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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8809 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2012-09-21 14:52:59 +00:00
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20
doc/replicate.html
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@ -47,6 +47,26 @@ 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 when replicating it in that dimension, as it may put atoms nearly on
top of each other. top of each other.
</P> </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
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.
</P>
<P>If the current simulation was read in from a restart file (before a <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 run is performed), there can have been no fix information stored in
the file for individual atoms. Similarly, no fixes can be defined at the file for individual atoms. Similarly, no fixes can be defined at

20
doc/replicate.txt
View File

@ -44,6 +44,26 @@ 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 when replicating it in that dimension, as it may put atoms nearly on
top of each other. 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
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.
If the current simulation was read in from a restart file (before a 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 run is performed), there can have been no fix information stored in
the file for individual atoms. Similarly, no fixes can be defined at the file for individual atoms. Similarly, no fixes can be defined at