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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3923 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2010-03-25 16:23:56 +00:00
parent eabe7d3166
commit 3a6ea84a72
4 changed files with 18 additions and 18 deletions
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16
doc/atom_modify.html
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@ -70,14 +70,14 @@ your input script. LAMMPS does not use the group until a simullation
is run. is run.
</P> </P>
<P>The <I>sort</I> keyword turns on a spatial sorting or reordering of atoms <P>The <I>sort</I> keyword turns on a spatial sorting or reordering of atoms
within each processor's sub-domain every <I>Nfreq</I> timesteps. This can within each processor's sub-domain every <I>Nfreq</I> timesteps. If
improve cache performance and thus speed-up a LAMMPS simulation, as <I>Nfreq</I> is set to 0, then sorting is turned off. Sorting can improve
discussed in a paper by <A HREF = "#Meloni">(Meloni)</A>. Its efficacy depends on cache performance and thus speed-up a LAMMPS simulation, as discussed
the problem size (atoms/processor), how quickly the system becomes in a paper by <A HREF = "#Meloni">(Meloni)</A>. Its efficacy depends on the problem
disordered, and various other factors. As a general rule, sorting is size (atoms/processor), how quickly the system becomes disordered, and
typically more effective at speeding up simulations of liquids as various other factors. As a general rule, sorting is typically more
opposed to solids. In tests we have done, the speed-up can range from effective at speeding up simulations of liquids as opposed to solids.
zero to 3-4x. In tests we have done, the speed-up can range from zero to 3-4x.
</P> </P>
<P>Reordering is peformed every <I>Nfreq</I> timesteps during a dynamics run <P>Reordering is peformed every <I>Nfreq</I> timesteps during a dynamics run
or iterations during a minimization. More precisely, reordering or iterations during a minimization. More precisely, reordering

16
doc/atom_modify.txt
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@ -64,14 +64,14 @@ your input script. LAMMPS does not use the group until a simullation
is run. is run.
The {sort} keyword turns on a spatial sorting or reordering of atoms The {sort} keyword turns on a spatial sorting or reordering of atoms
within each processor's sub-domain every {Nfreq} timesteps. This can within each processor's sub-domain every {Nfreq} timesteps. If
improve cache performance and thus speed-up a LAMMPS simulation, as {Nfreq} is set to 0, then sorting is turned off. Sorting can improve
discussed in a paper by "(Meloni)"_#Meloni. Its efficacy depends on cache performance and thus speed-up a LAMMPS simulation, as discussed
the problem size (atoms/processor), how quickly the system becomes in a paper by "(Meloni)"_#Meloni. Its efficacy depends on the problem
disordered, and various other factors. As a general rule, sorting is size (atoms/processor), how quickly the system becomes disordered, and
typically more effective at speeding up simulations of liquids as various other factors. As a general rule, sorting is typically more
opposed to solids. In tests we have done, the speed-up can range from effective at speeding up simulations of liquids as opposed to solids.
zero to 3-4x. 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 Reordering is peformed every {Nfreq} timesteps during a dynamics run
or iterations during a minimization. More precisely, reordering or iterations during a minimization. More precisely, reordering

2
doc/run_style.html
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@ -168,7 +168,7 @@ Kcal/mol, the following settings seem to work well:
<PRE>timestep 36.0 <PRE>timestep 36.0
run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
</PRE> </PRE>
<P><B>Restrictions:</B> none <P><B>Restrictions:</B>
</P> </P>
<P>Whenever using rRESPA, the user should experiment with trade-offs in <P>Whenever using rRESPA, the user should experiment with trade-offs in
speed and accuracy for their system, and verify that they are speed and accuracy for their system, and verify that they are

2
doc/run_style.txt
View File

@ -163,7 +163,7 @@ Kcal/mol, the following settings seem to work well:
timestep 36.0 timestep 36.0
run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre 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 Whenever using rRESPA, the user should experiment with trade-offs in
speed and accuracy for their system, and verify that they are speed and accuracy for their system, and verify that they are