New question #628595 on Yade:
https://answers.launchpad.net/yade/+question/628595
Hi everybody,
I have been using the agglomerate examples that can be found in the docs from
yadedaily, in order to generate a packed sample of clumped particles. In the
example this was done in three scripts (Makecloud, divide and compress) ,
creating at the end of each file a temporary file that was reloaded in the
subsequent simulation.
I figured that I would like to have those three scripts all in one go, in order
to launch this simulation, have the package and then save it to be used in
other simulations.
But I am having trouble when it comes to actually clump assemblies of particle.
The strange thing is I haven't been changing much of the existing code !
The code creates a list of groups of spheres, which are to be later on
assembled in a clump.
So the spheres are added one after another, based on their agglomerate number,
that has been set previously by creating an initial sphere pack, and then
packing in each of the spheres another sphere pack. So the agglomerate number
would be the id of the initials bigger spheres, I guess.
Once they are all stored in the same occurence of the list, each element of the
list ( that is, each group of spheres), is called in order to be clumped.
and then I get this error :
Traceback (most recent call last):
File "/usr/bin/yadedaily", line 182, in runScript
execfile(script,globals())
File "agglomerate.py", line 74, in <module>
O.bodies.appendClumped(g)
IndexError: Body already has id 0 set; appending such body (for the second
time) is not allowed.
I am not sure what this means, but it seems like the program is trying to
append the spheres once again, when they are already in the simulation. But
that results strange to me, since I thought the appendClumped function could
work with existing spheres..
Here is the full script :
# -*- coding: utf-8 -*-
from yade import export
from yade import export,ymport
import random
def getClumpInfo():
for b in O.bodies:
if b.isClump:
print 'Clump ',b.id,' has following members:'
keys = b.shape.members.keys()
for ii in range(0,len(keys)):
print '- Body ',keys[ii]
print 'inertia:',b.state.inertia
print 'mass:',b.state.mass,'\n'
else:
print 'no clumps'
dim = (15,15,15) # dimensions for makeCloud
radius = 1
fuzz = 0.2
# use of makeCloud function
sp = pack.SpherePack()
sp.makeCloud((0,0,0), dim, rMean=radius, rRelFuzz=fuzz, seed=1)
random.seed(1) # to make colors always the same
attrs = []
colors = [randomColor() for s in sp]
# each macroparticle is filled randomDensePack
for si,s in enumerate(sp):
sphere = pack.inSphere(s[0],s[1])
sp1 = pack.randomDensePack(
sphere,
spheresInCell = 500,
radius = .2,
memoizeDb = '/tmp/agglomeratepackaux.db',
returnSpherePack = True,
)
ids = sp1.toSimulation(color=colors[si]) # add the result to simulation
with uniform color
for i in ids:
O.bodies[i].agglomerate = si # tell each particle who is its
agglomerate
attrs.append(O.bodies[i].agglomerate)
#random.seed(1)
sp2 = []
for b in O.bodies :
sp2.append(b)
# add walls first
dim = (15,15,15)
walls = aabbWalls(((0,0,0),(dim)))
wallIds = O.bodies.append(walls)
# clump agglomerates
n = max(a for a in attrs)+1
colors = [randomColor() for _ in xrange(n)]
agglomerates = [[] for _ in xrange(n)]
for s,a in zip(sp2,attrs):
aa = a
s.agglomerate = aa
s.shape.color = colors[aa]
agglomerates[aa].append(s)
for g in agglomerates:
O.bodies.appendClumped(g)
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()]
),
TriaxialStressController(
thickness = 0,
stressMask = 7,
internalCompaction = False,
label = 'compressor',
),
NewtonIntegrator(damping=.6),
]
O.dt = PWaveTimeStep()
# compress the sample
compressor.goal1 = compressor.goal2 = compressor.goal3 = -1e-7
O.run(50000,True)
compressor.goal1 = compressor.goal2 = compressor.goal3 = -1e-5
O.run(30000,True)
# save the result, including information of agglomerates which the particle
belongs to
export.textExt('/tmp/compressed.txt','x_y_z_r_attrs',attrs=['b.agglomerate'])
try:
from yade import qt
qt.View()
except:
pass
Welle, if anybody has an idea, it would be of great help !
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