git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4926 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/prd.html

@@ -290,7 +290,7 @@ dt/reset</A> and <A HREF = "fix_deposit.html">fix deposit</A>.
 <P><A HREF = "compute_event_displace.html">compute event/displace</A>,
 <A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
 <A HREF = "run_style.html">run_style</A>, <A HREF = "minimize.html">minimize</A>,
-<A HREF = "velocity.html">velocity</A>
+<A HREF = "velocity.html">velocity</A>, <A HREF = "temper.html">temper</A>, <A HREF = "neb.html">neb</A>
 </P>
 <P><B>Default:</B> 
 </P>

doc/prd.txt

@@ -277,7 +277,7 @@ dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
 "compute event/displace"_compute_event_displace.html,
 "min_modify"_min_modify.html, "min_style"_min_style.html,
 "run_style"_run_style.html, "minimize"_minimize.html,
-"velocity"_velocity.html
+"velocity"_velocity.html, "temper"_temper.html, "neb"_neb.html
 
 [Default:] 
 

doc/temper.html

@@ -30,27 +30,27 @@ temper 40000 100 $t tempfix 0 32285 $w
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>Run a parallel tempering (replica exchange) simulation of multiple
+<P>Run a parallel tempering or replica exchange simulation using multiple
-ensembles (replicas) of a system on multiple partitions of processors.
+replicas (ensembles) of a system.  Two or more replicas must be used.
 </P>
-<P>The processor partitions are defined using the -partition command-line
+<P>Each replica runs on a partition of one or more processors.  Processor
-switch (see <A HREF = "Section_start.html#2_6">this section</A>).  Each partition
+partitions are defined at run-time using the -partition command-line
-(replica) can be assigned one or more processors.  Note that if you
+switch; see <A HREF = "Section_start.html#2_6">this section</A> of the manual.  Note
-have MPI installed, you can run a multi-partition simulation on more
+that if you have MPI installed, you can run a multi-replica simulation
-partitions than you have physical processors, e.g you can run a
+with more replicas (partitions) than you have physical processors, e.g
-10-replica simulation on one or two processors.  You will simply
+you can run a 10-replica simulation on one or two processors.  You
-not get the performance speed-up you would typically see with one or
+will simply not get the performance speed-up you would see with one or
 more physical processors per replica.  See <A HREF = "Section_howto.html#4_5">this
 section</A> of the manual for further discussion.
 </P>
-<P>Each ensemble's temperature is controlled at a different value by a
+<P>Each replica's temperature is controlled at a different value by a fix
-fix with ID <I>fix-ID</I> that controls temperature.  Possible fix styles
+with <I>fix-ID</I> that controls temperature.  Possible fix styles are
-are <A HREF = "fix_nh.html">nvt</A>, <A HREF = "fix_nh.html">temp/berendsen</A>,
+<A HREF = "fix_nh.html">nvt</A>, <A HREF = "fix_nh.html">temp/berendsen</A>,
 <A HREF = "fix_langevin.html">langevin</A> and <A HREF = "fix_temp_rescale.html">temp/rescale</A>.
 The desired temperature is specified by <I>temp</I>, which is typically a
 variable previously set in the input script, so that each partition is
 assigned a different temperature.  See the <A HREF = "variable.html">variable</A>
-command for more details. For example:
+command for more details.  For example:
 </P>
 <PRE>variable t world 300.0 310.0 320.0 330.0
 fix myfix all nvt $t $t 100.0
@@ -59,10 +59,10 @@ temper 100000 100 $t myfix 3847 58382
 <P>would define 4 temperatures, and assign one of them to the thermostat
 used by each replica, and to the temper command.
 </P>
-<P>As the tempering simulation runs for <I>N</I> timesteps, a swap between
+<P>As the tempering simulation runs for <I>N</I> timesteps, a temperature swap
-adjacent ensembles will be attempted every <I>M</I> timesteps.  If <I>seed1</I>
+between adjacent ensembles will be attempted every <I>M</I> timesteps.  If
-is 0, then the swap attempts will alternate between odd and even
+<I>seed1</I> is 0, then the swap attempts will alternate between odd and
-pairings.  If <I>seed1</I> is non-zero then it is used as a seed in a
+even pairings.  If <I>seed1</I> is non-zero then it is used as a seed in a
 random number generator to randomly choose an odd or even pairing each
 time.  Each attempted swap of temperatures is either accepted or
 rejected based on a Boltzmann-weighted Metropolis criterion which uses

doc/temper.txt

@@ -27,27 +27,27 @@ temper 40000 100 $t tempfix 0 32285 $w :pre
 
 [Description:]
 
-Run a parallel tempering (replica exchange) simulation of multiple
+Run a parallel tempering or replica exchange simulation using multiple
-ensembles (replicas) of a system on multiple partitions of processors.
+replicas (ensembles) of a system.  Two or more replicas must be used.
 
-The processor partitions are defined using the -partition command-line
+Each replica runs on a partition of one or more processors.  Processor
-switch (see "this section"_Section_start.html#2_6).  Each partition
+partitions are defined at run-time using the -partition command-line
-(replica) can be assigned one or more processors.  Note that if you
+switch; see "this section"_Section_start.html#2_6 of the manual.  Note
-have MPI installed, you can run a multi-partition simulation on more
+that if you have MPI installed, you can run a multi-replica simulation
-partitions than you have physical processors, e.g you can run a
+with more replicas (partitions) than you have physical processors, e.g
-10-replica simulation on one or two processors.  You will simply
+you can run a 10-replica simulation on one or two processors.  You
-not get the performance speed-up you would typically see with one or
+will simply not get the performance speed-up you would see with one or
 more physical processors per replica.  See "this
 section"_Section_howto.html#4_5 of the manual for further discussion.
 
-Each ensemble's temperature is controlled at a different value by a
+Each replica's temperature is controlled at a different value by a fix
-fix with ID {fix-ID} that controls temperature.  Possible fix styles
+with {fix-ID} that controls temperature.  Possible fix styles are
-are "nvt"_fix_nh.html, "temp/berendsen"_fix_nh.html,
+"nvt"_fix_nh.html, "temp/berendsen"_fix_nh.html,
 "langevin"_fix_langevin.html and "temp/rescale"_fix_temp_rescale.html.
 The desired temperature is specified by {temp}, which is typically a
 variable previously set in the input script, so that each partition is
 assigned a different temperature.  See the "variable"_variable.html
-command for more details. For example:
+command for more details.  For example:
 
 variable t world 300.0 310.0 320.0 330.0
 fix myfix all nvt $t $t 100.0
@@ -56,10 +56,10 @@ temper 100000 100 $t myfix 3847 58382 :pre
 would define 4 temperatures, and assign one of them to the thermostat
 used by each replica, and to the temper command.
 
-As the tempering simulation runs for {N} timesteps, a swap between
+As the tempering simulation runs for {N} timesteps, a temperature swap
-adjacent ensembles will be attempted every {M} timesteps.  If {seed1}
+between adjacent ensembles will be attempted every {M} timesteps.  If
-is 0, then the swap attempts will alternate between odd and even
+{seed1} is 0, then the swap attempts will alternate between odd and
-pairings.  If {seed1} is non-zero then it is used as a seed in a
+even pairings.  If {seed1} is non-zero then it is used as a seed in a
 random number generator to randomly choose an odd or even pairing each
 time.  Each attempted swap of temperatures is either accepted or
 rejected based on a Boltzmann-weighted Metropolis criterion which uses