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[Jan Stránský <question290950@xxxxxxxxxxxxxxxxxxxxx>]

Question #290950 on Yade changed:
https://answers.launchpad.net/yade/+question/290950

Jan Stránský proposed the following answer:
The script works fine for me (at least nothing disappears).
What version of Yade do you use?
What is the output of "O.bodies[top_id].state.mass" and
"O.bodies[top_id].state.inertia"?
thanks
Jan


2016-04-26 2:21 GMT+02:00 VG <question290950@xxxxxxxxxxxxxxxxxxxxx>:

> Question #290950 on Yade changed:
> https://answers.launchpad.net/yade/+question/290950
>
> VG posted a new comment:
> Thanks Jan!
> I modified the generation of top and bottom boxes as you suggested. The
> boxes seem to be generated the way they should be. However, as soon as the
> simulation starts, those boxes just disappear. I am not sure what is
> causing this behavior. Here is the updated MWE script:
>
>
> # Generate a periodic cell with few super-particles.
> # Each superparticle consists of smaller sub-particles of 75 microns
> # bonded with cohesive bonds.
>
> from yade import pack,qt,plot,utils,export,ymport
> from math import *
> from pylab import rand
> import datetime
> import os,shutil
>
>
> #############################################################################
> # Set up run
>
> #############################################################################
> run_name="PeriodicCohesive_MWE"
> data_root_dir="."
> if not os.path.exists(data_root_dir):
>   print "The data root directory you specified:"
>   print data_root_dir
>   print "does not exist. Exiting..."
>   exit()
> timestamp=datetime.datetime.now().strftime("%Y.%m.%d-%H%M%S")
> run_dir_name=timestamp+'-'+run_name
> data_dir_path=os.path.join(data_root_dir,run_dir_name)
> if not os.path.exists(data_dir_path):
>   os.makedirs(data_dir_path)
> else:
>   print("Something is really wrong if you get this message. Exiting...\n")
>   exit()
>
> run_name_base_path=os.path.join(data_dir_path,run_name+'-')
> # opts.script is defined in yade, which inserts the script file (e.g.
> # this file) into itself.
> this_script=os.path.abspath(opts.script)
> shutil.copy(this_script,data_dir_path)
>
>
>
> #############################################################################
> # Materials
>
> #############################################################################
> plate_material=CohFrictMat(
>     young=200e9
>    ,poisson=0.3
>    ,density=8000
>    ,frictionAngle=radians(30)
>    ,normalCohesion=1e10
>    ,shearCohesion=1e10
>    ,momentRotationLaw=True
>    ,label='plate_mat')
> O.materials.append(plate_material)
>
>
> sample_material=CohFrictMat(
>     young=4e9
>    ,poisson=0.25
>    ,density=1400
>    ,frictionAngle=radians(30)
>    ,normalCohesion=1e8*1.2
>    ,shearCohesion=.4e8*1.2
>    ,momentRotationLaw=True
>    ,label='sample_mat')
> O.materials.append(sample_material)
>
>
>
> #############################################################################
> # Component dimensions and operating condition
>
> #############################################################################
> # Granular material dimension
> sample_diameter=2e-4
> sample_radius=sample_diameter/2.0
> # Sub-particle dimension
> particle_diameter=74.e-6
> particle_radius=particle_diameter/2.
>
>
> #############################################################################
> # grinding plate dimension
>
> #############################################################################
>
> rotvel=2./3.*pi*(1.5+0.5)*.254
>
>
> #############################################################################
> # Periodic Geometry
>
> #############################################################################
>
>
> # Set up periodic boundary conditions
> O.periodic=True
> xExt=4*sample_diameter
> yExt=3.*sample_diameter*2 #to block the periodicity in y direction
> zExt=xExt
> xLim=xExt
> yLim=yExt/4
> zLim=zExt
> O.cell.hSize=Matrix3(
>   xExt, 0, 0,
>   0, yExt, 0,
>   0, 0, zExt)
>
>
> length=xExt
> height=yExt
> width=zExt
>
> # Top and bottom plate thickness
> thickness=0.1*height
>
>
> #########
> # Bottom
> #########
> #bottom=box(
> #    center=(length/2.0,yLim - thickness/2.0,width/2.0)
> #   ,extents=(4*length,thickness/2.0,width)
> #   ,wire=False
> #   ,material='plate_mat'
> #   )
>
> bottomBoxes = []
> for ix in (0,1,2):
>  for iz in (0,1,2):
>    bottomBoxes.append(box( # create 3x3 boxes with 1/3 cell size
>    center=(xExt/6.*(1+2*ix),yLim - thickness/2.0,zExt/6.*(1+2*iz))
>    ,extents=(xExt/6.,thickness/2.0,zExt/6.)
>    ,wire=False
>    ,material='plate_mat'
>    ))
>
> bottom_id,bottom_ids = O.bodies.appendClumped(bottomBoxes) # bottom_id
> is the clump id,
>
>
> O.bodies[bottom_id].state.blockedDOFs='xyzXYZ'
>
>
>
> #############################################################################
> # Particle Packing
>
> #############################################################################
>
> min_corner= (0,yLim,0)
> max_corner= (xLim, yExt-yLim, zLim)
>
> sp=pack.SpherePack()
> sp.makeCloud( min_corner,max_corner, rMean=sample_radius, periodic=False)
>
> print "Generated ",len(sp)," aggregates"
>
> ###########################################
> # Sample
> ###########################################
> for s in sp:
>   sphere=pack.inSphere((s[0][0],s[0][1],s[0][2]),s[1])
>   sp1=pack.randomDensePack(
>       sphere
>      ,spheresInCell=2000
>      ,radius=particle_radius
>      ,memoizeDb='/tmp/triaxPackCache.sqlite'
>      ,returnSpherePack=True
>      )
>
>   sp1.toSimulation(material='sample_mat',color=(0.9,0.8,0.6))
>   print 'Generated ',len(sp1),' particles'
>
> Gl1_Sphere(stripes=True)
>
> #########
> # Top
> #########
> #top=box(
> #    center=(length/2.0,yExt - yLim + thickness*2,width/2.0)
> #   ,extents=(0.16*length,thickness/2.0,0.16*width)
> #   ,wire=False
> #   ,material='plate_mat'
> #   )
>
> #top_id=O.bodies.append(top)
>
> #########
>  # Top
> #########
> topBoxes = []
> for ix in (0,1,2):
>  for iz in (0,1,2):
>    topBoxes.append(box( # create 3x3 boxes with 1/3 cell size
>    center=(xExt/6.*(1+2*ix),yExt - yLim + thickness/2.0,zExt/6.*(1+2*iz))
>    ,extents=(xExt/6.,thickness/2.0,zExt/6.)
>    ,wire=False
>    ,material='plate_mat'
>    ))
>
> top_id,top_ids = O.bodies.appendClumped(topBoxes) # top_id is the clump
> id,
>
>
> O.bodies[top_id].state.blockedDOFs='xzXYZ'
>
>
> plate_downforce=-0.0036
>
> O.forces.addF(top_id,(0,plate_downforce,0),permanent=True)
>
> O.bodies[top_id].state.vel[0]= rotvel
>
>
>
> #############################################################################
> # Run the simulation
>
> #############################################################################
>
>
> O.dt=0.5*PWaveTimeStep()
>
> O.engines=[
>   ForceResetter(),
>   InsertionSortCollider([
>     Bo1_Sphere_Aabb()
>    ,Bo1_Box_Aabb()
>    ], allowBiggerThanPeriod=True
>    ),
>   InteractionLoop(
>     [Ig2_Sphere_Sphere_ScGeom6D()
>     ,Ig2_Box_Sphere_ScGeom6D()
>     ],
>     [
>
>  Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,label="cohesiveIp")
>     ],
>     [
>      Law2_ScGeom6D_CohFrictPhys_CohesionMoment()
>     ]
>   ), # End InteractionLoop
>   NewtonIntegrator(damping=0.8,gravity=(0.,0.,0.)),
>
> ]
>
> O.saveTmp()
>
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