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[Irfaan Peerun <question683388@xxxxxxxxxxxxxxxxxxxxx>]

Question #683388 on Yade changed:
https://answers.launchpad.net/yade/+question/683388

Irfaan Peerun gave more information on the question:
Just an update:

I have managed to convert the .stl file to .gts using the following command: stl2gts -r < filename.stl > filename.gts
gmsh and libgts-bin need to be installed to do so.

So now I have a surface which was imported in .gts format using the
command: surf=gts.read(open('filename.gts'))

My next step is to fill the surface with spheres of various sizes and
clump them together to produce a body of the same volume and geometry as
the surface. This would require overlapping of spheres.

I used the pack.randomDensePack function with sphere radius=0.00005 and
realfuzz=0.000005. The average range diameter of the surface 2.36mm to
1.18mm.  Hence, my questions are:

[1] Is the pack.randomDensePack function appropriate for this situation?
Any rule of thumb in deciding the sphere radius? Does the function
include overlapping of spheres?

[2] By adding memoizeDb='/tmp/gts-packings.sqlite', does it mean that a
temporary sqlite file will be created to store the packing that will be
generated?

[3] Is there any function to obtain the clump volume as comparison to
the imported gts surface.

When running the script, I received the following error along with a blank view (no sphere or surface):
WARN  /build/yade-fDuCoe/yade-2018.02b/pkg/common/InsertionSortCollider.cpp:242 action: verletDist is set to 0 because no spheres were found. It will result in suboptimal performances, consider setting a positive verletDist in your script.

Appreciate if anyone could guide me in solving this. The script is as
follows:

# ========= Script ===================
from yade import pack,ymport
import gts

#Add material for spheres
m=FrictMat(young = 1E8, poisson = 0.25, frictionAngle = 0.0, density = 2650)

# import surface
surf=gts.read(open('/home/Desktop/SphereClumping/sample.gts'))

# parameters for radom packing in imported surface
memoizeDb='/tmp/gts-packings.sqlite'
sp=SpherePack()

# generate lists of spheres and outer surface
if surf.is_closed():
 O1=O.bodies.append(pack.gtsSurface2Facets(surf,fixed=False,noBound=True,material=m))
 sp=pack.randomDensePack(pack.inGtsSurface(surf),radius=0.00005,rRelFuzz=0.000005,memoizeDb=memoizeDb,returnSpherePack=True)
 Otemp=sp.toSimulation()
 
 #clump spheres and surface together
 idClump=O.bodies.clump(Otemp)

O.engines=[
   ForceResetter(),
   InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),
   InteractionLoop(
      # handle sphere+sphere and facet+sphere collisions
      [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()],
      [Ip2_FrictMat_FrictMat_FrictPhys()],
      [Law2_ScGeom_FrictPhys_CundallStrack()]
   ),
 NewtonIntegrator(gravity=(0,0,-9.81),damping=0.4),
]

# set timestep to a fraction of the critical timestep
O.dt=0.5*PWaveTimeStep()

# save the simulation, so that it can be reloaded later, for experimentation
O.saveTmp()

from yade import qt
qt.View()

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