Dear all,
Is there a way for LAMMPS (or perhaps VMD) to compute the molecules or fragments existing in each step of the dump file, for example, for the whole simulation?
With a specific determined cutoff distance, could the trajectory file interpret all the fragments/molecules present in each frame and export to a text file or plot it?
As I am currently working on small systems, I can make this evaluation manually, but as the system increases, would be better if the software could supply this info for each timestep.
Thanks.
Rene
The compute cluster/atom command can group atoms by
clusters and you can dump a cluster ID for each atom
in a dump file snapshot. All atoms with same ID = one cluster.
Steve
Dear all,
Is there a way for LAMMPS (or perhaps VMD) to compute the molecules or
fragments existing in each step of the dump file, for example, for the
whole simulation?
With a specific determined cutoff distance, could the trajectory file
interpret all the fragments/molecules present in each frame and export to a
text file or plot it?
As I am currently working on small systems, I can make this evaluation
manually, but as the system increases, would be better if the software
could supply this info for each timestep.
can you provide some more context? what kind of force field and type of
system are you talking about here.
for systems with only atomic interactions there is already compute
cluster/atom that steve pointed out and you can output the cluster id
together with the atom id.
however, for systems with explicit bonds, it has some limitations, since
this is based on a neighbor list where 1-2, 1-3, and 1-4 pairs may be
excluded.
it is straightforward to implement a similar compute fragment/atom that is
based on the information about explicit bonds rather than distance. please
see the attached files, that should be included in a future version of
LAMMPS
for systems based on ReaxFF, where bonds are implicit, there is fix
reax/c/species.
axel.
compute_fragment_atom.cpp.gz (1.79 KB)
compute_fragment_atom.h.gz (920 Bytes)
Thank you very much for the info, Steve and Axel,
I am simulating energetic materials explosion using ReaxFF. The condensed phase interacts with gaseous O2 and a small temperature pulse to ignite the material. As there is aluminum and C/H/O, several distinct species are being produced and consumed at high rates. So, I’d like to compute that and verify if my output matches the kinetic mechanism.
thanks
Rene
If you are using ReaxFF and would like to examine/output the resulting fragments, you should take a look at fix reax/c/species.
Ray