git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12134 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_start.html

@@ -1356,13 +1356,13 @@ sub-directory (-pscreen replica_files/screen).  If this option is not
 used the screen file for partition N is screen.N or whatever is
 specified by the -screen command-line option.
 </P>
-<PRE>-restart restartfile datafile keyword value ... 
+<PRE>-restart restartfile <I>remap</I> datafile keyword value ... 
 </PRE>
 <P>Convert the restart file into a data file and immediately exit.  This
 is the same operation as if the following 2-line input script were
 run:
 </P>
-<PRE>read_restart restartfile
+<PRE>read_restart restartfile <I>remap</I>
 write_data datafile keyword value ... 
 </PRE>
 <P>Note that the specified restartfile and datafile can have wild-card
@@ -1371,6 +1371,13 @@ characters ("*",%") as described by the
 commands.  But a filename such as file.* will need to be enclosed in
 quotes to avoid shell expansion of the "*" character.
 </P>
+<P>Note that following restartfile, the optional flag <I>remap</I> can be
+used.  This has the same effect as adding it to the
+<A HREF = "read_restart.html">read_restart</A> command, as explained on its doc
+page.  This is only useful if the reading of the restart file triggers
+an error that atoms have been lost.  In that case, use of the remap
+flag should allow the data file to still be produced.
+</P>
 <P>Also note that following datafile, the same optional keyword/value
 pairs can be listed as used by the <A HREF = "write_data.html">write_data</A>
 command.

doc/Section_start.txt

@@ -1350,13 +1350,13 @@ sub-directory (-pscreen replica_files/screen).  If this option is not
 used the screen file for partition N is screen.N or whatever is
 specified by the -screen command-line option.
 
--restart restartfile datafile keyword value ... :pre 
+-restart restartfile {remap} datafile keyword value ... :pre 
 
 Convert the restart file into a data file and immediately exit.  This
 is the same operation as if the following 2-line input script were
 run:
 
-read_restart restartfile
+read_restart restartfile {remap}
 write_data datafile keyword value ... :pre
 
 Note that the specified restartfile and datafile can have wild-card
@@ -1365,6 +1365,13 @@ characters ("*",%") as described by the
 commands.  But a filename such as file.* will need to be enclosed in
 quotes to avoid shell expansion of the "*" character.
 
+Note that following restartfile, the optional flag {remap} can be
+used.  This has the same effect as adding it to the
+"read_restart"_read_restart.html command, as explained on its doc
+page.  This is only useful if the reading of the restart file triggers
+an error that atoms have been lost.  In that case, use of the remap
+flag should allow the data file to still be produced.
+
 Also note that following datafile, the same optional keyword/value
 pairs can be listed as used by the "write_data"_write_data.html
 command.

doc/read_restart.html

@@ -13,16 +13,19 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>read_restart file 
+<PRE>read_restart file flag 
 </PRE>
 <UL><LI>file = name of binary restart file to read in 
 </UL>
+<P>flag = remap (optional)
+</P>
 <P><B>Examples:</B>
 </P>
 <PRE>read_restart save.10000
+read_restart save.10000 remap
 read_restart restart.*
 read_restart restart.*.mpiio
-read_restart poly.*.% 
+read_restart poly.*.% remap 
 </PRE>
 <PRE>
 </PRE>
@@ -40,6 +43,17 @@ number of processors in the current simulation and the settings of the
 changed by the <A HREF = "balance.html">balance</A> or <A HREF = "fix_balance.html">fix
 balance</A> commands.
 </P>
+<P>IMPORTANT NOTE: Normally, restart files are written by the
+<A HREF = "restart.html">restart</A> or <A HREF = "write_restart.html">write_restart</A> commands
+so that all atoms in the restart file are inside the simulation box.
+If this is not the case, the read_restart command will print an error
+that atoms were "lost" when the file is read.  This error should be
+reported to the LAMMPS developers so the invalid writing of the
+restart file can be fixed.  If you still wish to use the restart file,
+the optional <I>remap</I> flag can be appended to the read_restart command.
+This will avoid the error, by explicitly remapping each atom back into
+the simulation box, updating image flags for the atom appropriately.
+</P>
 <P>Restart files are saved in binary format to enable exact restarts,
 meaning that the trajectories of a restarted run will precisely match
 those produced by the original run had it continued on.

doc/read_restart.txt

@@ -10,16 +10,18 @@ read_restart command :h3
 
 [Syntax:]
 
-read_restart file :pre
+read_restart file flag :pre
 
 file = name of binary restart file to read in :ul
+flag = remap (optional)
 
 [Examples:]
 
 read_restart save.10000
+read_restart save.10000 remap
 read_restart restart.*
 read_restart restart.*.mpiio
-read_restart poly.*.% :pre
+read_restart poly.*.% remap :pre
 
 :pre
 
@@ -37,6 +39,17 @@ number of processors in the current simulation and the settings of the
 changed by the "balance"_balance.html or "fix
 balance"_fix_balance.html commands.
 
+IMPORTANT NOTE: Normally, restart files are written by the
+"restart"_restart.html or "write_restart"_write_restart.html commands
+so that all atoms in the restart file are inside the simulation box.
+If this is not the case, the read_restart command will print an error
+that atoms were "lost" when the file is read.  This error should be
+reported to the LAMMPS developers so the invalid writing of the
+restart file can be fixed.  If you still wish to use the restart file,
+the optional {remap} flag can be appended to the read_restart command.
+This will avoid the error, by explicitly remapping each atom back into
+the simulation box, updating image flags for the atom appropriately.
+
 Restart files are saved in binary format to enable exact restarts,
 meaning that the trajectories of a restarted run will precisely match
 those produced by the original run had it continued on.