[lammps-users] problem about shell command

Dear all,
Recently, I encountered a problem in using lammps. As we known, commands like “variable, jump, etc” could be combined together to perform a circular simulation in lamps input file. However, in my simulation, I want to make some changes about the atom coordinates in the “dump” file by converting dump file into “data” file during the intervals so that the next circulation could use it. In order to achieve this, I want to insert the script, such as “shell ./abc”, to execute it in the input file of lammps. However, lammps seems not cover this usage, so I wonder how can I solve this problem?

Dear all,
Recently, I encountered a problem in using lammps. As we known, commands
like "variable, jump, etc" could be combined together to perform a circular
simulation in lamps input file. However, in my simulation, I want to make
some changes about the atom coordinates in the "dump" file by converting
dump file into "data" file during the intervals so that the next circulation
could use it. In order to achieve this, I want to insert the script, such as
"shell ./abc", to execute it in the input file of lammps. However, lammps
seems not cover this usage, so I wonder how can I solve this problem?

update your lammps executable and check out the new read_dump command.
that would short cut the process.

axel.

oops - there is no read_dump command yet. If the doc page for
it slipped into the repository/distribution, then it's a mistake, since
the source code has not yet been finished/released. This
is a future command.

The reason you can't do this from LAMMPS:

I want to insert the script, such as
"shell ./abc", to execute it in the input file of lammps.

is that is non-portable, and is not even possible on some
parallel machines. Some OS's on parallel machines do
not support executing an arbitrary command for various
reasons. Also, it is unclear what it means in
parallel. Would every processor run "abc", or just one?

You can of course, write a script yourself (e.g. a batch submission
script on a parallel machine) to run LAMMPS, run some other
code, run LAMMPS some more, etc.

Steve

Thanks for your advice and explanation! I think I have to write a a batch submission
script instead.

Qingjie

2010/8/10 Steve Plimpton <[email protected]>