From 3a6ea84a7289b3582680c43c0cb14fb4d9fa012e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 25 Mar 2010 16:23:56 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3923 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/atom_modify.html | 16 ++++++++-------- doc/atom_modify.txt | 16 ++++++++-------- doc/run_style.html | 2 +- doc/run_style.txt | 2 +- 4 files changed, 18 insertions(+), 18 deletions(-) diff --git a/doc/atom_modify.html b/doc/atom_modify.html index 1292e43fbd..87331412bc 100644 --- a/doc/atom_modify.html +++ b/doc/atom_modify.html @@ -70,14 +70,14 @@ your input script. LAMMPS does not use the group until a simullation is run.

The sort keyword turns on a spatial sorting or reordering of atoms -within each processor's sub-domain every Nfreq timesteps. This can -improve cache performance and thus speed-up a LAMMPS simulation, as -discussed in a paper by (Meloni). Its efficacy depends on -the problem size (atoms/processor), how quickly the system becomes -disordered, and various other factors. As a general rule, sorting is -typically more effective at speeding up simulations of liquids as -opposed to solids. In tests we have done, the speed-up can range from -zero to 3-4x. +within each processor's sub-domain every Nfreq timesteps. If +Nfreq is set to 0, then sorting is turned off. Sorting can improve +cache performance and thus speed-up a LAMMPS simulation, as discussed +in a paper by (Meloni). Its efficacy depends on the problem +size (atoms/processor), how quickly the system becomes disordered, and +various other factors. As a general rule, sorting is typically more +effective at speeding up simulations of liquids as opposed to solids. +In tests we have done, the speed-up can range from zero to 3-4x.

Reordering is peformed every Nfreq timesteps during a dynamics run or iterations during a minimization. More precisely, reordering diff --git a/doc/atom_modify.txt b/doc/atom_modify.txt index c386d78f91..e6bc889048 100644 --- a/doc/atom_modify.txt +++ b/doc/atom_modify.txt @@ -64,14 +64,14 @@ your input script. LAMMPS does not use the group until a simullation is run. The {sort} keyword turns on a spatial sorting or reordering of atoms -within each processor's sub-domain every {Nfreq} timesteps. This can -improve cache performance and thus speed-up a LAMMPS simulation, as -discussed in a paper by "(Meloni)"_#Meloni. Its efficacy depends on -the problem size (atoms/processor), how quickly the system becomes -disordered, and various other factors. As a general rule, sorting is -typically more effective at speeding up simulations of liquids as -opposed to solids. In tests we have done, the speed-up can range from -zero to 3-4x. +within each processor's sub-domain every {Nfreq} timesteps. If +{Nfreq} is set to 0, then sorting is turned off. Sorting can improve +cache performance and thus speed-up a LAMMPS simulation, as discussed +in a paper by "(Meloni)"_#Meloni. Its efficacy depends on the problem +size (atoms/processor), how quickly the system becomes disordered, and +various other factors. As a general rule, sorting is typically more +effective at speeding up simulations of liquids as opposed to solids. +In tests we have done, the speed-up can range from zero to 3-4x. Reordering is peformed every {Nfreq} timesteps during a dynamics run or iterations during a minimization. More precisely, reordering diff --git a/doc/run_style.html b/doc/run_style.html index bb6e3951bb..f3f1e25acc 100644 --- a/doc/run_style.html +++ b/doc/run_style.html @@ -168,7 +168,7 @@ Kcal/mol, the following settings seem to work well: 

timestep  36.0  
 run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
-

Restrictions: none +

Restrictions:

Whenever using rRESPA, the user should experiment with trade-offs in speed and accuracy for their system, and verify that they are diff --git a/doc/run_style.txt b/doc/run_style.txt index f27a4b54eb..508f975642 100644 --- a/doc/run_style.txt +++ b/doc/run_style.txt @@ -163,7 +163,7 @@ Kcal/mol, the following settings seem to work well: timestep 36.0 run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre -[Restrictions:] none +[Restrictions:] Whenever using rRESPA, the user should experiment with trade-offs in speed and accuracy for their system, and verify that they are