Error on proc 1: Neighbor list overflow, boost neigh_modify one (../neigh_full.cpp:314)

Theo_Score's picture
Submitted by Theo_Score on Tue, 02/14/2017 - 06:44

Hi All,

Attached is the insertion face stl and give embedded is a full script where I want to have coordination number of particles in a multiple particle size distribution system;

# Testing Script

atom_style sphere
atom_modify map array
boundary f f f
newton off

communicate multi vel yes

units si

region reg block -0.1 0.1 0. 0.40 -0.1 0.1 units box
create_box 3 reg

neighbor 0.03 multi
neigh_modify delay 0 every 1 check yes

# Material properties required for new pair styles

fix m1 all property/global youngsModulus peratomtype 5.e6 5.e6 5.e6
fix m2 all property/global poissonsRatio peratomtype 0.24 0.24 0.24
fix m3 all property/global coefficientRestitution peratomtypepair 3 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25
fix m4 all property/global coefficientFriction peratomtypepair 3 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35
fix m5 all property/global coefficientRollingFriction peratomtypepair 3 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35

# New pair style
pair_style gran model hertz tangential history
pair_coeff * *

timestep 0.000015

fix gravi all gravity 9.81 vector 0.0 -1.0 0.0

# Define sphere/ primitive walls
fix ins_mesh all mesh/surface/planar file meshes/insertion_face.stl type 3
fix ywalls1 all wall/gran model hertz tangential history primitive type 3 yplane 0.0
fix cylwalls all wall/gran model hertz tangential history primitive type 3 ycylinder 0.1 0. 0.

# Distributions for insertion
fix pts1 all particletemplate/sphere 17599 atom_type 1 density constant 5000 radius constant 0.01500
fix pts2 all particletemplate/sphere 12041 atom_type 1 density constant 5000 radius constant 0.01250
fix pts3 all particletemplate/sphere 12043 atom_type 1 density constant 5000 radius constant 0.01000
fix pts4 all particletemplate/sphere 12049 atom_type 1 density constant 5000 radius constant 0.00750
fix pts5 all particletemplate/sphere 12071 atom_type 1 density constant 5000 radius constant 0.00500
fix pts6 all particletemplate/sphere 12073 atom_type 1 density constant 5000 radius constant 0.00250
fix pts7 all particletemplate/sphere 12097 atom_type 1 density constant 5000 radius constant 0.00125
fix pdd1 all particledistribution/discrete 12539 7 pts1 0.25 pts2 0.20 pts3 0.17 pts4 0.14 pts5 0.11 pts6 0.08 pts7 0.05

fix pts8 all particletemplate/sphere 19867 atom_type 2 density constant 5000 radius constant 0.01500
fix pts9 all particletemplate/sphere 12451 atom_type 2 density constant 5000 radius constant 0.01250
fix pts10 all particletemplate/sphere 12457 atom_type 2 density constant 5000 radius constant 0.01000
fix pts11 all particletemplate/sphere 12473 atom_type 2 density constant 5000 radius constant 0.00750
fix pts12 all particletemplate/sphere 12479 atom_type 2 density constant 5000 radius constant 0.00500
fix pts13 all particletemplate/sphere 12487 atom_type 2 density constant 5000 radius constant 0.00250
fix pts14 all particletemplate/sphere 12491 atom_type 2 density constant 5000 radius constant 0.00125
fix pdd2 all particledistribution/discrete 19889 7 pts8 0.25 pts9 0.20 pts10 0.17 pts11 0.14 pts12 0.11 pts13 0.08 pts14 0.05

# apply nve integration to all particles that are inserted as single particles
fix integr all nve/sphere

# Output settings, include total thermal energy
fix ts all check/timestep/gran 1000 0.15 0.15
compute rke all erotate/sphere
compute nconts all coord/atom 0.03 mix yes
thermo_style custom step atoms ke c_rke vol f_ts[1] f_ts[2]
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes

# Particle insertion
fix ins1 all insert/stream seed 17449 distributiontemplate pdd1 maxattempt 100 nparticles 16000 particlerate 16000 &
overlapcheck yes vel constant 0.0 -1.0 0.0 insertion_face ins_mesh extrude_length 0.050

fix ins2 all insert/stream seed 17761 distributiontemplate pdd2 maxattempt 100 nparticles 16000 particlerate 16000 &
overlapcheck yes vel constant 0.0 -1.0 0.0 insertion_face ins_mesh extrude_length 0.050

#Initialising dump file
run 1
dump dmp all custom 1000 post/dump*.data id type vx vy vz fx fy fz omegax omegay omegaz radius c_nconts

#Insert particles
run 100000

After running for 14 Time Steps, I got the error as in the subject of this thread and I am asking for the solution to my problem.

Thank you.

AttachmentSize
Plain text icon .stl File376 bytes
ckloss's picture

ckloss | Mon, 02/27/2017 - 20:33

Hi,

my guess is that your simulation produces a bad dynamics which leads to lots of neighbors. Try to step-wise debugging your simulation by starting with something that works, and try to find out where the issue comes in

Christoph

Theo_Score's picture

Theo_Score | Fri, 03/10/2017 - 03:28

Hi Christoph and All,

I have done some debugging and I realize the issue is with the coord/atom compute style.

If I run a simulation without

compute nconts all coord/atom 0.0315 mix yes

The simulation goes through well.

However including the coord/atom compute style, at some point, the error occurs.

I am using a multi-size component system with size range from 2.5 mm to 30 mm particles (2.5, 5, 10, 15, 20, 25, 30 mm). If I am using a mono-size system, the cut-off distance is easy to specify. My source of problem here is "how to specify cutoff distance in a multi-component system?", I am sure this is what is causing a bloated neighbor list with the coord/ atom compute style.

Your help will be appreciated.

Thank you.

NTT1508 | Wed, 03/15/2017 - 00:02

Hi,

I normally use cut-off distance with respect to the smallest diameter of particles in a multi-size system. Overflow error is possibly generated if there are too many particles in a sub-domain so that processor is overloaded. Reduce the cut-off distance (plus other dynamic parameters, e.g., reconstitution coefficient) might work although this will cost more time of computation.

How do you think ?

Regards,

Theo_Score's picture

Theo_Score | Wed, 03/15/2017 - 00:14

Hi,

I am working with minerals ores and I am currently using an admissibly low restitution coefficient between 0.15 - 0.30. Thank you for the suggestion to use cut-off based on the smallest element, I will try that and see the result.

Thank you and best regards,

Theo