Dear All,
I'm very new to LAMMPS and i'm not a chemist nor physicist (i do mechanics),
yet I have to work a little bit with MD.
When I run LAMMPS, I have the following error message:
LAMMPS (3 Jun 2011)
Scanning data file ...
1 = max bonds/atom
Reading data file ...
orthogonal box = (0 0 -1.3) to (59 60 1.3)
1 by 1 by 1 processor grid
Segmentation fault
In that thread, it was assumed that the position of atoms is too close
http://lammps.sandia.gov/threads/msg12247.html
My input file has coarse-grained polymer (30 chains with 10 monomers each, FENE).
In order for distance to be big, I put chains initially so that
they do not interact (distance between neighbor chains ~ 5-6).
And the distance between monomers in 1 chains is 1.3.
(LJ units with 2.5 and 1.5 cutoff for not bonded and bonded interactions respectively)
So it seems to me that the source of "segmentation fault" is different in my case.
I would be very much grateful for any income on that problem.
p/s/ I attach both input and data files.
Kind regards,
Denis.
data.2dPolyM30N10Lx59Ly60 (23.5 KB)
in.chainMy2D (1.36 KB)
dear denis,
Dear All,
I'm very new to LAMMPS and i'm not a chemist nor physicist (i do mechanics),
yet I have to work a little bit with MD.
When I run LAMMPS, I have the following error message:
LAMMPS (3 Jun 2011)
Scanning data file ...
1 = max bonds/atom
Reading data file ...
orthogonal box = (0 0 -1.3) to (59 60 1.3)
1 by 1 by 1 processor grid
Segmentation fault
In that thread, it was assumed that the position of atoms is too close
LAMMPS Molecular Dynamics Simulator
this is just speculation. segmentation faults can have diverse sources.
have a look at this e-mail describing how to use a debugger to
track down the real cause for a segfault.
My input file has coarse-grained polymer (30 chains with 10 monomers each,
FENE).
In order for distance to be big, I put chains initially so that
they do not interact (distance between neighbor chains ~ 5-6).
And the distance between monomers in 1 chains is 1.3.
(LJ units with 2.5 and 1.5 cutoff for not bonded and bonded interactions
respectively)
So it seems to me that the source of "segmentation fault" is different in my
case.
I would be very much grateful for any income on that problem.
i guess anybody in academia would be grateful for income. 
cheers,
axel.
Dear Axel,
Thank you for your advises and link on how to debug,
having found that thread I linked on some distance issues, i though
my problem can be solved without debugging, anyway...
I tried to update (svn) and then to recompile LAMMPS with CCFLAGS '-O -g' and that's what I have:
...
pair_airebo.cpp: In member function ‘virtual void LAMMPS_NS::PairAIREBO::compute(int, int)’:
pair_airebo.cpp:101:35: error: ‘virial_compute’ was not declared in this scope
has something been recently changed in that file?
p/s/ compiling without '-g' yields same error, as expected.
Regards,
Denis.
You need a blank line after the Atoms keyword.
Not sure why it is crashing instead of printing an error
message, but I'll look at it.
Steve
Dear Steve,
Thank you for finding my stupid mistake,
It does work now.
Regards,
Denis.