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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