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

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sjplimp
2011-06-07 17:15:11 +00:00
parent c76fd4256e
commit fd57c6d16b
6 changed files with 96 additions and 38 deletions
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12
doc/Section_commands.html
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@ -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_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_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_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_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_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_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_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_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_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.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

2
doc/Section_commands.txt
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@ -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,

58
doc/shell.html
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@ -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
@ -27,7 +27,8 @@
<I>rm</I> args = file1 file2 ...
file1,file2 = one or more filenames to delete
<I>rmdir</I> 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
</PRE>
</UL>
@ -38,37 +39,64 @@ shell cd ..
shell mkdir tmp1 tmp2 tmp3
shell rmdir tmp1
shell mv log.lammps hold/log.1
shell rm TMP/file1 TMP/file2
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
are supported, in Unix-style syntax. With the exception of <I>cd</I>, all
commands are executed by only a single processor, so that
<P>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.
</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
one or more directories.
<P>The <I>mkdir</I> cmd executes the Unix "mkdir" command to create one or
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>

58
doc/shell.txt
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@ -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

2
doc/variable.html
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@ -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

2
doc/variable.txt
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@ -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