Dear Lammps users
I used Reaxff force fied for my study and I also used fix/speices command to get the speices. I want to get the molecule ID corresponding to the species, including the new speices formed during the simulation. Then I want to dump the specified molecule ID to dump file to visulize the molecular structure. My idea is to get the per-atom molecule ID, then I will correspod the molecule ID to the species, then I will out put the specified molecule ID to dump file.
I have finished the simulation with following command
fix 3 all reax/c/species 1 1 100 species.tatb
dump 1 all custom 100 coro-xu.lammpstrj id type q xu yu zu ix iy iz f_3
I think I get the per-atom molecule ID in dump file. But I can not correspond the molecule ID to the species.My questions are
(1)How can I correspond the molecule ID to the species?After that, how to out put the specified the molecule ID?
(2)If I have done wrong things(I mean the fix/species and dump command), or my idea is wrong, which commamd should I use to dump the specified molecule ID, including the new speices formed during the simulation, to dump file in the in the input when I start the simulation?
My lammps version is 10-Aug15. The atom_style is charge. The attachment is my input and dump file.
Sincerely
Fan Li
从QQ邮箱发来的超大附件
coro-x.lammpstrj (81.01M, 2016年02月10日 17:32 到期)
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in.coro-oh (2.48 KB)
Current fix reax/c/species command does not have this function; meaning there is no direct correspondence of molecule ID to species type. Perhaps there is a way to add this function in as an additional keyword. Note that per-atom molecule ID is an instantaneous property; meaning it changes from step to step, which adds complexity to this keyword. If you want this function very bad, remind me in a week when I get back to my office and I will take a look.
Ray
Dear Lammps users
I used Reaxff force fied for my study and I also used fix/speices command
to get the speices. I want to get the molecule ID corresponding to the
species, including the new speices formed during the simulation. Then I
want to dump the specified molecule ID to dump file to visulize the
molecular structure. My idea is to get the per-atom molecule ID, then I
will correspod the molecule ID to the species, then I will out put the
specified molecule ID to dump file.
*is* there a visualization program that *can* read molecule ids from
LAMMPS dump file (in every time step) and make it available for
visualization?
i don't know of any. the only way i can imagine this to work, would be
with custom scripting and a scriptable viz program like VMD. in this case,
the species information would have to be processed independently with
script code and for that the existing output would be sufficient.
in order to simply track the changes in the bond topology, however, this is
not needed, but rather a visual representation that can recompute the
connectivity would be sufficient. most viz programs compute connectivity
based on (rather simple) heuristics anyway, and for visualization purposes
it is rarely needed to follow the details as meticulously.
axel.
Thanks for answering questions.
I just wonder whether lammps has this function.
Sincerly
Fan Li