git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10509 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/replicate.html

@@ -34,10 +34,12 @@ velocities, which may or may not be desirable.  New atom IDs are
 assigned to new atoms, as are molecule IDs.  Bonds and other topology
 interactions are created between pairs of new atoms as well as between
 old and new atoms.  This is done by using the image flag for each atom
-to "unwrap" it out of the periodic box before replicating it.  This
-means that molecular bonds you specify in the original data file that
-span the periodic box should be between two atoms with image flags
-that differ by 1.  This will allow them to be unwrapped appropriately.
+to "unwrap" it out of the periodic box before replicating it.
+</P>
+<P>This means that any molecular bond you specify in the original data
+file that crosses a periodic boundary should be between two atoms with
+image flags that differ by 1.  This will allow the bond to be
+unwrapped appropriately.
 </P>
 <P><B>Restrictions:</B>
 </P>
@@ -47,25 +49,27 @@ that differ by 1.  This will allow them to be unwrapped appropriately.
 when replicating it in that dimension, as it may put atoms nearly on
 top of each other.
 </P>
-<P>IMPORTANT NOTE: You cannot use the replicate command to replicate a
-molecule that is bonded to itself across a periodic boundary, so the
-molecule is efffectively a loop.  A simple example would be a linear
-polymer chain that spans the simulation box and bonds back to itself
-across the periodic boundary.  More realistic examples would be a CNT
-(meant to be an infinitely long CNT) or graphene sheet.  (Note that
-this only applies to such molecules that have permanent bonds as
-specified in the data file.  A CNT that is just atoms modeled with the
-<A HREF = "pair_airebo.html">AIREBO potential</A> has no such permanent bonds, so it
-is not a problem to replicate it.)  The reason replicate does not work
-with those systems is that the image flag settings described above
-cannot be made consistent.  I.e. it is not possible to have every pair
-of bonded atoms have the same image flags, when they are unwrapped so
-as to be close to each other.  The only way the replicate command
+<P>IMPORTANT NOTE: You cannot use the replicate command on a system which
+has a molecule that spans the box and is bonded to itself across a
+periodic boundary, so that the molecule is efffectively a loop.  A
+simple example would be a linear polymer chain that spans the
+simulation box and bonds back to itself across the periodic boundary.
+More realistic examples would be a CNT (meant to be an infinitely long
+CNT) or a graphene sheet or a bulk periodic crystal where there are
+explicit bonds specified between near neighbors.  (Note that this only
+applies to systems that have permanent bonds as specified in the data
+file.  A CNT that is just atoms modeled with the <A HREF = "pair_airebo.html">AIREBO
+potential</A> has no such permanent bonds, so it can be
+replicated.)  The reason replication does not work with those systems
+is that the image flag settings described above cannot be made
+consistent.  I.e. it is not possible to define images flags so that
+when every pair of bonded atoms is unwrapped (using the image flags),
+they will be close to each other.  The only way the replicate command
 could work in this scenario is for it to break a bond, insert more
-atoms, and re-connect the loop for the larger simulation box.  It is
-not clever enough to do this.  So you will have to construct a larger
-version of your molecule as a pre-processing step and input a new data
-file to LAMMPS.
+atoms, and re-connect the loop for the larger simulation box.  But it
+is not clever enough to do this.  So you will have to construct a
+larger version of your molecule as a pre-processing step and input a
+new data file to LAMMPS.
 </P>
 <P>If the current simulation was read in from a restart file (before a
 run is performed), there can have been no fix information stored in

doc/replicate.txt

@@ -31,10 +31,12 @@ velocities, which may or may not be desirable.  New atom IDs are
 assigned to new atoms, as are molecule IDs.  Bonds and other topology
 interactions are created between pairs of new atoms as well as between
 old and new atoms.  This is done by using the image flag for each atom
-to "unwrap" it out of the periodic box before replicating it.  This
-means that molecular bonds you specify in the original data file that
-span the periodic box should be between two atoms with image flags
-that differ by 1.  This will allow them to be unwrapped appropriately.
+to "unwrap" it out of the periodic box before replicating it.
+
+This means that any molecular bond you specify in the original data
+file that crosses a periodic boundary should be between two atoms with
+image flags that differ by 1.  This will allow the bond to be
+unwrapped appropriately.
 
 [Restrictions:]
 
@@ -44,25 +46,27 @@ If a simulation is non-periodic in a dimension, care should be used
 when replicating it in that dimension, as it may put atoms nearly on
 top of each other.
 
-IMPORTANT NOTE: You cannot use the replicate command to replicate a
-molecule that is bonded to itself across a periodic boundary, so the
-molecule is efffectively a loop.  A simple example would be a linear
-polymer chain that spans the simulation box and bonds back to itself
-across the periodic boundary.  More realistic examples would be a CNT
-(meant to be an infinitely long CNT) or graphene sheet.  (Note that
-this only applies to such molecules that have permanent bonds as
-specified in the data file.  A CNT that is just atoms modeled with the
-"AIREBO potential"_pair_airebo.html has no such permanent bonds, so it
-is not a problem to replicate it.)  The reason replicate does not work
-with those systems is that the image flag settings described above
-cannot be made consistent.  I.e. it is not possible to have every pair
-of bonded atoms have the same image flags, when they are unwrapped so
-as to be close to each other.  The only way the replicate command
+IMPORTANT NOTE: You cannot use the replicate command on a system which
+has a molecule that spans the box and is bonded to itself across a
+periodic boundary, so that the molecule is efffectively a loop.  A
+simple example would be a linear polymer chain that spans the
+simulation box and bonds back to itself across the periodic boundary.
+More realistic examples would be a CNT (meant to be an infinitely long
+CNT) or a graphene sheet or a bulk periodic crystal where there are
+explicit bonds specified between near neighbors.  (Note that this only
+applies to systems that have permanent bonds as specified in the data
+file.  A CNT that is just atoms modeled with the "AIREBO
+potential"_pair_airebo.html has no such permanent bonds, so it can be
+replicated.)  The reason replication does not work with those systems
+is that the image flag settings described above cannot be made
+consistent.  I.e. it is not possible to define images flags so that
+when every pair of bonded atoms is unwrapped (using the image flags),
+they will be close to each other.  The only way the replicate command
 could work in this scenario is for it to break a bond, insert more
-atoms, and re-connect the loop for the larger simulation box.  It is
-not clever enough to do this.  So you will have to construct a larger
-version of your molecule as a pre-processing step and input a new data
-file to LAMMPS.
+atoms, and re-connect the loop for the larger simulation box.  But it
+is not clever enough to do this.  So you will have to construct a
+larger version of your molecule as a pre-processing step and input a
+new data file to LAMMPS.
 
 If the current simulation was read in from a restart file (before a
 run is performed), there can have been no fix information stored in