Re: [Yade-users] [Question #680397]: Kn and Ks value for Hertz-Mindilin model

2019-04-23 Thread Robert Caulk
Question #680397 on Yade changed:
https://answers.launchpad.net/yade/+question/680397

Status: Open => Answered

Robert Caulk proposed the following answer:
Nope, I believe you need to make your own material class in C++.
FrictMat uses the values Young and Poisson in collaboration with
interacting particle radii to estimate Kn and Ks [1]. There are a couple
benefits to particle size based stiffnesses, one of which is the scale
independence of macroscopic behaviors IINM, the other being the radii
distribution based stiffness heterogeneity distribution.

[1]https://yade-
dev.gitlab.io/-/trunk/-/jobs/200298968/artifacts/install/share/doc/yade-
ci/html/formulation.html#stiffnesses

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Re: [Yade-users] [Question #680397]: Kn and Ks value for Hertz-Mindilin model

2019-04-23 Thread SayedHessam
Question #680397 on Yade changed:
https://answers.launchpad.net/yade/+question/680397

SayedHessam posted a new comment:
Dear Robert,

thanks for your quick response.

BTW, for Hertz-Mindlin there are these parameters kn and ks [1], but you
say I should make my material class in C++.


Cheers
Sam


[1] https://yade-
dev.gitlab.io/trunk/yade.wrapper.html?highlight=frictmat#yade.wrapper.MindlinPhys

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Re: [Yade-users] [Question #680375]: How to delete 10% percent of small particles?

2019-04-23 Thread Robert Caulk
Question #680375 on Yade changed:
https://answers.launchpad.net/yade/+question/680375

Status: Open => Answered

Robert Caulk proposed the following answer:
I guess it's a python question.

import numpy as np

def delBelowPercentile(a, q):
maxRad = np.percentile(a,q)
for b in bodyRadius:
   if b[0].shape.radius <= maxRad:
   O.bodies.erase(b[0].id)

bodyRadius = []
for b in O.bodies:
if isinstance(b.shape,Sphere):
bodyRadius.append([b,b.shape.radius])

bodyRadius.sort(key=lambda x: x[1])
delBelowPercentile(bodyRadius,10)

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Re: [Yade-users] [Question #680334]: cohesion between polyhedral particles

2019-04-23 Thread Robert Caulk
Question #680334 on Yade changed:
https://answers.launchpad.net/yade/+question/680334

Status: Open => Answered

Robert Caulk proposed the following answer:
Does it answer your question [1]?

[1]https://answers.launchpad.net/yade/+question/255247

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Re: [Yade-users] [Question #680397]: Kn and Ks value for Hertz-Mindilin model

2019-04-23 Thread Robert Caulk
Question #680397 on Yade changed:
https://answers.launchpad.net/yade/+question/680397

Robert Caulk proposed the following answer:
You reference the physics of a single interaction, those values are
computed inside Yade. Now that I think about it, you could let Yade
compute those values and then overwrite them by looping through all
interactions. From what I can see in the source, you will only need to
do this once anytime new interactions are created.

for i in O.interactions:
i.phys.kn = 10
i.phys.ks = 5

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Re: [Yade-users] [Question #680334]: cohesion between polyhedral particles

2019-04-23 Thread Jan Stránský
Question #680334 on Yade changed:
https://answers.launchpad.net/yade/+question/680334

Jan Stránský proposed the following answer:
Hello,
try to use Ig2_Polyhedra_Polyhedra_ScGeom [1] and then materials, Ip2 and Law2 
as if you simulate cohesive spheres.
cheers
Jan

[1] https://yade-
dem.org/doc/yade.wrapper.html#yade.wrapper.Ig2_Polyhedra_Polyhedra_ScGeom

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Re: [Yade-users] [Question #680307]: How can I applied PeriTriaxController on a box of polyhedras?

2019-04-23 Thread Jérôme Duriez
Question #680307 on Yade changed:
https://answers.launchpad.net/yade/+question/680307

Status: Open => Answered

Jérôme Duriez proposed the following answer:
Then, the question looks to be "how to generate walls surrounding a
sample of polyhedra" ?

Indeed, aabbWalls(), the way you called it, needed to call aabbExtrema()
which does not "work" for something else than spheres (or clump of
spheres) [*]

Solution looks to be to just define yourself some extrema attribute when
you call aabbWalls().

But, if we are now speaking about boundary walls, your question has
nothing to do with "PeriTriaxController" (which would be for periodic
boundary conditions, without boundary walls..)


[*]  https://gitlab.com/yade-dev/trunk/blob/master/pkg/dem/Shop_02.cpp#L883

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Re: [Yade-users] [Question #680375]: How to delete 10% percent of small particles?

2019-04-23 Thread Jan Stránský
Question #680375 on Yade changed:
https://answers.launchpad.net/yade/+question/680375

Jan Stránský proposed the following answer:
Hello,

use PyRunner [1]:
###
def getSmallParticles():
   ret = []
   # fill ret with particles satisfying "10% percent of small particles"
   return ret

def deleteSmallParticles():
   for b in getSmallParticles():
  O.bodies.erase(b.id)

O.engines = [
   ...
   PyRunner(iterPeriod=100,command="deleteSmallParticles()"),
]
###

cheers
Jan

[1] https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.PyRunner

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Re: [Yade-users] [Question #680295]: how to set the shear and normal bond strength between sticky particles

2019-04-23 Thread Jan Stránský
Question #680295 on Yade changed:
https://answers.launchpad.net/yade/+question/680295

Status: Open => Needs information

Jan Stránský requested more information:
Hello,

please be more specific [1], mainly if you know already which material, Ip2 and 
Law2 you will use (setting strengths depends very much on them).
Different strengths between different materials can be set e.g. using match 
makers, "manually" in the loop over interactions.

cheers
Jan

[1] https://yade-dem.org/wiki/Howtoask

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Re: [Yade-users] [Question #680398]: Inertia Tensor for clumps with Intersecting Spheres

2019-04-23 Thread Robert Caulk
Question #680398 on Yade changed:
https://answers.launchpad.net/yade/+question/680398

Status: Open => Answered

Robert Caulk proposed the following answer:
It looks like a mistake in the code. In fact, both terms were originally
multiplied by dv. I think this commit [1] was aiming to fix it but only
noticed the first term.

Can you confirm, Jan?

[1]https://gitlab.com/yade-
dev/trunk/commit/5fef57e3a925e803e6c5009f7ec30884a2cb9c37

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Re: [Yade-users] [Question #680398]: Inertia Tensor for clumps with Intersecting Spheres

2019-04-23 Thread Jan Stránský
Question #680398 on Yade changed:
https://answers.launchpad.net/yade/+question/680398

Jan Stránský posted a new comment:
Hello,
good point, it looks like a mistake, definitely there should be m instead of 
dv..

2 points:
- the term tends to zero as discretization tends to infinity
- at the moment I have no idea why it is computed with respect to principal 
axes of the voxel, I **think** it should be computed with respect to global 
coordinate system..

cheers
Jan

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Re: [Yade-users] [Question #680398]: Inertia Tensor for clumps with Intersecting Spheres

2019-04-23 Thread Robert Caulk
Question #680398 on Yade changed:
https://answers.launchpad.net/yade/+question/680398

Robert Caulk proposed the following answer:
Thanks Bokkisa, I submitted the merge request for changing dv to m [1].

[1]https://gitlab.com/yade-dev/trunk/merge_requests/101

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Re: [Yade-users] [Question #680398]: Inertia Tensor for clumps with Intersecting Spheres

2019-04-23 Thread Bokkisa Srinivas Vivek
Question #680398 on Yade changed:
https://answers.launchpad.net/yade/+question/680398

Status: Answered => Solved

Bokkisa Srinivas Vivek confirmed that the question is solved:
Thanks Robert Caulk, that solved my question.

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Re: [Yade-users] [Question #680398]: Inertia Tensor for clumps with Intersecting Spheres

2019-04-23 Thread Bokkisa Srinivas Vivek
Question #680398 on Yade changed:
https://answers.launchpad.net/yade/+question/680398

Bokkisa Srinivas Vivek posted a new comment:
Dear Jan, thanks for your confirmation.

I think inertia of all the voxels are calculated w.r.t Global Coordinate
System (GCS) only. Using parallel axis theorem inertia at principal axis
of voxel is translated to GCS.   (Line 178)

After computing the centre of mass (C.O.M) of the clump, the inertia is
translated again to the C.O.M.  (Line 215)

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Re: [Yade-users] [Question #680398]: Inertia Tensor for clumps with Intersecting Spheres

2019-04-23 Thread Jan Stránský
Question #680398 on Yade changed:
https://answers.launchpad.net/yade/+question/680398

Jan Stránský posted a new comment:
Yes, sorry, just ignore this part of my answer :-)
Jan

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Re: [Yade-users] [Question #680375]: How to delete 10% percent of small particles?

2019-04-23 Thread zheng
Question #680375 on Yade changed:
https://answers.launchpad.net/yade/+question/680375

Status: Answered => Open

zheng is still having a problem:
Thanks Caulk and Jan, this solved most of my question. However, deleting
particles by sizes may not be suitable for all cases. For example, how
to delete 10% of particles by number if I only have one particle size?
This time the "percentile(a,q)” may not work. Could you please give me
any clues? Thanks so much.

Best regards,
Zheng

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Re: [Yade-users] [Question #680375]: How to delete 10% percent of small particles?

2019-04-23 Thread Robert Caulk
Question #680375 on Yade changed:
https://answers.launchpad.net/yade/+question/680375

Status: Open => Answered

Robert Caulk proposed the following answer:
Why don't you give that a shot and tell us where the difficulties lie?

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[Yade-users] [Question #680409]: Inertia Tensor of the "Tetra" shape class

2019-04-23 Thread Vasileios Angelidakis
New question #680409 on Yade:
https://answers.launchpad.net/yade/+question/680409

Hi,

I think I have spotted a mistake in the calculation of the Inertia Tensor for 
the "Tetra" shape class (since the day calls for inertia-related amendments :) 
). In the Tetra.cpp script, the Inertia Tensor is calculated exactly as in [1]. 
The thing is, this paper has a typo, and although the non-diagonal inertia 
values "a', b', c'" (stated in the source code as: "a__ , b__ , c__") are 
calculated correctly, their position in the Inertia tensor seems to be false. 
In particular, the terms "-b__" and "-c__" should be in each other's place, 
since these terms are defined as:

b' (=b__) term: $$b' = \int_{D} μ*x*z dD $$ : Involving x-z coordinates: should 
be present in the (0,2) (2,0) cells of the tensor
c' (=c__) term:  $$c' = \int_{D} μ*x*y dD $$ : Involving x-y coordinates: 
should be present in the (0,1) (1,0) cells of the tensor

I see this has also been spotted in the Polyhedra_support.cpp script, where the 
correct tensor is used:

Matrix3r ret; ret<<
a   , -c__, -b__,
-c__, b   , -a__,
-b__, -a__, c   ;
return ret;


[1] https://thescipub.com/pdf/10.3844/jmssp.2005.8.11

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[Yade-users] [Question #680414]: Creating a FCC structued packing and applying confining stress

2019-04-23 Thread Anqi H
New question #680414 on Yade:
https://answers.launchpad.net/yade/+question/680414

Hey everyone! I've been trying to create a cubic rock sample of FCC structure, 
and apply a 0.5 MPa confining stress to prepare the sample for other 
simulations. I tried following the periodic triaxial testing script but 
something is not correct in my setup as I'm getting an error message 
"PeriTriaxController run on aperiodic simulation".  I set up the FCC structure 
in the rock sample by specifying the centroid position and radius of every 
sphere particle, however I'm sure if this is the correct way to create the 
packing. I have attached the my code below, if anyone could show me some 
pointers I would really appreciate it.


from yade import pack, qt, plot

r = 0.45
L = 2*sqrt(2)*r
sigmaIso = -5e5

# rock material 
rockID = 
O.materials.append(CpmMat(young=15e6,poisson=.4,frictionAngle=radians(atan(0.5)),density=2650,label='spheres'))
#wall material
O.materials.append(FrictMat(young=15e6,poisson=.4,frictionAngle=0,density=0,label='frictionless'))

sphereArr = []

for m in range(0,46): #y axis
for j in range(0,30): #z  axis
for i in range(0,15): #x axis
if j%2==0:
sphereArr.append((L*i,m*L/2,j*L/2))
else:
sphereArr.append((L*(i+(.5)),m*L/2,j*L/2))


O.bodies.append([sphere(center, r,material='spheres',color = (0.42,0.06,0.51) 
)for center in sphereArr])

## create walls around the packing
walls=aabbWalls([(0,0,0),(20,30,20)],thickness=1e-10,material='frictionless')
wallIds=O.bodies.append(walls)

O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()],
[Law2_ScGeom_FrictPhys_CundallStrack()] 
),
PeriTriaxController(label='triax',
goal=(sigmaIso,sigmaIso,sigmaIso),stressMask=7,
dynCell=True, maxStrainRate=(10,10,10),
# wait until the unbalanced force goes below this value
maxUnbalanced=.1,relStressTol=1e-3,
# call this function when goal is reached and the packing is stable
doneHook='compactionFinished()'
),
NewtonIntegrator(damping=.2),
PyRunner(command='GlobalData()',iterPeriod=500),
]

O.dt=.5*PWaveTimeStep()

def GlobalData():
print 'porosity '+utils.porosity()
print 'coord #' +utils.avgNumInteractions()



def compactionFinished():
# set the current cell configuration to be the reference one
O.cell.trsf=Matrix3.Identity
# change control type: keep constant confinement in x,y, 20% 
compression in z
triax.goal=(sigmaIso,sigmaIso,-.2)
triax.stressMask=3
# allow faster deformation along x,y to better maintain stresses
triax.maxStrainRate=(1.,1.,.1)
# next time, call triaxFinished instead of compactionFinished
triax.doneHook='triaxFinished()'
# do not wait for stabilization before calling triaxFinished
triax.maxUnbalanced=10

def triaxFinished():
print 'Finished'
O.pause()

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Re: [Yade-users] [Question #680414]: Creating a FCC structued packing and applying confining stress

2019-04-23 Thread Anqi H
Question #680414 on Yade changed:
https://answers.launchpad.net/yade/+question/680414

Description changed to:
Hey everyone!

I've been trying to create a cubic rock sample of FCC structure, and
apply a 0.5 MPa confining stress to prepare the sample for other
simulations. I tried following the periodic triaxial testing script but
something is not correct in my setup as I'm getting an error message
"body larger than half of the cell size encountered".  I set up the FCC
structure in the rock sample by specifying the centroid position and
radius of every sphere particle, however I'm not sure if this is the
correct way to create the packing. I have attached the my code below, if
anyone could show me some pointers I would really appreciate it.


from yade import pack, qt, plot

r = 0.45
L = 2*sqrt(2)*r
sigmaIso = -5e5

# rock material 
rockID = 
O.materials.append(CpmMat(young=15e6,poisson=.4,frictionAngle=radians(atan(0.5)),density=2650,label='spheres'))
#wall material
O.materials.append(FrictMat(young=15e6,poisson=.4,frictionAngle=0,density=0,label='frictionless'))
O.periodic = Trus

sphereArr = []

for m in range(0,46): #y axis
for j in range(0,30): #z  axis
for i in range(0,15): #x axis
if j%2==0:
sphereArr.append((L*i,m*L/2,j*L/2))
else:
sphereArr.append((L*(i+(.5)),m*L/2,j*L/2))


O.bodies.append([sphere(center, r,material='spheres',color = (0.42,0.06,0.51) 
)for center in sphereArr])

## create walls around the packing
walls=aabbWalls([(0,0,0),(20,30,20)],thickness=1e-10,material='frictionless')
wallIds=O.bodies.append(walls)

O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys()],
[Law2_ScGeom_FrictPhys_CundallStrack()] 
),
PeriTriaxController(label='triax',
goal=(sigmaIso,sigmaIso,sigmaIso),stressMask=7,
dynCell=True, maxStrainRate=(10,10,10),
# wait until the unbalanced force goes below this value
maxUnbalanced=.1,relStressTol=1e-3,
# call this function when goal is reached and the packing is stable
doneHook='compactionFinished()'
),
NewtonIntegrator(damping=.2),
PyRunner(command='GlobalData()',iterPeriod=500),
]

O.dt=.5*PWaveTimeStep()

def GlobalData():
print 'porosity '+utils.porosity()
print 'coord #' +utils.avgNumInteractions()


def compactionFinished():
# set the current cell configuration to be the reference one
O.cell.trsf=Matrix3.Identity
# change control type: keep constant confinement in x,y, 20% 
compression in z
triax.goal=(sigmaIso,sigmaIso,-.2)
triax.stressMask=3
# allow faster deformation along x,y to better maintain stresses
triax.maxStrainRate=(1.,1.,.1)
# next time, call triaxFinished instead of compactionFinished
triax.doneHook='triaxFinished()'
# do not wait for stabilization before calling triaxFinished
triax.maxUnbalanced=10

def triaxFinished():
print 'Finished'
O.pause()

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Re: [Yade-users] [Question #680307]: How can I applied PeriTriaxController on a box of polyhedras?

2019-04-23 Thread Gavin He
Question #680307 on Yade changed:
https://answers.launchpad.net/yade/+question/680307

Status: Answered => Open

Gavin He is still having a problem:
Hello Jérôme,

With your responses, I have been able to generate aabbwalls surrounding
polyhedra specimen.

However, after I modify the code of triax-basic.py, trying to run fast
triaxial test on polyhedrons, I found the aabbwalls cannot run as the
same way as the example does. Eventually I found I need an IPhysFunctor
like "Ig2_Box_Polyhedra_ScGeom" (like "Ig2_Box_Sphere_ScGeom" when
simulating with spheres or clumps) to make the aabbwalls able to
interact with polyhedras, which I cannot find.

So now the question looks to be "how to make aabbwalls able to interact
with polyhedras"?

Could you help me with this problem?

___

CODE:

from yade import pack,polyhedra_utils

gravel = PolyhedraMat()
gravel.density = 2600 #kg/m^3 
gravel.young = 1E7 #Pa
gravel.poisson = 2/1E7
gravel.frictionAngle = 0.5 #rad

mn,mx=Vector3(0,0,0),Vector3(10,10,10)

O.materials.append(PolyhedraMat(young=15e6,poisson=.4,frictionAngle=0,density=0,label='frictionless'))

walls=aabbWalls(extrema=(mn,mx),thickness=1e-10,material='frictionless')
wallIds=O.bodies.append(walls)

polyhedra_utils.fillBox((0,0,0),
(10,10,10),gravel,sizemin=[1,1,1],sizemax=[0.1,0.1,0.1],seed=4)

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=False,
## 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=-50e3,
sigmaLateralConfinement=-50e3,
max_vel=10,
strainRate=0.01,
label="triax"
)

O.engines=[
ForceResetter(),

InsertionSortCollider([Bo1_Polyhedra_Aabb(),Bo1_Wall_Aabb(),Bo1_Facet_Aabb()],verletDist=5e-6),
InteractionLoop(
[Ig2_Wall_Polyhedra_PolyhedraGeom(), 
Ig2_Polyhedra_Polyhedra_PolyhedraGeom(), Ig2_Facet_Polyhedra_PolyhedraGeom()], 
[Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], # collision "physics"
[Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()]   # contact law -- 
apply forces
),

GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
triax,
# you can add TriaxialStateRecorder and such here…
NewtonIntegrator(damping=.4)
]
O.dt=polyhedra_utils.PWaveTimeStep()

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Re: [Yade-users] [Question #680397]: Kn and Ks value for Hertz-Mindilin model

2019-04-23 Thread SayedHessam
Question #680397 on Yade changed:
https://answers.launchpad.net/yade/+question/680397

Status: Answered => Solved

SayedHessam confirmed that the question is solved:
Thanks Robert, that solved my question.

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Re: [Yade-users] [Question #680307]: How can I applied PeriTriaxController on a box of polyhedras?

2019-04-23 Thread Gavin He
Question #680307 on Yade changed:
https://answers.launchpad.net/yade/+question/680307

Gavin He posted a new comment:
Also, it seems that TriaxialCompressionEngine can only use aabbwall
(boxes) as its boundary walls. I tried to set the wallID of the engine
as the ID of some other shape objects (including walls and polyhedras),
but it cannot run.

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