Hi, All:
I am trying to read particles from file using an external data file (see attached LIGGGHTS input files), however I am getting neighbor error problems, I have attached the file below, could anyone tell the exact problem? Thanks in advance.
The Error I got is pasted below:
run 1 upto
Setting up run ...
INFO: more than 15 touching neighbor atoms found, growing contact history.
INFO: more than 30 touching neighbor atoms found, growing contact history.
INFO: more than 45 touching neighbor atoms found, growing contact history.
INFO: more than 60 touching neighbor atoms found, growing contact history.
INFO: more than 75 touching neighbor atoms found, growing contact history.
INFO: more than 90 touching neighbor atoms found, growing contact history.
INFO: more than 105 touching neighbor atoms found, growing contact history.
INFO: more than 120 touching neighbor atoms found, growing contact history.
INFO: more than 135 touching neighbor atoms found, growing contact history.
INFO: more than 150 touching neighbor atoms found, growing contact history.
INFO: more than 165 touching neighbor atoms found, growing contact history.
INFO: more than 180 touching neighbor atoms found, growing contact history.
INFO: more than 195 touching neighbor atoms found, growing contact history.
INFO: more than 210 touching neighbor atoms found, growing contact history.
INFO: more than 225 touching neighbor atoms found, growing contact history.
INFO: more than 240 touching neighbor atoms found, growing contact history.
INFO: more than 255 touching neighbor atoms found, growing contact history.
INFO: more than 270 touching neighbor atoms found, growing contact history.
INFO: more than 285 touching neighbor atoms found, growing contact history.
INFO: more than 300 touching neighbor atoms found, growing contact history.
INFO: more than 315 touching neighbor atoms found, growing contact history.
INFO: more than 330 touching neighbor atoms found, growing contact history.
INFO: more than 345 touching neighbor atoms found, growing contact history.
INFO: more than 360 touching neighbor atoms found, growing contact history.
INFO: more than 375 touching neighbor atoms found, growing contact history.
INFO: more than 390 touching neighbor atoms found, growing contact history.
INFO: more than 405 touching neighbor atoms found, growing contact history.
INFO: more than 420 touching neighbor atoms found, growing contact history.
INFO: more than 435 touching neighbor atoms found, growing contact history.
INFO: more than 450 touching neighbor atoms found, growing contact history.
INFO: more than 465 touching neighbor atoms found, growing contact history.
INFO: more than 480 touching neighbor atoms found, growing contact history.
INFO: more than 495 touching neighbor atoms found, growing contact history.
INFO: more than 510 touching neighbor atoms found, growing contact history.
INFO: more than 525 touching neighbor atoms found, growing contact history.
INFO: more than 540 touching neighbor atoms found, growing contact history.
INFO: more than 555 touching neighbor atoms found, growing contact history.
INFO: more than 570 touching neighbor atoms found, growing contact history.
INFO: more than 585 touching neighbor atoms found, growing contact history.
INFO: more than 600 touching neighbor atoms found, growing contact history.
INFO: more than 615 touching neighbor atoms found, growing contact history.
INFO: more than 630 touching neighbor atoms found, growing contact history.
INFO: more than 645 touching neighbor atoms found, growing contact history.
INFO: more than 660 touching neighbor atoms found, growing contact history.
INFO: more than 675 touching neighbor atoms found, growing contact history.
INFO: more than 690 touching neighbor atoms found, growing contact history.
INFO: more than 705 touching neighbor atoms found, growing contact history.
INFO: more than 720 touching neighbor atoms found, growing contact history.
INFO: more than 735 touching neighbor atoms found, growing contact history.
INFO: more than 750 touching neighbor atoms found, growing contact history.
INFO: more than 765 touching neighbor atoms found, growing contact history.
INFO: more than 780 touching neighbor atoms found, growing contact history.
INFO: more than 795 touching neighbor atoms found, growing contact history.
INFO: more than 810 touching neighbor atoms found, growing contact history.
INFO: more than 825 touching neighbor atoms found, growing contact history.
INFO: more than 840 touching neighbor atoms found, growing contact history.
INFO: more than 855 touching neighbor atoms found, growing contact history.
INFO: more than 870 touching neighbor atoms found, growing contact history.
INFO: more than 885 touching neighbor atoms found, growing contact history.
INFO: more than 900 touching neighbor atoms found, growing contact history.
INFO: more than 915 touching neighbor atoms found, growing contact history.
INFO: more than 930 touching neighbor atoms found, growing contact history.
INFO: more than 945 touching neighbor atoms found, growing contact history.
INFO: more than 960 touching neighbor atoms found, growing contact history.
INFO: more than 975 touching neighbor atoms found, growing contact history.
INFO: more than 990 touching neighbor atoms found, growing contact history.
INFO: more than 1005 touching neighbor atoms found, growing contact history.
INFO: more than 1020 touching neighbor atoms found, growing contact history.
INFO: more than 1035 touching neighbor atoms found, growing contact history.
INFO: more than 1050 touching neighbor atoms found, growing contact history.
INFO: more than 1065 touching neighbor atoms found, growing contact history.
INFO: more than 1080 touching neighbor atoms found, growing contact history.
INFO: more than 1095 touching neighbor atoms found, growing contact history.
[ccav-3:16519] *** Process received signal ***
[ccav-3:16519] Signal: Segmentation fault (11)
[ccav-3:16519] Signal code: Address not mapped (1)
[ccav-3:16519] Failing at address: 0xfffffffe02a02eec
[ccav-3:16519] [ 0] /lib64/libpthread.so.0() [0x3658a0f500]
[ccav-3:16519] [ 1] liggghts() [0x6b67ba]
[ccav-3:16519] [ 2] liggghts() [0x65dbf6]
[ccav-3:16519] [ 3] liggghts() [0x6afc04]
[ccav-3:16519] [ 4] liggghts() [0x52a782]
[ccav-3:16519] [ 5] liggghts() [0x5df854]
[ccav-3:16519] [ 6] liggghts() [0x4433ab]
[ccav-3:16519] [ 7] liggghts() [0x444ff8]
[ccav-3:16519] [ 8] liggghts() [0x40daa9]
[ccav-3:16519] [ 9] /lib64/libc.so.6(__libc_start_main+0xed) [0x3657e2169d]
[ccav-3:16519] [10] liggghts() [0x40edc1]
[ccav-3:16519] *** End of error message ***
Segmentation fault (core dumped)
If I enable the cutoff value in in.liggghts_init.txt in line 33 and line 35 and then use a large ${rcut} value, say rcut=1, I get a different error:
Step Atoms KinEng 1 Volume
0 2800 0 0 0.001
1 2800 -1.#IND -1.#IND 0.001
Loop time of 0.157753 on 1 procs for 1 steps with 2800 atoms
Pair time (%) = 0.156258 (99.0525)
Neigh time (%) = 0 (0)
Comm time (%) = 2.5683e-006 (0.00162805)
Outpt time (%) = 0.00033088 (0.209746)
Other time (%) = 0.00116129 (0.736146)
Nlocal: 2800 ave 2800 max 2800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.22515e+006 ave 2.22515e+006 max 2.22515e+006 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2225149
Ave neighs/atom = 794.696
Neighbor list builds = 0
Dangerous builds = 0
dump dmp all custom 1 post/dump.liggghts_init id type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius density q
run 100 upto
Setting up run ...
#insert the first particles so that dump is not empty
run 1
Setting up run ...
ERROR on proc 0: Neighbor list overflow, boost neigh_modify one (neigh_half_bin.cpp:112)
--------------------------------------------------------------------------
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.
--------------------------------------------------------------------------
From googling the problem I guess the "Neighbor list overflow" problem might be relate to the neighbor skin value problem however I cannot figure out the exact value I should use.
Any suggestions are welcome, thanks in advance!
Roy
| Attachment | Size |
|---|---|
 clump_data_bond.txt | 224.6 KB |
| in.liggghts_init_0.txt | 1.93 KB |
sbateman | Thu, 04/25/2013 - 20:19
Well, the first thing I
Well, the first thing I notice is that you are using an old version of LIGGGHTS with the "granular" atom style. You should upgrade to the latest version 2.3.2, which uses "sphere".
Secondly, the atoms in your data file are highly overlapped, in fact many particles are in the exact same position. Also, the z positions are all 3.000e+03. Surely this is not what you intended?
dbxmcf | Thu, 04/25/2013 - 22:15
Hi, sbateman
Hi, sbateman
Thank you for the reply, I am trying to test bonded model proposed in here: https://github.com/Polyun/LIGGGHTS-PUBLIC, therefore the granular atom style is still used, I believe it should still compatible with the newest LIGGGHTS 2.3.2 (actually I am using the newest version of LIGGGHTS), the meaning of the data file with the "granular" keyword is (e.g. for one atom line):
id, type, x, y, z, diameter, density, charge
1 1 4.750000e-02 1.375000e-02 4.750000e-02 1.000000e-04 3.000e+03 -3.930000e-13
I ran this format using one particle and I am sure the dumped results are correct (e.g. the 3.0e+3 is density instead of z), so actually there should be no overlapping between particles.
Is there any other reason that could cause the problem?
Thank you so much!
Roy
sbateman | Fri, 04/26/2013 - 17:35
Okay, that data file format
Okay, that data file format makes more sense. I've never used the atom_style hybrid before, so I'm used to "id, type, diameter, density, x, y, z".
I ran your input and got this important section before the error about neighbors:
#insert the first particles so that dump is not empty
run 1
Setting up run ...
Memory usage per processor = 5.37105 Mbytes
Step Atoms KinEng 1 Volume
0 2800 0 0 0.001
1 2800 nan nan 0.001
Loop time of 0.00156307 on 1 procs for 1 steps with 2800 atoms
The energies are nan, which means there was some bad dynamics and/or lost atoms. Probably either some overlapped particles (though I didn't see any), or some particles are overlapped with the walls, and the simulation "exploded". That would mess up the neighbor list building.
dbxmcf | Fri, 04/26/2013 - 20:29
Thanks a lot, sbateman, I
Thanks a lot, sbateman, I searched web and found a very similar post here:
http://lammps.sandia.gov/threads/msg21595.html
I bluntly guess there might be bug in the original LAMMPS neighbor search algorithm, I manually changed the page and one value:
neigh_modify page 100000 one 10000
and it went through, although the output of Ave neighs/atom 1399.5 actually does not make any sense, I am also wondering if anyone has met such kind of problem before?
//--------------------------------------------------------
...
run 100 upto
Setting up run ...
Memory usage per processor = 136.224 Mbytes
Step Atoms KinEng 1 Volume
1 2800 1.7359162e-016 1.4469277e-021 0.001
100 2800 5.4345469e-013 2.9473368e-016 0.001
Loop time of 12.1122 on 1 procs for 99 steps with 2800 atoms
Pair time (%) = 8.80404 (72.6872)
Neigh time (%) = 0 (0)
Comm time (%) = 7.57644e-005 (0.000625521)
Outpt time (%) = 3.21341 (26.5303)
Other time (%) = 0.094705 (0.781896)
Nlocal: 2800 ave 2800 max 2800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3.9186e+006 ave 3.9186e+006 max 3.9186e+006 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3918600
Ave neighs/atom = 1399.5
Neighbor list builds = 0
Dangerous builds = 0
//----------------------------------------------------------------------------------------------
Roy
sbateman | Fri, 04/26/2013 - 22:45
In that thread on the lammps
In that thread on the lammps mailing list, the neighbor list issue was just a symptom of the real problem: bad dynamics. The output from LIGGGHTS before the neighbor list errors shows that the particle energies become nan (not-a-number) during the first timestep, which indicates that there is something crazy going on with your initial configuration. Like I said in my previous post, probably an overlap between the particles and/or the walls.
Welcome to the wonderful world of debugging! :)
ckloss | Thu, 05/02/2013 - 11:51
>>In that thread on the
>>In that thread on the lammps mailing list, the neighbor list issue was just a symptom of the real problem: bad dynamics
That's what I would guess too. I suggest you debug your system step-by-step
Cheers
Christoph