Hi All,
I have 2 questions related to dumping and I could not find their answers on manual.
1-) I want to dump atoms velocities and positions after certain time step ( lets say after running the simulation 10000 steps). How can I do that?
2-) For now, I am only dumping the atom velocities and positions when the atoms are in the region I specify. But for other time steps ( when atoms are not in the specified region) it is still dumping
ITEM: BOX BOUNDS pp pp pp
0 14.9341
0 17.2444 ( lattice constants)
0 35
I do not want to dump them for each time step because it makes my file too big. How can I get rid off them?
Thanks,
Rose
Hi All,
I have 2 questions related to dumping and I could not find their answers on manual.
1-) I want to dump atoms velocities and positions after certain time step ( lets say after running the simulation 10000 steps). How can I do that?
the question is not entirely clear. do you want to *start* dumping
after a certain point that then do it regularly at a known interval,
or do you want to write out selected frames at specific time step
counts that are not regular?
in *both* cases, there *is* an answer in the manual: you can just run
for a given number of steps and only then define the dump and start
dumping. also, you can always use the write_dump command to output the
current state to a dump file.
for the second case, you can also look for dump_modify every in the
documentation. this can refer to a variable, which in turn can either
compute the sequence of steps where you want to have output or even
read it from a file.
2-) For now, I am only dumping the atom velocities and positions when the atoms are in the region I specify. But for other time steps ( when atoms are not in the specified region) it is still dumping
ITEM: BOX BOUNDS pp pp pp
0 14.9341
0 17.2444 ( lattice constants)
0 35
I do not want to dump them for each time step because it makes my file too big. How can I get rid off them?
i don't know any answer for that, but if you output frames *that*
frequently, you are likely doing something wrong. in MD consecutive
frames are *highly* correlated and thus have very little statistical
relevance and thus i would suspect that you output the dump to
frequently. other than that, you could output each frame to a separate
file and then just delete all "short" files before you combine them to
a trajectory with the data you want to keep. and beyond that, there is
always the option to modify the code. it may be worth to add an option
to dump_modify to tell it to not output the box information (at all).
axel.
It’s pretty clear in the lammps documentation… http://lammps.sandia.gov/doc/dump.html
dump ID group-ID style N file args
- N = dump every this many timesteps
- group-ID = ID of the group of atoms to be dumped
so if you did:
dump region_atoms <group-id for atoms in region> custom 10000 region_atoms.lammpstrj id x y z ix iy iz vx vy vz
you should get what you are after... But I would probably read through the documentation a bit more carefully if you are struggling to understand how to dump only certain atoms..