git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1379 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/dump.html

@@ -30,8 +30,7 @@
 <PRE>  <I>atom</I> args = none
   <I>bond</I> args = none
   <I>dcd</I> args = none
-  <I>xtc</I> args = precision (optional)
-    precision = power-of-10 value from 10 to 1000000 (default = 1000)
+  <I>xtc</I> args = none
   <I>xyz</I> args = none
   <I>custom</I> args = list of atom attributes
     possible attributes = tag, mol, type,
@@ -138,16 +137,31 @@ below.
 <P>The <I>dcd</I> style writes DCD files, a standard atomic trajectory format
 used by the CHARMM, NAMD, and XPlor molecular dynamics packages.  DCD
 files are binary and thus may not be portable to different machines.
-The dump group must be <I>all</I> for the <I>dcd</I> style.
+The dump group must be <I>all</I> for the <I>dcd</I> style.  The <I>unwrap</I> option
+of the <A HREF = "dump_modify.html">dump_modify</A> command allows DCD coordinates
+to be written "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 these
+coordinates may thus be far outside the box size stored with the
+snapshot.
 </P>
 <P>The <I>xtc</I> style writes XTC files, a compressed trajectory format used
 by the GROMACS molecular dynamics package, and described
 <A HREF = "http://www.gromacs.org/documentation/reference_3.3/online/xtc.html">here</A>.
-The precision used in XTC files can be specified; for example, a value
-of 100 means that coordinates are stored to 1/100 nanometer accuracy.
-XTC files are portable binary files written in the NFS XDR data
-format, so that any machine which supports XDR should be able to read
-them.  The dump group must be <I>all</I> for the <I>xtc</I> style.
+The precision used in XTC files can be adjusted via the
+<A HREF = "dump_modify.html">dump_modify</A> command.  The default value of 1000
+means that coordinates are stored to 1/1000 nanometer accuracy.  XTC
+files are portable binary files written in the NFS XDR data format, so
+that any machine which supports XDR should be able to read them.  The
+dump group must be <I>all</I> for the <I>xtc</I> style.  The <I>unwrap</I> option of
+the <A HREF = "dump_modify.html">dump_modify</A> command allows XTC coordinates to
+be written "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 these
+coordinates may thus be far outside the box size stored with the
+snapshot.
 </P>
 <P>The <I>xyz</I> style writes XYZ files, which is a simple text-based
 coordinate format that many codes can read.
@@ -310,12 +324,14 @@ some machines may not support the lo-level XDR data format that XTC
 files are written with, which will result in a compile-time error when
 a lo-level include file is not found.  Putting this style in a package
 makes it easy to exclude from a LAMMPS build for those machines.
-</P>
-<P>Some pair potentials do not allow the calculation of per-atom energy
-and stress via the <I>epair</I>, <I>etotal</I>, <I>sxx</I>, etc keywords.  One of
-these are the granular pair potentials.  However, for those
-potentials, the <A HREF = "fix_gran_diag.html">fix gran/diag</A> command can be used
-instead.
+However, the XTC package also includes two compatibility header files
+and associated functions, which should be a suitable substitute on
+machines that do not have the appropriate native header files.  This
+option can be invoked at build time by adding -DLAMMPS_XDR to the
+CCFLAGS variable in the appropriate lo-level Makefile,
+e.g. src/MAKE/Makefile.foo.  This compatability mode has been tested
+successfully on Cray XT3 and IBM BlueGene/L machines and should also
+work on the Cray XT4, IBM BG/P, and Windows XP machines.
 </P>
 <P><B>Related commands:</B>
 </P>