[Yade-users] [Question #700963]: Pore size distribution

2022-03-16 Thread Soheil Safari
New question #700963 on Yade:
https://answers.launchpad.net/yade/+question/700963

Dear all,

I want to obtain the pore size distribution of a sphere packing.

Does anyone have any suggestions for this purpose?

Thank you so much in advance.

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

2022-03-16 Thread Soheil Safari
Question #700953 on Yade changed:
https://answers.launchpad.net/yade/+question/700953

Soheil Safari posted a new comment:
Dear Robert and Bruno;

Thank you very much for your kind reply and valuable information.

I am so sorry for asking several questions here.

Fortunately, I could add the PSD arguments to the makeCloud function and
it works.[1]

Regarding the FlowEngine, as I am fresh in yade, I do not know what
function is proper for compression specially in oedometer test.

For the oedometer test, I used 03-oedometric-test.py [2] which has
gravity composition.

Would you please let me know what your recommendation is for the
oedometer test?

[1] https://gitlab.com/yade-dev/trunk/-/blob/master/examples/test/psd.py
[2] 
https://gitlab.com/yade-dev/trunk/blob/master/doc/sphinx/tutorial/03-oedometric-test.py

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

2022-03-16 Thread Xifan Li
Question #700931 on Yade changed:
https://answers.launchpad.net/yade/+question/700931

Status: Answered => Solved

Xifan Li confirmed that the question is solved:
Thanks Bruno Chareyre, that solved my question.

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[Yade-users] [Question #700957]: How to simulate the cyclic loading during the biaxial test?

2022-03-16 Thread Xifan Li
New question #700957 on Yade:
https://answers.launchpad.net/yade/+question/700957

I took the triaxial compression code (3d) and modified it to end up with the 
biaxial compression simulation (2d), but now I want to go a step further and 
get cyclic loading while doing biaxial compression (which means to allow the 
sigmaIsoCompaction and sigmaLateralConfinement are not constantly).

Here is the code (The code works fine and completes the biaxial compression 
test, but it doesn't load the loop, so I'd like to know what the problem is.):

from yade import pack

sp=pack.SpherePack()
## corners of the initial packing
mn,mx=Vector3(0,0,0),Vector3(10,10,.1)

## box between mn and mx, avg radius ± ½(20%), 2k spheres
sp.makeCloud(minCorner=mn,maxCorner=mx,rRelFuzz=0,num=2000)

## create material #0, which will be used as default
O.materials.append(FrictMat(young=15e6,poisson=.4,frictionAngle=radians(30),density=2600,label='spheres'))
O.materials.append(FrictMat(young=15e6,poisson=.4,frictionAngle=0,density=0,label='frictionless'))


## copy spheres from the packing into the scene
## use default material, don't care about that for now
O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp])
## create walls around the packing
walls=aabbWalls(thickness=1e-10,material='frictionless')
wallIds=O.bodies.append(walls)

triax=TriaxialCompressionEngine(
wall_bottom_id=wallIds[2],
wall_top_id=wallIds[3],
wall_left_id=wallIds[0],
wall_right_id=wallIds[1],
wall_back_id=wallIds[4],
wall_front_id=wallIds[5],
internalCompaction=True,
## define the rest of triax params here
## see in pkg/dem/PreProcessor/TriaxialTest.cpp:524 etc
## which are assigned in the c++ preprocessor actually
sigmaIsoCompaction=-5e4,
sigmaLateralConfinement=-5e4,
max_vel=10,
strainRate=0.01,
label="triax"
)

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()]
),

GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
triax,
TriaxialStateRecorder(iterPeriod=100, file='Stresses(d.id).txt'),
NewtonIntegrator(damping=.4),
PyRunner(command='checkUnbalanced()',realPeriod=1,label='checker'),
]

O.dt=.5*PWaveTimeStep()


def checkUnbalanced():

if O.iter < 5000:
return

if unbalancedForce() > .1:
return
checker.command ='unload'


def unload():

if triax.stress(2)[1] > 6e4:
sigmaIsoCompaction /= 2
sigmaLateralConfinement /= 2
checker.command = 'load'

def load():

if triax.stress(2)[1]  < 3e4:
sigmaIsoCompaction *= 2
sigmaLateralConfinement *= 2

from yade import plot



O.engines=O.engines[0:5]+[PyRunner(iterPeriod=20,command='history()',label='recorder')]+O.engines[5:7]
def history():
plot.addData(e11=triax.strain[0], 
e22=-triax.strain[1], 
s11=-triax.stress(0)[0],
s22=-triax.stress(2)[1],

i=O.iter)

plot.plots={'e11': ('s11',),'e22': ('s22',)}

O.saveTmp()
plot.plot()


#
Many thanks for your help.


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

2022-03-16 Thread 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)

2022-03-16 Thread 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 #700953]: Oedometer test based on PSD

2022-03-16 Thread Robert Caulk
Question #700953 on Yade changed:
https://answers.launchpad.net/yade/+question/700953

Status: Open => Needs information

Robert Caulk requested more information:
Hello,

Welcome to Yade! You are asking quite a few disparate questions here, so
please in the future, limit your threads to a single question each. Open
as many threads as you want. We have other important forum guidelines
that you should keep in mind if you desire quick and efficient help [3].

>>how can I change the sphere packing function (makeCloud)) based on the
PSD?

You can add the PSD arguments to the makeCloud function. Please refer to
the documentation [1].

>>  And how can I fix the side walls to obtain the oedometric condition
(just vertical force)?

You can activate and deactivate walls, please refer to the documentation
[2].

>>Now I am using [1] code.

But you want to use FlowEngine? I do not see how your referenced script
(save_then_reload.py) has anything to do with your proposed simulation.
By the way, saving and reloading does not work "out of the box" with
FlowEngine.

>> I should mention that I tried the oedometric sample on the yade
website but it is not proper for me due to its gravity composition.
Also, I tried to mix some PSD functions with this code but I could not
get any result.

It seems the main question here has to do with your "P.S." But as is,
you have not provided enough information for us to help you. For example
what does "could not get any result" mean? Which script are you
referring to? The odeometer.py does not have gravity composition.


Cheers,

Robert


[1]https://yade-dem.org/doc/yade.pack.html#yade._packSpheres.SpherePack.makeCloud
[2]https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.TriaxialStressController.wall_back_activated
[3]https://www.yade-dem.org/wiki/Howtoask

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

2022-03-16 Thread Soheil Safari
New question #700953 on Yade:
https://answers.launchpad.net/yade/+question/700953

Dear all,

I am a new user of YADE. A part of my PhD project is investigation of the 
effects of compaction on pore structure and soil hydraulic properties. To this 
aim, we want to follow the DEM approach proposed by ”Mahmoodlu, M. G., Raoof, 
A., Sweijen, T., & Van Genuchten, M. T. (2016). Effects of sand compaction and 
mixing on pore structure and the unsaturated soil hydraulic properties. Vadose 
Zone Journal, 15(8).” which is done using YADE.

I am trying to reproduce the compaction process of a granular material under 
oedometric conditions based on my desired pore size distribution (PSD).

Now I am using [1] code. My first question is how can I change the sphere 
packing function (makeCloud)) based on the PSD? And how can I fix the side 
walls to obtain the oedometric condition (just vertical force)?

P.S. I should mention that I tried the oedometric sample on the yade website 
but it is not proper for me due to its gravity composition. Also, I tried to 
mix some PSD functions with this code but I could not get any result.

[1] 
https://gitlab.com/yade-dev/trunk/-/blob/3e9a209234b7f23241d5f4bdef1b586056e97582/examples/simple-scene/save-then-reload.py

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Re: [Yade-users] [Question #700944]: VTKRecorder is not defined

2022-03-16 Thread Jan Stránský
Question #700944 on Yade changed:
https://answers.launchpad.net/yade/+question/700944

Status: Open => Needs information

Jan Stránský requested more information:
Hello,

> but VTK_dir was not detected automatically during make process.

what is the output of cmake?

> So, I manually set the direction of VTK.

to what value?
My is (automatically detected, on Ubuntu 18.04)
VTK_DIR:PATH=/usr/lib/cmake/vtk-6.3

> I installed VTK9.1.0 and this version is available to YADE?

I think it should work..
but anyway I would start with the "system default" libraries.

Anyway, I strongly recommend to compile and install such libraries in
more "logical" way, e.g. not all compilation/installation in $HOME/bin.

Cheers
Jan

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Re: [Yade-users] [Question #700944]: VTKRecorder is not defined

2022-03-16 Thread Jeseung Moon
Question #700944 on Yade changed:
https://answers.launchpad.net/yade/+question/700944

Status: Needs information => Open

Jeseung Moon gave more information on the question:
Thanks Jan,

First of all, I am making different contact and bonding model, so I need to 
compile yade to check the new model.
Also, I have already tried to use yadedaily and a system VTK, but VTK_dir was 
not detected automatically during make process. So, I manually set the 
direction of VTK.
One question regarding VTK:
I installed VTK9.1.0 and this version is available to YADE?

Best regards,
Jeseung Moon

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Re: [Yade-users] [Question #700944]: VTKRecorder is not defined

2022-03-16 Thread Jan Stránský
Question #700944 on Yade changed:
https://answers.launchpad.net/yade/+question/700944

Status: Open => Needs information

Jan Stránský requested more information:
As you see, VTK is not present in the output of printAllVersions().
I.e., Yade was compiled without VTK.

What is the output of cmake?

Can you try a system VTK, instead of self-installed version?

Why are you compiling Yade? Would a package [3], yadedaily for example,
be an option?

Cheers
Jan

[3] https://yade-dem.org/doc/installation.html#packages

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Re: [Yade-users] [Question #700946]: Simulation rectangle

2022-03-16 Thread Fereshteh Salehi
Question #700946 on Yade changed:
https://answers.launchpad.net/yade/+question/700946

Summary changed to:
Simulation rectangle 

Description changed to:
Hello I'm beginner in yade and I am student. I want to simulation  rectangle 
tire shred , but l don't know how to simulate rectangle tire shred. Tire shred  
is a particles tire in range of 50 to 305 mm.
Please guide me. 
Thank you.

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Re: [Yade-users] [Question #700944]: VTKRecorder is not defined

2022-03-16 Thread Jeseung Moon
Question #700944 on Yade changed:
https://answers.launchpad.net/yade/+question/700944

Status: Needs information => Open

Jeseung Moon gave more information on the question:
Hello, Jan!

I compiled the VTK installation to the bin folder. And when choosing
VTK_dir, other directories were not detected as a VTK_dir.

I attatched printAllVersion()
```
Yade version   :  2022-01-18.git-4be27ac
Yade features  :  LOGGER USEFUL_ERRORS COMPLEX_MP MPFR MPC OPENMP GTS QT5 CGAL 
PFVFLOW PFVFLOW LINSOLV MPI TWOPHASEFLOW LS_DEM FEMLIKE GL2PS LBMFLOW THERMAL 
POTENTIAL_PARTICLES POTENTIAL_BLOCKS
Yade config dir:  ~/.yade-2022-01-18.git-4be27ac
Yade precision :  53 bits, 15 decimal places, without mpmath, PrecisionDouble
```

Libraries used :

| library   | cmake  | C++ |
| - | -- | --- |
| boost | 107800 | 1.78.0  |
| cgal  || 4.11|
| clp   | 1.16.11| 1.16.11 |
| cmake | 3.10.2 | |
| coinutils | 2.10.14| 2.10.14 |
| compiler  | /usr/bin/g++-7 7.5.0   | gcc 7.5.0   |
| eigen | 3.4.0  | 3.4.0   |
| freeglut  | 2.8.1  | |
| gl|| 20190911|
| ipython   | 5.5.0  | |
| metis || 5.1.0   |
| mpc   | 1.1.0  | 1.1.0   |
| mpfr  | 4.0.1  | 4.0.1   |
| mpi   | 3.1| ompi:2.1.1  |
| mpi4py| 2.0.0  | |
| mpmath| 1.0.0  | |
| openblas  ||  OpenBLAS 0.2.20|
| python| 3.6.9  | 3.6.9   |
| qglviewer || 2.6.3   |
| qt|| 5.9.5   |
| sphinx| 1.6.7-final-0  | |
| sqlite|| 3.22.0  |
| suitesparse   | 5.1.2  | 5.1.2   |

```
Linux version  :  Ubuntu 18.04.4 LTS
Architecture   :  amd64
Little endian  :  True

Best regards,

Jeseung Moon

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Re: [Yade-users] [Question #700944]: VTKRecorder is not defined

2022-03-16 Thread Jan Stránský
Question #700944 on Yade changed:
https://answers.launchpad.net/yade/+question/700944

Status: Open => Needs information

Jan Stránský requested more information:
Hello,

what is the output of printAllVersions() from yade [2]?

> //The directory containing a CMake configuration file for VTK.
> VTK_DIR:PATH=/home/jsmoon/bin/VTK910

this seems very suspicious.
At least it should not be in "bin", but rather something like "lib".
Could you try using a system-wide VTK?

Cheers
Jan

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Re: [Yade-users] [Question #700946]: Simulation three axial test

2022-03-16 Thread Jan Stránský
Question #700946 on Yade changed:
https://answers.launchpad.net/yade/+question/700946

Status: Open => Needs information

Jan Stránský requested more information:
Hello,

please read [1] and follow the instructions.
Try to read your question as somebody, who have no experience with your problem 
(as we are).
Then provide more information, E.g.:
- what shape are the tire particles? truely rectangle (2D zero thickness)?
- how should they behave other then sand? I expect less stiffness, something 
else?
- are they randomly placed, or somehow clustered?
- how much of it is there? How probable is their mutual interaction?
- ... ?

Please provide requested information from [2]

The help with lack of information is of course possible, but then rather
try "Paid support and Consulting" link [3,4].

Cheers
Jan

[1] https://www.yade-dem.org/wiki/Howtoask
[2] https://answers.launchpad.net/yade/+question/700800
[3] https://yade-dem.org/doc/
[4] https://yade-dem.org/doc/consulting.html

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Re: [Yade-users] [Question #700944]: VTKRecorder is not defined

2022-03-16 Thread Jeseung Moon
Question #700944 on Yade changed:
https://answers.launchpad.net/yade/+question/700944

Status: Needs information => Open

Jeseung Moon gave more information on the question:
Thanks Jan,

I can share the CMakeCache which includes library information.
I installed in Ubuntu 20.04.

# This is the CMakeCache file.
# For build in directory: /home/jsmoon/download/build
# It was generated by CMake: /usr/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
# VALUE is the current value for the KEY.


# EXTERNAL cache entries


//Path to a library.
AMD_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libamd.so

//Path to a file.
BLAS_INCLUDE_DIR:PATH=/usr/include/x86_64-linux-gnu

//Path to a library.
BLAS_goto2_LIBRARY:FILEPATH=BLAS_goto2_LIBRARY-NOTFOUND

//Path to a library.
BLAS_openblas_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libopenblas.so

//The threading library used by boost-thread
BOOST_THREAD_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpthread.so

//Path to a file.
BZIP2_INCLUDE_DIR:PATH=/usr/include

//Path to a library.
BZIP2_LIBRARY_DEBUG:FILEPATH=BZIP2_LIBRARY_DEBUG-NOTFOUND

//Path to a library.
BZIP2_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64-linux-gnu/libbz2.so

//Boost atomic library (debug)
Boost_ATOMIC_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_atomic.so

//Boost atomic library (release)
Boost_ATOMIC_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_atomic.so

//Boost chrono library (debug)
Boost_CHRONO_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_chrono.so

//Boost chrono library (release)
Boost_CHRONO_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_chrono.so

//Boost date_time library (debug)
Boost_DATE_TIME_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_date_time.so

//Boost date_time library (release)
Boost_DATE_TIME_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_date_time.so

//Boost filesystem library (debug)
Boost_FILESYSTEM_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_filesystem.so

//Boost filesystem library (release)
Boost_FILESYSTEM_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_filesystem.so

//Path to a file.
Boost_INCLUDE_DIR:PATH=/usr/local/include

//Boost iostreams library (debug)
Boost_IOSTREAMS_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_iostreams.so

//Boost iostreams library (release)
Boost_IOSTREAMS_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_iostreams.so

//Boost library directory DEBUG
Boost_LIBRARY_DIR_DEBUG:PATH=/usr/local/lib

//Boost library directory RELEASE
Boost_LIBRARY_DIR_RELEASE:PATH=/usr/local/lib

//Boost log library (debug)
Boost_LOG_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_log.so

//Boost log library (release)
Boost_LOG_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_log.so

//Boost log_setup library (debug)
Boost_LOG_SETUP_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_log_setup.so

//Boost log_setup library (release)
Boost_LOG_SETUP_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_log_setup.so

//Boost python36 library (debug)
Boost_PYTHON36_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_python36.so

//Boost python36 library (release)
Boost_PYTHON36_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_python36.so

//Boost regex library (debug)
Boost_REGEX_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_regex.so

//Boost regex library (release)
Boost_REGEX_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_regex.so

//Boost serialization library (debug)
Boost_SERIALIZATION_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_serialization.so

//Boost serialization library (release)
Boost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_serialization.so

//Boost system library (debug)
Boost_SYSTEM_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_system.so

//Boost system library (release)
Boost_SYSTEM_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_system.so

//Boost thread library (debug)
Boost_THREAD_LIBRARY_DEBUG:FILEPATH=/usr/local/lib/libboost_thread.so

//Boost thread library (release)
Boost_THREAD_LIBRARY_RELEASE:FILEPATH=/usr/local/lib/libboost_thread.so

//Path to a library.
CAMD_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libcamd.so

//Path to a library.
CCOLAMD_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libccolamd.so

//Path to a file.
CGAL_INCLUDE_DIR:PATH=/usr/include

//Path to a library.
CGAL_LIBRARIES:FILEPATH=/usr/lib/x86_64-linux-gnu/libCGAL.so

//Enable GPU acceleration flow engine direct solver
CHOLMOD_GPU:BOOL=OFF

//Path to a file.
CHOLMOD_INCLUDE_DIR:PATH=/usr/include/suitesparse

//Path to a library.
CHOLMOD_LIBRARIES:FILEPATH=/usr/lib/x86_64-linux-gnu/libcholmod.so

//Path to a file.

Re: [Yade-users] [Question #700947]: 2D direct shear test

2022-03-16 Thread Jan Stránský
Question #700947 on Yade changed:
https://answers.launchpad.net/yade/+question/700947

Status: Open => Answered

Jan Stránský proposed the following answer:
Hello,
see [1], where the direct shear test was recently discussed, and links therein.
Cheers
Jan

[1] https://answers.launchpad.net/yade/+question/700924

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Re: [Yade-users] [Question #700903]: How to call the set function again

2022-03-16 Thread Jan Stránský
Question #700903 on Yade changed:
https://answers.launchpad.net/yade/+question/700903

Status: Open => Answered

Jan Stránský proposed the following answer:
Just call call the function again when you want the second output..

For better answer, please provide requested information:
> ... provide a MWE [1], illustrating "operation" ..., how you run and stop the 
> simulation, ... etc. etc.

Cheers
Jan

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Re: [Yade-users] [Question #700944]: VTKRecorder is not defined

2022-03-16 Thread Jan Stránský
Question #700944 on Yade changed:
https://answers.launchpad.net/yade/+question/700944

Status: Open => Needs information

Jan Stránský requested more information:
Hello,

please provide more information: what system you use, how you installed Yade, 
how you run Yade, output of printAllVersions() [2], a MWE [1] (or at least 
actual python script)...
A MWE in this case would be just one line script:
###
VTKRecorder()
###

Cheers
Jan

[1] https://www.yade-dem.org/wiki/Howtoask
[2] 
https://yade-dem.org/doc/yade.libVersions.html#yade.libVersions.printAllVersions

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[Yade-users] [Question #700947]: 2D direct shear test

2022-03-16 Thread Huchao
New question #700947 on Yade:
https://answers.launchpad.net/yade/+question/700947

Hi, I'm looking for the scripts of direct shear test, but I only find the PFC's 
scripts. Is there any example in YADE? Can YADE simulate 2D  direct shear test? 
Thank you.

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[Yade-users] [Question #700946]: Simulation three axial test

2022-03-16 Thread Fereshteh Salehi
New question #700946 on Yade:
https://answers.launchpad.net/yade/+question/700946

Hello I'm beginner in yade and I am student. I want to simulation three axial 
test with rectangle tire shred and sand, but l don't know how to simulate 
rectangle tire shred. Tire shred  is a particles tire in range of 50 to 305 mm.
Please guide me. 
Thank you. 

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