[lammps-users] dump dcd option

Dear all,
Currently, the dump group must be all for the dcd style. I just wonder if it can be modified to dump selected group into DCD format. It may help to reduce the file size in case there is massive solvent, which is not important. Thanks!

best,
Zhenlong

Dear all,

dear zhenlong,

    Currently, the dump group must be *all* for the *dcd* style. I just
wonder if it can be modified to dump selected group into DCD format. It may
help to reduce the file size in case there is massive solvent, which is not
important. Thanks!

yes. it should be doable. you have to take your favorite editor
load the dump_dcd.* files and implement it. :wink:

you have to make sure, though, that the group that you use
does not change the number of atoms and their identity, as
a .dcd file does not "allow" this.

cheers,
   axel.

p.s.: and if you're done with that, please apply the same
change to xtc format dumps. i know some people that would
be very thankful. :wink:

Since dcd and xtc formats sort their output by allocating
one big array for all the atoms (on a single proc), the issue
is how to map a subset of atoms into a linear compact array in a
consistent fashion. If you could do this, it probably wouldn't
be too hard to add the feature you describe to dump_xtc and dump_dcd

Steve

Thank, Axel and Steve. In my case, all the atoms other than the solvent are located at the
very beginning of the coordinate file, so it is really straightforward to modify the program, without
the trouble to orderly sort the atom into a compact array.

best,
Zhenlong

Thank, Axel and Steve. In my case, all the atoms other than the solvent are
located at the
very beginning of the coordinate file, so it is really straightforward to
modify the program, without
the trouble to orderly sort the atom into a compact array.

zhenlong,

well, feel free to hack it your way, but this kind of hack
cannot be included into any official version.

anyways, this discussion is pretty much pointless, since i
have already implemented a proper group dump option for both
xtc and dcd (we need this for ultra-large coarse-graind MD
runs on memory constrained platforms) and sent the resulting
modifications to steve for inclusion into the official LAMMPS
distribution.

cheers,
   axel.