilibrium (not the case here since there are 
drag forces not counted in the stress, second problem).
That's why I would really refrain from simulating consolidation with periodic 
boundaries.

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Re: [Yade-users] [Question #703284]: If the PeriodicFlowEngine can simulate the oedometer test

[Bruno Chareyre]

Question #703284 on Yade changed:
https://answers.launchpad.net/yade/+question/703284

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,

Q1." flow.gradP？or flow.imposePressure() ?" both work and they are
compatible with each other. Typically, you can assign P somewhere and
its derivative at the macroscale (the gradient).

Q2. "flow.averageVelocity() achieve it or not.". Yes. The average
velocity is the output if you assign gradP as input.

Q3. "if the PeriTriaxController and PeriodicFlowEngine can reproduce the 
oedometer test" 
Easy answer: "no". The oedometer is a diffusion problem and a diffusion problem 
is not periodic in general.
Tedious answer: in fact you could impose fluid pressure along a plane cutting 
through the period, and impose the average effective stress with PeriTriax (how 
exactly, I'm not sure). That would somehow approach an oedometer situation, and 
it would be consistent with the general theory of consolidation. But in fact it 
would only make things more complex, and in the end you would just simulate the 
periodic superposition of independent consolidating layers. I don't see a clear 
progress.

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Re: [Yade-users] [Question #703276]: The problem in PeritriaxController

[Bruno Chareyre]

Question #703276 on Yade changed:
https://answers.launchpad.net/yade/+question/703276

Bruno Chareyre proposed the following answer:
Thanks for finding that.
I fixed PeriTriaxController in another merge request. [1]
B

[1] https://gitlab.com/yade-dev/trunk/-/merge_requests/892

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Re: [Yade-users] [Question #703169]: Energy conservation of clump

[Bruno Chareyre]

Question #703169 on Yade changed:
https://answers.launchpad.net/yade/+question/703169

Status: Open => Answered

Bruno Chareyre proposed the following answer:
It will be fixed with https://gitlab.com/yade-dev/trunk/-/merge_requests/891. 
I confirmed the fix with a modified version of #10.

Note that this example with walls has another issue (which does not
affect periodic BCs): the volume computed by default in getStress is
overestimated because it includes enlarged bounding boxes. When  passing
tha actual volume as argument, like below, the error falls to 1% with
the new version (still high, but that's because equilibrium is only
approximately satisfied).

Bruno


from yade import pack, plot

useClumps = True

readParamsFromTable(rMean=.075, rRelFuzz=.3, maxLoad=1e5)

from yade.params.table import *

# create box with free top, and ceate loose packing inside the box
O.bodies.append(geom.facetBox((.5, .5, 1), (.5, .5, 1), wallMask=31))
sp = pack.SpherePack()
sp.makeCloud((0, 0, 0), (1, 1, 2), rMean=rMean, rRelFuzz=rRelFuzz)
sp.toSimulation()
# make material frictionless to avoid force acting on vert walls
O.materials[0].frictionAngle = 0

# I just make spheres smaller to avoid overlapping after replacing by clumps
for b in O.bodies:
 if isinstance(b.shape, Sphere):
  b.shape.radius*=0.8

if useClumps:

 relRadList2 = [0.8,0.8,0.8,0.8]
 relPosList2 = [[0.6,0,0],[-0.6,0,0],[0,0.7,0],[0,0.25,0.7]]
 templates= []
 templates.append(clumpTemplate(relRadii=relRadList2,relPositions=relPosList2))
 O.bodies.replaceByClumps(templates,[1.],discretization=10)

O.engines = [
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(), Bo1_Facet_Aabb(), 
Bo1_Wall_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom(), 
Ig2_Wall_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()],
[Law2_ScGeom_FrictPhys_CundallStrack()]
),
NewtonIntegrator(gravity=(0, 0, 0), damping=0.2),
PyRunner(command='checkUnbalanced()', iterPeriod=20, label='checker'),
]
O.dt = .5 * PWaveTimeStep()

def checkUnbalanced():
 # add plate at the position on the top of the packing
 # the maximum finds the z-coordinate of the top of the topmost particle
 O.bodies.append(wall(max([b.state.pos[2] + b.shape.radius for b in O.bodies if 
isinstance(b.shape, Sphere)]), axis=2, sense=-1))
 global plate # without this line, the plate variable would only exist inside 
this function
 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, -.3)
 # start plotting the data now, it was not interesting before
 O.engines = O.engines + [PyRunner(command='addPlotData()', iterPeriod=20)]
 # next time, do not call this function anymore, but the next one (unloadPlate) 
instead
 checker.command = 'unloadPlate()'

def unloadPlate():
 # if the force on plate exceeds maximum load, start unloading
 if abs(O.forces.f(plate.id)[2]) > maxLoad:
  plate.state.vel = (0,0,0)
 elif plate.state.vel[2]==0 and unbalancedForce() < 0.01:
  O.pause()
  print('Stress underestimated by the factor 
{:.2f}'.format(max(plot.data['Fz'])/max(plot.data['szz'])))

def addPlotData():
 if not isinstance(O.bodies[-1].shape, Wall):
  plot.addData()
  return
 Fz = O.forces.f(plate.id)[2]
 szz=-1*utils.getStress(plate.state.pos[2])[2,2]
 plot.addData(Fz=Fz,szz=szz, w=plate.state.pos[2] - plate.state.refPos[2], 
unbalanced=unbalancedForce(), i=O.iter)

# besides unbalanced force evolution, also plot the displacement-force diagram
plot.plots = {'w': ('Fz','szz')}
plot.plot()

O.run()



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Re: [Yade-users] [Question #703169]: Energy conservation of clump

[Bruno Chareyre]

Question #703169 on Yade changed:
https://answers.launchpad.net/yade/+question/703169

Bruno Chareyre posted a new comment:
I found the problem, getStress does not handle clumps...

In the product f*branch, "branch" should point to one single point per
body (in this case: per clump). Instead, the function implementation
disregards the clump status and uses the center of the clump members.

I reported the issue here: https://gitlab.com/yade-
dev/trunk/-/issues/289

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Re: [Yade-users] [Question #703169]: Energy conservation of clump

[Bruno Chareyre]

Question #703169 on Yade changed:
https://answers.launchpad.net/yade/+question/703169

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi, that changing members size results in different stiffness is a correct 
observation.
It is not "wrong", in the sense that it's a default behavior and you can always 
counter this effect by adapting Young parameter of the material.
Anyway, that stiffness is different is not a reason for not conserving energy.
I noticed that you don't take kinetic energy into account, is it negligible?
Bruno

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Re: [Yade-users] [Question #702448]: 2PFV - update Triangulation

[Bruno Chareyre]

Question #702448 on Yade changed:
https://answers.launchpad.net/yade/+question/702448

Status: Open => Answered

Bruno Chareyre proposed the following answer:
updateTriangulation is inherited from one-phase flow engine. If it is triggered 
in the 2-phase child class  (not tested) the best thing it can do is to give a 
virgin network - i.e. previous imbibition history is erased.
That was actually part of the trick we used iirc: generate a new network and 
imbibe it up to a saturation a bit larger than previous value, so we could 
incrementally build a pseudo-sequence with increasing saturation.

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Re: [Yade-users] [Question #702448]: 2PFV - update Triangulation

[Bruno Chareyre]

Question #702448 on Yade changed:
https://answers.launchpad.net/yade/+question/702448

Bruno Chareyre proposed the following answer:
Hi,
The simple answer, not very satisfying I'm afraid, is "mesh doesn't evolve".
The engine builds a static pore network. How to update the network in a 
situation of partial saturation is still an open issue, and a tough one. It 
needs to decide where the phases go when one pore is splitted into multiple 
pores (or the opposite).

We used some tricks before to handle the update "somehow" but they are
very difficult to generalize. If you have sound physical arguments to
come up with an update logic we can discuss implementation, but right
now yade will not solve this for you.

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Re: [Yade-users] [Question #702418]: About flow.bndCondIsPressure and flow.bndCondValue in flowengine

[Bruno Chareyre]

Question #702418 on Yade changed:
https://answers.launchpad.net/yade/+question/702418

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,

1- Is "osmotic pressure" just the fluid pressure? ("osmotic" is strange in this 
context).
2- your problem statement is self-contradictory: if there is only one permeable 
boundary [0,0,0,0,0,1] is the correct setting, yes, but  how would you estimate 
permeability from "the other end" (which is no-flux) in such case?

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Re: [Yade-users] [Question #702412]: O.interactions[0, 1] is unable to detect the interactions between sphere and wall, throwing an error stating "No such interaction"

[Bruno Chareyre]

Question #702412 on Yade changed:
https://answers.launchpad.net/yade/+question/702412

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,

If there are only two bodies O.forces.f(0) and O.interactions[0,1] should be 
the same.
Except that the first will not give an error when there is no interaction.

Alternatively, this boolean could help: 
O.interactions.has(0,1) 
Cheers
Bruno

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Re: [Yade-users] [Question #702411]: Calculation of a time averaging of a physical quantity

[Bruno Chareyre]

Question #702411 on Yade changed:
https://answers.launchpad.net/yade/+question/702411

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,

Something like this?

timeSeries = []

while totalRotationhttps://launchpad.net/~yade-users
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Re: [Yade-users] [Question #702407]: CGAL ERROR: assertion violation! when running HM coupling

[Bruno Chareyre]

Question #702407 on Yade changed:
https://answers.launchpad.net/yade/+question/702407

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
This error suggests huge overlaps between some spheres, such that in some pore 
throats the intersected solid area is more than the area of the triangle 
connecting sphere centers (hence a negative area left for the fluid).
It may come from a small stress to stiffness ratio, or more simply a numerical 
instability.
Try with a smaller time-step?
 Bruno

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[Yade-users] PDoc position in Grenoble (SPH-DEM)

[Bruno Chareyre]

Dear All

A 1-year post-doctoral position is available for developing a 3D coupled 
model of creeping snow. This position is part of a project which final 
goal is to improve the design of snow avalanches protective structures. 
Indeed, these structures are confronted with the change in snow mantle 
mechanical characteristics resulting from climate change.


An outline can be found here 
 [1].


This position is proposed by ETNA-INRAE and 3SR, both located in 
Grenoble, and is funded by TEC21.


The attached document gives further details on the context and aim of 
this position, together the required qualifications for applying.


Interested people are invited to apply via the platform:

https://academicpositions.com/ad/universite-grenoble-alpes/2022/post-doctoral-position-creeping-snow-modelling-the-force-induced-on-structures/181144

Thanks for sharing this announcement with potential candidates!

Best regards

S. LAMBERT and B. CHAREYRE

[1] https://cloud.univ-grenoble-alpes.fr/s/yGrdzxQPWxwcagN
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Re: [Yade-users] [Question #702047]: Parametric study with yade-batch

[Bruno Chareyre]

Question #702047 on Yade changed:
https://answers.launchpad.net/yade/+question/702047

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
Please show example scripts.
Bruno

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Re: [Yade-users] [Question #701938]: Large size cylinderConnection in periodic scene

[Bruno Chareyre]

Question #701938 on Yade changed:
https://answers.launchpad.net/yade/+question/701938

Bruno Chareyre proposed the following answer:
Indeed, enlarged bboxes and cell distorsions may make 4 not enough, but you get 
the idea. 
B

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Re: [Yade-users] [Question #701938]: Large size cylinderConnection in periodic scene

[Bruno Chareyre]

Question #701938 on Yade changed:
https://answers.launchpad.net/yade/+question/701938

Bruno Chareyre proposed the following answer:
Welcome.
If you define at least 3 (or maybe 4) you could turn off 
"allowBiggerThanPeriod".
But as long it detects contacts properly it should be the same.
B

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Re: [Yade-users] [Question #658938]: Modeling presence of water( a degree of saturation) in consolidation test

[Bruno Chareyre]

Question #658938 on Yade changed:
https://answers.launchpad.net/yade/+question/658938

Bruno Chareyre proposed the following answer:
Hi, please open a new question if you have one. 
Bruno

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Re: [Yade-users] [Question #701938]: Large size cylinderConnection in periodic scene

[Bruno Chareyre]

Question #701938 on Yade changed:
https://answers.launchpad.net/yade/+question/701938

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
I've seen working examples where the cylinder was discretized into multiple 
connexions, all smaller than period. It could workaround your issue.
Even this trick is not tested extensively, yo uwill have to try and see by 
yourself.
Regards
BRuno

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Re: [Yade-users] [Question #701743]: Alternative permeability values during the compaction

[Bruno Chareyre]

Question #701743 on Yade changed:
https://answers.launchpad.net/yade/+question/701743

Bruno Chareyre posted a new comment:
Hi,
Please explain what is wrong in you opinion and how it can be reproduced. The 
script you pasted will not work for anyone else because of this line: 
spheres = ymport.text('filename.txt', shift=Vector3(0, 0, 0), scale=1.0)

Bruno

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[Yade-users] A PhD position in Limoge (France)

[Bruno Chareyre]

Hi,
Please find the announcement below and feel free to forward.
Regards

Bruno


--
Dear Yade users,

please find below an open position about Discrete Element modeling. The 
targeted Discrete Element code is officially "GranOO" but it is open to 
other opensource codes (as Yade).


https://www.cesaref.eu/wp-content/uploads/sites/23/2022/04/08-CESAREF-Flyer-PhD8-Position-IRCER-IMERYS.pdf 



This PhD is part of the CESAREF EU doctoral network.
https://www.cesaref.eu/

Kind regards,
--
Damien ANDRÉ,
Associate professor,
ENSIL-ENSCI, Limoges university, IRCER,
12 Rue Atlantis, 87068 Limoges, France.
+33 5 87 50 24 42
http://www.unilim.fr/pages_perso/damien.andre/



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Re: [Yade-users] [Question #701782]: O.cell.volume=0 during flipCell

[Bruno Chareyre]

Question #701782 on Yade changed:
https://answers.launchpad.net/yade/+question/701782

Bruno Chareyre proposed the following answer:
At the moment it is a bit convolved to read your changes but it seems I was 
able to break your algorithm.
A suspicious feature of yours is that it tries to align the period on the 
reference frame, which isn't helping in general.
Try a rigid body rotation (velGrad = [[0,1,0], [-1,0,0], [0,0,0]] ) and you 
will see the problem:
- older version leads to zero volume (wrong)
- new version does flip without "zero volume" error, but it shouldn't: it turns 
the cube into a more elongated thing, the opposite of what we want; it also 
breaks my contact model (most likely a problem in updating cellDist). 
My impression is that there must be is a much simpler fix to the issue.
I'll need to cleam my test script before showing (right now it's a mess).
Let's continue the discussion on gitlab?

B

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Re: [Yade-users] [Question #701845]: Has ZeroInitForce been implemented?

[Bruno Chareyre]

Question #701845 on Yade changed:
https://answers.launchpad.net/yade/+question/701845

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
The documentation should tell you if it is implemented for a particular functor.
If it isn't, an easy way to offset is explained in #1 of the discussion you are 
linking [1] (the rest of the discussion is worth a read too).
Bruno

[1] https://answers.launchpad.net/yade/+question/619109

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Re: [Yade-users] [Question #701782]: O.cell.volume=0 during flipCell

[Bruno Chareyre]

Question #701782 on Yade changed:
https://answers.launchpad.net/yade/+question/701782

Bruno Chareyre proposed the following answer:
See more here:
https://www.sciencedirect.com/science/article/abs/pii/030193229290074Q

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Re: [Yade-users] [Question #701836]: size vs. hSize vs. hSize0 vs. refSize in "Cell"

[Bruno Chareyre]

Question #701836 on Yade changed:
https://answers.launchpad.net/yade/+question/701836

Bruno Chareyre proposed the following answer:
Hi,

"size, hSize, hSize0, and refSize"

The simple answer is: "hSize" gives the current shape.
You can ignore the others.
Their documentation is short but accurate, seemes to me.

Bruno

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Re: [Yade-users] [Question #701782]: O.cell.volume=0 during flipCell

[Bruno Chareyre]

Question #701782 on Yade changed:
https://answers.launchpad.net/yade/+question/701782

Bruno Chareyre posted a new comment:
Hi,

I'll check the suggested MR whenever I have a chance.

The case of stretching can be overcomed in a few special cases. It needs
to define an initial cell size not aligned with the principal strain
axis. It has limitations and it will probably not work for non-monotonic
multi-directional deformation.

B

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Re: [Yade-users] [Question #701782]: O.cell.volume=0 during flipCell

[Bruno Chareyre]

Question #701782 on Yade changed:
https://answers.launchpad.net/yade/+question/701782

Status: Open => Answered

Bruno Chareyre proposed the following answer:
In principle all cells can be flipped, yes. What  you get suggests that the 
automatic determination of the flip matrix fails.
Not sure why right now.  You could pass one flip matrix explicitly.
Is cell.velGrad always symmetric or arbitrary (do you have rotation)?

Thanks for posting example numbers, it might help investigating.

Bruno

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Re: [Yade-users] [Question #701764]: Use flipCell in periodic simulations

[Bruno Chareyre]

Question #701764 on Yade changed:
https://answers.launchpad.net/yade/+question/701764

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
[1] is outdated, or maybe just misleading (it says "it needs to be done", not 
"it's not done").
And, yes, [2] is safe, I'm using this mechanism routinely and I never 
distinguished any sort of discontinuity or weird response associated to 
flipping.
We could probably implement it as a Cell method since currently everyone has to 
re-type something like:
O.engines=O.engines+[PyRunner(command='if O.cell.hSize[0,1]>O.cell.hSize[0,0]: 
flipCell()',iterPeriod=20)]

Bruno

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Re: [Yade-users] [Question #701670]: Wrong permeability values during compaction

[Bruno Chareyre]

Question #701670 on Yade changed:
https://answers.launchpad.net/yade/+question/701670

Status: Open => Answered

Bruno Chareyre proposed the following answer:
In the above code fragment (#11) you block DOFs but you don't solve any
fluid flow after that, so it's completely ineffective.

In #10 you set "flow.bndCondIsPressure = [0, 0, 0, 1, 0, 0]", which
means there is an inlet but no outlet. I would expect 0-flux from this.

You should step back and check detailed results. For instance, do you get Qin = 
Qout? else why? Etc.
So iteratively you will understand what goes wrong.

Bruno

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Re: [Yade-users] [Question #701670]: Wrong permeability values during compaction

[Bruno Chareyre]

Question #701670 on Yade changed:
https://answers.launchpad.net/yade/+question/701670

Status: Open => Answered

Bruno Chareyre proposed the following answer:
If I understand well, you are compressing a packing with an imposed velocity  
of 0.3.
As a result, the fluid goes out through the boundaries where pressure is 
imposed (top and bottom). 
You then take one of these outward flux and you deduce permeability from it. 
But in fact the flux in your case is controlled by the imposed velocity (0.3). 
That's not how permeability can be determined.

For correct evaluation see the example script you started from and alternate 
steps B and C.
You need to make sure no deformation is going on when you evaluate 
permeability. A sure way is to fix DOFs and set all velocities to zero. 

Bruno

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Re: [Yade-users] [Question #701670]: Wrong permeability values during compaction

[Bruno Chareyre]

Question #701670 on Yade changed:
https://answers.launchpad.net/yade/+question/701670

Status: Open => Answered

Bruno Chareyre proposed the following answer:
> in the oedometer section there is also triaxial load and unload for 
> compaction.
> But I need just vertical load for compaction. Because of this I add the 
> ‘top.state.vel = (0, 0, -0.06)’

An "oedometer" implies a uniaxial deformation, that's what the script does.
And you want a uniaxial deformation. 
I don't know why you are trying something else.

B

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Re: [Yade-users] [Question #701670]: Wrong permeability values during compaction

[Bruno Chareyre]

Question #701670 on Yade changed:
https://answers.launchpad.net/yade/+question/701670

Status: Open => Answered

Bruno Chareyre proposed the following answer:
I don't know what you "should" use. It all depends on what you want to
simulate. Which direction for the pressure gradient? Which stress in
each direction?

Independently: I see, now, that you are inserting  walls twice, that's
the main change compared to original script. I really don't understand
why doing that. Prescribing boundary conditions just needs to assign
triax.goal's and stressMask as you wish, not to add more walls.

B

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Re: [Yade-users] [Question #701670]: Wrong permeability values during compaction

[Bruno Chareyre]

Question #701670 on Yade changed:
https://answers.launchpad.net/yade/+question/701670

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
The example script oedometer.py is doing exactly what you are asking and 
apparently you re-used it. 
But at the same time you seem to have doubts on walls numbering, why? What did 
you change in the script?
B

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Re: [Yade-users] [Question #701666]: How to present the pore network model in flowengine

[Bruno Chareyre]

Question #701666 on Yade changed:
https://answers.launchpad.net/yade/+question/701666

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi, 
There is indeed an export function for paraview:
https://yade-dem.org/doc/yade.wrapper.html?highlight=flow%20engine#yade.wrapper.FlowEngine.saveVtk

Regards

Bruno

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Re: [Yade-users] [Question #701641]: Non-Newtonian fluids in PFV model

[Bruno Chareyre]

Question #701641 on Yade changed:
https://answers.launchpad.net/yade/+question/701641

Bruno Chareyre posted a new comment:
Hi there,
Just a quick comment: non-newtonian fluid flow at the pore scale sounds very 
interesting but right now I have no idea how to achieve that. It would need, I 
presume, to solve a non-linear system of equations, which will be very 
different.
There is nowhere a single line of code that you could tweek to turn the fluid 
non-newtonian. 
Bruno

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Re: [Yade-users] [Question #701581]: Difference between FrictMat and cohFrictMat without cohesion and moment

[Bruno Chareyre]

Question #701581 on Yade changed:
https://answers.launchpad.net/yade/+question/701581

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
Unless you found a bug, yes, the two cases should be equivalent.
It's hard to know if you made a mistake in converting materials or if there is 
really a difference due to the code.

Currently, your scripts are way too complex to dive in. If you could
elaborate a simpler example maybe someone could check in more details.

Bruno

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Re: [Yade-users] [Question #701438]: Why particle velocity varies with time step

[Bruno Chareyre]

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

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Re: [Yade-users] [Question #700953]: Oedometer test based on PSD

[Bruno Chareyre]

Question #700953 on Yade changed:
https://answers.launchpad.net/yade/+question/700953

Bruno Chareyre proposed the following answer:
This example is an oedometer with fluid coupling:

https://gitlab.com/yade-
dev/trunk/-/blob/master/examples/FluidCouplingPFV/oedometer.py

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Re: [Yade-users] [Question #700953]: Oedometer test based on PSD

[Bruno Chareyre]

Question #700953 on Yade changed:
https://answers.launchpad.net/yade/+question/700953

Status: Needs information => Answered

Bruno Chareyre proposed the following answer:
For PSD there is a good example here:
https://gitlab.com/yade-dev/trunk/-/blob/master/examples/test/psd.py

Bruno

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Re: [Yade-users] [Question #700931]: How to colour in the particles in my own specific way (sequence)

[Bruno Chareyre]

Question #700931 on Yade changed:
https://answers.launchpad.net/yade/+question/700931

Status: Needs information => Answered

Bruno Chareyre proposed the following answer:
Hi,

That's how bodies are colored based on their subdomain in the mpi
module, it should apply for anything else with appropriate tuning:

import colorsys
colorScale = [Vector3(colorsys.hsv_to_rgb(value*1.0/numThreads, 1, 1)) for 
value in range(0, numThreads)]
for b in O.bodies:
   b.shape.color = colorScale[b.subdomain]

Bruno

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Re: [Yade-users] [Question #700924]: soil stucture interaction

[Bruno Chareyre]

Question #700924 on Yade changed:
https://answers.launchpad.net/yade/+question/700924

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
TriaxialStressController can be used for 2D cases but it still requires that 
you place 6 walls (in fact boxes), not 4.
Also, if the the walls have custom numbering (i.e. not what  you get by 
inserting "O.bodies.append(aabbWalls(...))" first) you need to set correct 
values for the wall_ids.

For further solution I would suggest to not split the thing in two files, 
example how to avoid that is in [1].
You can actually start from [1] and make it 2D.

Note: pasting code fragments in a question is not appropriate [2].

[1] 
https://gitlab.com/yade-dev/trunk/-/blob/3e9a209234b7f23241d5f4bdef1b586056e97582/examples/simple-scene/save-then-reload.py
[2] https://www.yade-dem.org/wiki/Howtoask

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Re: [Yade-users] [Question #700861]: an installation problem

[Bruno Chareyre]

Question #700861 on Yade changed:
https://answers.launchpad.net/yade/+question/700861

Status: Open => Answered

Bruno Chareyre proposed the following answer:
That company will have to find out the problem or report it.
I don't know that we can fix problems when we are completely blind on the 
OS+install procedure.
B

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Re: [Yade-users] [Question #700889]: Output collsions particles-walls and particle-particle per cycle

[Bruno Chareyre]

Question #700889 on Yade changed:
https://answers.launchpad.net/yade/+question/700889

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
How do you distinguish a collision from a contact?
Bruno

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Re: [Yade-users] [Question #700847]: access friction and inelastic collision contributions in the total loss of energy of the system

[Bruno Chareyre]

Question #700847 on Yade changed:
https://answers.launchpad.net/yade/+question/700847

Status: Open => Answered

Bruno Chareyre proposed the following answer:
As pointed out by Jan, there is no contact damping in Yade's CundallStrack.
If Newton.damping =0 (which I recommend in quastistatic simulations) then the 
only dissipation is frictional.
And the collisions conserve kinetic energy (at least if they do not lead to 
plastic slip).
Bruno

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Re: [Yade-users] [Question #700830]: Is there any way to generate voronoi tessellation diagram?

[Bruno Chareyre]

Question #700830 on Yade changed:
https://answers.launchpad.net/yade/+question/700830

Status: Open => Answered

Bruno Chareyre proposed the following answer:
FlowEngine has more features to visit the graph.

Something like this should work (not tested but the needed functions are
there):

for k in range(f.nCells): #where "f" is FlowEngine
point1 = f.getCellCenter(k)
others = f.getNeighbors(k)
 for j in others:
if ihttps://launchpad.net/~yade-users
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Re: [Yade-users] [Question #700861]: an installation problem

[Bruno Chareyre]

Question #700861 on Yade changed:
https://answers.launchpad.net/yade/+question/700861

Bruno Chareyre requested more information:
Hi,
What's that "cloud computing platform", which OS?
How do you install?
Bruno

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Re: [Yade-users] [Question #700761]: about measure seepage discharge in triaxial test

[Bruno Chareyre]

Question #700761 on Yade changed:
https://answers.launchpad.net/yade/+question/700761

Status: Open => Needs information

Bruno Chareyre requested more information:
> I tried changing flow.permeabilityFactor to a positive value and other
values.However,It seems that the data I record is always constant

Please post a script showing what you say.
You "tried changing" or you "changed"?
It "seems" it is the same or it "is" the same?
Etc.

Bruno

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Re: [Yade-users] [Question #700830]: Is there any way to generate voronoi tessellation diagram?

[Bruno Chareyre]

Question #700830 on Yade changed:
https://answers.launchpad.net/yade/+question/700830

Status: Needs information => Answered

Bruno Chareyre proposed the following answer:
Hi,
The image [1] was generated semi-automatically with POV-ray, using data 
generated collected from FlowEngine.
There is no builtin function for doing that in Yade directly.
It seems your question has two sides:
1/ how to get the data
2/ how to display it

For 1/, it's pretty easy in C++ to iterate on the triangulation's facets
and output a dual segment for each (one branch in Voronoi), but there is
currently no python wrapping for such operation in TesselationWrapper.
You may need to code a little within TessealationWrapper, or switch to
FlowEngine. I can advise a bit more if needed.

For 2/, it is up to you. I'm not quite sure POV-ray still works on
modern systems. There could be other softwares doing 3D rendering.
There's paraview but I'm not sure precisely how to achieve [1] in
paraview. Blender is another one but I have no experience.

Bruno

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Re: [Yade-users] [Question #700611]: TwoPhaseFlow - double free or corruption

[Bruno Chareyre]

Question #700611 on Yade changed:
https://answers.launchpad.net/yade/+question/700611

Status: Open => Needs information

Bruno Chareyre requested more information:
Oh... but I thought the question was about "large number of particles".
Now it's about "packs".

what do these packs look like? Would they contain overlapping spheres?
B

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Re: [Yade-users] [Question #700761]: about measure seepage discharge in triaxial test

[Bruno Chareyre]

Question #700761 on Yade changed:
https://answers.launchpad.net/yade/+question/700761

Bruno Chareyre proposed the following answer:
> the unit of the value measured by flow.getBoundaryFlux

It is in velocity * area.
B

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Re: [Yade-users] [Question #700611]: TwoPhaseFlow - double free or corruption

[Bruno Chareyre]

Question #700611 on Yade changed:
https://answers.launchpad.net/yade/+question/700611

Bruno Chareyre requested more information:
> Yes

Your question states the opposite it seems...
Can you be more specific on which number of particles gives the problem and 
provide a script showing the problem?
Bruno

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Re: [Yade-users] [Question #678523]: frictionAngle vs μ(interparticle friction coefficient)

[Bruno Chareyre]

Question #678523 on Yade changed:
https://answers.launchpad.net/yade/+question/678523

Bruno Chareyre proposed the following answer:
Please don't re-use a 3-year old thread for asking a question.
B

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Re: [Yade-users] [Question #700748]: how to calculate the plastic part of shear displacement in law2-cohesionMoment

[Bruno Chareyre]

Question #700748 on Yade changed:
https://answers.launchpad.net/yade/+question/700748

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
No, I don't see a simple way to track this "per contact".
Energy tracking would give a total for all contacts, not what you want.
You'll have to modify the source code a little.
For instance, add a "Real dissipation" attribute to interaction physics and 
accumulate there.
I hope it helps.
Bruno

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Re: [Yade-users] [Question #700743]: Errors during step-by-step particle deletion of consolidated specimen

[Bruno Chareyre]

Question #700743 on Yade changed:
https://answers.launchpad.net/yade/+question/700743

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
I ran your script and I didn't see a problem on yade side 
(20211216-6185~d81270c~focal1 here).
The timestep is stable.
It runs until a dense state is reached then it stops. It seems to be the 
behaviour of your algorithm. 
Cheers
Bruno

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Re: [Yade-users] [Question #700611]: TwoPhaseFlow - double free or corruption

[Bruno Chareyre]

Question #700611 on Yade changed:
https://answers.launchpad.net/yade/+question/700611

Bruno Chareyre requested more information:
Indeed. It's a glibc error [1] even if it sounds mechanical ("consolidation").
So you have crashes without MPI and without aggregates when using many 
particles?
B

[1] https://stackoverflow.com/questions/49628615/understanding-
corrupted-size-vs-prev-size-glibc-error

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Re: [Yade-users] [Question #700617]: core dumped after replacing boundary walls

[Bruno Chareyre]

Question #700617 on Yade changed:
https://answers.launchpad.net/yade/+question/700617

Bruno Chareyre posted a new comment:
> b.shape.extents = b.shape.extents * 10

Perfect answer.
Remember that it only works if thickness is null.

B

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Re: [Yade-users] [Question #700611]: TwoPhaseFlow - double free or corruption

[Bruno Chareyre]

Question #700611 on Yade changed:
https://answers.launchpad.net/yade/+question/700611

Status: Open => Answered

Bruno Chareyre proposed the following answer:
> still it works for lower number of particles

You mean it doesn't crash, right? Even so, I don't see it giving
consistent results.

> "corrupted size vs. prev_size while consolidating"

I don't find this text anywhere in the source code... this is puzzling.
Which version is that?

Please choose a topic: is it MPI or is aggregates, or is it something
else??

Bruno

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Re: [Yade-users] [Question #700617]: core dumped after replacing boundary walls

[Bruno Chareyre]

Question #700617 on Yade changed:
https://answers.launchpad.net/yade/+question/700617

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
This script will not run with python3.

Questions coming to mind, though:
- why not defining larger walls in the first place?
- why not changing the size of the existing walls instead of erasing them and 
inserting new ones with different "id's" (that's most likely the core dump 
explanation since TriaxialStressController  keeps looking for the older ones).

Bruno

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Re: [Yade-users] [Question #700611]: TwoPhaseFlow - double free or corruption

[Bruno Chareyre]

Question #700611 on Yade changed:
https://answers.launchpad.net/yade/+question/700611

Status: Open => Answered

Bruno Chareyre proposed the following answer:
Hi,
This has 0% chances to work.
MPI uses a domain decomposition with one yade instance running each subdomain.
What happens in your script is that each yade instance has its own 2PFV engine 
trying to triangulate+solve a flow problem in a subset of particles with no 
walls, and with no knowledge of what happens in the other subdomains (hence 
inconsistent triangulations,  no connectivity of fluxes accross subdomains, 
etc.).
Worth than that, particles can be exchanged between subdomains, so 2PFV may 
look for positions of particles which are no longer in the scene.

You need to think about what really happens with domain decomposition if you 
want to understand what can/cannot work.
In this case it would need a specific implementation of 2PFV in order support 
MPI.

Bruno

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Re: [Yade-users] [Question #700587]: My fluid-solid coupling script run very slowly

[Bruno Chareyre]

Question #700587 on Yade changed:
https://answers.launchpad.net/yade/+question/700587

Status: Needs information => Answered

Bruno Chareyre proposed the following answer:
> flow.meshUpdateInterval=2

This is an enormous workload, it means to rebuild a mesh, a permeability 
matrix, and factorize it, every 2 iterations. It can only be very slow. See [1] 
for a more detailed understanding.
Bruno

[1]
https://www.sciencedirect.com/science/article/abs/pii/S0010465519303340

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Re: [Yade-users] [Question #700434]: InsertionSortCollider SortAxis : does axis choice make a difference to speed?

[Bruno Chareyre]

Question #700434 on Yade changed:
https://answers.launchpad.net/yade/+question/700434

Bruno Chareyre posted a new comment:
Hi, thanks for report. It is interesting to see the effect on initSort but it 
is in fact not the important question.
It occurs only at iteration 1, then never again (also I don't think I 
parallelized it).
Since you found no difference for the next iterations I guess you confirm that 
there is little to gain here.
Bruno

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Re: [Yade-users] [Question #700531]: Contacts in function getStress()

[Bruno Chareyre]

Question #700531 on Yade changed:
https://answers.launchpad.net/yade/+question/700531

Bruno Chareyre posted a new comment:
Hi,
Using the position of the wall instead of the contact point is perfectly fine.
The sum of f*l really runs over all interacting pairs regardless of the shapes 
of the objects.
The nice thing with this expression is it doesn't require the notion of a 
"contact point", at all. Which is great when the interactions are remote 
(capillary forces, electrostatic, lubrication, etc.).

In general it would be wrong to select different reference points for
one single object when defining "l". It is correct in the particular
case of an external wall, though. And therefore the suggestion by Jan
and Jerome are correct too (at least for those interaction models which
define a contact point, not always the case). It gives the same result
in practice.

Bruno

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