Question #665540 on Yade changed:
https://answers.launchpad.net/yade/+question/665540

    Status: Open => Solved

JOHN confirmed that the question is solved:
minimal working example follows


def run(name,boundaries,r,gap,numStepsPerIteration):


                facets = ymport.stl(name)

                rod1 = O.bodies.append(facets)



                # converts facets to gts (see the other question)

                s = gts.Surface()

                for facet in facets:

                   vs = [facet.state.pos + facet.state.ori*v for v in
facet.shape.vertices]

                   vs = [gts.Vertex(v[0],v[1],v[2]) for v in vs]

                   es = [gts.Edge(vs[i],vs[j]) for i,j in
((0,1),(1,2),(2,0))]

                   f = gts.Face(es[0],es[1],es[2])

                   s.add(f)

                print s.is_closed()

                threshold = 1e-3

                s.cleanup(threshold)

                print s.is_closed()

                assert s.is_closed()

                # use gts to filter spheres

                pred = inGtsSurface(s)




                


sp=pack.regularHexa(pack.inAlignedBox((boundaries[0],boundaries[2],boundaries[4]),(boundaries[1],boundaries[3],boundaries[5])),radius=r,gap=gap)



                # remove spheres completely inside walls

                for b in sp:

                   if pred(b.state.pos,0):

                      continue

                   O.bodies.append(b)


                # remove spheres partially inside walls

                O.dt = 0

                O.step() # interactions are created afterwards

                toErase = set()

                for i in O.interactions:

                   b1,b2 = [O.bodies[i] for i in (i.id1,i.id2)]

                   if any(isinstance(b.shape,Facet) for b in (b1,b2)): #
if facet is involved, delete

                      toErase.add(b1)

                      toErase.add(b2)

                toErase = [b for b in toErase if
isinstance(b.shape,Sphere)] # delete just spheres


                if not restart:

                        for b in toErase: # delete the spheres

                           O.bodies.erase(b.id)


                #generate the initial global index list

                for b in O.bodies:

                    if isinstance(b.shape,Sphere):

                        loc2glob.append(b.id)




                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,-9.81,0),damping=0.4,
label='newtonInt'),







                ]

                O.dt=.8*PWaveTimeStep()

                O.step()

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