yade-users team mailing list archive

[mrhappy <question690925@xxxxxxxxxxxxxxxxxxxxx>]

New question #690925 on Yade:
https://answers.launchpad.net/yade/+question/690925

Hi all,

I am running my Yade model. when the Yade model is small (8000 particles), the code works well. But when the same model has 1000000 particles, I get the following error:

corrupted double-linked list
Aborted (core dumped)

Can anyone help me understand why I get this error? The model compiles well, but when the first iteration is solved, the error appears. 

Thank you for your help.

MY CODE:

#MATERIAL PROPERTIES 
intR =   0.20 #connectivity parameter 
DENS = 2500.00 #Density (kg/mm^3) 
YOUNG = 1800.00 #Young's modulus (N/mm^2) 
FRICT =  18.00 #Friction angle (degrees) 
ALPHA =   0.20 #Poisson's ratio 
TENS = 100.00 #Tensile strength (N/mm^2) 
COH = 1000.00 #Shear strength (N/mm^2) 

mn,mx=Vector3(-0.500000,-0.500000,-0.500000),Vector3(100.500000,86.525190,86.236515) # corners of the initial packing

#CREATING NODES 
with open('Nodes.txt') as f:
  Nodes = [[float(x) for x in line.split()] for line in f]

O.materials.append(JCFpmMat(type=1,density=DENS,young=YOUNG,poisson=ALPHA,frictionAngle=radians(FRICT),tensileStrength=TENS,cohesion=COH,label='mat1'))

walls=aabbWalls([mn,mx],thickness=0,material='mat1') 
wallIds=O.bodies.append(walls) 

# PARTICLES 
for i in range(1000000):
  if Nodes[i][3] == 1:
    O.bodies.append([ sphere(center=(Nodes[i][0],Nodes[i][1],Nodes[i][2]),radius=0.50,color = (1,0,0),material='mat1'),])
  else:
    O.bodies.append([ sphere(center=(Nodes[i][0],Nodes[i][1],Nodes[i][2]),radius=0.50,color = (0,1,0),material='mat1'),])

nbSpheres = 1000000.00

# PRINTING 
from yade import plot 
from pprint import pprint 

# SIMULATION LOOP 
O.engines=[ 
    ForceResetter(), 
    InsertionSortCollider([Bo1_Sphere_Aabb()]), 
    InteractionLoop( 
        [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intR)], 
        [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1)], 
        [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM()] 
    ), 
    GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=10,timestepSafetyCoefficient=0.5, defaultDt=utils.PWaveTimeStep()), 
    DFNFlowEngine(dead=1,label="flow"),
    NewtonIntegrator(damping=  0.80), 
    PyRunner(command='BreakingBonds()',iterPeriod=1), 
    PyRunner(command='Writting()',iterPeriod=   500), 
]

#WRITTING RESULTS 
number = 0 
def Writting(): 
  global number 
  number = number + 1 
  f= open("Info%d.txt" %(number),"w+")
  f.write("%5.10f \n" % (O.time)) 
  f.write("%5.10f \n" % (flow.getPorePressure((50.000,43.013,42.868)))) 
  for i in range (20000):
    f.write("%5.10f \n" % (SaveDataNodes[i][0])) 
  f.close() 

def history(): 
  plot.addData(t=O.time,p=flow.getPorePressure((50.000,43.013,42.868)))
 
#Apply Qin (volume flow rate) in the center of the model. 
flow.dead = 0 
flow.defTolerance=0.3 
flow.meshUpdateInterval=1 
flow.useSolver=3 
flow.permeabilityFactor=1 
flow.viscosity=10 
flow.bndCondIsPressure=[1,1,1,1,1,1] 
flow.bndCondValue=[0,0,0,0,0,0] 
flow.boundaryUseMaxMin=[0,0,0,0,0,0] 
O.dt= 0.0010000000 
O.dynDt=False 

ti = O.time 
O.engines=O.engines+[PyRunner(iterPeriod=2,command='history()')] 
O.engines=O.engines+[PyRunner(iterPeriod=1,command='Pumping()')] 
def Pumping(): 
  if O.time<(ti+0.2): 
    flow.imposeFlux(Vector3(50.000,43.013,42.868),-1.0000000000) 
  else: 
    flow.imposeFlux(Vector3(50.000,43.013,42.868),0) 
 

def BreakingBonds():
  global Bonds0
  CurrentBonds = 0
  for ii in O.interactions: 
    CurrentBonds+=1 
  if Bonds0 > CurrentBonds:
    Bonds0 = CurrentBonds
    print("BROKEN!") 
    print(O.time)
    Writting()

#PLOTTING 
plot.plots={'t':('p')} 
plot.plot() 

#CREATING CONNECTIVITY 
with open('Connectivity.txt') as f:
  Connectivity = [[int(x) for x in line.split()] for line in f]

#CREATING INTERACTIONS 
for i in range(5905449):
  if Connectivity[i][2] == 1:
    createInteraction(Connectivity[i][0],Connectivity[i][1])

Connectivity.clear() 

#CREATING SAVEDATA 
with open('SaveDataNodes.txt') as f:
  SaveDataNodes = [[int(x) for x in line.split()] for line in f]

#BOUND COUNT 
Bonds0=0
for i in O.interactions:
  Bonds0+=1
print (Bonds0)

-- 
You received this question notification because your team yade-users is
an answer contact for Yade.