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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9584 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-03-06 16:46:43 +00:00
parent 18a04f2c5c
commit 4819ef9e1e
6 changed files with 56 additions and 4 deletions
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2
doc/Section_start.html
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@ -287,7 +287,7 @@ This should create a libmpi_stubs.a file suitable for linking to
LAMMPS. If the build fails, you will need to edit the STUBS/Makefile
for your platform.
</P>
<P>The file STUBS/mpi.cpp provides a CPU timer function called
<P>The file STUBS/mpi.c provides a CPU timer function called
MPI_Wtime() that calls gettimeofday() . If your system doesn't
support gettimeofday() , you'll need to insert code to call another
timer. Note that the ANSI-standard function clock() rolls over after

2
doc/Section_start.txt
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@ -281,7 +281,7 @@ This should create a libmpi_stubs.a file suitable for linking to
LAMMPS. If the build fails, you will need to edit the STUBS/Makefile
for your platform.
The file STUBS/mpi.cpp provides a CPU timer function called
The file STUBS/mpi.c provides a CPU timer function called
MPI_Wtime() that calls gettimeofday() . If your system doesn't
support gettimeofday() , you'll need to insert code to call another
timer. Note that the ANSI-standard function clock() rolls over after

4
doc/read_dump.html
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@ -51,6 +51,10 @@
<P><B>Examples:</B>
</P>
<PRE>read_dump dump.file 5000 x y z
read_dump dump.xyz 5 x y z format xyz box no
read_dump dump.xyz 10 x y z format molfile box no reader xyz "../plugins"
read_dump dump.dcd 0 x y z format molfile box yes reader dcd
read_dump dump.file 1000 x y z vx vy vz format molfile box yes reader lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
read_dump dump.file 5000 x y vx vy trim yes
read_dump ../run7/dump.file.gz 10000 x y z box yes
read_dump dump.xyz 5 x y z box no format xyz

4
doc/read_dump.txt
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@ -41,6 +41,10 @@ keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled
[Examples:]
read_dump dump.file 5000 x y z
read_dump dump.xyz 5 x y z format xyz box no
read_dump dump.xyz 10 x y z format molfile box no reader xyz "../plugins"
read_dump dump.dcd 0 x y z format molfile box yes reader dcd
read_dump dump.file 1000 x y z vx vy vz format molfile box yes reader lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
read_dump dump.file 5000 x y vx vy trim yes
read_dump ../run7/dump.file.gz 10000 x y z box yes
read_dump dump.xyz 5 x y z box no format xyz

24
doc/run_style.html
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@ -15,7 +15,7 @@
</P>
<PRE>run_style style args
</PRE>
<UL><LI>style = <I>verlet</I> or <I>verlet/split</I> or <I>respa</I>
<UL><LI>style = <I>verlet</I> or <I>verlet/split</I> or <I>respa</I> or <I>respa/omp</I>
<PRE> <I>verlet</I> args = none
<I>verlet/split</I> args = none
@ -235,6 +235,28 @@ run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
</PRE>
<HR>
<P>The <I>respa/omp</I> styles is a variant of <I>respa</I> adapted for use with
pair, bond, angle, dihedral, improper, or kspace styles with an <I>omp</I>
suffix. It is functionally to <I>respa</I> but performs additional required
operations. For more on <I>omp</I> styles see the
<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual.
Accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
</P>
<P>The <I>respa/omp</I> style is part of the USER-OMP packages. It is only
enabled if LAMMPS was built with this package included. See the
<A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>You can specify <I>respa/omp</I> explicitly in your input script, or
you can use the <A HREF = "Section_start.html#start_7">-suffix command-line switch</A>
when you invoke LAMMPS, or you can use the <A HREF = "suffix.html">suffix</A>
command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>The <I>verlet/split</I> style can only be used if LAMMPS was built with the

24
doc/run_style.txt
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@ -12,7 +12,7 @@ run_style command :h3
run_style style args :pre
style = {verlet} or {verlet/split} or {respa} :ulb,l
style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
{verlet} args = none
{verlet/split} args = none
{respa} args = N n1 n2 ... keyword values ...
@ -230,6 +230,28 @@ run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre
:line
The {respa/omp} styles is a variant of {respa} adapted for use with
pair, bond, angle, dihedral, improper, or kspace styles with an {omp}
suffix. It is functionally to {respa} but performs additional required
operations. For more on {omp} styles see the
"Section_accelerate"_Section_accelerate.html of the manual.
Accelerated styles take the same arguments and should produce the same
results, except for round-off and precision issues.
The {respa/omp} style is part of the USER-OMP packages. It is only
enabled if LAMMPS was built with this package included. See the
"Making LAMMPS"_Section_start.html#start_3 section for more info.
You can specify {respa/omp} explicitly in your input script, or
you can use the "-suffix command-line switch"_Section_start.html#start_7
when you invoke LAMMPS, or you can use the "suffix"_suffix.html
command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
The {verlet/split} style can only be used if LAMMPS was built with the