Re: [Yade-users] [Question #657677]: How to export and import a irregular shape particles model.

2017-09-06 Thread Jan Stránský
Question #657677 on Yade changed:
https://answers.launchpad.net/yade/+question/657677

Status: Open => Answered

Jan Stránský proposed the following answer:
Hello,

this is correct approach. Before export.textPolyhedra, there should probably be 
some running, in the script e.g.
O.run(N,True)

export.textPolyhedra [1] and ymport.textPolyhedra [2] should fit
together.

cheers
Jan

[1] https://yade-dem.org/doc/yade.export.html#yade.export.textPolyhedra
[2] https://yade-dem.org/doc/yade.ymport.html#yade.ymport.textPolyhedra

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[Yade-users] [Question #657677]: How to export and import a irregular shape particles model.

2017-09-06 Thread Kun Zeng
New question #657677 on Yade:
https://answers.launchpad.net/yade/+question/657677

Hi all,

I am a new user of yade. I tried polyhedra particles falling down into a box. I 
am wondering how can I export this model after it finishes this falling process 
and how to import it and down the next simulation? For example, generate a beam 
on this aggregates.

I used this code and yade.export.textPolyhedra. I don't know whether it is 
right or not.

##
# INPUTS
##
gravity = 100

# box dimensions
widthl = .3
widthr = .3
widthc = .3
height = .3
thick = .5
deep = -.2

# size of grains
sizeMin = 40e-3
sizeMax = 60e-3

frictionAngle = .5
young = 1e8 # stiffness

dt = 1e-3 # time step

nGravityDeposition = 250 # how long to run initial gravity deposition
nCycles = 3 # how many jumps to run afterwards
nStepsBetweenCycles = 200 # number of time steps between jumps
dspl = 20e-3

# how much larger the initial make box should be
fillBoxHFactor = 3
##
from yade import polyhedra_utils, export

width = widthl+widthc+widthr

# mat, engines, ...
mat = PolyhedraMat(young=young,poisson=10,frictionAngle=frictionAngle)
O.materials.append(mat)
O.engines=[
   ForceResetter(),
   InsertionSortCollider([Bo1_Polyhedra_Aabb(),Bo1_Facet_Aabb()]),
   InteractionLoop(
  [Ig2_Polyhedra_Polyhedra_PolyhedraGeom(), 
Ig2_Facet_Polyhedra_PolyhedraGeom()],
  [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()],
  [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()],
   ),
   NewtonIntegrator(damping=0.4,gravity=(0,0,-gravity)),
 PyRunner(iterPeriod=1,command='checker()'),
]
O.dt = dt
def checker():
 for i in range(nCycles):
  ii = nGravityDeposition+i*nStepsBetweenCycles
  if O.iter == ii:
   moveBottom()
  if O.iter == ii+1:
   stopBottom()
 if O.iter == nGravityDeposition+nCycles*nStepsBetweenCycles:
  O.pause()
def moveBottom():
 v = dspl / O.dt
 for b in movables:
  b.state.vel = (0,0,-v)
def stopBottom():
 for b in movables:
  b.state.vel = (0,0,0)

# box
p000 = Vector3(0,0,0)
p100 = Vector3(widthl,0,0)
p200 = Vector3(widthl+widthc,0,0)
p300 = Vector3(widthl+widthc+widthr,0,0)
pxs = (p000,p100,p200,p300)
p001,p101,p201,p301 = [p+Vector3(0,0,height) for p in pxs]
p010,p110,p210,p310 = [p+Vector3(0,thick,0) for p in pxs]
p011,p111,p211,p311 = [p+Vector3(0,thick,height) for p in pxs]
p00b,p10b,p20b,p30b = [p+Vector3(0,0,deep) for p in pxs]
p01b,p11b,p21b,p31b = [p+Vector3(0,thick,deep) for p in pxs]
def rect(vs,**kw):
 v1,v2,v3,v4 = vs
 return [
  facet((v1,v2,v3),**kw),
  facet((v1,v3,v4),**kw),
 ]
movables = rect((p100,p200,p210,p110)) # bottom center
rects = (
 (p000,p100,p110,p010), # bottom left
 (p200,p300,p310,p210), # bottom left
 (p000,p010,p011,p001), # left
 (p300,p310,p311,p301), # right
 (p000,p100,p101,p001), # front left
 (p100,p200,p201,p101), # front center
 (p200,p300,p301,p201), # front right
 (p010,p110,p111,p011), # back left
 (p110,p210,p211,p111), # back center
 (p210,p310,p311,p211), # back right
 (p100,p200,p20b,p10b), # front center below
 (p110,p210,p21b,p11b), # back center below
 (p100,p110,p11b,p10b), # left below
 (p200,p210,p21b,p20b), # right below
)
rects = movables + sum((rect(r) for r in rects),[])
O.bodies.append(rects)

# gravel
polyhedra_utils.fillBox((0,0,0),(width,thick,fillBoxHFactor*height),mat,sizemin=3*[sizeMin],sizemax=3*[sizeMax],seed=1)

yade.export.textPolyhedra('try2.txt', comment='try2', mask=-1, 
explanationComment=True, attrs=[])


Thanks.

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Re: [Yade-users] [Question #657063]: unconsolidated undrained triaxial test

2017-09-06 Thread Seti
Question #657063 on Yade changed:
https://answers.launchpad.net/yade/+question/657063

Status: Answered => Open

Seti is still having a problem:
Thanks Bruno,

It  makes sense -  Considering your comments- my physical samples be
completely aggregated,  if  I want to skip the consolidation part ( I
know by this assumption we change the condition to USC test when there
is confining pressure around the sample) - how should I edit the current
script  to address my requirements -

P.S. I need to model UU & CU.


Thanks 

Seti

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Re: [Yade-users] [Question #657564]: continuous creation and destruction of bodies

2017-09-06 Thread Bruno Chareyre
Question #657564 on Yade changed:
https://answers.launchpad.net/yade/+question/657564

Bruno Chareyre proposed the following answer:
Hi,
I would suggest to check examples/spheresFactory.py which combines the engines 
DomainLimiter and BoxFactory to delete/insert particles. It will be more 
flexible and computationally much more efficient than anything you can wruite 
in python.
Bruno

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Re: [Yade-users] [Question #657564]: continuous creation and destruction of bodies

2017-09-06 Thread Jan Stránský
Question #657564 on Yade changed:
https://answers.launchpad.net/yade/+question/657564

Jan Stránský posted a new comment:
Hello,

>  "b->id=-1;//else it sits in the python scope without a chance to be
inserted again"

this is just that you can re-append erased body if you have it in Python
##
s = sphere((0,0,0),1)
O.bodies.append(s)
#O.bodies.append(s) # would be error
print s.id
O.bodies.erase(0)
print s.id
O.bodies.append(s)
print s.id
##

> and intelligently reallocates free ids for newly added ones
> One explanation could be that your example is too small, i.e. the engine of 
> shared_ptr allocation does not reuse old (freed) memory until it is really 
> necessary, that is after many new insertions

according to the source code, the sentence of "intelligent reallocation"
is not true (perhaps was some time ago), no matter if the example is too
small or not..

However, my comment was really theoretical, practically it has no effect. I 
have tried the following code, 10e6 append/erase has no significant effect on 
memory. Assuming sizeof(shared_ptr)=16, it occupies 10e6*16=160e6=160MB, almost 
nothing)
##
while True:
   i = O.bodies.append(sphere((0,0,0),1))
   O.bodies.erase(i)
   if i%100==0:
  print i, len(O.bodies)
##

so, go in the direction append/erase without any worries :-)

cheers
Jan

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Re: [Yade-users] [Question #657564]: continuous creation and destruction of bodies

2017-09-06 Thread Andrea Puglisi
Question #657564 on Yade changed:
https://answers.launchpad.net/yade/+question/657564

Andrea Puglisi posted a new comment:
Dear Jan
thanks also for your message. Your conclusion is puzzling, i.e. it seems to 
contradict some statements found in the .cpp and .hpp linked by Jerome above.

Indeed in [2] at line 60 I read  
"b->id=-1;//else it sits in the python scope without a chance to be 
inserted again"

And in [1] at line 22 I read

 "Container of bodies implemented as flat std::vector. It handles body removal 
and
 intelligently reallocates free ids for newly added ones. 
 The nested iterators and the specialized FOREACH_BODY macros above will 
silently skip null body pointers which may exist after 
 removal. The null pointers can still be accessed via the [] operator. "


One explanation could be that your example is too small, i.e. the engine
of shared_ptr allocation does not reuse old (freed) memory until it is
really necessary, that is after many new insertions. As soon as I have
time I will try to conceive a modification of Jan's example with a much
larger number of bodies deleted and inserted.

Any other ideas?

Thanks a lot to everybody for the prompt help

Andrea


[1] https://github.com/yade/trunk/blob/master/core/BodyContainer.hpp
[2] https://github.com/yade/trunk/blob/master/core/BodyContainer.cpp

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Re: [Yade-users] [Question #657637]: Applying confinement (rigid boundary) to a cylindrical sample

2017-09-06 Thread Jan Stránský
Question #657637 on Yade changed:
https://answers.launchpad.net/yade/+question/657637

Jan Stránský proposed the following answer:
Hi,

> O.forces.addF(f.id,preStress*a*n) --> I am confused about the
application of forces using the facetcylinder as a whole. The
(f.id,Prestress*a*n) used here is when we apply forces through each
facet.

You can apply force to the cylinder as a whole, but then it would not
apply confining pressure, but tried to move as a rigid body in the
direction of the force, so very different result than confining
boundary..

> In order to apply force from the facetcylinder as a whole (such that
each facet does the same) can I use: O.forces.addF(facets.id,0.20)
where, for e.g., 0.20 represents the magnitude of force(stress) applied.

no
- facets.id would give error as facets is a list of bodies, not body.
- O.forces.addF accepts vector, not only magnitude

Jan

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Re: [Yade-users] [Question #657126]: Performing a penetration test

2017-09-06 Thread Swapnil
Question #657126 on Yade changed:
https://answers.launchpad.net/yade/+question/657126

Swapnil posted a new comment:
[1] is still on mate ;)

I have been trying to save it as you said but I am getting errors with the 
syntax.
Will reattempt on Monday..

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Re: [Yade-users] [Question #657637]: Applying confinement (rigid boundary) to a cylindrical sample

2017-09-06 Thread Swapnil
Question #657637 on Yade changed:
https://answers.launchpad.net/yade/+question/657637

Swapnil posted a new comment:
Would be trying the rest on Monday when I return to the system ;)

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Re: [Yade-users] [Question #657637]: Applying confinement (rigid boundary) to a cylindrical sample

2017-09-06 Thread Swapnil
Question #657637 on Yade changed:
https://answers.launchpad.net/yade/+question/657637

Swapnil posted a new comment:
Yes mate it works with the inclusion of those engines. Foolishly, I completely 
forgot about those for the new facet bodies.
Thanks :)


Yes, I am first trying the static boundary case ( where the material of the 
facetCylinder itself holds the spheres intact). Thanks to you, that appears to 
work successfully now.


As you are suggesting, for the active confining pressure case we can directly 
use the facetCylinder as one body and apply the desired stress, isn't it? Then 
should I try the following in addition to [1]:


 facets.state.blockedDOFs='XYZz'  --> this command seems okay

O.forces.addF(f.id,preStress*a*n)--> I am confused about the
application of forces using the facetcylinder as a whole. The
(f.id,Prestress*a*n) used here is when we apply forces through each
facet. In order to apply force from the facetcylinder as a whole (such
that each facet does the same) can I use:  O.forces.addF(facets.id,0.20)
where, for e.g., 0.20 represents the magnitude of force(stress) applied.

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Re: [Yade-users] [Question #657637]: Applying confinement (rigid boundary) to a cylindrical sample

2017-09-06 Thread Jan Stránský
Question #657637 on Yade changed:
https://answers.launchpad.net/yade/+question/657637

Jan Stránský proposed the following answer:
> I do not want the spheres to move out of the boundary

in both cases, you will have to use different engines, namely Bo1_Facet,
Ig2_Facet_Sphere, see [2]

> Using [1] creates a default set of facets and combines them to form a
cylindrical boundary of the prescribed dimensions. Isn't it?

yes

>On the other hand in [2], the user is creating facets (using vectors)
and then combining them followed by application of pre defined
stresses(confining pressure). My question here is can this operation be
performed like in [1]? that is using a simpler way to create facets and
then applying stresses.

yes, you can use facetCylinder and then apply force on resulting facets
in the same way as in [2]

> In short, I am looking for a simpler way to perform the application of
laterally confining pressures.

Do you really want active confining pressure? Wouldn't static boundary
be enough? At least for beginning, I would try the static boundary..

cheers
Jan

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Re: [Yade-users] [Question #657637]: Applying confinement (rigid boundary) to a cylindrical sample

2017-09-06 Thread Swapnil
Question #657637 on Yade changed:
https://answers.launchpad.net/yade/+question/657637

Swapnil posted a new comment:
Thanks Jan.
Option [1] leads to the movement of spheres out of the boundary (I tried the 
script). I do not want the spheres to move out of the boundary. Therefore, I 
would have to go for application of lateral confining pressure. That you say is 
depicted in [2]. 


# facets division
nw = 24,
nh = 15,

# facets
facets = []
if testType == 'cyl':
rCyl2 = .5*width / cos(pi/float(nw))
for r in xrange(nw):
for h in xrange(nh):
v1 = Vector3( rCyl2*cos(2*pi*(r+0)/float(nw)), 
rCyl2*sin(2*pi*(r+0)/float(nw)), height*(h+0)/float(nh) )
v2 = Vector3( rCyl2*cos(2*pi*(r+1)/float(nw)), 
rCyl2*sin(2*pi*(r+1)/float(nw)), height*(h+0)/float(nh) )
v3 = Vector3( rCyl2*cos(2*pi*(r+1)/float(nw)), 
rCyl2*sin(2*pi*(r+1)/float(nw)), height*(h+1)/float(nh) )
v4 = Vector3( rCyl2*cos(2*pi*(r+0)/float(nw)), 
rCyl2*sin(2*pi*(r+0)/float(nw)), height*(h+1)/float(nh) )
f1 = facet((v1,v2,v3),color=(0,0,1),material=frictMat)
f2 = facet((v1,v3,v4),color=(0,0,1),material=frictMat)
facets.extend((f1,f2))
O.bodies.append(facets)
mass = O.bodies[0].state.mass
for f in facets:
f.state.mass = mass
f.state.blockedDOFs = 'XYZz'

# apply prestress to facets
def addForces():
for f in facets:
n = f.shape.normal
a = f.shape.area
O.forces.addF(f.id,preStress*a*n)


As I can understand from reading this:

Using [1] creates a default set of facets and combines them to form a 
cylindrical boundary of the prescribed dimensions. Isn't it?
On the other hand in [2], the user is creating facets (using vectors) and then 
combining them followed by application of pre-defined stresses(confining 
pressure). My question here is can this operation be performed like in [1]? 
that is using a simpler way to create facets and then applying stresses. 

For e.g something like (just an idea to keep it simple):

#create facet sets and combine them to form a cylindrical shaped
boundary around the sample.

facets = geom.facetCylinder((0,0,0.125),0.1,0.25,wallMask=2|4)
O.bodies.append(facets)   

# for all facets block restrain the desired motion 
facets.state.blockedDOFs='XYZz'   

#apply prestress to each one
O.forces.addF(f.id,preStress*a*n)

In short, I am looking for a simpler way to perform the application of
laterally confining pressures.

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Re: [Yade-users] [Question #656657]: tension test on grids

2017-09-06 Thread Jan Stránský
Question #656657 on Yade changed:
https://answers.launchpad.net/yade/+question/656657

Jan Stránský posted a new comment:
Hello,
I have tried your script. The "instant" velocity you see is due to gravity. You 
don't see the effect of the "permanent" velocity, because for some reason 
state.dynamic=False does not have desired effect here
use gravity=(0,0,0) if you find it irrelevant in your calibration and inside 
history1:
O.bodies[i].state.blockedDOFs='xyzXYZ' # instead of 
O.bodies[i].state.dynamic=False
cheers
Jan

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Re: [Yade-users] [Question #656657]: tension test on grids

2017-09-06 Thread Launchpad Janitor
Question #656657 on Yade changed:
https://answers.launchpad.net/yade/+question/656657

Status: Open => Expired

Launchpad Janitor expired the question:
This question was expired because it remained in the 'Open' state
without activity for the last 15 days.

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Re: [Yade-users] [Question #657637]: Applying confinement (rigid boundary) to a cylindrical sample

2017-09-06 Thread Jan Stránský
Question #657637 on Yade changed:
https://answers.launchpad.net/yade/+question/657637

Status: Open => Answered

Jan Stránský proposed the following answer:
Hello,
you can use walls or facets or boxes. See e.g. [1] for static boundary or [2] 
for active boundary applying lateral confining pressure.
cheers
Jan

###
from yade import pack, geom
pred = pack.inCylinder((0,0,0),(0,0,0.25),0.10)
sp = pack.randomDensePack(pred,radius=0.01,spheresInCell=300)
O.bodies.append(sp)
facets = geom.facetCylinder((0,0,0.125),0.1,0.25,wallMask=2|4)
O.bodies.append(facets)
###

[1] https://yade-dem.org/doc/yade.geom.html#yade.geom.facetCylinder
[2] https://github.com/yade/trunk/blob/master/examples/concrete/triax.py

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[Yade-users] [Question #657637]: Applying confinement (rigid boundary) to a cylindrical sample

2017-09-06 Thread Swapnil
New question #657637 on Yade:
https://answers.launchpad.net/yade/+question/657637

How can we apply a confining cylindrical boundary to a cylindrical
arrangement (packing) of the spheres ( in order to constrain the motion of
spheres outwards when a compressive load is applied) ? I have been searching 
but can only find information
about 'Wall'.

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Re: [Yade-users] [Question #657560]: Plotting force & displacement of impactor in a penetration test

2017-09-06 Thread Jan Stránský
Question #657560 on Yade changed:
https://answers.launchpad.net/yade/+question/657560

Jan Stránský proposed the following answer:
This time the question is completely unrelated to Plotting force & 
displacement, so next time please open a new question.
https://github.com/yade/trunk/blob/master/examples/concrete/triax.py
Jan

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Re: [Yade-users] [Question #657564]: continuous creation and destruction of bodies

2017-09-06 Thread Jan Stránský
Question #657564 on Yade changed:
https://answers.launchpad.net/yade/+question/657564

Jan Stránský posted a new comment:
Hi guys,
just a theoretical comment concerning O.bodies.erase,. The memory of erased 
body is freed, but the space in BodyContainer remains (O.bodies.append does not 
reuse ids) and the size of BodyContainer itself is continuously increasing. So 
with continuous adding and deleting bodies, the simulation theoretically cannot 
be run indefinitely, but practically yes :-)
cheers
Jan

###
sphs = [sphere((2*i,0,0),1) for i in (0,1,2,3,4)]
s0,s1,s2,s3,s4 = sphs

O.bodies.append(s0)
O.bodies.append(s1)
O.bodies.append(s2)

print O.bodies[0], O.bodies[0].id
print O.bodies[1], O.bodies[1].id
print O.bodies[2], O.bodies[2].id
print len(O.bodies), len([b for b in O.bodies])

O.bodies.erase(0)
print len(O.bodies), len([b for b in O.bodies])
O.bodies.erase(1)
print len(O.bodies), len([b for b in O.bodies])
O.bodies.erase(2)
print len(O.bodies), len([b for b in O.bodies])

O.bodies.append(s3)
O.bodies.append(s4)
print len(O.bodies), len([b for b in O.bodies])
print O.bodies[0]
print O.bodies[4], O.bodies[4].id
###

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Re: [Yade-users] [Question #657564]: continuous creation and destruction of bodies

2017-09-06 Thread Andrea Puglisi
Question #657564 on Yade changed:
https://answers.launchpad.net/yade/+question/657564

Andrea Puglisi posted a new comment:
Thanks to both Duriez and Caulk, your answers seem very useful. I study
them and I will let you know if everything is ok (as it seems from your
discussion).

Andrea

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Re: [Yade-users] [Question #657560]: Plotting force & displacement of impactor in a penetration test

2017-09-06 Thread Swapnil
Question #657560 on Yade changed:
https://answers.launchpad.net/yade/+question/657560

Swapnil posted a new comment:
Thanks Jan, you saved me again :-) That part works now.

How can we apply a confining cylindrical boundary to the cylindrical
arrangement of the spheres here ( in order to constrain the motion of
spheres outwards) ? I have been searching but can only find information
about 'Wall'?

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Re: [Yade-users] [Question #657126]: Performing a penetration test

2017-09-06 Thread Jan Stránský
Question #657126 on Yade changed:
https://answers.launchpad.net/yade/+question/657126

Jan Stránský proposed the following answer:
> Also, how does one reach the file where the data is stored?

after the simulation, you can save data with

plot.saveDataTxt(fileName)

then you simply reach it in the location you specified, e.g.
'results.dat' would be save to the directory from where you started
yade, '/tmp/results.dat' to /tmp directory, '/home/swapnil/mydir' would
save it there etc.

Is the rest of the question solved in [1]?
cheers
Jan

[1] https://answers.launchpad.net/yade/+question/657560

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Re: [Yade-users] [Question #657560]: Plotting force & displacement of impactor in a penetration test

2017-09-06 Thread Jan Stránský
Question #657560 on Yade changed:
https://answers.launchpad.net/yade/+question/657560

Jan Stránský proposed the following answer:
Once again, take care of errors :-)

I got:
TypeError
...
---> 14   Dz=hammer.state.displ[2]

should be Dz=hammer.state.displ()[2] # state.displ() is a fanction,
therefore called by (), than you can extract z component by [2]

cheers
Jan

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Re: [Yade-users] [Question #657560]: Plotting force & displacement of impactor in a penetration test

2017-09-06 Thread Swapnil
Question #657560 on Yade changed:
https://answers.launchpad.net/yade/+question/657560

Swapnil posted a new comment:
Hi Jerome, thanks a lot for the correction. Now, it runs and I can see
the plot window but I cannot see any changes occuring0 on the plot.
Looks like the values are not updated on the plot somehow. Where could I
be going wrong with the script?

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