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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