jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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

This commit is contained in:
sjplimp 2009-04-22 23:33:07 +00:00
parent 2391d7655a
commit 70e7709d2e
2 changed files with 38 additions and 16 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

27
doc/fix_deform.html
View File

@ -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
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
re-mapped; otherwise they are not. If <I>remap</I> is set to <I>v</I>, then any
atom in the fix group that crosses a periodic boundary will have a
delta added to its velocity equal to the difference in velocities
between the lo and hi boundaries. Note that this velocity difference
can include tilt components, e.g. a delta in the x velocity 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.
re-mapped; otherwise they are not. Note that their velocities are not
changed, just their positions are altered. If <I>remap</I> is set to <I>v</I>,
then any atom in the fix group that crosses a periodic boundary will
have a delta added to its velocity equal to the difference in
velocities between the lo and hi boundaries. Note that this velocity
difference can include tilt components, e.g. a delta in the x velocity
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>IMPORTANT NOTE: When non-equilibrium MD (NEMD) simulations are
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
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
be remapped by fix deform, but velocities SHOULD be when atoms cross
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
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
re-mapped; otherwise they are not. If {remap} is set to {v}, then any
atom in the fix group that crosses a periodic boundary will have a
delta added to its velocity equal to the difference in velocities
between the lo and hi boundaries. Note that this velocity difference
can include tilt components, e.g. a delta in the x velocity when an
atom crosses the y periodic boundary. If {remap} is set to {none},
then neither of these remappings take place.
re-mapped; otherwise they are not. Note that their velocities are not
changed, just their positions are altered. If {remap} is set to {v},
then any atom in the fix group that crosses a periodic boundary will
have a delta added to its velocity equal to the difference in
velocities between the lo and hi boundaries. Note that this velocity
difference can include tilt components, e.g. a delta in the x velocity
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
performed using this fix, the option "remap v" should normally be
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
be remapped by fix deform, but velocities SHOULD be when atoms cross
periodic boundaries, since that is consistent with maintaining the