git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@319 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_recenter.html

@@ -74,6 +74,14 @@ means a fractional distance between the lo/hi box boundaries, e.g. 0.5
 <P>Note that the <A HREF = "velocity.html">velocity</A> command can be used to create
 velocities with zero aggregate linear and/or angular momentum.
 </P>
+<P>IMPORTANT NOTE: This fix performs its operations at the same point in
+the timestep as other time integration fixes, such as <A HREF = "fix_nve.html">fix
+nve</A>, <A HREF = "fix_nvt.html">fix nvt</A>, or <A HREF = "fix_npt.html">fix npt</A>.
+Thus fix recenter should normally be the last such fix specified in
+the input script, since the adjustments it makes to atom coordinates
+should come after the changes made by time integration.  LAMMPS will
+warn you if your fixes are not ordered this way.
+</P>
 <P><B>Restrictions:</B>
 </P>
 <P>This fix should not be used with an x,y,z setting that causes a large
@@ -83,12 +91,6 @@ be lost,especially in parallel.  Instead, use the
 <A HREF = "displace_atoms.html">displace_atoms</A> command, which can be used
 several times in succession to move atoms a large distance.
 </P>
-<P>This fix should be specified after integration fixes (<A HREF = "fix_nve.html">fix
-nve</A>, <A HREF = "fix_nvt.html">fix_nvt</A>, <A HREF = "fix_npt.html">fix npt</A>,
-etc), because the adjustments it makes to atom coordinates should come
-after atom coordinates are changed due to time integration.  LAMMPS
-will warn you if your fixes are not ordered this way.
-</P>
 <P><B>Related commands:</B>
 </P>
 <P><A HREF = "fix_momentum.html">fix momentum</A>, <A HREF = "velocity.html">velocity</A>

doc/fix_recenter.txt

@@ -66,6 +66,14 @@ means a fractional distance between the lo/hi box boundaries, e.g. 0.5
 Note that the "velocity"_velocity.html command can be used to create
 velocities with zero aggregate linear and/or angular momentum.
 
+IMPORTANT NOTE: This fix performs its operations at the same point in
+the timestep as other time integration fixes, such as "fix
+nve"_fix_nve.html, "fix nvt"_fix_nvt.html, or "fix npt"_fix_npt.html.
+Thus fix recenter should normally be the last such fix specified in
+the input script, since the adjustments it makes to atom coordinates
+should come after the changes made by time integration.  LAMMPS will
+warn you if your fixes are not ordered this way.
+
 [Restrictions:]
 
 This fix should not be used with an x,y,z setting that causes a large
@@ -75,12 +83,6 @@ be lost,especially in parallel.  Instead, use the
 "displace_atoms"_displace_atoms.html command, which can be used
 several times in succession to move atoms a large distance.
 
-This fix should be specified after integration fixes ("fix
-nve"_fix_nve.html, "fix_nvt"_fix_nvt.html, "fix npt"_fix_npt.html,
-etc), because the adjustments it makes to atom coordinates should come
-after atom coordinates are changed due to time integration.  LAMMPS
-will warn you if your fixes are not ordered this way.
-
 [Related commands:]
 
 "fix momentum"_fix_momentum.html, "velocity"_velocity.html

doc/fix_wall_reflect.html

@@ -38,12 +38,13 @@ by a distance delta (e.g. due to <A HREF = "fix_nve.html">fix nve</A>), then it
 put back inside the box by the same delta and the sign of the
 corresponding component of its velocity is flipped.
 </P>
-<P>This fix performs its operations at the same point in the timestep as
-other time integration fixes, such as <A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nvt.html">fix
-nvt</A>, or <A HREF = "fix_npt.html">fix npt</A>.  It is important that it
-be the last such fix specified in the input script, since it changes
-the atom positions set by those fixes to insure atoms stay within the
-simulation box.
+<P>IMPORTANT NOTE: This fix performs its operations at the same point in
+the timestep as other time integration fixes, such as <A HREF = "fix_nve.html">fix
+nve</A>, <A HREF = "fix_nvt.html">fix nvt</A>, or <A HREF = "fix_npt.html">fix npt</A>.
+Thus fix wall/reflect should normally be the last such fix specified
+in the input script, since the adjustments it makes to atom
+coordinates should come after the changes made by time integration.
+LAMMPS will warn you if your fixes are not ordered this way.
 </P>
 <P><B>Restrictions:</B> none
 </P>

doc/fix_wall_reflect.txt

@@ -35,12 +35,13 @@ by a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is
 put back inside the box by the same delta and the sign of the
 corresponding component of its velocity is flipped.
 
-This fix performs its operations at the same point in the timestep as
-other time integration fixes, such as "fix nve"_fix_nve.html, "fix
-nvt"_fix_nvt.html, or "fix npt"_fix_npt.html.  It is important that it
-be the last such fix specified in the input script, since it changes
-the atom positions set by those fixes to insure atoms stay within the
-simulation box.
+IMPORTANT NOTE: This fix performs its operations at the same point in
+the timestep as other time integration fixes, such as "fix
+nve"_fix_nve.html, "fix nvt"_fix_nvt.html, or "fix npt"_fix_npt.html.
+Thus fix wall/reflect should normally be the last such fix specified
+in the input script, since the adjustments it makes to atom
+coordinates should come after the changes made by time integration.
+LAMMPS will warn you if your fixes are not ordered this way.
 
 [Restrictions:] none
 

doc/pair_lj_smooth.html

@@ -34,10 +34,12 @@ applied between the inner and outer cutoff.
 <P>The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to
 cause the force to vary smoothly from Rin to Rc.  At Rin the force and
 its 1st derivative will match the unsmoothed LJ formula.  At Rc the
-force and its 1st derivative will be 0.0.  IMPORTANT NOTE: this force
-smoothing causes the energy to be discontinuous both in its values and
-1st derivative.  This can lead to poor energy conservation.  Plot the
-energy and force resulting from this formula via the
+force and its 1st derivative will be 0.0.
+</P>
+<P>IMPORTANT NOTE: this force smoothing causes the energy to be
+discontinuous both in its values and 1st derivative.  This can lead to
+poor energy conservation and may require the use of a thermostat.
+Plot the energy and force resulting from this formula via the
 <A HREF = "pair_write.html">pair_write</A> command to see the effect.
 </P>
 <P>The following coefficients must be defined for each pair of atoms

doc/pair_lj_smooth.txt

@@ -31,10 +31,12 @@ applied between the inner and outer cutoff.
 The polynomial coefficients C1, C2, C3, C4 are computed by LAMMPS to
 cause the force to vary smoothly from Rin to Rc.  At Rin the force and
 its 1st derivative will match the unsmoothed LJ formula.  At Rc the
-force and its 1st derivative will be 0.0.  IMPORTANT NOTE: this force
-smoothing causes the energy to be discontinuous both in its values and
-1st derivative.  This can lead to poor energy conservation.  Plot the
-energy and force resulting from this formula via the
+force and its 1st derivative will be 0.0.
+
+IMPORTANT NOTE: this force smoothing causes the energy to be
+discontinuous both in its values and 1st derivative.  This can lead to
+poor energy conservation and may require the use of a thermostat.
+Plot the energy and force resulting from this formula via the
 "pair_write"_pair_write.html command to see the effect.
 
 The following coefficients must be defined for each pair of atoms