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shell command

Syntax

shell command args

command = cd or mkdir or mv or rm or rmdir or putenv or arbitrary command

cd arg = dir
  dir = directory to change to
mkdir args = dir1 dir2 ...
  dir1,dir2 = one or more directories to create
mv args = old new
  old = old filename
  new = new filename or destination folder
rm args = [-f] file1 file2 ...
  -f = turn off warnings (optional)
  file1,file2 = one or more filenames to delete
rmdir args = dir1 dir2 ...
  dir1,dir2 = one or more directories to delete
putenv args = var1=value1 var2=value2
  var=value = one of more definitions of environment variables
anything else is passed as a command to the shell for direct execution

Examples

shell cd sub1
shell cd ..
shell mkdir tmp1 tmp2/tmp3
shell rmdir tmp1 tmp2
shell mv log.lammps hold/log.1
shell rm TMP/file1 TMP/file2
shell putenv LAMMPS_POTENTIALS=../../potentials
shell my_setup file1 10 file2
shell my_post_process 100 dump.out

Description

Execute a shell command. A few simple file-based shell commands are supported directly, in Unix-style syntax. Any command not listed above is passed as-is to the C-library system() call, which invokes the command in a shell. To use the external executable instead of the built-in version one needs to use a full path, for example /bin/rm instead of rm. The built-in commands will also work on operating systems, that do not - by default - provide the corresponding external executables (like mkdir on Windows).

This command provides a ways to invoke custom commands or executables from your input script. For example, you can move files around in preparation for the next section of the input script. Or you can run a program that pre-processes data for input into LAMMPS. Or you can run a program that post-processes LAMMPS output data.

With the exception of cd, all commands, including ones invoked via a system() call, are executed by only a single processor, so that files/directories are not being manipulated by multiple processors concurrently which may result in unexpected errors or corrupted files.

The cd command changes the current working directory similar to the cd command. All subsequent LAMMPS commands that read/write files will use the new directory. All processors execute this command.

The mkdir command creates directories similar to the Unix mkdir -p command. That is, it will attempt to create the entire path of subdirectories if they do not exist yet.

The mv command renames a file and/or moves it to a new directory. It cannot rename files across filesystem boundaries or between drives.

The rm command deletes file similar to the Unix rm command.

The rmdir command deletes directories similar to Unix rmdir command. If a directory is not empty, its contents are also removed recursively similar to the Unix rm -r command.

The putenv command defines or updates an environment variable directly. Since this command does not pass through the shell, no shell variable expansion or globbing is performed, only the usual substitution for LAMMPS variables defined with the variable command is performed. The resulting string is then used literally.

Any other command is passed as-is to the shell along with its arguments as one string, invoked by the C-library system() call. For example, these lines in your input script:

variable n equal 10
variable foo string file2
shell my_setup file1 $n ${foo}

would be the same as invoking

my_setup file1 10 file2

from a command-line prompt. The executable program “my_setup” is run with 3 arguments: file1 10 file2.

Restrictions

LAMMPS will do a best effort to detect errors and print suitable warnings, but due to the nature of delegating commands to the C-library system() call, this is not always reliable.

Default

none