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[Daniel Kiracofe <question690691@xxxxxxxxxxxxxxxxxxxxx>]

Question #690691 on Yade changed:
https://answers.launchpad.net/yade/+question/690691

    Status: Answered => Open

Daniel Kiracofe is still having a problem:
Jan, I appreciate the quick reply.  Here are some more details.

I was originally running with "yade -j 4".  I tried it with just "yade",
but that did not change anything.

The original code was quite complicated. I tried to create a stripped
down version of my code to produce the minimum possible bug report.  I
stripped it down to code #1 below.  In that code, I create 4 walls which
are clumped together. if I apply the setPermF to the clump, it does not
work.  If I apply the setPermF to an individual wall that is a member of
the clump, it does work.

However, in my original code, neither one of these worked.  So I went
back to my original code again, and started stripping it down again to
try to get the minimum possible bug report for a single body that is not
part of a clump.  I got code #2 below.  In this code, I create a single
wall, and then either 0, 1 or a bunch of spheres.  If I create a bunch
of spheres, then setPermF (on the wall) does not work.  If I create 0 or
1 sphere, then it does work.  Not quite sure what is going on here.

So, unless I'm doing something wrong or misunderstanding, it looks like there may be three separate bugs with setPermF
1) the parallel vs single-threaded issue raised above
2) the clump vs single body issue demonstrated in code #1 below
3) the still unknown issue demonstrated in code #2 below

Please let me know if you need any more details.

Daniel


#########################################
#code #1
#in this version, setPermF works if I apply to one of the members of the clump
#but does not work if apply it directly to the clump

###############################################3
box_x = 0.00025
box_y = 0.0013
box_z = box_y
f_sweep_start = 45.5 #
f_sweep_stop  = 52 #Hertz
f_sweep_rate  = 1  #Hertz/second
out_file_name = "TestOutput.txt"
F_amp = 4e-6
grav_y=0
damp = 0.000 
ball_gen_method=1
                
#################################################

import qt, plot
qt.View() #open the controlling and visualization interfaces
                
finalFricDegree = atan(0.25) #contact friction during the deviatoric loading

young2 = 200e9 #the walls' Young's modulus, same as the spheres
rho    = 8230 #

mn = Vector3(0,      box_y,      0)
mx = Vector3(box_x,2*box_y,  box_z) #corners of the initial packing
thick = 0.010 # the thickness of the walls

nat_freq_hz = 50.0
nat_period = 1 / nat_freq_hz
nat_freq_rad = nat_freq_hz * 2 * math.pi

#GENERATING BODIES #####

O.dt = nat_period / 100
plotDataPeriod = 10
        
#special 4 walls case for 2D because of all of the blocked DOF
expand=1.5

walls_density = 8000

wallIds = []

O.materials.append(FrictMat(young=young2,poisson=0.7,frictionAngle=0,
density=walls_density ,   label='walls'))

# yade.utils.box(  center                             extents= half sizes!
topWall   = yade.utils.box( (box_x/2,2*box_y+thick/2,box_z/2), (box_x/2*expand,thick/2,box_z/2*expand), material='walls')
topWallId =  O.bodies.append(topWall)
wallIds.append(topWallId)

botWall   = yade.utils.box( (box_x/2,box_y-thick/2,box_z/2), (box_x/2*expand,thick/2, box_z/2*expand), material='walls')
botWallId =  O.bodies.append(botWall)
wallIds.append(botWallId)

rightWall   = yade.utils.box( (box_x+thick/2,1.5*box_y,box_z/2), (thick/2,box_y/2*expand, box_z/2*expand), material='walls')
rightWallId =  O.bodies.append(rightWall)
wallIds.append(rightWallId)

leftWall   = yade.utils.box( (-thick/2,1.5*box_y,box_z/2), (thick/2,box_y/2*expand, box_z/2*expand), material='walls')
leftWallId =  O.bodies.append(leftWall)
wallIds.append(leftWallId)

wallClump=O.bodies.clump(wallIds)

for i in wallIds:
        O.bodies[i].state.blockedDOFs = 'xzXYZ' #fixme is this needed with clumping?

#DEFINING ENGINES ####

newton=NewtonIntegrator(damping=damp, gravity=(0,grav_y,0))

O.engines=[
 ForceResetter(),
 PyRunner(command='swing()',iterPeriod=100),
 newton,
   PyRunner(command='addPlotData()',iterPeriod=plotDataPeriod),
]

def swing():
        force = 5
        #this works
        #O.forces.addF( wallClump, ( 0, force , 0) )

        #this does not work
        O.forces.setPermF( wallClump , ( 0, force , 0) )

        #this does work
        #O.forces.setPermF( topWallId , ( 0, force , 0) )

        
def addPlotData():
        position=O.bodies[topWallId].state.pos[1]       

        plot.addData(freq=O.time , position=position)

plot.plots={'freq':('position')}
plot.plot()



###################################################################################
###################################################################################
#code #2
from yade import pack

#this variable selection between three cases
#ball_gen_method=0, generates one wall and zero spheres, then setPermF on the wall works
#ball_gen_method=1, generates one wall and one spheres, then setPermF on the wall works
#ball_gen_method=2, generates one wall and many spheres, then setPermF on the wall does NOT work
ball_gen_method=1


###############################################3
box_x = 0.00025
box_y = 0.0013
f_sweep_start = 45.5 #Hertz
f_sweep_stop  = 52 #Hertz
f_sweep_rate  = 1  #Hertz/second
periodic_bc = 2
particle_dia = 2.5e-5
grav_y=0
damp = 0.000
                
box_z = particle_dia*1.01
                
#################################################
##### DEFINING VARIABLES AND MATERIALS ######
#################################################

import qt, plot
qt.View() #open the controlling and visualization interfaces

                
finalFricDegree = atan(0.25) #contact friction during the deviatoric loading


young1 = 200e9 #the spheres' Young's modulus, Pa. AFRL published papers used Inco718. young's modulus about 29e6 psi at room temp, or 200 GPa
young2 = 200e9 #the walls' Young's modulus, same as the spheres
rho    = 8230 #generic inco 718, kg/m^3

mn = Vector3(0,      box_y,      0)
mx = Vector3(box_x,2*box_y,  box_z) #corners of the initial packing
thick = 2*particle_dia # the thickness of the walls

dia = [particle_dia, particle_dia * 1.001 ]  #these are the points on a distribution, but for now we basically have them all the same size
phi = [0.0,   1.0]


O.materials.append(FrictMat(young=young1,poisson=0.7,frictionAngle=finalFricDegree,density=rho,label='spheres'))


#GENERATING BODIES #####

ballIds = ()
if (ball_gen_method==2):
        #for this setting, setPermF does not work        
        sp=pack.SpherePack()
        sp.makeCloud(minCorner=mn,maxCorner=mx,periodic=False,psdSizes=dia,psdCumm=phi,distributeMass=True,seed=1)
        
        ballIds = O.bodies.append([sphere(center,rad,material='spheres',color=(0,0,1)) for center,rad in sp])                
elif (ball_gen_method == 1):
        #only only 1 single ball.
        #with this setting setPermF does work
        center = ( (mn[0]+mx[0])/2,  (mn[1]+mx[1])/2,  (mn[2]+mx[2])/2)
        rad = 0.01
        ballIds = O.bodies.append(sphere(center,rad,material='spheres',color=(0,0,1)))
elif (ball_gen_method == 0):
        #turn off all spheres.  this is only for debugging
        # for this setting, setPermF does work
        print('this space intentionally left blank')


timestepper =  GlobalStiffnessTimeStepper(active=False,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8)
O.dt = 2e-9

        
plotDataPeriod = 10
expand=1.5

walls_density = 8000

O.materials.append(FrictMat(young=young2,poisson=0.7,frictionAngle=0,
density=walls_density ,   label='walls'))

# yade.utils.box(  center                             extents= half sizes!
topWall   = yade.utils.box( (box_x/2,2*box_y+thick/2,box_z/2), (box_x/2*expand,thick/2,box_z/2*expand), material='walls')
topWallId =  O.bodies.append(topWall)

x0 = O.bodies[topWallId].state.pos[1]


newton=NewtonIntegrator(damping=damp, gravity=(0,grav_y,0))


O.engines=[
 ForceResetter(),
 InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]),
 InteractionLoop(
   [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()],
   [Ip2_FrictMat_FrictMat_FrictPhys()],
   [Law2_ScGeom_FrictPhys_CundallStrack()] ),
 timestepper,
 PyRunner(command='swing()',iterPeriod=100),
 newton,
   PyRunner(command='addPlotData()',iterPeriod=plotDataPeriod),
]


def swing():
        F = 100

#this works, always
#        O.forces.addF(topWallId , ( 0, F , 0))
#works when there is only 0 or 1 sphere, but not when there are a bunch
        O.forces.setPermF(topWallId , ( 0, F , 0) )

                
def addPlotData():
        position=O.bodies[topWallId].state.pos[1]-x0
        
        plot.addData(freq=O.time , position=position)
                
        if (O.time > 8):
                O.pause()

plot.plots={'freq':('position')}
plot.plot()

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