git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6316 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -379,9 +379,9 @@ each style or click on the style itself for a full description:
 <TR ALIGN="center"><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A> 
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A> 
 </TD></TR></TABLE></DIV>
 
 <P>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:
 <TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A> 
+<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A> 
 </TD></TR></TABLE></DIV>
 
 <P>These are pair styles contributed by users, which can be used if

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,

doc/shell.html

@@ -13,9 +13,9 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>shell style args 
+<PRE>shell cmd args 
 </PRE>
-<UL><LI>style = <I>cd</I> or <I>mkdir</I> or <I>mv</I> or <I>rm</I> or <I>rmdir</I> 
+<UL><LI>cmd = <I>cd</I> or <I>mkdir</I> or <I>mv</I> or <I>rm</I> or <I>rmdir</I> or arbitrary command 
 
 <PRE>  <I>cd</I> arg = dir
     dir = directory to change to
@@ -28,6 +28,7 @@
     file1,file2 = one or more filenames to delete
   <I>rmdir</I> args = dir1 dir2 ...
     dir1,dir2 = one or more directories to delete
+  anything else is passed as a command to the shell for direct execution 
 </PRE>
 
 </UL>
@@ -39,36 +40,63 @@ shell mkdir tmp1 tmp2 tmp3
 shell rmdir tmp1
 shell mv log.lammps hold/log.1
 shell rm TMP/file1 TMP/file2
+shell my_setup file1 10 file2
+shell my_post_process 100 dump.out 
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>Execute a shell command.  Only a few simple file-based shell commands
+<P>Execute a shell command.  A few simple file-based shell commands are
-are supported, in Unix-style syntax.  With the exception of <I>cd</I>, all
+supported directly, in Unix-style syntax.  Any command not listed
-commands are executed by only a single processor, so that
+above is passed as-is to the C-library system() call, which invokes
+the command in a shell.
+</P>
+<P>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.
+</P>
+<P>With the exception of <I>cd</I>, 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.
 </P>
-<P>The <I>cd</I> style executes the Unix "cd" command to change the working
+<P>The <I>cd</I> 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.
 </P>
-<P>The <I>mkdir</I> style executes the Unix "mkdir" command to create
+<P>The <I>mkdir</I> cmd executes the Unix "mkdir" command to create one or
-one or more directories.
+more directories.
 </P>
-<P>The <I>mv</I> style executes the Unix "mv" command to rename a file and/or
+<P>The <I>mv</I> cmd executes the Unix "mv" command to rename a file and/or
 move it to a new directory.
 </P>
-<P>The <I>rm</I> style executes the Unix "rm" command to remove one or more
+<P>The <I>rm</I> cmd executes the Unix "rm" command to remove one or more
 files.
 </P>
-<P>The <I>rmdir</I> style executes the Unix "rmdir" command to remove one or
+<P>The <I>rmdir</I> cmd executes the Unix "rmdir" command to remove one or
 more directories.  A directory must be empty to be successfully
 removed.
 </P>
+<P>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:
+</P>
+<PRE>variable n equal 10
+variable foo string file2
+shell my_setup file1 $n ${foo} 
+</PRE>
+<P>would be the same as invoking
+</P>
+<PRE>% my_setup file1 10 file2 
+</PRE>
+<P>from a command-line prompt.  The executable program "my_setup" is run
+with 3 arguments: file1 10 file2.
+</P>
 <P><B>Restrictions:</B>
 </P>
-<P>LAMMPS does not detect errors or print warnings when any of these Unix
+<P>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 <I>cd</I> command will silently not do anything.
+executing the <I>cd</I> command will silently do nothing.
 </P>
 <P><B>Related commands:</B> none
 </P>

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
+Execute a shell command.  A few simple file-based shell commands are
-are supported, in Unix-style syntax.  With the exception of {cd}, all
+supported directly, in Unix-style syntax.  Any command not listed
-commands are executed by only a single processor, so that
+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
+The {mkdir} cmd executes the Unix "mkdir" command to create one or
-one or more directories.
+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
 

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

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