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Re: [lammps-users] molindex and identifying atoms on the same molecule
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Re: [lammps-users] molindex and identifying atoms on the same molecule


From: Jeff Towers <jeff.towers66@...24...>
Date: Mon, 27 Nov 2017 14:37:14 +0900

Dear Axel,

Thank you so much for your quick reply. That's really helpful.

I don't fully understand what you mean by "molecule IDs in LAMMPS are purely indicating molecules by convention and thus may not be tied to individual molecules at all". Would you mind elaborating further? Based on my reading of compute_pe_mol_tally, I assume that all the atoms in the same molecule will always have the same molecule ID as each other.

Thanks again.
Best,
Jeff

On Mon, Nov 27, 2017 at 1:09 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Sun, Nov 26, 2017 at 9:25 PM, Jeff Towers <jeff.towers66@...24...> wrote:
Dear LAMMPS users and developers,

I am trying to add a new compute to LAMMPS, and I need to be able to identify which atoms are part of the same molecule.

Under atom_style "full", the molecule number of each atom is defined in the data file so I am thinking to do a comparison of molecule numbers for each atom. I would like to ask:

Is the molecule number assigned to each atom held in atom->molindex?

​no.​


The array is empty when called from a typical compute like
  compute_pe_atom.cpp's ComputePEAtom::compute_peratom()
or
  compute X/tally

​if you'd looked closer at compute_pe_mol_tally.cpp,​ you'd have seen, that what you are looking for is stored in atom->molecule and that when atom->molecule_flag is non-zero, this information is available.

axel.

p.s.: please note, that molecule IDs in LAMMPS are purely indicating molecules by convention and thus may not be tied to individual molecules at all.

 

In each case I get
(gdb) print(atom->molindex)
$1 = (int *) 0x0

My guess is that either

(1) An array different to molindex holds the molecule-member information
(2) Lammps doesn't hold molecule-member information beyond the initial read_data (in which case, any suggestion about a different way to do this would be appreciated)
(3) molindex is correct but I need to do something to make this information available within the computes above.

I would really appreciate any guidance on this issue.

Thank you,
Best,

Jeff

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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.