Hi ,
I am trying to run a simulation in LAMMPS and successively trying to dump
the values of the atom coordinates in dump files by following command .
dump 1 all custom 5000 dump.lammps.* id type x y
Now, after the simulation it is coming out that they are not getting
saved in the file in a precise manner. I want to get it in an ascending
way of atom id. How does it possible to correct it ?
Moreover, if i wish not to write the items, like timestep, box size
etc.(first few lines before the atomic information) what I have to do ?
Thanks in advance.
Best,
From the LAMMPS manual at http://lammps.sandia.gov/doc/dump.html:
For the atom, custom, cfg, and local styles, sorting is off by default. For the dcd, xtc, xyz, and molfile styles, sorting by atom ID is on by default. See the dump_modify doc page for details
sorting -> ascending atom id.
choose “style” xyz if you do not want the items, like timestep, box size etc.
From the LAMMPS manual at http://lammps.sandia.gov/doc/dump.html:
For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by
default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting by
atom
ID is on by default. See the
dump_modify<http://lammps.sandia.gov/doc/dump_modify.html>doc page for
details
sorting -> ascending atom id.
Yes, I understood your point. But particularly for my case, arguments are
required. So I must have to go for *custom* style. Anyway it can be
resolved by some means.
choose "style" xyz if you do not want the items, like timestep, box size
etc.
But , basically I want to include only the following args in my dump m
files
atom id,atom type,x,y,z
But style *xyz* doesn't allow any arguments. Am I right ?
then what to do ?
Best,
Saikat
> From the LAMMPS manual at http://lammps.sandia.gov/doc/dump.html:
> For the *atom*, *custom*, *cfg*, and *local* styles, sorting is off by
> default. For the *dcd*, *xtc*, *xyz*, and *molfile* styles, sorting by
> atom
> ID is on by default. See the
> dump_modify<http://lammps.sandia.gov/doc/dump_modify.html>doc page for
> details
> sorting -> ascending atom id.
Yes, I understood your point. But particularly for my case, arguments are
required. So I must have to go for *custom* style. Anyway it can be
resolved by some means.
>
> choose "style" xyz if you do not want the items, like timestep, box size
> etc.
But , basically I want to include only the following args in my dump m
files
atom id,atom type,x,y,z
But style *xyz* doesn't allow any arguments. Am I right ?
then what to do ?
jump into ganges river and hope for inspiration?
why the hell do you need to insist on outputting data
in such a stupid and useless unstructured format??
if you absolutely need it, you can write a few lines of
python or perl or whatever script code that removes
those lines, but if i remember correctly, you want to
read the data into a program of your own, right?
then i don't see the problem. just skip those lines.
this is *trivial* to program. or write your own custom
dump style (that nobody can or wants to read).
please don't waste people's time
and bandwidth with being so inflexible
and bone headed.
thanks a lot.
axel.
your original Q was simply about getting
the atoms ordered (sorted) by atom ID.
The dump_modify command has an option
for that which works for several styles - it's off by
default b/c it is extra work.
Steve