particle position data

Hello,
please provide a complete MWE [1], otherwise we can just guess..
thanks
Jan

[1] https://www.yade-dem.org/wiki/Howtoask

Hello, Jan Stránský,

I am sorry for this inconvenience. I have attached the simple version of my simulation code below. It also have the same issue with mine.... It looks like having weird data at iteration of 14, 25, 36, 47 .... (I am using Yade 1.20.0.)

#################################
import math
import numpy as np
import sys
import os.path
def saveData():
   global ids
   global i
   p_num=ids+1
   pkdID=np.zeros((p_num,1))
   p_radii=np.zeros((p_num,1))
   x_pos=np.zeros((p_num,1))
   y_pos=np.zeros((p_num,1))
   z_pos=np.zeros((p_num,1))
   x_vel=np.zeros((p_num,1))
   y_vel=np.zeros((p_num,1))
   z_vel=np.zeros((p_num,1))
   x_ang=np.zeros((p_num,1))
   y_ang=np.zeros((p_num,1))
   z_ang=np.zeros((p_num,1))
   p_mass=np.zeros((p_num,1))
   eflag=np.zeros((p_num,1))
   print(p_num)
   for k in range(p_num):
       pkdID[k][0]=O.bodies[k].id
       x_pos[k][0]=O.bodies[k].state.pos[0]
       y_pos[k][0]=O.bodies[k].state.pos[1]
       z_pos[k][0]=O.bodies[k].state.pos[2]
       x_vel[k][0]=O.bodies[k].state.vel[0]
       y_vel[k][0]=O.bodies[k].state.vel[1]
       z_vel[k][0]=O.bodies[k].state.vel[2]
       x_ang[k][0]=O.bodies[k].state.angVel[0]
       y_ang[k][0]=O.bodies[k].state.angVel[1]
       z_ang[k][0]=O.bodies[k].state.angVel[2]
       p_mass[k][0]=O.bodies[k].state.mass
       p_radii[k][0]=O.bodies[k].shape.radius
   f1=open(os.path.join("/home/ae_h1/yzk0056/Desktop/Semesters/2019 Summer Semester/DEM Project/DEMsimulation/Obtain_initial_position/Sim_regular_rotation_Apophis/constant_gravity_2/","Output_"+str(i)+".txt"),"w")
   for p in range(p_num):
       f1.write("%d\t%e\t%e\t%e\t%e\t%e\t%e\t%e\t%e\t%e\t%e\t%e\n" % (pkdID[p][0],p_mass[p][0],p_radii[p][0],x_pos[p][0],y_pos[p][0],z_pos[p][0],x_vel[p][0],y_vel[p][0],z_vel[p][0],x_ang[p][0],y_ang[p][0],z_ang[p][0]))
   f1.close()
   i+=1
Density=2900
Young=3.3e7
poisson=0.3
c_r = 0.1
r_fc = 0.0 #1st case: low angle of repose
frictionAngle=radians(35)
sphereColor = (.8,.8,0.)#dirty yellow
i=0
from yade import pack, plot, ymport, export
## Import particles
iron_ore=FrictMat(young=Young,poisson=poisson,density=Density,frictionAngle=frictionAngle)
Mat=O.materials.append(iron_ore)
from yade import pack, plot, ymport, export
sp=pack.SpherePack()
ids=sp.makeCloud(minCorner=(-0.4,-0.2,0.01),maxCorner=(0.4,0.2,1),rMean=2.0e-2,rRelFuzz=0.,num=250000,periodic=False)
sp.toSimulation(material=Mat)
for pp in O.bodies:
   ids=pp.id
## Import wall's geometry
O.materials.append(FrictMat(young=Young,poisson=poisson,density=Density,frictionAngle=frictionAngle,label='frictionlessWalls'))
fctIds = O.bodies.append(geom.facetBox((0.,0.,-0.01),(0.8,0.4,0.0),wallMask=0b110011,color=(1,0,0),wire=False))
g=6.5e-2
itr_num=30000
## Engines
O.engines=[
   ForceResetter(),
   InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),
   InteractionLoop(
       [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()],
       [Ip2_FrictMat_FrictMat_MindlinCapillaryPhys(krot=r_fc,en=c_r,es=c_r)],
       [Law2_ScGeom_MindlinPhys_Mindlin(includeMoment=True)]
       ),
   NewtonIntegrator(damping=0,gravity=(0,0,-g),label='NI'),
   PyRunner(iterPeriod=itr_num,command='saveData()')
]
## time step (how to run the script)
O.dt=2.0e-4 # should be 1.0e-6
O.run(14400000)
from yade import qt
qt.View()
#####################################################

Thank you for your help in advance.

Sincerely,
Jinny Kim

Hello,
I have tried your code (using Yade 2018.02b), but found no "weird data" (did not try too much, thought).. Please be more specific (I don't want to check 2500 lines of data file to find one discrepancy :-)
It would help, if you could create a MWE [1], i.e. minimal from point of both code and simulation (number of particles, running time).
cheers
Jan

[1] https://www.yade-dem.org/wiki/Howtoask

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