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[rhaven <question645503@xxxxxxxxxxxxxxxxxxxxx>]

New question #645503 on Yade:
https://answers.launchpad.net/yade/+question/645503

Hi There,
I am working on generating a compressed packing of aggregates.  I am currently using /examples/agglomerate as a basis. 
I am using makeClumpCloud to fill a cuboid with clumps which I generated. Then I would like to run them through /examples/agglomerate/compress.py and generate a dense packing of these aggregates. 

I would like the method to work for just a few aggregates as well as for a larger number. 
The result using just a few looks like http://pasteall.org/pic/index.php?id=116817 
(When I generate a larger number of particles things look better http://pasteall.org/pic/index.php?id=116816)

As you see from the first image, there are fewer particles left after the compression. Why is this the case? 

Does this have something to do with periodicity? Am I only seeing some of the particles? If so, how do I export all particles within my volume. 
In case I am going about this wrong, how should I generate the packing of aggregates and then compress them such that I end up with a cuboid of packed aggregates (when the total number of particles is ~200)

many thanks in advance!
Jesse

the compress code is shown below. 





from yade import export,ymport
	import random
	random.seed(1)

	# add walls first
	#dim = (15,15,15)
	dim = (1e-6,1e-6,1e-6)
	walls = aabbWalls(((0,0,0),(dim)))
	wallIds = O.bodies.append(walls)

	# load spheres from file, including information of their agglomerates ids
	attrs = []
	sp = ymport.textExt('/tmp/divided.txt',format='x_y_z_r_attrs',attrs=attrs)
	n = max(int(a[0]) for a in attrs)+1
	colors = [randomColor() for _ in xrange(n)]
	agglomerates = [[] for _ in xrange(n)]
	for s,a in zip(sp,attrs):
		aa = int(a[0])
		s.agglomerate = aa
		s.shape.color = colors[aa]
		agglomerates[aa].append(s)
	for a in agglomerates:
		O.bodies.appendClumped(a)

	#getClumpInfo()


	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
	#compressor.goal1 = compressor.goal2 = compressor.goal3 = 1e-10
	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'])



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