git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4410 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_adapt.html

@@ -53,6 +53,10 @@ command will change the simulation box size/shape and the "fix move"
 command will change atom positions and velocities in prescribed
 manners.
 </P>
+<P>IMPORTANT NOTE: Any settings changed by fix adapt are not reset to
+their original values at the end of a simulation.  They remain changed
+to the final values they were set to at the end of the run.
+</P>
 <P>The <I>pair</I> keyword enables various parameters of potentials defined by
 the <A HREF = "pair_style.html">pair_style</A> command to be changed, if the pair
 style supports it.  The <I>pstyle</I> argument is the name of the pair
@@ -73,7 +77,11 @@ viscosity setting "mu" for <A HREF = "pair_lubricate.html">pair_style lubricate<
 Other parameters apply to pairs of atom types within the pair style,
 e.g. the prefactor "a" for <A HREF = "pair_soft.html">pair_style soft</A>.  If a
 type pair parameter is specified, the <I>I</I> and <I>J</I> settings should be
-specified to indicate which pair(s) to apply it to.
+specified to indicate which pair(s) to apply it to.  Note that in all
+cases, the <A HREF = "pair_style.html">pair_style</A> and
+<A HREF = "pair_coeff.html">pair_coeff</A> commands must be used in the usual manner
+to specify these parameters; the fix adapt command simply overrides
+the parameters.
 </P>
 <P>Similar to the <A HREF = "pair_coeff.html">pair_coeff command</A>, I and J can be
 specified in one of two ways.  Explicit numeric values can be used for

doc/fix_adapt.txt

@@ -43,6 +43,10 @@ command will change the simulation box size/shape and the "fix move"
 command will change atom positions and velocities in prescribed
 manners.
 
+IMPORTANT NOTE: Any settings changed by fix adapt are not reset to
+their original values at the end of a simulation.  They remain changed
+to the final values they were set to at the end of the run.
+
 The {pair} keyword enables various parameters of potentials defined by
 the "pair_style"_pair_style.html command to be changed, if the pair
 style supports it.  The {pstyle} argument is the name of the pair
@@ -61,7 +65,11 @@ viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html.
 Other parameters apply to pairs of atom types within the pair style,
 e.g. the prefactor "a" for "pair_style soft"_pair_soft.html.  If a
 type pair parameter is specified, the {I} and {J} settings should be
-specified to indicate which pair(s) to apply it to.
+specified to indicate which pair(s) to apply it to.  Note that in all
+cases, the "pair_style"_pair_style.html and
+"pair_coeff"_pair_coeff.html commands must be used in the usual manner
+to specify these parameters; the fix adapt command simply overrides
+the parameters.
 
 Similar to the "pair_coeff command"_pair_coeff.html, I and J can be
 specified in one of two ways.  Explicit numeric values can be used for

doc/pair_lubricate.html

@@ -31,6 +31,11 @@
 pair_coeff 1 1 1.8 2.0
 pair_coeff * * 
 </PRE>
+<PRE>pair_style lubricate 1.0 1 1 1 0 2.3 2.4 1.3 5878598
+pair_coeff * *
+variable vmu equal 1.0+elapsed/10000
+fix 1 all adapt 1 pair lubricate mu * * vmu 
+</PRE>
 <P><B>Description:</B>
 </P>
 <P>Style <I>lubricate</I> computes pairwise interactions between mono-disperse
@@ -44,8 +49,9 @@ viscosity mu.  Note that this is dynamic viscosity which has units of
 mass/distance/time, not kinematic viscosity.
 </P>
 <P>The viscosity mu can be varied in a time-dependent manner over the
-course of a simluation.  See the <A HREF = "fix_adapt.html">fix adapt</A> command
-for details.
+course of a simluation, in which case in which case the pair_style
+setting for mu will be overridden.  See the <A HREF = "fix_adapt.html">fix adapt</A>
+command for details.
 </P>
 <P>Rc is the outer cutoff specified in the pair_style command, the
 translational velocities of the 2 particles are v1 and v2, the angular

doc/pair_lubricate.txt

@@ -28,6 +28,11 @@ pair_style lubricate 1.5 1 1 1 0 2.3 2.4 1.3 5878598
 pair_coeff 1 1 1.8 2.0
 pair_coeff * * :pre
 
+pair_style lubricate 1.0 1 1 1 0 2.3 2.4 1.3 5878598
+pair_coeff * *
+variable vmu equal 1.0+elapsed/10000
+fix 1 all adapt 1 pair lubricate mu * * vmu :pre
+
 [Description:]
 
 Style {lubricate} computes pairwise interactions between mono-disperse
@@ -41,8 +46,9 @@ viscosity mu.  Note that this is dynamic viscosity which has units of
 mass/distance/time, not kinematic viscosity.
 
 The viscosity mu can be varied in a time-dependent manner over the
-course of a simluation.  See the "fix adapt"_fix_adapt.html command
-for details.
+course of a simluation, in which case in which case the pair_style
+setting for mu will be overridden.  See the "fix adapt"_fix_adapt.html
+command for details.
 
 Rc is the outer cutoff specified in the pair_style command, the
 translational velocities of the 2 particles are v1 and v2, the angular

doc/pair_soft.html

@@ -49,10 +49,12 @@ commands, or by mixing as described below:
 <P>The last coefficient is optional.  If not specified, the global soft
 cutoff is used.
 </P>
-<P>The <A HREF = "fix_adapt.html">fix adapt</A> command can be used to vary A over the
-course of a simulation.  For example these commands will vary the
-prefactor A for all pairwise interactions from 0.0 at the beginning to
-30.0 at the end of a 10,000 step run:
+<P>The <A HREF = "fix_adapt.html">fix adapt</A> command can be used to vary A for one
+or more pair types over the course of a simulation, in which case the
+pair_coeff setting for A must still be specified, but will be
+overridden.  For example these commands will vary the prefactor A for
+all pairwise interactions from 0.0 at the beginning to 30.0 at the end
+of a 10,000 step run:
 </P>
 <PRE>variable prefactor equal 30.0*elapsed/10000
 fix 1 all adapt 1 pair soft a * * prefactor 

doc/pair_soft.txt

@@ -46,10 +46,12 @@ cutoff (distance units) :ul
 The last coefficient is optional.  If not specified, the global soft
 cutoff is used.
 
-The "fix adapt"_fix_adapt.html command can be used to vary A over the
-course of a simulation.  For example these commands will vary the
-prefactor A for all pairwise interactions from 0.0 at the beginning to
-30.0 at the end of a 10,000 step run:
+The "fix adapt"_fix_adapt.html command can be used to vary A for one
+or more pair types over the course of a simulation, in which case the
+pair_coeff setting for A must still be specified, but will be
+overridden.  For example these commands will vary the prefactor A for
+all pairwise interactions from 0.0 at the beginning to 30.0 at the end
+of a 10,000 step run:
 
 variable prefactor equal 30.0*elapsed/10000
 fix 1 all adapt 1 pair soft a * * prefactor :pre