git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2456 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/dump.html

@@ -229,22 +229,30 @@ styles.
 <P>This section explains the atom quantities that can be specified as
 part of the <I>custom</I> style.
 </P>
-<P>The <I>id</I>, <I>mol</I>, <I>type</I>, <I>x</I>, <I>y</I>, <I>z</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
-<I>fz</I>, <I>q</I> keywords are self-explanatory.  <I>Id</I> is the atom ID.  <I>Mol</I>
-is the molecule ID, included in the data file for molecular systems.
-The <I>x</I>, <I>y</I>, <I>z</I> keywords write atom coordinates "unscaled", in the
+<P>The <I>id</I>, <I>mol</I>, <I>type</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
+<I>fz</I>, <I>q</I> keywords are self-explanatory.
+</P>
+<P><I>Id</I> is the atom ID.  <I>Mol</I> is the molecule ID, included in the data
+file for molecular systems.  <I>Type</I> is the atom type.  <I>Vx</I>, <I>vy</I>,
+<I>vz</I>, <I>fx</I>, <I>fy</I>, <I>fz</I>, and <I>q</I> are components of atom velocity and
+force and atomic charge.
+</P>
+<P>There are several options for outputting atom coordinates.  The <I>x</I>,
+<I>y</I>, <I>z</I> keywords write atom coordinates "unscaled", in the
 appropriate distance <A HREF = "units.html">units</A> (Angstroms, sigma, etc).  Use
 <I>xs</I>, <I>ys</I>, <I>zs</I> if you want the coordinates "scaled" to the box size,
-so that each value is 0.0 to 1.0.  Use <I>xu</I>, <I>yu</I>, <I>zu</I> if you want
-the coordinates "unwrapped" by the image flags for each atom.
-Unwrapped means that if the atom has passed thru a periodic boundary
-one or more times, the value is printed for what the coordinate would
-be if it had not been wrapped back into the periodic box.  Note that
-using <I>xu</I>, <I>yu</I>, <I>zu</I> means that the coordinate values may be far
-outside the box size printed with the snapshot.  The image flags can
-be printed directly using the <I>ix</I>, <I>iy</I>, <I>iz</I> keywords. The
-<A HREF = "dump_modify.html">dump_modify</A> command describes in more detail what
-is meant by scaled vs unscaled coordinates and the image flags.
+so that each value is 0.0 to 1.0.  If the simluation box is triclinic
+(tilted), then all atom coords will still be between 0.0 and 1.0.  Use
+<I>xu</I>, <I>yu</I>, <I>zu</I> if you want the coordinates "unwrapped" by the image
+flags for each atom.  Unwrapped means that if the atom has passed thru
+a periodic boundary one or more times, the value is printed for what
+the coordinate would be if it had not been wrapped back into the
+periodic box.  Note that using <I>xu</I>, <I>yu</I>, <I>zu</I> means that the
+coordinate values may be far outside the box size printed with the
+snapshot.  The image flags can be printed directly using the <I>ix</I>,
+<I>iy</I>, <I>iz</I> keywords. The <A HREF = "dump_modify.html">dump_modify</A> command
+describes in more detail what is meant by scaled vs unscaled
+coordinates and the image flags.
 </P>
 <P>The <I>mux</I>, <I>muy</I>, <I>muz</I> keywords are specific to dipolar systems
 defined with an atom style of <I>dipole</I>.  They give the orientation of
@@ -323,13 +331,6 @@ per-atom quantities which could then be output into dump files.
 
 <P><B>Restrictions:</B>
 </P>
-<P>Scaled coordinates cannot be writted to dump files when the simulation
-box is triclinic (non-orthogonal).  Note that this is the default for
-dump style <I>atom</I>; the <A HREF = "dump_modify.html">dump_modify command</A> must be
-used to change it.  The exception is DCD files which store the tilt
-factors for subsequent visualization by programs like
-<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
-</P>
 <P>To write gzipped dump files, you must compile LAMMPS with the
 -DLAMMPS_GZIP option - see the <A HREF = "Section_start.html#2_2">Making LAMMPS</A>
 section of the documentation.

doc/dump.txt

@@ -219,22 +219,30 @@ styles.
 This section explains the atom quantities that can be specified as
 part of the {custom} style.
 
-The {id}, {mol}, {type}, {x}, {y}, {z}, {vx}, {vy}, {vz}, {fx}, {fy},
-{fz}, {q} keywords are self-explanatory.  {Id} is the atom ID.  {Mol}
-is the molecule ID, included in the data file for molecular systems.
-The {x}, {y}, {z} keywords write atom coordinates "unscaled", in the
+The {id}, {mol}, {type}, {vx}, {vy}, {vz}, {fx}, {fy},
+{fz}, {q} keywords are self-explanatory.
+
+{Id} is the atom ID.  {Mol} is the molecule ID, included in the data
+file for molecular systems.  {Type} is the atom type.  {Vx}, {vy},
+{vz}, {fx}, {fy}, {fz}, and {q} are components of atom velocity and
+force and atomic charge.
+
+There are several options for outputting atom coordinates.  The {x},
+{y}, {z} keywords write atom coordinates "unscaled", in the
 appropriate distance "units"_units.html (Angstroms, sigma, etc).  Use
 {xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size,
-so that each value is 0.0 to 1.0.  Use {xu}, {yu}, {zu} if you want
-the coordinates "unwrapped" by the image flags for each atom.
-Unwrapped means that if the atom has passed thru a periodic boundary
-one or more times, the value is printed for what the coordinate would
-be if it had not been wrapped back into the periodic box.  Note that
-using {xu}, {yu}, {zu} means that the coordinate values may be far
-outside the box size printed with the snapshot.  The image flags can
-be printed directly using the {ix}, {iy}, {iz} keywords. The
-"dump_modify"_dump_modify.html command describes in more detail what
-is meant by scaled vs unscaled coordinates and the image flags.
+so that each value is 0.0 to 1.0.  If the simluation box is triclinic
+(tilted), then all atom coords will still be between 0.0 and 1.0.  Use
+{xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the image
+flags for each atom.  Unwrapped means that if the atom has passed thru
+a periodic boundary one or more times, the value is printed for what
+the coordinate would be if it had not been wrapped back into the
+periodic box.  Note that using {xu}, {yu}, {zu} means that the
+coordinate values may be far outside the box size printed with the
+snapshot.  The image flags can be printed directly using the {ix},
+{iy}, {iz} keywords. The "dump_modify"_dump_modify.html command
+describes in more detail what is meant by scaled vs unscaled
+coordinates and the image flags.
 
 The {mux}, {muy}, {muz} keywords are specific to dipolar systems
 defined with an atom style of {dipole}.  They give the orientation of
@@ -313,13 +321,6 @@ per-atom quantities which could then be output into dump files.
 
 [Restrictions:]
 
-Scaled coordinates cannot be writted to dump files when the simulation
-box is triclinic (non-orthogonal).  Note that this is the default for
-dump style {atom}; the "dump_modify command"_dump_modify.html must be
-used to change it.  The exception is DCD files which store the tilt
-factors for subsequent visualization by programs like
-"VMD"_http://www.ks.uiuc.edu/Research/vmd.
-
 To write gzipped dump files, you must compile LAMMPS with the
 -DLAMMPS_GZIP option - see the "Making LAMMPS"_Section_start.html#2_2
 section of the documentation.

doc/dump_modify.html

@@ -59,16 +59,20 @@ format string.  This option has no effect on the <I>dcd</I> and <I>xtc</I> dump
 styles since they write binary files.
 </P>
 <P>The <I>scale</I> and <I>image</I> keywords apply only to the dump <I>atom</I> style.
-A scale value of <I>yes</I> means atom coords are written in normalized
-units from 0.0 to 1.0 in each box dimension.  A value of <I>no</I> means
-they are written in absolute distance units (e.g. Angstroms or sigma).
-If the image value is <I>yes</I>, 3 flags are appended to each atom's
+</P>
+<P>A scale value of <I>yes</I> means atom coords are written in normalized
+units from 0.0 to 1.0 in each box dimension.  If the simluation box is
+triclinic (tilted), then all atom coords will still be between 0.0 and
+1.0.  A value of <I>no</I> means they are written in absolute distance
+units (e.g. Angstroms or sigma).
+</P>
+<P>If the image value is <I>yes</I>, 3 flags are appended to each atom's
 coords which are the absolute box image of the atom in each dimension.
 For example, an x image flag of -2 with a normalized coord of 0.5
 means the atom is in the center of the box, but has passed thru the
 box boundary 2 times and is really 2 box lengths to the left of its
-current coordinate.  Note that for dump style <I>custom</I> these values
-can be printed in the dump file by using the appropriate atom
+current coordinate.  Note that for dump style <I>custom</I> these various
+values can be printed in the dump file by using the appropriate atom
 attributes in the dump command itself.
 </P>
 

doc/dump_modify.txt

@@ -52,16 +52,20 @@ format string.  This option has no effect on the {dcd} and {xtc} dump
 styles since they write binary files.
 
 The {scale} and {image} keywords apply only to the dump {atom} style.
+
 A scale value of {yes} means atom coords are written in normalized
-units from 0.0 to 1.0 in each box dimension.  A value of {no} means
-they are written in absolute distance units (e.g. Angstroms or sigma).
+units from 0.0 to 1.0 in each box dimension.  If the simluation box is
+triclinic (tilted), then all atom coords will still be between 0.0 and
+1.0.  A value of {no} means they are written in absolute distance
+units (e.g. Angstroms or sigma).
+
 If the image value is {yes}, 3 flags are appended to each atom's
 coords which are the absolute box image of the atom in each dimension.
 For example, an x image flag of -2 with a normalized coord of 0.5
 means the atom is in the center of the box, but has passed thru the
 box boundary 2 times and is really 2 box lengths to the left of its
-current coordinate.  Note that for dump style {custom} these values
-can be printed in the dump file by using the appropriate atom
+current coordinate.  Note that for dump style {custom} these various
+values can be printed in the dump file by using the appropriate atom
 attributes in the dump command itself.
 
 :link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)