velocity profile already created by fix nvt/sllod.  LAMMPS will warn

you if the <I>remap</I> setting is not consistent with fix nvt/sllod.

</P>

<P>IMPORTANT NOTE: If a <A HREF = "fix_rigid.html">fix rigid</A> is defined for rigid

bodies, and <I>remap</I> is set to <I>x</I>, then the center-of-mass coordinates

of rigid bodies will be remapped to the changing simulation box.  This

will be done regardless of whether atoms in the rigid bodies are in

the fix deform group or not.  The velocity of the centers of mass are

not remapped even if <I>remap</I> is set to <I>v</I>, since <A HREF = "fix_nvt_sllod.html">fix

nvt/sllod</A> does not currently do anything special

for rigid particles.  If you wish to perform a NEMD simulation of

rigid particles, you can either thermostat them independently or

include a background fluid and thermostat the fluid via <A HREF = "fix_nvt_sllod">fix

nvt/sllod</A>.

</P>

<P>The <I>units</I> keyword determines the meaning of the distance units used

to define various arguments.  A <I>box</I> value selects standard distance

units as defined by the <A HREF = "units.html">units</A> command, e.g. Angstroms for

velocity profile already created by fix nvt/sllod.  LAMMPS will warn

you if the {remap} setting is not consistent with fix nvt/sllod.

IMPORTANT NOTE: If a "fix rigid"_fix_rigid.html is defined for rigid

bodies, and {remap} is set to {x}, then the center-of-mass coordinates

of rigid bodies will be remapped to the changing simulation box.  This

will be done regardless of whether atoms in the rigid bodies are in

the fix deform group or not.  The velocity of the centers of mass are

not remapped even if {remap} is set to {v}, since "fix

nvt/sllod"_fix_nvt_sllod.html does not currently do anything special

for rigid particles.  If you wish to perform a NEMD simulation of

rigid particles, you can either thermostat them independently or

include a background fluid and thermostat the fluid via "fix

nvt/sllod"_fix_nvt_sllod.

The {units} keyword determines the meaning of the distance units used

to define various arguments.  A {box} value selects standard distance

units as defined by the "units"_units.html command, e.g. Angstroms for

</P>

<P>IMPORTANT NOTE: If you want the atom/indenter interaction energy to be

included in the total potential energy of the system (the quantity

being minimized), you MUST enable the <A HREF = "fix_modify.html">fix_modify</A>

being minimized), you must enable the <A HREF = "fix_modify.html">fix_modify</A>

<I>energy</I> option for this fix.

</P>

<P><B>Restrictions:</B> none

IMPORTANT NOTE: If you want the atom/indenter interaction energy to be

included in the total potential energy of the system (the quantity

being minimized), you MUST enable the "fix_modify"_fix_modify.html

being minimized), you must enable the "fix_modify"_fix_modify.html

{energy} option for this fix.

[Restrictions:] none

</PRE>

<P><B>Description:</B>

</P>

<P>Compute the mean-squared displacement of the group of atoms every N

steps, including all effects due to atoms passing thru periodic

boundaries.  The slope of the mean-squared displacement versus time is

proportional to the diffusion coefficient of the diffusing atoms.  The

"origin" of the displacement for each atom is its position at the time

the fix command was issued.  Write the results to the specified file.

<P>Compute the mean-squared displacement (MSD) of the group of atoms

every N steps, including all effects due to atoms passing thru

periodic boundaries.  The slope of the mean-squared displacement

versus time is proportional to the diffusion coefficient of the

diffusing atoms.  The "origin" of the displacement for each atom is

its position at the time the fix command was issued.  Write the

results to the specified file.

</P>

<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix

rigid</A> command), it's periodic image flags are altered,

and the computed MSD will not reflect its true displacement.  See the

<A HREF = "fix_rigid.html">fix rigid</A> command for details.  Thus, to compute the

MSD of rigid bodies as they cross periodic boundaries, you will need

to post-process a <A HREF = "dump.html">dump file</A> containing coordinates of the

atomss in the bodies.

</P>

<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>

</P>