New question #692476 on Yade:
https://answers.launchpad.net/yade/+question/692476

How to define geometry in case of flow around a cylinder?
If you set the geometry the way I do it, then the time step becomes nan.

###
def __init__(self):
                O.periodic = True
                O.cell.setBox(0.4,0.4,0.4)

                numspheres=1000
                young = 5e6
                density = 1000

                mat1 = 
FrictMat(young=young,poisson=0.5,frictionAngle=radians(15),density=density,label='spheremat')
                O.materials.append(mat1)
                mat2 = 
FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='wallmat')
                O.materials.append(mat2)

                epsilon = 1e-08
                minval = 0 + epsilon
                maxval = 0.4 - epsilon
                #wall coords, use facets for wall BC:
                v0 = Vector3(minval, minval, minval)
                v1 = Vector3(minval,minval,maxval)
                v2 = Vector3(maxval,minval,minval)
                v3 = Vector3(maxval,minval,maxval)

                v4 = Vector3(minval,maxval,minval)
                v5 = Vector3(minval,maxval,maxval)
                v6 = Vector3(maxval,maxval,minval)
                v7 = Vector3(maxval, maxval, maxval)

                lf0 = facet(vertices=[v0,v1,v2], material='wallmat')
                O.bodies.append(lf0)
                lf1 = facet(vertices=[v0,v2,v3], material='wallmat')
                O.bodies.append(lf1)

                uf0 = facet(vertices=[v4,v5,v6], material='wallmat')
                O.bodies.append(uf0)
                uf1 = facet(vertices=[v4,v6,v7], material='wallmat')
                O.bodies.append(uf1)

                ff0 = facet(vertices=[v1,v2,v6], material='wallmat')
                O.bodies.append(ff0)
                ff1 = facet(vertices=[v1,v6,v5], material='wallmat')
                O.bodies.append(ff1)

                bf0 = facet(vertices=[v0,v3,v7], material='wallmat')
                O.bodies.append(bf0)
                bf1 = facet(vertices=[v0,v7,v4], material='wallmat')
                O.bodies.append(bf1)

                ######cylinder######
                cyl = Cylinder(segment=[0,0,1],radius=0.05)
                b = Body()
                b.shape = cyl
                b.mat = O.materials['wallmat']
                O.bodies.append(b)

                #spheres
                mn, mx= Vector3(minval + epsilon, minval + epsilon, minval + 
epsilon), Vector3(-0.06, maxval - epsilon, maxval - epsilon)
                sp = pack.SpherePack();
                sp.makeCloud(mn,mx,rMean=0.00075,rRelFuzz=0.10, num=numspheres)
                O.bodies.append([sphere(center,rad,material='spheremat') for 
center,rad in sp])
                sphereIDs = [b.id for b in O.bodies if type(b.shape)==Sphere]

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