A project by DCS Computing and CFDEMresearch
Hello,
i get the Assertion Error, when i want to simulate on periodic boundary dircetion. If i set all boundaries to fff it works fine. Only when i set ffp, it throws me the error. Can anybody hint me wo where this comes from?
Thanks a lot for your help!
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mschramm | Thu, 07/08/2021 - 16:26
post error in script
Hello,
could you post your log file with the "echo both" flag enabled?
David Thomas | Wed, 11/10/2021 - 12:12
Assertion Failed Error with periodic Boundary
Hi,
I too experience "Assertion error" when simulating using periodic boundary condition. Simulation runs fine with fixed boundary condition. The log file content (with echo both flag) with error is as follows:
hard_particles yes
communicate single vel yes
processors * * *
units si
region reg block -0.002e-2 1.56e-2 0 0.08e-2 -0.02e-2 0.430e-2 units box
#create_box 2 reg
read_restart restart.fillone3
Reading restart file ...
version 3 8
WARNING: Restart file used different # of processors (../read_restart.cpp:574)
orthogonal box = (-2e-05 0 -0.0002) to (0.0156 0.0008 0.0043)
1 by 1 by 1 MPI processor grid
WARNING:
The contact model you specified is not located in any whitelist.
Because of this the model will be run in an unoptimized version (increasing runtime by up to 20%).
In order to optimize this model you have the following options:
(i) Run the genAutoExamplesWhitelist.sh script in your LIGGGHTS(R) source folder to automatically parse the input script
(ii) Add the model combination by hand to your style_contact_model_user.whitelist that can be found in your LIGGGHTS(R) source folder
If you perform one of the steps above LIGGGHTS(R) needs to be recompiled to generate the optimized code.
(../contact_models.h:364)
30000 atoms
neighbor 50e-6 bin
neigh_modify delay 0 one 5000
fix m1 all property/global youngsModulus peratomtype 3e9 210e9
fix m2 all property/global poissonsRatio peratomtype 0.3 0.3
fix m3 all property/global coefficientRestitution peratomtypepair 2 0.5 0.5 0.5 0.5
fix m4 all property/global coefficientFriction peratomtypepair 2 0.5 0.5 0.5 0.5
fix m5 all property/global coefficientRollingFriction peratomtypepair 2 0.1 0.1 0.1 0.1
fix m6 all property/global HamakerConstant scalar 0.1e-20
fix m7 all property/global maxSurfaceDistance scalar 1e-6
fix m8 all property/global minSurfaceDistance scalar 1.65e-10
fix m9 all property/global userConstantDistfactor scalar 2
#New pair style
pair_style gran model hertz tangential history cohesion vdw3 rolling_friction cdt
WARNING:
The contact model you specified is not located in any whitelist.
Because of this the model will be run in an unoptimized version (increasing runtime by up to 20%).
In order to optimize this model you have the following options:
(i) Run the genAutoExamplesWhitelist.sh script in your LIGGGHTS(R) source folder to automatically parse the input script
(ii) Add the model combination by hand to your style_contact_model_user.whitelist that can be found in your LIGGGHTS(R) source folder
If you perform one of the steps above LIGGGHTS(R) needs to be recompiled to generate the optimized code.
(../contact_models.h:364)
pair_coeff * *
timestep 1e-8
fix gravi all gravity 9.81 vector 0.0 0.0 -1.0
fix cad1 all mesh/surface file meshes/container.stl type 1 scale 0.002e-2 curvature 1e-5
INFO: mesh file (meshes/container.stl) is required, but data will be taken from restart file (../fix_mesh.cpp:417)
Resetting global state of Fix cad1 Style mesh/surface from restart file info
fix granwalls all wall/gran model hertz tangential history mesh n_meshes 1 meshes cad1
Resetting global state of Fix n_neighs_mesh_cad1 Style property/atom from restart file info
Resetting per-atom state of Fix n_neighs_mesh_cad1 Style property/atom from restart file info
Resetting global state of Fix tracker_cad1 Style contacthistory/mesh from restart file info
Resetting per-atom state of Fix tracker_cad1 Style contacthistory/mesh from restart file info
unfix granwalls
unfix cad1
fix cad3 all mesh/surface file meshes/p_bed.stl type 1 precision 1e-12 element_exclusion_list read blacklist_combase.txt scale 0.002e-2 curvature 1e-5
Reading STL file 'meshes/p_bed.stl' (mesh processing step 1/3)
fix cad4 all mesh/surface file meshes/layering_base.stl type 1 scale 0.002e-2 move 0 0 -69.6e-6 curvature 1e-5
Reading STL file 'meshes/layering_base.stl' (mesh processing step 1/3)
fix cad5 all mesh/surface file meshes/left_blade_NF.stl type 1 scale 0.002e-2 curvature 1e-5
Reading STL file 'meshes/left_blade_NF.stl' (mesh processing step 1/3)
fix granwalls all wall/gran model hertz tangential history mesh n_meshes 3 meshes cad3 cad4 cad5
#apply nve integration to all particles
fix integr all nve/sphere
#output settings, include total thermal energy
compute rke all erotate/sphere
thermo_style custom step atoms ke c_rke vol
thermo 5000
thermo_modify lost ignore norm no
# Check time step and initialize dump file
fix ctg all check/timestep/gran 1 0.01 0.01
run 1
Resetting global state of Fix contacthistory Style contacthistory from restart file info
Resetting per-atom state of Fix contacthistory Style contacthistory from restart file info
Setting up run at Wed Nov 10 16:34:03 2021
ERROR on proc 0: assertion failed (../region_neighbor_list_I.h:165)
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
Thank you,
Thomas.