save spheres coordinates to a file

Hi,

O.bodies[b].radius does not exist. It should be O.bodies[b].shape.radius (if O.bodies[b] is a sphere).
Regards
Bruno

Ah... and in O.bodies[b] 'b' should be an integer, not a body.

Else it is a bit like O.bodies[O.bodies[O.bodies[O.bodies[....]]]]]]]]]]]]

Bb]

hi Bruno ,
thank you for answer me , i changed the script like you advise me to :

#saving parameters of spheres in file
def myaddData():
   for b in O.bodies:
      idt,rad=b.id,b.shape.radius
      x,y,z=b.state.pos[0],b.state.pos[1],b.state.pos[2]
      veloc,force=b.vel[2],O.forces.f(b.id)
   fil.write("{:e} {:e} {:e} {:e} {:e} {:e} {:e}\n".format(idt,x,y,z,veloc,rad,force)) # ( .format = % )

but still have problem on radius :

AttributeError Traceback (most recent call last)
/usr/bin/yade in <module>()

/usr/bin/yade in myaddData()
     43 def myaddData():
     44 for b in O.bodies:
---> 45 idt,rad=b.id,b.shape.radius
     46 x,y,z=b.state.pos[0],b.state.pos[1],b.state.pos[2]
     47 veloc,force=b.vel[2],O.forces.f(b.id)

AttributeError: 'Facet' object has no attribute 'radius'

and in wpapper.Record () :

  File "save.py", line 51, in <module>
    yade.wrapper.Recorder(addIternNum=True,file=fil)
AttributeError: No such attribute: addIternNum.
[[ ^L clears screen, ^U kills line. F12 controller, F11 3d view (use h-key for showing help), F10 both, F9 generator, F8 plot. ]]

Thanks in advance.

O.bodies contains all bodies, including any walls (Facet) you might have appended. I guess walls don't have radii :-)

You can use a check like this:

def myaddData():
   for b in O.bodies:
      if not isinstance(b.shape,sphere): continue
      idt,rad=b.id,b.shape.radius
      x,y,z=b.state.pos[0],b.state.pos[1],b.state.pos[2]
      veloc,force=b.vel[2],O.forces.f(b.id)
      fil.write("{:e} {:e} {:e} {:e} {:e} {:e} {:e}\n".format(idt,x,y,z,veloc,rad,force)) # ( .format = % )

>> yade.wrapper.Recorder(addIternNum=True,file=fil)

Recorder is a separate engine in Yade [1], one that appears to have very little documentation associated with it. I've never used it, I use VTKRecorder for this type of data collection [2].

[1]https://yade-dev.gitlab.io/trunk/yade.wrapper.html#yade.wrapper.Recorder
[2]https://yade-dev.gitlab.io/trunk/user.html#saving-data-during-the-simulation

hi Robert ,
thank you for answer me , i changed O.bodies like you said and it's work so thank you a obtain file (vibration.txt) contains properties
but the problem that ( id ) start with 192 not by zero . and i used VTKRecorder but i don't know how to add this properties .
Any idea ?

Thanks in advance.

there's my code :
from yade import pack,plot,export,wrapper

#material of cylinder
Mat1 = O.materials.append(ViscElMat(kn=10.0e4,ks=10.0e4,frictionAngle=0.455,density=2650.0))

# create Cylinder
Cylinder=O.bodies.append(geom.facetCylinder((0,0,1.5),2.0,height=3.0,wallMask=6,segmentsNumber=64,material=Mat1))

# create sphere packing
sp=pack.SpherePack()
sp.makeCloud((-1.2,-1.2,1.5),(1.2,1.2,8.0),rMean=.2,rRelFuzz=.1,num=128)
sp.toSimulation(color=(0,1,0))

O.engines=[
    ForceResetter(),
    InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),
    InteractionLoop(

        [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()],
        [Ip2_FrictMat_FrictMat_FrictPhys()],
        [Law2_ScGeom_FrictPhys_CundallStrack()]
    ),
    NewtonIntegrator(gravity=(0,0,-9.81),damping=0.3),
    HarmonicMotionEngine(A=[0,0,0.5], f=[0,0,1.0], fi = [0.0,0.0,pi],ids =Cylinder),# vertical vibration
    # HarmonicMotionEngine(A = (0,0.002,0),f = (0,50,0),fi = (0,-0.5*math.pi,0),ids =Cylinder), horizontal vibration
    PyRunner(command='myaddData()',realPeriod=1,initRun=True), #call def fonction every second
    VTKRecorder(iterPeriod=100,recorders=['myaddData()'],fileName='vibrations.txt-') # add iteration number to basename
 ]

O.dt=utils.PWaveTimeStep() #to slow down the motion O.dt=.9*PWaveTimeStep()
O.resetTime()

# open file
fil=open("vibrations.txt.bz","a+")
fil.write ('id \t x \t y \t z \t velocity \t radius \t force \n')

#saving parameters of spheres in file
def myaddData():
   for b in O.bodies:
      if isinstance(b.shape,Sphere):
         number,rad=b.id,b.shape.radius
         x,y,z=b.state.pos[0],b.state.pos[1],b.state.pos[2]
         veloc,force=b.state.vel[2],O.forces.f(b.id)
         fil.write("{:d}\t{:.3g}\t{:.3g}\t{:.3g}\t{:.3g}\t{:.3g}\t{}\n".format(number,x,y,z,veloc,rad,force)) # ( .format = % )

O.saveTmp()
.

> ( id ) start with 192 not by zero
> Cylinder=O.bodies.append(geom.facetCylinder(...

because the first 192 bodies are facets created by the facetCylinder command.
cheers
Jan

thank Jan my problem is solved
for the person who wont saved properties of spheres in cylinder there's my code :

from yade import pack,plot,export,wrapper

#material of cylinder
Mat1 = O.materials.append(ViscElMat(kn=10.0e4,ks=10.0e4,frictionAngle=0.455,density=2650.0))

# create sphere packing
sp=pack.SpherePack()
sp.makeCloud((-1.2,-1.2,1.5),(1.2,1.2,8.0),rMean=.2,rRelFuzz=.1,num=128)
sp.toSimulation(color=(0,1,0))

# create Cylinder
Cylinder=O.bodies.append(geom.facetCylinder((0,0,1.5),2.0,height=3.0,wallMask=6,segmentsNumber=64,material=Mat1))

#time of simulation
O.stopAtIter=5000

# interactions
O.engines=[
    ForceResetter(),
    InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),
    InteractionLoop(

        [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()],
        [Ip2_FrictMat_FrictMat_FrictPhys()],
        [Law2_ScGeom_FrictPhys_CundallStrack()]
    ),
    NewtonIntegrator(gravity=(0,0,-9.81),damping=0.3),
    HarmonicMotionEngine(A=[0,0,0.5], f=[0,0,1.0], fi = [0.0,0.0,0.0],ids =Cylinder),# vertical vibration
    # HarmonicMotionEngine(A = (0,0.002,0),f = (0,50,0),fi = (0,-0.5*math.pi,0),ids =Cylinder), horizontal vibration
    PyRunner(command='myaddData()',iterPeriod=100,initRun=True), #call def fonction
 ]

O.dt=utils.PWaveTimeStep() #to slow down the motion O.dt=.9*PWaveTimeStep()
O.resetTime()

#saving parameters of spheres in file
def myaddData():
   if (O.iter%8==0):
      # open file
      fil=open("vibs_."+str(O.iter),"a+")
      fil.write ('id \t x \t y \t z \t vz \t radius \t force \n')
      for b in O.bodies:
         if (type(b.shape)==Sphere):
            number,rad=b.id,b.shape.radius
            x,y,z=b.state.pos[0],b.state.pos[1],b.state.pos[2]
            veloc,force=b.state.vel[2],O.forces.f(b.id)
            fil.write("{:d}\t{:.3g}\t{:.3g}\t{:.3g}\t{:.3g}\t{:.3g}\t{}\n".format(number,x,y,z,veloc,rad,force)) # ( .format = % )

O.saveTmp()

thank you Jan