problem in import and paralization of certain mesh elements

Submitted by atul2018 on Wed, 05/04/2022 - 11:24

Hello

I am facing all of a sudden problem in importing and paralization of cetain elements of meshes (.stl geometry). Previously I have done it with smaller geometry (.stl file) and corresponding simulation box. Now, I have increased my geometry size and also accordingly the simulation box. Periodic bounadries (p) are provided x- and z-dir and fixed boundaries (f) in y-dir of the simulation box. More specifically, elements (top, front and back stl files) are having problems in importing and paralization, while the remaining elements (inlet, outlet, channelbottom_1, channleBottom_2, bedbottom, insertion_face) are imported are paralized without any issue. The error produced looks like this:

ERROR on proc 1: assertion failed (../region_neighbor_list_I.h:165)
...
...

It is quite strange that with bigger geometry, the error occurs when importing some elements of mesh (.stl files), while in smaller geometry the import and paralization of all mesh elements work properly and simulation starts without any issue. The liggghts input scripts is provided below:

echo both
log ../DEM/log.liggghts
thermo_log ../DEM/post/thermo.txt

atom_style granular
atom_modify map array
communicate single vel yes

boundary p f p
newton off

units si
processors 14 4 2

#simulation box ranging whole CFD geometry (slightly grater than CFD domain ~0.02m in y- and z-dir, periodic cfd boubdaries almost coincide with periodic simulation box boundaries in x-dir)
region reg block -0.2 0.2 -0.02 0.26 -0.02 0.17 units box
create_box 2 reg

neighbor 0.006 bin #avg particle dia (2*avg radius) of gravel bed
neigh_modify delay 0

# Material properties required for granular pair styles

fix m1 all property/global youngsModulus peratomtype 5.e6 5.e6
fix m2 all property/global poissonsRatio peratomtype 0.45 0.45
fix m3 all property/global coefficientRestitution peratomtypepair 2 0.3 0.3 0.3 0
fix m4 all property/global coefficientFriction peratomtypepair 2 0.08 0.08 0.08 0

# pair style
pair_style gran model hertz tangential history # Hertzian without cohesion
pair_coeff * *

# timestep, gravity
timestep 0.0000001
fix ts_check all check/timestep/gran 1000 0.1 0.1
fix gravi all gravity 9.81 vector 0.0 -1.0 0.0

# Defining the walls that can be in contact with the particles; those come from the STL folder

fix inlet all mesh/surface/surface file STL/inlet.stl type 1 curvature_tolerant yes
fix outlet all mesh/surface/surface file STL/outlet.stl type 1 curvature_tolerant yes
fix top all mesh/surface/surface file STL/top.stl type 1 curvature_tolerant yes
fix channelBottom_1 all mesh/surface/surface file STL/channelBottom_1.stl type 1 curvature_tolerant yes
fix channelBottom_2 all mesh/surface/surface file STL/channelBottom_2.stl type 1 curvature_tolerant yes
fix bedBottom all mesh/surface/surface file STL/bedBottom.stl type 1 curvature_tolerant yes
fix front all mesh/surface/surface file STL/front.stl type 1 curvature_tolerant yes
fix back all mesh/surface/surface file STL/back.stl type 1 curvature_tolerant yes
fix insFace all mesh/surface/surface file STL/insertion_face.stl type 1 curvature_tolerant yes

# The wall contacts are only allowed at the box walls
fix wall all wall/gran model hertz tangential history mesh n_meshes 8 meshes inlet outlet top channelBottom_1 channelBottom_2 bedBottom front back
fix xwalls1 all wall/gran model hertz tangential history primitive type 1 xplane 0.0
fix xwalls2 all wall/gran model hertz tangential history primitive type 1 xplane 0.15

# particle distributions and insertion
region bc block 0.0 0.15 0.0 0.1 0.0 0.15 units box
fix pts1 all particletemplate/sphere 15485863 atom_type 1 density constant 2650 radius constant 0.00616
fix pts2 all particletemplate/sphere 15485867 atom_type 1 density constant 2650 radius constant 0.00459
fix pts3 all particletemplate/sphere 32452843 atom_type 1 density constant 2650 radius constant 0.00394
fix pts4 all particletemplate/sphere 32452867 atom_type 1 density constant 2650 radius constant 0.00339
fix pts5 all particletemplate/sphere 49979687 atom_type 1 density constant 2650 radius constant 0.00290
fix pts6 all particletemplate/sphere 49979693 atom_type 1 density constant 2650 radius constant 0.00236
fix pts7 all particletemplate/sphere 67867967 atom_type 1 density constant 2650 radius constant 0.00196
fix pts8 all particletemplate/sphere 67867979 atom_type 1 density constant 2650 radius constant 0.00098
fix pts9 all particletemplate/sphere 86028121 atom_type 1 density constant 2650 radius constant 0.00049
fix pdd1 all particledistribution/discrete 86028157 9 pts1 18.5 pts2 25.7 pts3 19.7 pts4 7.2 pts5 21 pts6 4.7 pts7 2.9 pts8 0.2 pts9 0.1

# bed is packed with 60 % of its volume with solid particles, let it settle under gravity, zero initial velocity, overlapping packing is generated>might need time to come to equilibrium
fix ins all insert/pack seed 91428863 distributiontemplate pdd1 vel constant 0. 0. 0. insert_every once overlapcheck no all_in yes volumefraction_region 0.6 region bc #generate the bed but also in the inlet and outlet section some layering is observed

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

# screen output
compute rke all erotate/sphere
thermo_style custom step atoms ke c_rke vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes

# insert the first particles so that dump is not empty
run 1
#dump dmp all custom 5000 post/dump.liggghts_init id type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius

dump dmpvtk all custom/vtk 50000 post/particles_pre_*.vtk id type x y z vx vy vz fx fy fz radius mass

run 100000 upto

write_restart post/restart/liggghts.restart

I am stuck here and not able to find cause of the error, I would be grateful if someone can look into it and probably help me to solve the issue.

Best Regards
Atul

atul2018 | Wed, 05/04/2022 - 18:01

I am not sure about why is was happening but I managed to solve the issue somehow. I extended the simulation box in z-direction from (-0.02 0.17) to (-0.05 0.2) and now that error is not acuuring anymore.

It is strange that stl bounadries (front and back) are located at z=0.15 and z=0, which was also within the previously defined simulation box boundaries. i am not sure about both the cause of error and the solution I found. Any expert comment?

Best Regards
Atul