Dear all,
ellipsoid.dat (2.35 KB)
ellipsoid_test2.in (803 Bytes)
To me, it seems like a lot of your atoms start in exactly the same position? This will of course result in INF/NAN for your interactions… I guess there is something wrong with how you generate your data file.
Thanks Stefan,
From documentation, I found that in “atom_style hybrid angle ellipsoid” the idea is to have the atom ID, type, x y z first and after that molecule ID, ellipsoid flag,density. Or am I misinterpreting something?
With best wishes,
Anna
You’re right, according to the documentation that is the way it should be. I do seem to recall something differently, maybe this got changed recently? What version of LAMMPS are you using?
The way I remember it, you needed to list all properties the first style expected, and then all the arguments the second style expected except those already specified by the first.
Dear Stefan,
I am using the latest version for Ubuntu.
Ok, it also crashes on the latest version for me. gdb shows something like this:
Program received signal SIGSEGV, Segmentation fault.
0x000000000052b8bf in LAMMPS_NS::shape_consistency (this=0x168cc70, itype=itype@…4654…=2,
shapex=@…5777…: 3.1829936873866332e-313, shapey=@…5778…: 3.395193266532567e-313,
shapez=@…5779…: 3.6073928456785008e-313) at …/atom.cpp:1466
1466 else shape = bonus[ellipsoid[i]].shape;
(gdb) print shape
$1 =
(gdb) print bonus
$2 = (LAMMPS_NS::AtomVecEllipsoid::Bonus *) 0x0
I don’t think that bonus should be a NULL-pointer at this point, since it is dereferenced in order to set shape. Maybe this is a bug instead of faulty input?
Ok, it also crashes on the latest version for me. gdb shows something like
this:
FYI, the term "the latest version" is very vague. it would be more helpful
to quote the specific version string.
Program received signal SIGSEGV, Segmentation fault.
0x000000000052b8bf in LAMMPS_NS::shape_consistency (this=0x168cc70,
[email protected]...=2,
[email protected]...: 3.1829936873866332e-313, [email protected]...:
3.395193266532567e-313,
[email protected]...: 3.6073928456785008e-313) at ../atom.cpp:1466
1466 else shape = bonus[ellipsoid[i]].shape;
(gdb) print shape
$1 = <optimized out>
(gdb) print bonus
$2 = (LAMMPS_NS::AtomVecEllipsoid::Bonus *) 0x0I don't think that bonus should be a NULL-pointer at this point, since it
is dereferenced in order to set shape. Maybe this is a bug instead of
faulty input?
you could call it a bug that LAMMPS doesn't provide a better check for
inconsistent data, but the core problem is that the data file is missing
some entries.
the header should have an entry for "ellipsoids" that specifies how many
ellipsoids are there (55 i guess). that will trigger allocating the bonus
structs.
also there needs to be an Ellipsoids section defining the shape of the
ellipsoids and their orientation.
please see the read_data docs for more details.
axel.
Ooooh, I get it now I think. You also need to specify an “Ellipsoids” section in your data file, in which you specify the diameters and orientation of the ellipsoids, see the part on Ellipsoids here: http://lammps.sandia.gov/doc/read_data.html
Wow, Axel beat me to it with a few seconds.
Thank you Axel and Stefan! That helped me a lot!