git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11025 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/dump.html

@@ -109,8 +109,8 @@ timesteps in one of several styles.  The <I>image</I> style is the
 exception; it creates a JPG or PPM image file of the atom
 configuration every N timesteps, as discussed on the <A HREF = "dump_image.html">dump
 image</A> doc page.  The timesteps on which dump output
-is written can also be controlled by a variable. See the <A HREF = "dump_modify.html">dump_modify
+is written can also be controlled by a variable; see the <A HREF = "dump_modify.html">dump_modify
-every</A> command.
+every</A> command for details.
 </P>
 <P>Only information for atoms in the specified group is dumped.  The
 <A HREF = "dump_modify.html">dump_modify thresh and region</A> commands can also
@@ -119,7 +119,7 @@ options; see details below.
 </P>
 <P>As described below, the filename determines the kind of output (text
 or binary or gzipped, one big file or one per timestep, one big file
-or one per processor).
+or multiple smaller files).
 </P>
 <P>IMPORTANT NOTE: Because periodic boundary conditions are enforced only
 on timesteps when neighbor lists are rebuilt, the coordinates of an
@@ -134,7 +134,7 @@ if the <A HREF = "atom_modify.html">atom_modify sort</A> option is on, which it
 by default.  In this case atoms are re-ordered periodically during a
 simulation, due to spatial sorting.  It is also true when running in
 parallel, because data for a single snapshot is collected from
-multiple processors.
+multiple processors, each of which owns a subset of the atoms.
 </P>
 <P>For the <I>atom</I>, <I>custom</I>, <I>cfg</I>, and <I>local</I> styles, sorting is off by
 default.  For the <I>dcd</I>, <I>xtc</I>, <I>xyz</I>, and <I>molfile</I> styles, sorting by
@@ -293,11 +293,12 @@ from using the (numerical) atom type to an element name (or some
 other label). This will help many visualization programs to guess
 bonds and colors.
 </P>
-<P>Note that <I>atom</I>, <I>custom</I>, <I>dcd</I>, <I>xtc</I>, and <I>xyz</I> style dump files can
+<P>Note that <I>atom</I>, <I>custom</I>, <I>dcd</I>, <I>xtc</I>, and <I>xyz</I> style dump files
-be read directly by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> (a popular
+can be read directly by <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>, a
-molecular viewing program).  See <A HREF = "Section_tools.html#vmd">Section tools</A>
+popular molecular viewing program.  See <A HREF = "Section_tools.html#vmd">Section
-of the manual and the tools/lmp2vmd/README.txt file for more information
+tools</A> of the manual and the
-about support in VMD for reading and visualizing LAMMPS dump files.
+tools/lmp2vmd/README.txt file for more information about support in
+VMD for reading and visualizing LAMMPS dump files.
 </P>
 <HR>
 
@@ -330,7 +331,7 @@ tmp.dump.20000, etc.  This option is not available for the <I>dcd</I> and
 <I>xtc</I> styles.  Note that the <A HREF = "dump_modify.html">dump_modify pad</A>
 command can be used to insure all timestep numbers are the same length
 (e.g. 00010), which can make it easier to read a series of dump files
-in order by some post-processing tools.
+in order with some post-processing tools.
 </P>
 <P>If a "%" character appears in the filename, then each of P processors
 writes a portion of the dump file, and the "%" character is replaced

doc/dump.txt

@@ -97,8 +97,8 @@ timesteps in one of several styles.  The {image} style is the
 exception; it creates a JPG or PPM image file of the atom
 configuration every N timesteps, as discussed on the "dump
 image"_dump_image.html doc page.  The timesteps on which dump output
-is written can also be controlled by a variable. See the "dump_modify
+is written can also be controlled by a variable; see the "dump_modify
-every"_dump_modify.html command.
+every"_dump_modify.html command for details.
 
 Only information for atoms in the specified group is dumped.  The
 "dump_modify thresh and region"_dump_modify.html commands can also
@@ -107,7 +107,7 @@ options; see details below.
 
 As described below, the filename determines the kind of output (text
 or binary or gzipped, one big file or one per timestep, one big file
-or one per processor).
+or multiple smaller files).
 
 IMPORTANT NOTE: Because periodic boundary conditions are enforced only
 on timesteps when neighbor lists are rebuilt, the coordinates of an
@@ -122,7 +122,7 @@ if the "atom_modify sort"_atom_modify.html option is on, which it is
 by default.  In this case atoms are re-ordered periodically during a
 simulation, due to spatial sorting.  It is also true when running in
 parallel, because data for a single snapshot is collected from
-multiple processors.
+multiple processors, each of which owns a subset of the atoms.
 
 For the {atom}, {custom}, {cfg}, and {local} styles, sorting is off by
 default.  For the {dcd}, {xtc}, {xyz}, and {molfile} styles, sorting by
@@ -281,11 +281,12 @@ from using the (numerical) atom type to an element name (or some
 other label). This will help many visualization programs to guess
 bonds and colors.
 
-Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files can
+Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files
-be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular
+can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a
-molecular viewing program).  See "Section tools"_Section_tools.html#vmd
+popular molecular viewing program.  See "Section
-of the manual and the tools/lmp2vmd/README.txt file for more information
+tools"_Section_tools.html#vmd of the manual and the
-about support in VMD for reading and visualizing LAMMPS dump files.
+tools/lmp2vmd/README.txt file for more information about support in
+VMD for reading and visualizing LAMMPS dump files.
 
 :line
 
@@ -318,7 +319,7 @@ tmp.dump.20000, etc.  This option is not available for the {dcd} and
 {xtc} styles.  Note that the "dump_modify pad"_dump_modify.html
 command can be used to insure all timestep numbers are the same length
 (e.g. 00010), which can make it easier to read a series of dump files
-in order by some post-processing tools.
+in order with some post-processing tools.
 
 If a "%" character appears in the filename, then each of P processors
 writes a portion of the dump file, and the "%" character is replaced

doc/dump_modify.html

@@ -100,9 +100,9 @@
   <I>color</I> args = name R G B
     name = name of color
     R,G,B = red/green/blue numeric values from 0.0 to 1.0
-</PRE>
   <I>framerate</I> arg = fps
     fps = frames per second for movie 
+</PRE>
 
 </UL>
 <P><B>Examples:</B>
@@ -245,6 +245,8 @@ the first two fields (atom id and type) are not actually written into
 the CFG file, though you must include formats for them in the format
 string.
 </P>
+<HR>
+
 <P>The <I>fileper</I> keyword is documented below with the <I>nfile</I> keyword.
 </P>
 <HR>
@@ -262,7 +264,7 @@ attributes in the dump command itself.
 <HR>
 
 <P>The <I>label</I> keyword applies only to the dump <I>local</I> style.  When
-it writes local informatoin, such as bond or angle topology
+it writes local information, such as bond or angle topology
 to a dump file, it will use the specified <I>label</I> to format
 the header.  By default this includes 2 lines:
 </P>
@@ -359,7 +361,7 @@ cost, as well as memory, versus unsorted output.
 <HR>
 
 <P>The <I>thresh</I> keyword only applies to the dump <I>custom</I>, <I>cfg</I>,
-<I>image</I>, and <I>mvoie</I> styles.  Multiple thresholds can be specified.
+<I>image</I>, and <I>movie</I> styles.  Multiple thresholds can be specified.
 Specifying "none" turns off all threshold criteria.  If thresholds are
 specified, only atoms whose attributes meet all the threshold criteria
 are written to the dump file or included in the image.  The possible

doc/dump_modify.txt

@@ -89,9 +89,9 @@ keyword = {acolor} or {adiam} or {amap} or {bcolor} or {bdiam} or {backcolor} or
     color = name of color for box lines
   {color} args = name R G B
     name = name of color
-    R,G,B = red/green/blue numeric values from 0.0 to 1.0 :pre
+    R,G,B = red/green/blue numeric values from 0.0 to 1.0
   {framerate} arg = fps
-    fps = frames per second for movie
+    fps = frames per second for movie :pre
 :ule
 
 [Examples:]
@@ -233,6 +233,8 @@ the first two fields (atom id and type) are not actually written into
 the CFG file, though you must include formats for them in the format
 string.
 
+:line
+
 The {fileper} keyword is documented below with the {nfile} keyword.
 
 :line
@@ -250,7 +252,7 @@ attributes in the dump command itself.
 :line
 
 The {label} keyword applies only to the dump {local} style.  When
-it writes local informatoin, such as bond or angle topology
+it writes local information, such as bond or angle topology
 to a dump file, it will use the specified {label} to format
 the header.  By default this includes 2 lines:
 
@@ -347,7 +349,7 @@ cost, as well as memory, versus unsorted output.
 :line
 
 The {thresh} keyword only applies to the dump {custom}, {cfg},
-{image}, and {mvoie} styles.  Multiple thresholds can be specified.
+{image}, and {movie} styles.  Multiple thresholds can be specified.
 Specifying "none" turns off all threshold criteria.  If thresholds are
 specified, only atoms whose attributes meet all the threshold criteria
 are written to the dump file or included in the image.  The possible

doc/neb.html

@@ -71,11 +71,11 @@ for further discussion.
 there to be one processor per replica.
 </P>
 <P>IMPORTANT NOTE: As explained below, a NEB calculation perfoms a
-damped-dynamics minimization across all the replicas.  This uses
+damped-dynamics minimization across all the replicas.  This will use
 whatever timestep you have defined in your input script, via the
-<A HREF = "timestep.html">timestep</A> command.  You may get faster convergence if
+<A HREF = "timestep.html">timestep</A> command.  You may get faster convergence for
-you use a larger timestep than you would normally use for dynamics
+a NEB calculation if you use a larger timestep than you would normally
-with the same system.
+use for dynamics with the same system.
 </P>
 <P>When a NEB calculation is performed, it is assumed that each replica
 is running the same system, though LAMMPS does not check for this.

doc/neb.txt

@@ -61,11 +61,11 @@ IMPORTANT NOTE: The current NEB implementation in LAMMPS only allows
 there to be one processor per replica.
 
 IMPORTANT NOTE: As explained below, a NEB calculation perfoms a
-damped-dynamics minimization across all the replicas.  This uses
+damped-dynamics minimization across all the replicas.  This will use
 whatever timestep you have defined in your input script, via the
-"timestep"_timestep.html command.  You may get faster convergence if
+"timestep"_timestep.html command.  You may get faster convergence for
-you use a larger timestep than you would normally use for dynamics
+a NEB calculation if you use a larger timestep than you would normally
-with the same system.
+use for dynamics with the same system.
 
 When a NEB calculation is performed, it is assumed that each replica
 is running the same system, though LAMMPS does not check for this.

doc/variable.html

@@ -418,8 +418,8 @@ would occur with the default precedence.
 <P>IMPORTANT NOTE: Because a unary minus is higher precedence than
 exponentiation, the formula "-2^2" will evaluate to 4, not -4.  This
 convention is compatible with some programming languages, but not
-others.  This behavior can be overridden with parenthesis; the formula
+others.  As mentioned, this behavior can be easily overridden with
-"-(2^2)" will evaluate to -4.
+parenthesis; the formula "-(2^2)" will evaluate to -4.
 </P>
 <P>The 6 relational operators return either a 1.0 or 0.0 depending on
 whether the relationship between x and y is TRUE or FALSE.  For

doc/variable.txt

@@ -418,8 +418,8 @@ would occur with the default precedence.
 IMPORTANT NOTE: Because a unary minus is higher precedence than
 exponentiation, the formula "-2^2" will evaluate to 4, not -4.  This
 convention is compatible with some programming languages, but not
-others.  This behavior can be overridden with parenthesis; the formula
+others.  As mentioned, this behavior can be easily overridden with
-"-(2^2)" will evaluate to -4.
+parenthesis; the formula "-(2^2)" will evaluate to -4.
 
 The 6 relational operators return either a 1.0 or 0.0 depending on
 whether the relationship between x and y is TRUE or FALSE.  For