These are compute styles contributed by users, which can be used if @@ -419,9 +419,9 @@ potentials. Click on the style itself for a full description:
These are pair styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 8689da8499..f2761fec9d 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -553,6 +553,7 @@ each style or click on the style itself for a full description: "rdf"_compute_rdf.html, "reduce"_compute_reduce.html, "reduce/region"_compute_reduce.html, +"slice"_compute_slice.html, "stress/atom"_compute_stress_atom.html, "temp"_compute_temp.html, "temp/asphere"_compute_temp_asphere.html, @@ -642,6 +643,7 @@ potentials. Click on the style itself for a full description: "peri/lps"_pair_peri.html, "peri/pmb"_pair_peri.html, "reax"_pair_reax.html, +"rebo"_pair_airebo.html, "resquared"_pair_resquared.html, "soft"_pair_soft.html, "sw"_pair_sw.html, diff --git a/doc/shell.html b/doc/shell.html index 7129ee596e..7953130af2 100644 --- a/doc/shell.html +++ b/doc/shell.html @@ -13,9 +13,9 @@
Syntax:
-shell style args +shell cmd args-
cd arg = dir
dir = directory to change to
@@ -27,7 +27,8 @@
rm args = file1 file2 ...
file1,file2 = one or more filenames to delete
rmdir args = dir1 dir2 ...
- dir1,dir2 = one or more directories to delete
+ dir1,dir2 = one or more directories to delete
+ anything else is passed as a command to the shell for direct execution
Description:
-Execute a shell command. Only a few simple file-based shell commands -are supported, in Unix-style syntax. With the exception of cd, all -commands are executed by only a single processor, so that +
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 style executes the Unix "cd" command to change the working +
The cd cmd 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 style executes the Unix "mkdir" command to create -one or more directories. +
The mkdir cmd executes the Unix "mkdir" command to create one or +more directories.
-The mv style executes the Unix "mv" command to rename a file and/or +
The mv cmd executes the Unix "mv" command to rename a file and/or move it to a new directory.
-The rm style executes the Unix "rm" command to remove one or more +
The rm cmd executes the Unix "rm" command to remove one or more files.
-The rmdir style executes the Unix "rmdir" command to remove one or +
The rmdir cmd executes the Unix "rmdir" command to remove one or more directories. A directory must be empty to be successfully removed.
+Any other cmd 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 Unix +
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 not do anything. +executing the cd command will silently do nothing.
Related commands: none
diff --git a/doc/shell.txt b/doc/shell.txt index fe1dbf3c2a..1369df80a9 100644 --- a/doc/shell.txt +++ b/doc/shell.txt @@ -10,9 +10,9 @@ shell command :h3 [Syntax:] -shell style args :pre +shell cmd args :pre -style = {cd} or {mkdir} or {mv} or {rm} or {rmdir} :ulb,l +cmd = {cd} or {mkdir} or {mv} or {rm} or {rmdir} or arbitrary command :ulb,l {cd} arg = dir dir = directory to change to {mkdir} args = dir1 dir2 ... @@ -23,7 +23,8 @@ style = {cd} or {mkdir} or {mv} or {rm} or {rmdir} :ulb,l {rm} args = file1 file2 ... file1,file2 = one or more filenames to delete {rmdir} args = dir1 dir2 ... - dir1,dir2 = one or more directories to delete :pre + dir1,dir2 = one or more directories to delete + anything else is passed as a command to the shell for direct execution :pre :ule [Examples:] @@ -33,37 +34,64 @@ shell cd .. shell mkdir tmp1 tmp2 tmp3 shell rmdir tmp1 shell mv log.lammps hold/log.1 -shell rm TMP/file1 TMP/file2 :pre +shell rm TMP/file1 TMP/file2 +shell my_setup file1 10 file2 +shell my_post_process 100 dump.out :pre [Description:] -Execute a shell command. Only a few simple file-based shell commands -are supported, in Unix-style syntax. With the exception of {cd}, all -commands are executed by only a single processor, so that +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} style executes the Unix "cd" command to change the working +The {cd} cmd 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} style executes the Unix "mkdir" command to create -one or more directories. +The {mkdir} cmd executes the Unix "mkdir" command to create one or +more directories. -The {mv} style executes the Unix "mv" command to rename a file and/or +The {mv} cmd executes the Unix "mv" command to rename a file and/or move it to a new directory. -The {rm} style executes the Unix "rm" command to remove one or more +The {rm} cmd executes the Unix "rm" command to remove one or more files. -The {rmdir} style executes the Unix "rmdir" command to remove one or +The {rmdir} cmd executes the Unix "rmdir" command to remove one or more directories. A directory must be empty to be successfully removed. +Any other cmd 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\} :pre + +would be the same as invoking + +% my_setup file1 10 file2 :pre + +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 Unix +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 not do anything. +executing the {cd} command will silently do nothing. [Related commands:] none diff --git a/doc/variable.html b/doc/variable.html index ec3f1c8578..d0da5e792e 100644 --- a/doc/variable.html +++ b/doc/variable.html @@ -78,7 +78,7 @@ variable b1 equal "x[234] + 0.5*vol" variable b equal xcm(mol1,x)/2.0 variable b equal c_myTemp variable b atom x*y/vol -variable foo myfile +variable foo string myfile variable temp world 300.0 310.0 320.0 ${Tfinal} variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 variable x uloop 15 pad diff --git a/doc/variable.txt b/doc/variable.txt index a1924d93cb..340f8539de 100644 --- a/doc/variable.txt +++ b/doc/variable.txt @@ -72,7 +72,7 @@ variable b1 equal "x\[234\] + 0.5*vol" variable b equal xcm(mol1,x)/2.0 variable b equal c_myTemp variable b atom x*y/vol -variable foo myfile +variable foo string myfile variable temp world 300.0 310.0 320.0 $\{Tfinal\} variable x universe 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 variable x uloop 15 pad