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[Deepak <question683336@xxxxxxxxxxxxxxxxxxxxx>]

Question #683336 on Yade changed:
https://answers.launchpad.net/yade/+question/683336

    Status: Open => Answered

Deepak proposed the following answer:
Hello,

There could be several reasons for this :

Have you checked for the stability of the system ? Do particles 'fly' out
of the domain within a few timesteps ? Have you made sure the courant
number/time step in the fluid side is an acceptable value (<0.5) ?
If all these are okay, then I suspect it is with the deletePar function as
it may not be in sync with coupling.  One way to ensure this is to add an
if condition to  check whether coupling occurs in the present time step..

def deletePar(self) :
     if (O.iter%fluidCoupling.dataExchangeInterval==0) :
               ...
try it and let me know..





On Tue, Sep 3, 2019 at 10:33 AM Anqi H <question683336@xxxxxxxxxxxxxxxxxxxxx>
wrote:

> Question #683336 on Yade changed:
> https://answers.launchpad.net/yade/+question/683336
>
>     Status: Answered => Open
>
> Anqi H is still having a problem:
> Hi Deepak,
>
> Thank you so much for your help so far. I've modified my script based on
> your comment to check if a body does not have any cohesive bonds in its
> interactions, if true then delete this sphere from fluidcoupling IDs. In
> the first openFoam time step, some spheres were deleted as expected,
> however, after the deletions and in the same foam timestep, it seems the
> program hangs after 500 yade iterations and in the fluidCoupling step (I
> have put the particle deletion pyrunner before calling fluidCoupling). I
> have copied my python script below. I am sorry it's probably difficult
> to run this script as it requires two other txt files that stored the
> sphere locations. I was wondering if it was due to some obvious errors
> in my script that I haven't noticed?
>
>
> from __future__ import print_function
> import sys
> from yadeimport import *
> from yade.utils import *
> from yade import ymport
>
> initMPI()                           #Initialize the mpi environment,
> always required.
> fluidCoupling = yade.FoamCoupling();     #Initialize the engine
> fluidCoupling.getRank();            #part of Initialization.
>
>
> #example of spheres in shear flow : two-way point force coupling
> class simulation():
>
>   def __init__(self):
>
>     O.periodic = True;
>
>     #proppant properties
>     FrictAng_p = 0.9
>     Density_p = 2650
>     Young_p = 100e6
>     TensileStr_p=3000
>     Cohesion_p=3000
>
>     Young = 57e8 #apparent modulus
>     FrictAng = 0.5
>     Density = 2650
>     Poisson = 0.28
>     Cohesion = 38e6 # pa
>     TensileStr = 38e6 # pa
>
>     rock =
> JCFpmMat(type=1,young=Young,frictionAngle=FrictAng,density=Density,poisson=Poisson,tensileStrength=TensileStr,cohesion=Cohesion,label='rock')
>     proppant =
> JCFpmMat(type=2,young=Young_p,frictionAngle=FrictAng_p,density=Density_p,tensileStrength=TensileStr_p,cohesion=Cohesion_p,label='proppant')
>
> O.materials.append(JCFpmMat(young=Young_p,frictionAngle=0,density=0,label='wallmat'))
>
>     O.materials.append(proppant)
>     O.materials.append(rock)
>
>     rock_assembly =
>
> O.bodies.append(ymport.textExt('new_rock.txt','x_y_z_r',shift=Vector3(0,0,0),scale=1,material=rock))
>
>     for b in O.bodies:
>       if b.state.pos[1]>0.017 or b.state.pos[1]<0.0135:
>         O.bodies.erase(b.id)
>       #if (b.state.pos[1]>0.0135 and b.state.pos[1]<0.015) :
>        # b.groupMask=2
>       else:
>         b.dynamic = False
>         b.state.vel=(0, 0, 0)
>
>     proppant_assembly =
> O.bodies.append(ymport.textExt('new_prop.txt','x_y_z_r',shift=Vector3(0,0,0),scale=1,material=proppant,color=(1.00,0.67,0.50)))
>     print ('length of bodies proppant '+str(len(O.bodies)))
>
>     for b in proppant_assembly:
>       O.bodies[b].groupMask=2
>       if O.bodies[b].state.pos[0] < 0:
>         print("found it ")
>         O.bodies.erase(b)
>
>
>     sphereIDs = [b.id for b in O.bodies if (type(b.shape)==Sphere and
> b.material.label=='proppant')]
>
>     #coupling engine settings
>     fluidCoupling.setNumParticles(len(sphereIDs))
>     fluidCoupling.setIdList(sphereIDs)
>     fluidCoupling.isGaussianInterp=False;  #use pimpleFoamYade for
> gaussianInterp
>
>     # Integrator
>     newton=NewtonIntegrator(damping=0.0, gravity = (0.0 ,0.0, 0.0))
>      # add small damping in case of stability issues.. ~ 0.1 max, also
> note : If gravity is needed, set it in constant/g dir.
>
>
>     O.engines=[
>   ForceResetter(),
>   InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=1.2,
> label="bols"),Bo1_Facet_Aabb()], allowBiggerThanPeriod=True),
>   InteractionLoop(
>     [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=1.2,
> label="ig2s"),Ig2_Facet_Sphere_ScGeom()],
>     [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1)],
>
> [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(recordCracks=True,label='lawFunctor')]
>   ),
>   GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.7, label = "ts"),
>         PyRunner(command='sim.deletePar()',iterPeriod=30,
> label='checkPar'),
>         fluidCoupling, #to be called after timestepper
>         PyRunner(command='sim.printMessage()', iterPeriod= 1000,
> label='outputMessage'),
>   newton,
>         #PyRunner(command='sim.deletePar()',iterPeriod=50,
> label='checkPar'),
>         VTKRecorder(fileName='yadep/3d-vtk-',mask =
> 2,recorders=['spheres','colors'],iterPeriod=1000)
>     ]
>
>
>   def printMessage(self):
>
>      print("********************************YADE-ITER = " + str(O.iter) +"
> **********************************")
>      if O.iter == 4000:
>          maxVel = 0.05
>          for b in O.bodies:
>              if type(b.shape)==Sphere:
>                  bodyVel = abs(b.state.vel.norm())
>                  if bodyVel > maxVel:
>                      raise ValueError("Body velocity exceeds imposed shear
> velocity by ", abs(bodyVel-maxVel))
>
>   def deletePar(self):
>     ids = fluidCoupling.getIdList()
>     for b in ids:
>       temp=0
>       for i in O.bodies[b].intrs():
>         if i.phys.isCohesive==True:
>           temp+=1
>       if temp==0:
>         fluidCoupling.eraseId(b)
>         print('deleted '+str(b))
>     print("******YADE-ITER = " + str(O.iter) +" **********")
>
>     #if O.bodies[b].state.nbInitBonds==0 or
> (O.bodies[b].state.nbInitBonds==O.bodies[b].state.nbBrokenBonds):
>
>
>   def steprun(self):
>     O.step()
>     bols.aabbEnlargeFactor = 1
>     ig2s.interactionDetectionFactor = 1
>     print('-------------------reset aabbEnlargeFactor------------------')
>
>   def irun(self,num):
>       O.run(num,1)
>
>
> if __name__=="__main__":
>     sim = simulation()
>     sim.steprun()
>     sim.irun(5000) #run 5000 iteration and wait
>     # print("body id = ", O.bodies[34].id)
>     fluidCoupling.killMPI()
>
> import builtins
> builtins.sim=sim
>
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