polymer and ellipsoid simulation in 3D

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::atom::shape_consistency (this=0x168cc70, [email protected]…4654…=2,
[email protected]…5777…: 3.1829936873866332e-313, [email protected]…5778…: 3.395193266532567e-313,
[email protected]…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::atom::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 *) 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?

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. :wink:

Thank you Axel and Stefan! That helped me a lot!