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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2773 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2009-04-22 23:33:07 +00:00
parent 2391d7655a
commit 70e7709d2e
2 changed files with 38 additions and 16 deletions
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27
doc/fix_deform.html
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@ -354,18 +354,29 @@ remapped into the new box in the appropriate manner.
<P>Each time the box size or shape is changed, the <I>remap</I> keyword <P>Each time the box size or shape is changed, the <I>remap</I> keyword
determines whether atom positions are re-mapped to the new box. If determines whether atom positions are re-mapped to the new box. If
<I>remap</I> is set to <I>x</I> (the default), atoms in the fix group are <I>remap</I> is set to <I>x</I> (the default), atoms in the fix group are
re-mapped; otherwise they are not. If <I>remap</I> is set to <I>v</I>, then any re-mapped; otherwise they are not. Note that their velocities are not
atom in the fix group that crosses a periodic boundary will have a changed, just their positions are altered. If <I>remap</I> is set to <I>v</I>,
delta added to its velocity equal to the difference in velocities then any atom in the fix group that crosses a periodic boundary will
between the lo and hi boundaries. Note that this velocity difference have a delta added to its velocity equal to the difference in
can include tilt components, e.g. a delta in the x velocity when an velocities between the lo and hi boundaries. Note that this velocity
atom crosses the y periodic boundary. If <I>remap</I> is set to <I>none</I>, difference can include tilt components, e.g. a delta in the x velocity
then neither of these remappings take place. when an atom crosses the y periodic boundary. If <I>remap</I> is set to
<I>none</I>, then neither of these remappings take place.
</P>
<P>Conceptually, setting <I>remap</I> to <I>x</I> is forcing the atoms to deform
via an affine transformation that exactly matches the box deformation.
Though the atoms are moving, it is not due to them having a velocity
that matches the box change. This setting is typically appropriate
for solids. Setting <I>remap</I> to <I>v</I> is typically appropriate for
fluids, where you want the atoms to respond to the change in box
size/shape on their own and acquire a velocity that matches the box
change, so that they will naturally move with the box without explicit
remapping of their coordinates.
</P> </P>
<P>IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are <P>IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are
performed using this fix, the option "remap v" should normally be performed using this fix, the option "remap v" should normally be
used. This is because <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> adjusts the used. This is because <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> adjusts the
atom positions and velocities to provide a velocity profile that atom positions and velocities to induce a velocity profile that
matches the changing box size/shape. Thus atom coordinates should NOT matches the changing box size/shape. Thus atom coordinates should NOT
be remapped by fix deform, but velocities SHOULD be when atoms cross be remapped by fix deform, but velocities SHOULD be when atoms cross
periodic boundaries, since that is consistent with maintaining the periodic boundaries, since that is consistent with maintaining the

27
doc/fix_deform.txt
View File

@ -344,18 +344,29 @@ remapped into the new box in the appropriate manner.
Each time the box size or shape is changed, the {remap} keyword Each time the box size or shape is changed, the {remap} keyword
determines whether atom positions are re-mapped to the new box. If determines whether atom positions are re-mapped to the new box. If
{remap} is set to {x} (the default), atoms in the fix group are {remap} is set to {x} (the default), atoms in the fix group are
re-mapped; otherwise they are not. If {remap} is set to {v}, then any re-mapped; otherwise they are not. Note that their velocities are not
atom in the fix group that crosses a periodic boundary will have a changed, just their positions are altered. If {remap} is set to {v},
delta added to its velocity equal to the difference in velocities then any atom in the fix group that crosses a periodic boundary will
between the lo and hi boundaries. Note that this velocity difference have a delta added to its velocity equal to the difference in
can include tilt components, e.g. a delta in the x velocity when an velocities between the lo and hi boundaries. Note that this velocity
atom crosses the y periodic boundary. If {remap} is set to {none}, difference can include tilt components, e.g. a delta in the x velocity
then neither of these remappings take place. when an atom crosses the y periodic boundary. If {remap} is set to
{none}, then neither of these remappings take place.
Conceptually, setting {remap} to {x} is forcing the atoms to deform
via an affine transformation that exactly matches the box deformation.
Though the atoms are moving, it is not due to them having a velocity
that matches the box change. This setting is typically appropriate
for solids. Setting {remap} to {v} is typically appropriate for
fluids, where you want the atoms to respond to the change in box
size/shape on their own and acquire a velocity that matches the box
change, so that they will naturally move with the box without explicit
remapping of their coordinates.
IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are
performed using this fix, the option "remap v" should normally be performed using this fix, the option "remap v" should normally be
used. This is because "fix nvt/sllod"_fix_nvt_sllod.html adjusts the used. This is because "fix nvt/sllod"_fix_nvt_sllod.html adjusts the
atom positions and velocities to provide a velocity profile that atom positions and velocities to induce a velocity profile that
matches the changing box size/shape. Thus atom coordinates should NOT matches the changing box size/shape. Thus atom coordinates should NOT
be remapped by fix deform, but velocities SHOULD be when atoms cross be remapped by fix deform, but velocities SHOULD be when atoms cross
periodic boundaries, since that is consistent with maintaining the periodic boundaries, since that is consistent with maintaining the