git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12944 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_adapt.html

@@ -234,6 +234,12 @@ over the course of a 1000-step simulation:
 <PRE>variable size equal ramp(1.0,0.1)
 fix 1 center adapt 10 atom diameter v_size 
 </PRE>
+<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, this fix changes
+parameters only on the outer loop (largest) timesteps, which means
+that the frequency parameter <I>N</I> has to be commensurate with the step
+numbers for those outer steps. Otherwise invocation will be less
+frequent than expected.
+</P>
 <HR>
 
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
@@ -246,7 +252,11 @@ commands</A>.  No parameter of this fix can
 be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
 This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
-<P><B>Restrictions:</B> none
+<P><B>Restrictions:</B>
+</P>
+<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, this fix is only
+invoked on outer loop time steps that are also commensurate with
+the frequency parameter <I>N</I>.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/fix_adapt.txt

@@ -220,6 +220,12 @@ over the course of a 1000-step simulation:
 variable size equal ramp(1.0,0.1)
 fix 1 center adapt 10 atom diameter v_size :pre
 
+When the "run style"_run_style.html is {respa}, this fix changes
+parameters only on the outer loop (largest) timesteps, which means
+that the frequency parameter {N} has to be commensurate with the step
+numbers for those outer steps. Otherwise invocation will be less
+frequent than expected.
+
 :line
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
@@ -232,7 +238,11 @@ commands"_Section_howto.html#howto_15.  No parameter of this fix can
 be used with the {start/stop} keywords of the "run"_run.html command.
 This fix is not invoked during "energy minimization"_minimize.html.
 
-[Restrictions:] none
+[Restrictions:]
+
+When the "run style"_run_style.html is {respa}, this fix is only
+invoked on outer loop time steps that are also commensurate with
+the frequency parameter {N}.
 
 [Related commands:]
 

doc/fix_adapt_fep.html

@@ -246,6 +246,12 @@ over the course of a 1000-step simulation:
 <PRE>variable size equal ramp(1.0,0.1)
 fix 1 center adapt 10 atom diameter * v_size 
 </PRE>
+<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, this fix changes
+parameters only on the outer loop (largest) timesteps, which means
+that the frequency parameter <I>N</I> has to be commensurate with the step
+numbers for those outer steps. Otherwise invocation will be less
+frequent than expected.
+</P>
 <HR>
 
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
@@ -258,7 +264,11 @@ commands</A>.  No parameter of this fix can
 be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
 This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
 </P>
-<P><B>Restrictions:</B> none
+<P><B>Restrictions:</B>
+</P>
+<P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, this fix is only
+invoked on outer loop time steps that are also commensurate with
+the frequency parameter <I>N</I>.
 </P>
 <P><B>Related commands:</B>
 </P>

doc/fix_adapt_fep.txt

@@ -232,6 +232,12 @@ over the course of a 1000-step simulation:
 variable size equal ramp(1.0,0.1)
 fix 1 center adapt 10 atom diameter * v_size :pre
 
+When the "run style"_run_style.html is {respa}, this fix changes
+parameters only on the outer loop (largest) timesteps, which means
+that the frequency parameter {N} has to be commensurate with the step
+numbers for those outer steps. Otherwise invocation will be less
+frequent than expected.
+
 :line
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
@@ -244,7 +250,11 @@ commands"_Section_howto.html#howto_15.  No parameter of this fix can
 be used with the {start/stop} keywords of the "run"_run.html command.
 This fix is not invoked during "energy minimization"_minimize.html.
 
-[Restrictions:] none
+[Restrictions:]
+
+When the "run style"_run_style.html is {respa}, this fix is only
+invoked on outer loop time steps that are also commensurate with
+the frequency parameter {N}.
 
 [Related commands:]
 

doc/fix_ave_spatial.html

@@ -93,8 +93,8 @@ commands</A> such as <A HREF = "thermo_style.html">thermo_style
 custom</A>, and can also be written to a file.
 </P>
 <P>The group specified with the command means only atoms within the group
-contribute to bin averages.  If the <I>region</I> keyword is used, the
+contribute to bin averages.  If the <I>region</I> keyword is used, the atom
-atom must be in both the group and the specified geometric
+must be in both the specified group and the specified geometric
 <A HREF = "region.html">region</A> in order to contribute to bin averages.
 </P>
 <P>Each listed value can be an atom attribute (position, velocity, force

doc/fix_ave_spatial.txt

@@ -78,8 +78,8 @@ commands"_Section_howto.html#howto_15 such as "thermo_style
 custom"_thermo_style.html, and can also be written to a file.
 
 The group specified with the command means only atoms within the group
-contribute to bin averages.  If the {region} keyword is used, the
+contribute to bin averages.  If the {region} keyword is used, the atom
-atom must be in both the group and the specified geometric
+must be in both the specified group and the specified geometric
 "region"_region.html in order to contribute to bin averages.
 
 Each listed value can be an atom attribute (position, velocity, force

doc/minimize.html

@@ -50,6 +50,11 @@ slowly drains all kinetic energy from the system.  The <A HREF = "pair_soft.html
 soft</A> potential can be used to un-overlap atoms while
 running dynamics.
 </P>
+<P>Note that you can minimize some atoms in the system while holding the
+coordiates of other atoms fixed by applying <A HREF = "fix_setforce.html">fix
+setforce</A> to the other atoms.  See a fuller
+discussion of using fixes while minimizing below.
+</P>
 <P>The <A HREF = "min_style.html">minimization styles</A> <I>cg</I>, <I>sd</I>, and <I>hftn</I>
 involves an outer iteration loop which sets the search direction along
 which atom coordinates are changed.  An inner iteration is then
@@ -211,8 +216,23 @@ during the minimization.
 </P>
 <P>Only a few other fixes (typically those that apply force constraints)
 are invoked during minimization.  See the doc pages for individual
-<A HREF = "fix.html">fix</A> commands to see which ones are relevant.
+<A HREF = "fix.html">fix</A> commands to see which ones are relevant.  Current
+examples of fixes that can be used include:
 </P>
+<UL><LI><A HREF = "fix_addforce.html">fix addforce</A>
+<LI><A HREF = "fix_addtorque.html">fix addtorque</A>
+<LI><A HREF = "fix_efield.html">fix efield</A>
+<LI><A HREF = "fix_enforce2d.html">fix enforce2d</A>
+<LI><A HREF = "fix_indent.html">fix indent</A>
+<LI><A HREF = "fix_lineforce.html">fix lineforce</A>
+<LI><A HREF = "fix_planeforce.html">fix planeforce</A>
+<LI><A HREF = "fix_setforce.html">fix setforce</A>
+<LI><A HREF = "fix_spring.html">fix spring</A>
+<LI><A HREF = "fix_spring_self.html">fix spring/self</A>
+<LI><A HREF = "fix_viscous.html">fix viscous</A>
+<LI><A HREF = "fix_wall.html">fix wall</A>
+<LI><A HREF = "fix_wall_region.html">fix wall/region</A> 
+</UL>
 <P>IMPORTANT NOTE: Some fixes which are invoked during minimization have
 an associated potential energy.  For that energy to be included in the
 total potential energy of the system (the quantity being minimized),

doc/minimize.txt

@@ -47,6 +47,11 @@ slowly drains all kinetic energy from the system.  The "pair_style
 soft"_pair_soft.html potential can be used to un-overlap atoms while
 running dynamics.
 
+Note that you can minimize some atoms in the system while holding the
+coordiates of other atoms fixed by applying "fix
+setforce"_fix_setforce.html to the other atoms.  See a fuller
+discussion of using fixes while minimizing below.
+
 The "minimization styles"_min_style.html {cg}, {sd}, and {hftn}
 involves an outer iteration loop which sets the search direction along
 which atom coordinates are changed.  An inner iteration is then
@@ -208,7 +213,22 @@ during the minimization.
 
 Only a few other fixes (typically those that apply force constraints)
 are invoked during minimization.  See the doc pages for individual
-"fix"_fix.html commands to see which ones are relevant.
+"fix"_fix.html commands to see which ones are relevant.  Current
+examples of fixes that can be used include:
+
+"fix addforce"_fix_addforce.html
+"fix addtorque"_fix_addtorque.html
+"fix efield"_fix_efield.html
+"fix enforce2d"_fix_enforce2d.html
+"fix indent"_fix_indent.html
+"fix lineforce"_fix_lineforce.html
+"fix planeforce"_fix_planeforce.html
+"fix setforce"_fix_setforce.html
+"fix spring"_fix_spring.html
+"fix spring/self"_fix_spring_self.html
+"fix viscous"_fix_viscous.html
+"fix wall"_fix_wall.html
+"fix wall/region"_fix_wall_region.html :ul
 
 IMPORTANT NOTE: Some fixes which are invoked during minimization have
 an associated potential energy.  For that energy to be included in the