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[Jan Stránský <question229898@xxxxxxxxxxxxxxxxxxxxx>]

Question #229898 on Yade changed:
https://answers.launchpad.net/yade/+question/229898

    Status: Open => Answered

Jan Stránský proposed the following answer:
Hello,

if you comment O.run(), you may see the particles and all walls before
simulation starts. After running one step, all particles AND 4 walls (out
of 6) disappears.. If you print

for b in O.bodies: print b.state.pos

you will see that most of the positions are full of NaN. I would guess,
that it is caused somehow by TriaxialStressController (perhaps by wrong
parameters??), but just now I can't say anything more. maybe somebody else
could? :-)

Jan


2013/6/3 Fu zuoguang <question229898@xxxxxxxxxxxxxxxxxxxxx>

> Question #229898 on Yade changed:
> https://answers.launchpad.net/yade/+question/229898
>
> Fu zuoguang gave more information on the question:
> Dear Jan Stránský and Bruno Chareyre:
>      Thanks for helping me last time, so in order to achieve "clumps in 2D
> simulation", I should try my best to test "particles-generation from PFC to
> YADE", but at the beginning of this task, I failed to import the "particles
> information.txt" to YADE and the question can be described as that:
> (1). There is a "particles information.txt" recording the basic infomation
> about the particles with the format "x_y_z_r", there is nothing wrong in it.
> (2). I employ these orders "O.bodies.append(ymport.text('qq.txt'))" to
> make a correct importing.
> (3). After importing finished(all the particles can be recogized by
> YADE),I wanna start my 2D-simulation but fail, because all the particles
> disaapear at the beginning of simulation, so I can see nothing but the
> walls in screen.
> (4). there may be something wrong in my script, since the importing order
> can be sucessfully used in examples provided by YADE.
> I don know where is wrong and seek your help!(all script and sphere.txt
> are below)
>
> Filename='2D-simulation-vertex'
> from yade import pack,os,utils,ymport
>
> ################################# preprocessing for simulation
> ##########################################
> ### prescribing variables and functions for simulation controller ###
> # material defination
> spheremat =
> O.materials.append(FrictMat(poisson=0.5,density=2500,young=1e10,frictionAngle=0.5))
> wallmat =
> O.materials.append(FrictMat(poisson=0.5,density=0,young=1e10,frictionAngle=0))
> # walls defination
> mn,mx=Vector3(0,0,0),Vector3(0.06,0.06,0.1)
>
> wallids=O.bodies.append(utils.aabbWalls([mn,mx],thickness=.00001,material=wallmat))
> # ThreeDTriaxialEngine defination for initial-state determination(the
> first calculation step)
> triax01=TriaxialStressController(
>         wall_bottom_id=wallids[2],wall_top_id=wallids[3],
>         wall_left_id=wallids[0],wall_right_id=wallids[1],
>         wall_back_id=wallids[4],wall_front_id=wallids[5],
>         wall_front_activated = False,wall_back_activated = False,
>         internalCompaction=False,
>         stressMask=7,
>         goal1=30000,
>         goal2=30000,
>         goal3=30000,
>         max_vel=5,
> )
> # ThreeDTriaxialEngine defination for triaxial compression(the second
> calculation step)
> triax02=TriaxialStressController(
>         wall_bottom_id=wallids[2],wall_top_id=wallids[3],
>         wall_left_id=wallids[0],wall_right_id=wallids[1],
>         wall_back_id=wallids[4],wall_front_id=wallids[5],
>         wall_front_activated = False,wall_back_activated = False,
>         internalCompaction=False,
>         stressMask = 5,
>         goal2=-100,
>         goal1=30000,
>         goal3=30000,
> )
> ################################# control flow for simulation
> ##########################################
> # particles generation
> O.periodic=1
> O.cell.setBox(0.06,0.06,0.06)
> sp=pack.SpherePack()
> O.bodies.append(ymport.text('sphere.txt'))
> sp.toSimulation(material=spheremat)
> # determining colors for particles in different aeras of the cell
> for b in O.bodies:
>     if isinstance(b.shape,Sphere):
>          pos = b.state.pos
>          if pos[0] <0.03 and pos[1] < 0.03: b.shape.color = (1,0,0)
> # area 1
>          elif pos[0] >= 0.03 and pos[1] <0.03: b.shape.color = (0,1,0)
>  # area 2
>          elif pos[0] >= 0.03 and pos[1] >= 0.03: b.shape.color = (0,0,1)
>  # area 3
>          elif pos[0] < 0.03 and pos[1] >= 0.03: b.shape.color = (0,10,1)
>  # area 4
>          else: b.shape.pos = (1,1,0)
> O.periodic=0
> # blockedDOFs
> for b in O.bodies:
>         if isinstance(b.shape,Sphere):
>                  b.state.blockedDOFs='zXY'
> # Simulation assembly for the first step
> O.engines=[
>         ForceResetter(),
>
> InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb(),Bo1_Wall_Aabb()]),
>         InteractionLoop(
>                 [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
>                 [Ip2_FrictMat_FrictMat_FrictPhys()],
>                 [Law2_ScGeom_FrictPhys_CundallStrack()]
>         ),
>
> GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8),
>         triax01,
>         NewtonIntegrator(damping=.1),
>         PyRunner(command='resultfirst()',iterPeriod=1000)
> ]
> # first step of simulation startting with a correct inheriting for the
> next step
> O.dt=utils.PWaveTimeStep()
> def resultfirst():
>         f = file("/home/fzg/fu/result-first-01.dat",'w')
>         wall_left = O.bodies[0].state.pos[0]
>         wall_right = O.bodies[1].state.pos[0]
>         wall_bottom = O.bodies[2].state.pos[1]
>         wall_top = O.bodies[3].state.pos[1]
>         wall_back = O.bodies[4].state.pos[2]
>         wall_front = O.bodies[5].state.pos[2]
>         x_dimension = wall_right - wall_left
>         y_dimension = wall_top - wall_bottom
>         #z_dimension = wall_front - wall_back
>         area = x_dimension * y_dimension
>         porosity = (area-sum(pi*b.shape.radius**2 for b in O.bodies if
> isinstance(b.shape,Sphere)))/area
>         print porosity
> #       f.write('%-16g %-16g %-16g %-16g
> \n'%(area,porosity,x_dimension,y_dimension)),
> #       f.close()
> O.run(30000,True)
> O.wait()
>
> sphere.txt:
> 0.019 0.001 0.05 0.0008
> 0.021 0.001 0.05 0.0008
> 0.023 0.001 0.05 0.0008
> 0.025 0.001 0.05 0.0008
> 0.027 0.001 0.05 0.0008
> 0.029 0.001 0.05 0.0008
> 0.031 0.001 0.05 0.0008
> 0.033 0.001 0.05 0.0008
> 0.035 0.001 0.05 0.0008
> 0.037 0.001 0.05 0.0008
> 0.039 0.001 0.05 0.0008
> 0.041 0.001 0.05 0.0008
> 0.043 0.001 0.05 0.0008
> 0.045 0.001 0.05 0.0008
> 0.047 0.001 0.05 0.0008
> 0.049 0.001 0.05 0.0008
> 0.051 0.001 0.05 0.0008
> 0.053 0.001 0.05 0.0008
> 0.055 0.001 0.05 0.0008
> 0.057 0.001 0.05 0.0008
> 0.059 0.001 0.05 0.0008
> 0.001 0.003 0.05 0.0008
> 0.003 0.003 0.05 0.0008
> 0.005 0.003 0.05 0.0008
>
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