git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@826 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_deform.html

@@ -341,6 +341,18 @@ periodic boundaries, since that is consistent with maintaining the
 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

doc/fix_deform.txt

@@ -331,6 +331,18 @@ periodic boundaries, since that is consistent with maintaining the
 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

doc/fix_indent.html

@@ -122,7 +122,7 @@ indenter always has a radius of its final value R in that case.
 </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

doc/fix_indent.txt

@@ -113,7 +113,7 @@ indenter always has a radius of its final value R in that case.
 
 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

doc/fix_msd.html

@@ -26,12 +26,21 @@
 </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>

doc/fix_msd.txt

@@ -23,12 +23,21 @@ fix 1 all msd 100 diff.out :pre
 
 [Description:]
 
-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.
+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.
+
+IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
+rigid"_fix_rigid.html command), it's periodic image flags are altered,
+and the computed MSD will not reflect its true displacement.  See the
+"fix rigid"_fix_rigid.html command for details.  Thus, to compute the
+MSD of rigid bodies as they cross periodic boundaries, you will need
+to post-process a "dump file"_dump.html containing coordinates of the
+atomss in the bodies.
 
 [Restart, fix_modify, thermo output, run start/stop, minimize info:]
 

doc/fix_rigid.html

@@ -87,6 +87,17 @@ effectively immersed in an implicit solvent, i.e. a Brownian dynamics
 model.  Or you can thermostat additional atoms of an explicit solvent
 directly.
 </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 = "fix_msd.html">fix
+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.
+</P>
 <P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
 </P>
 <P>No information about this fix is written to <A HREF = "restart.html">binary restart

doc/fix_rigid.txt

@@ -80,6 +80,17 @@ effectively immersed in an implicit solvent, i.e. a Brownian dynamics
 model.  Or you can thermostat additional atoms of an explicit solvent
 directly.
 
+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 "fix
+msd"_fix_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.
+
 [Restart, fix_modify, thermo output, run start/stop, minimize info:]
 
 No information about this fix is written to "binary restart