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

doc/Section_start.html

@@ -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

doc/Section_start.txt

@@ -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

doc/read_dump.html

@@ -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

doc/read_dump.txt

@@ -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

doc/run_style.html

@@ -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

doc/run_style.txt

@@ -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