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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4994 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-10-07 14:59:11 +00:00
parent db3d5fa0b5
commit e20c035199
2 changed files with 44 additions and 32 deletions
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38
doc/fix_rigid.html
View File

@ -242,18 +242,22 @@ not do this automatically.
also accounted for by this fix.
</P>
<P>IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are
modified when the center-of-mass of the rigid body moves across a
periodic boundary. They are not incremented/decremented as they would
be for non-rigid atoms. This change does not affect dynamics, but
means that any diagnostic computation based on the atomic image flag
values must be adjusted accordingly. For example, the <A HREF = "compute_msd.html">compute
msd</A> will not compute the expected mean-squared
displacement for such atoms, and the image flag values written to a
<A HREF = "dump.html">dump file</A> will be different than they would be if the
atoms were not in a rigid body. It also means that if you have bonds
altered so that the rigid body can be reconstructed correctly when it
straddles periodic boundaries. The atom image flags are not
incremented/decremented as they would be for non-rigid atoms. This
means you cannot interpret them as you normally would. For example,
the image flag values written to a <A HREF = "dump.html">dump file</A> will be
different than they would be if the atoms were not in a rigid body.
Likewise the <A HREF = "compute_msd.html">compute msd</A> will not compute the
expected mean-squared displacement for such atoms if the body moves
across periodic boundaries. It also means that if you have bonds
between a pair of rigid bodies and the bond straddles a periodic
boundary, you cannot use the <A HREF = "replicate.html">replicate</A> command to
increase the system size.
increase the system size. Note that this fix does define image flags
for each rigid body, which are incremented when the rigid body crosses
a periodic boundary in the usual way. These image flags have the same
meaning as atom images (see the "dump" command) and can be accessed
and output as described below.
</P>
<HR>
@ -273,13 +277,15 @@ fixes.
<P>These fixes compute a global array of values which can be accessed by
various <A HREF = "Section_howto.html#4_15">output commands</A>. The number of rows
in the array is equal to the number of rigid bodies. The number of
columns is 12. Thus for each rigid body, 12 values are stored: the
columns is 15. Thus for each rigid body, 12 values are stored: the
xyz coords of the center of mass (COM), the xyz components of the COM
velocity, the xyz components of the force acting on the COM, and the
xyz components of the torque acting on the COM. The force and torque
values in the array are not affected by the <I>force</I> and <I>torque</I>
keywords in the fix rigid command; they reflect values before any
changes are made by those keywords.
velocity, the xyz components of the force acting on the COM, the xyz
components of the torque acting on the COM, and the xyz image flags of
the COM, which have the same meaning as image flags for atom positions
(see the "dump" command). The force and torque values in the array
are not affected by the <I>force</I> and <I>torque</I> keywords in the fix rigid
command; they reflect values before any changes are made by those
keywords.
</P>
<P>The ordering of the rigid bodies (by row in the array) is as follows.
For the <I>single</I> keyword there is just one rigid body. For the

38
doc/fix_rigid.txt
View File

@ -231,18 +231,22 @@ The rigid body contribution to the pressure of the system (virial) is
also accounted for by this fix.
IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are
modified when the center-of-mass of the rigid body moves across a
periodic boundary. They are not incremented/decremented as they would
be for non-rigid atoms. This change does not affect dynamics, but
means that any diagnostic computation based on the atomic image flag
values must be adjusted accordingly. For example, the "compute
msd"_compute_msd.html will not compute the expected mean-squared
displacement for such atoms, and the image flag values written to a
"dump file"_dump.html will be different than they would be if the
atoms were not in a rigid body. It also means that if you have bonds
altered so that the rigid body can be reconstructed correctly when it
straddles periodic boundaries. The atom image flags are not
incremented/decremented as they would be for non-rigid atoms. This
means you cannot interpret them as you normally would. For example,
the image flag values written to a "dump file"_dump.html will be
different than they would be if the atoms were not in a rigid body.
Likewise the "compute msd"_compute_msd.html will not compute the
expected mean-squared displacement for such atoms if the body moves
across periodic boundaries. It also means that if you have bonds
between a pair of rigid bodies and the bond straddles a periodic
boundary, you cannot use the "replicate"_replicate.html command to
increase the system size.
increase the system size. Note that this fix does define image flags
for each rigid body, which are incremented when the rigid body crosses
a periodic boundary in the usual way. These image flags have the same
meaning as atom images (see the "dump" command) and can be accessed
and output as described below.
:line
@ -262,13 +266,15 @@ fixes.
These fixes compute a global array of values which can be accessed by
various "output commands"_Section_howto.html#4_15. The number of rows
in the array is equal to the number of rigid bodies. The number of
columns is 12. Thus for each rigid body, 12 values are stored: the
columns is 15. Thus for each rigid body, 12 values are stored: the
xyz coords of the center of mass (COM), the xyz components of the COM
velocity, the xyz components of the force acting on the COM, and the
xyz components of the torque acting on the COM. The force and torque
values in the array are not affected by the {force} and {torque}
keywords in the fix rigid command; they reflect values before any
changes are made by those keywords.
velocity, the xyz components of the force acting on the COM, the xyz
components of the torque acting on the COM, and the xyz image flags of
the COM, which have the same meaning as image flags for atom positions
(see the "dump" command). The force and torque values in the array
are not affected by the {force} and {torque} keywords in the fix rigid
command; they reflect values before any changes are made by those
keywords.
The ordering of the rigid bodies (by row in the array) is as follows.
For the {single} keyword there is just one rigid body. For the