git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2514 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_spring.html

@@ -104,11 +104,19 @@ energy as part of <A HREF = "thermo_style.html">thermodynamic output</A>.
 <A HREF = "Section_howto.html#4_15">output commands</A>.  This energy is spring
 energy = 0.5 * K * r^2.
 </P>
-<P>This fix computes a 3-vector of forces, which can be accessed by
+<P>This fix also computes 4 output quantities stored in a vector of
-various <A HREF = "Section_howto.html#4_15">output commands</A>.  This is the total
+length 4, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
-force on the group of atoms by the spring.  In the case of the
+commands</A>.  The first 3 quantities are xyz
-<I>couple</I> style, it is the force on the fix group (group-ID) or the
+components of the total force added to the group of atoms by the
-negative of the force on the 2nd group (group-ID2).
+spring.  In the case of the <I>couple</I> style, it is the force on the fix
+group (group-ID) or the negative of the force on the 2nd group
+(group-ID2).  The 4th quantity is the magnitude of the force added by
+the spring, as a positive value if (r-R0) > 0 and a negative value if
+(r-R0) < 0.  This sign convention can be useful when using the spring
+force to compute a potential of mean force (PMF).
+</P>
+<P>The scalar and vector values calculated by this fix are "extensive",
+meaning they scale with the number of atoms in the simulation.
 </P>
 <P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
 the <A HREF = "run.html">run</A> command.

doc/fix_spring.txt

@@ -97,11 +97,19 @@ This fix computes a scalar energy which can be accessed by various
 "output commands"_Section_howto.html#4_15.  This energy is spring
 energy = 0.5 * K * r^2.
 
-This fix computes a 3-vector of forces, which can be accessed by
+This fix also computes 4 output quantities stored in a vector of
-various "output commands"_Section_howto.html#4_15.  This is the total
+length 4, which can be accessed by various "output
-force on the group of atoms by the spring.  In the case of the
+commands"_Section_howto.html#4_15.  The first 3 quantities are xyz
-{couple} style, it is the force on the fix group (group-ID) or the
+components of the total force added to the group of atoms by the
-negative of the force on the 2nd group (group-ID2).
+spring.  In the case of the {couple} style, it is the force on the fix
+group (group-ID) or the negative of the force on the 2nd group
+(group-ID2).  The 4th quantity is the magnitude of the force added by
+the spring, as a positive value if (r-R0) > 0 and a negative value if
+(r-R0) < 0.  This sign convention can be useful when using the spring
+force to compute a potential of mean force (PMF).
+
+The scalar and vector values calculated by this fix are "extensive",
+meaning they scale with the number of atoms in the simulation.
 
 No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.

doc/pair_tersoff.html

@@ -131,8 +131,7 @@ using the Tersoff_2 mixing rules:
 </P>
 <CENTER><IMG SRC = "Eqs/pair_tersoff_2.jpg">
 </CENTER>
-<P>Values not shown are determined by the first atom type. Finally, the
+<P>Tersoff_2 parameters R and S must be converted to the LAMMPS
-Tersoff_2 parameters R and S must be converted to the LAMMPS
 parameters R and D (R is different in both forms), using the following
 relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the
 Tersoff_2 parameters.

doc/pair_tersoff.txt

@@ -128,7 +128,6 @@ using the Tersoff_2 mixing rules:
 
 :c,image(Eqs/pair_tersoff_2.jpg)
 
-Values not shown are determined by the first atom type. Finally, the
 Tersoff_2 parameters R and S must be converted to the LAMMPS
 parameters R and D (R is different in both forms), using the following
 relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the