Commit 4b2e7583 authored by sjplimp's avatar sjplimp
Browse files

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1251 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent db10083b
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+26 −13
Original line number Diff line number Diff line
@@ -30,7 +30,7 @@
  <I>post</I> value = <I>no</I> or <I>yes</I> 
  <I>every</I> values = M command
    M = break the run into M-timestep segments and invoke command between them
    command = a single LAMMPS command (enclosed in double quotes if multiple words)
    command = a single LAMMPS command listed the same as if on a line by itself
              NULL means no command will be invoked 
</PRE>

@@ -41,7 +41,7 @@
run 1000000 upto
run 100 start 0 stop 1000
run 1000 pre no post yes
run 100000 start 0 stop 1000000 every 1000 "print Protein Rg = $r"
run 100000 start 0 stop 1000000 every 1000 print "Protein Rg = $r"
run 100000 every 1000 NULL 
</PRE>
<P><B>Description:</B>
@@ -112,20 +112,26 @@ only a one-line summary timing is printed. Note that if <I>pre</I> is set
to "no" for the 1st run LAMMPS performs, then it is overridden, since
the initial setup computations must be done.
</P>
<P>The <I>every</I> option provides a means of interleaving LAMMPS runs with a
command.  This can be a short-hand abbreviation to avoid listing a
long series of runs in your input script.  Or it can be useful for
invoking a command that wraps some other code (e.g. as a library) to
perform a computation periodically during a long LAMMPS run.  See
<P>The <I>every</I> option provides a means of breaking a LAMMPS run into a
series of shorter runs.  Optionally a single LAMMPS command can be
executed in between the short runs.  This is a means to avoid listing
a long series of runs and commands in your input script.  For example,
a <A HREF = "print.html">print</A> command could be invoked or a <A HREF = "fix.html">fix</A>
could be redefined, e.g. to reset a thermostat temperature.  Or it
could be useful for invoking a command you write that wraps some other
code (e.g. as a library) to perform a computation periodically during
a long LAMMPS run.  See <A HREF = "Section_modify.html">this section</A> of the
documentation for info about how to add new commands to LAMMPS.  See
<A HREF = "Section_howto.html#4_10">this section</A> of the documentation for ideas
about how to couple LAMMPS to other codes.
</P>
<P>N total steps are simulated, in shorter runs of M steps each.  After
each M-length run, the command is invoked.  If the command is
specified as NULL, no command is invoked.  Thus these lines:
<P>With the <I>every</I> option, N total steps are simulated, in shorter runs
of M steps each.  After each M-length run, the command is invoked.  If
the command is specified as NULL, no command is invoked.  Thus these
lines:
</P>
<PRE>variable q equal x[100]
run 6000 every 2000 "print Coord = $q" 
run 6000 every 2000 print "Coord = $q" 
</PRE>
<P>are the equivalent of:
</P>
@@ -138,10 +144,17 @@ run 2000
print Coord = $q 
</PRE>
<P>which does 3 runs of 2000 steps and prints the x-coordinate of a
particular atom between runs.  Note that the command can contain
<A HREF = "variable.html">variables</A> of style <I>equal</I> which will be evaluated
particular atom between runs.  Note that, as in this example, the
command can contain <A HREF = "variable.html">variables</A> which will be evaluated
each time the command is invoked.
</P>
<P>IMPORTANT NOTE: For the <I>every</I> option, all remaining arguments after
the M value are considerd part of the LAMMPS command (e.g. print
"Protein Rg = $r" as in the example above).  This means that, if
specified, the <I>every</I> option must be the last keyword used.  The
command should be listed exactly as it would appear if it were on a
line by itself in the input script.
</P>
<P>If the <I>pre</I> and <I>post</I> options are set to "no" when <I>every</I> is used,
then the 1st run will do the full setup and the last run will print
the full timing summary, but these operations will be skipped for
+26 −13
Original line number Diff line number Diff line
@@ -24,7 +24,7 @@ keyword = {upto} or {start} or {stop} or {pre} or {post} or {every} :l
  {post} value = {no} or {yes} 
  {every} values = M command
    M = break the run into M-timestep segments and invoke command between them
    command = a single LAMMPS command (enclosed in double quotes if multiple words)
    command = a single LAMMPS command listed the same as if on a line by itself
              NULL means no command will be invoked :pre
:ule

@@ -34,7 +34,7 @@ run 10000
run 1000000 upto
run 100 start 0 stop 1000
run 1000 pre no post yes
run 100000 start 0 stop 1000000 every 1000 "print Protein Rg = $r"
run 100000 start 0 stop 1000000 every 1000 print "Protein Rg = $r"
run 100000 every 1000 NULL :pre

[Description:]
@@ -105,20 +105,26 @@ only a one-line summary timing is printed. Note that if {pre} is set
to "no" for the 1st run LAMMPS performs, then it is overridden, since
the initial setup computations must be done.

The {every} option provides a means of interleaving LAMMPS runs with a
command.  This can be a short-hand abbreviation to avoid listing a
long series of runs in your input script.  Or it can be useful for
invoking a command that wraps some other code (e.g. as a library) to
perform a computation periodically during a long LAMMPS run.  See
The {every} option provides a means of breaking a LAMMPS run into a
series of shorter runs.  Optionally a single LAMMPS command can be
executed in between the short runs.  This is a means to avoid listing
a long series of runs and commands in your input script.  For example,
a "print"_print.html command could be invoked or a "fix"_fix.html
could be redefined, e.g. to reset a thermostat temperature.  Or it
could be useful for invoking a command you write that wraps some other
code (e.g. as a library) to perform a computation periodically during
a long LAMMPS run.  See "this section"_Section_modify.html of the
documentation for info about how to add new commands to LAMMPS.  See
"this section"_Section_howto.html#4_10 of the documentation for ideas
about how to couple LAMMPS to other codes.

N total steps are simulated, in shorter runs of M steps each.  After
each M-length run, the command is invoked.  If the command is
specified as NULL, no command is invoked.  Thus these lines:
With the {every} option, N total steps are simulated, in shorter runs
of M steps each.  After each M-length run, the command is invoked.  If
the command is specified as NULL, no command is invoked.  Thus these
lines:

variable q equal x\[100\]
run 6000 every 2000 "print Coord = $q" :pre
run 6000 every 2000 print "Coord = $q" :pre

are the equivalent of:

@@ -131,10 +137,17 @@ run 2000
print Coord = $q :pre

which does 3 runs of 2000 steps and prints the x-coordinate of a
particular atom between runs.  Note that the command can contain
"variables"_variable.html of style {equal} which will be evaluated
particular atom between runs.  Note that, as in this example, the
command can contain "variables"_variable.html which will be evaluated
each time the command is invoked.

IMPORTANT NOTE: For the {every} option, all remaining arguments after
the M value are considerd part of the LAMMPS command (e.g. print
"Protein Rg = $r" as in the example above).  This means that, if
specified, the {every} option must be the last keyword used.  The
command should be listed exactly as it would appear if it were on a
line by itself in the input script.

If the {pre} and {post} options are set to "no" when {every} is used,
then the 1st run will do the full setup and the last run will print
the full timing summary, but these operations will be skipped for