From d514f55bb69035e9aa541b3461e9a657990e25b1 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 30 Sep 2010 23:52:53 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4926 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/prd.html | 2 +- doc/prd.txt | 2 +- doc/temper.html | 34 +++++++++++++++++----------------- doc/temper.txt | 34 +++++++++++++++++----------------- 4 files changed, 36 insertions(+), 36 deletions(-) diff --git a/doc/prd.html b/doc/prd.html index 96fa80609a..02fd16ab12 100644 --- a/doc/prd.html +++ b/doc/prd.html @@ -290,7 +290,7 @@ dt/reset and fix deposit.

compute event/displace, min_modify, min_style, run_style, minimize, -velocity +velocity, temper, neb

Default:

diff --git a/doc/prd.txt b/doc/prd.txt index 7ac5461b47..efe5fedb86 100644 --- a/doc/prd.txt +++ b/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:] diff --git a/doc/temper.html b/doc/temper.html index 7e828b4ddb..ff67dbc3fa 100644 --- a/doc/temper.html +++ b/doc/temper.html @@ -30,27 +30,27 @@ temper 40000 100 $t tempfix 0 32285 $w

Description:

-

Run a parallel tempering (replica exchange) simulation of multiple -ensembles (replicas) of a system on multiple partitions of processors. +

Run a parallel tempering or replica exchange simulation using multiple +replicas (ensembles) of a system. Two or more replicas must be used.

-

The processor partitions are defined using the -partition command-line -switch (see this section). Each partition -(replica) can be assigned one or more processors. Note that if you -have MPI installed, you can run a multi-partition simulation on more -partitions than you have physical processors, e.g you can run a -10-replica simulation on one or two processors. You will simply -not get the performance speed-up you would typically see with one or +

Each replica runs on a partition of one or more processors. Processor +partitions are defined at run-time using the -partition command-line +switch; see this section of the manual. Note +that if you have MPI installed, you can run a multi-replica simulation +with more replicas (partitions) than you have physical processors, e.g +you can run a 10-replica simulation on one or two processors. You +will simply not get the performance speed-up you would see with one or more physical processors per replica. See this section of the manual for further discussion.

-

Each ensemble's temperature is controlled at a different value by a -fix with ID fix-ID that controls temperature. Possible fix styles -are nvt, temp/berendsen, +

Each replica's temperature is controlled at a different value by a fix +with fix-ID that controls temperature. Possible fix styles are +nvt, temp/berendsen, langevin and temp/rescale. 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 -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
@@ -59,10 +59,10 @@ temper 100000 100 $t myfix 3847 58382
 
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
-adjacent ensembles will be attempted every M timesteps.  If seed1
-is 0, then the swap attempts will alternate between odd and even
-pairings.  If seed1 is non-zero then it is used as a seed in a
+
As the tempering simulation runs for N timesteps, a temperature swap
+between adjacent ensembles will be attempted every M timesteps.  If
+seed1 is 0, then the swap attempts will alternate between odd and
+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
diff --git a/doc/temper.txt b/doc/temper.txt
index 978930ff1b..4f6ba7179c 100644
--- a/doc/temper.txt
+++ b/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
-ensembles (replicas) of a system on multiple partitions of processors.
+Run a parallel tempering or replica exchange simulation using multiple
+replicas (ensembles) of a system.  Two or more replicas must be used.
 
-The processor partitions are defined using the -partition command-line
-switch (see "this section"_Section_start.html#2_6).  Each partition
-(replica) can be assigned one or more processors.  Note that if you
-have MPI installed, you can run a multi-partition simulation on more
-partitions than you have physical processors, e.g you can run a
-10-replica simulation on one or two processors.  You will simply
-not get the performance speed-up you would typically see with one or
+Each replica runs on a partition of one or more processors.  Processor
+partitions are defined at run-time using the -partition command-line
+switch; see "this section"_Section_start.html#2_6 of the manual.  Note
+that if you have MPI installed, you can run a multi-replica simulation
+with more replicas (partitions) than you have physical processors, e.g
+you can run a 10-replica simulation on one or two processors.  You
+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
-fix with ID {fix-ID} that controls temperature.  Possible fix styles
-are "nvt"_fix_nh.html, "temp/berendsen"_fix_nh.html,
+Each replica's temperature is controlled at a different value by a fix
+with {fix-ID} that controls temperature.  Possible fix styles are
+"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
-adjacent ensembles will be attempted every {M} timesteps.  If {seed1}
-is 0, then the swap attempts will alternate between odd and even
-pairings.  If {seed1} is non-zero then it is used as a seed in a
+As the tempering simulation runs for {N} timesteps, a temperature swap
+between adjacent ensembles will be attempted every {M} timesteps.  If
+{seed1} is 0, then the swap attempts will alternate between odd and
+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