The identification of atom in simulations by lammps

Dear everyone,

Now I have a question to consult.When I did simulations using the lammps,I colored an atom in a nanowire model.Then after slight deformations,the positions of the colored atom have dramaticlly changed.And I wonder whether it is physically reasonable.

So my question is:Whether the atoms in simulations which using lammps,each have a permanent fixed identification? In other words,for example,do the atoms with the same serial numbers in different frames of a ‘pdb’ trajectory file represent the same atoms?

I would appreciate if somebody could help me.

Thank you very much in advance and best regards,

Nianke Chen

2012/2/9 陈念科 <[email protected]>:

Dear everyone,

Now I have a question to consult.When I did simulations using the lammps,I colored an atom in a nanowire model.Then after slight deformations,the positions of the colored atom have dramaticlly changed.And I wonder whether it is physically reasonable.

probably not. difficult to tell from afar, though.

So my question is:Whether the atoms in simulations which using lammps,each have a permanent fixed identification? In other words,for example,do the atoms with the same serial numbers in different frames of a 'pdb' trajectory
file represent the same atoms?

lammps doesn't produce a pdb format trajectory. so how should this be.
the order of atoms in dump files can change due to atoms movement
between parallelization domains and atom sorting to improve cache
efficiency, but the mapping of atom tags to atoms doesn't.

for more details, please consult the documentation on the dump command
and the comments on the dump_modify sort option.

axel.

If you do a dump in the native LAMMPS format
you can dump the atom ID. As Axel said, that
ID is fixed for the duration of the simulation. So you
can easily monitor how far the atom you care about
has moved. Or use compute displace/atom and
either do it for a single atom (if you know the ID), or
take the max of the result via compute reduce, and print
out the max distance any atom has moved as your
simulation runs.

Steve

Dear Axel,

Thank you very much for your help!I have consulted the manual about dump and dump_modify sort commands as you suggested.
Yes,I made a mistake before.The pdb format trajectory file is produced by VMD.So the serial numbers of atoms are rebuilt by VMD based on the atom order in dump file which is indeterminate unless the dump_modify sort option is invoked.It means the serial numbers are disorder,either.In my previous simulation,the same serial number doesn’t represent the same atoms.Is my comprehension right? And if I add this command ‘dump_modify dump-ID sort id’ on the condition of dumping the atom ID as Steve said,will it be OK?

And than I tryed another simulation as above mentioned.I find the positions of the colored atom doesn’t change so much already.I think it is more reasonable than before.

Thanks again,

Nianke Chen

2012/2/10 陈念科 <[email protected]>:

Dear Axel,

Thank you very much for your help!I have consulted the manual about dump and
dump_modify sort commands as you suggested.
Yes,I made a mistake before.The pdb format trajectory file is produced by
VMD.So the serial numbers of atoms are rebuilt by VMD based on the atom
order in dump file which is indeterminate unless the dump_modify sort option
is invoked.It means the serial numbers are disorder,either.In my previous
simulation,the same serial number doesn't represent the same
atoms.Is my comprehension right? And if I add this command 'dump_modify

the reader for native lammps trajectories in VMD does
sort atoms by atom id upon reading if the information
is present (in case of a custom dump). same goes for
dcd and xtc, where the conserved order (and number)
of atoms is part of the file format.

it does not hold for .xyz format dumps, because the
file format doesn't provide this information.

dump-ID sort id' on the condition of dumping the atom ID as Steve said,will
it be OK?

as i wrote above, in VMD it doesn't matter for atom
or custom style dumps, if the atom id is contained.

And than I tryed another simulation as above mentioned.I find the positions
of the colored atom doesn't change so much already.I think it is more
reasonable than before.

i don't know your simulation, so i cannot comment
on whether what you see is reasonable or not.

axel.