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
  rm args = file1 file2 ...
    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
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.

This is means to invoke other commands 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.

The cd command executes the Unix “cd” command to change the working directory. All subsequent LAMMPS commands that read/write files will use the new directory. All processors execute this command.

The mkdir command executes the Unix “mkdir” command to create one or more directories.

The mv command executes the Unix “mv” command to rename a file and/or move it to a new directory.

The rm command executes the Unix “rm” command to remove one or more files.

The rmdir command executes the Unix “rmdir” command to remove one or more directories. A directory must be empty to be successfully removed.

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 does not detect errors or print warnings when any of these commands execute. E.g. if the specified directory does not exist, executing the cd command will silently do nothing.

Related commands

none

Default

none