git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8097 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/compute_pe.html

@@ -45,8 +45,7 @@ then only those components are summed to compute the potential energy.
 per-atom energy is calculated, if using the PPPM solver via the
 <A HREF = "kspace_style.html">kspace_style pppm</A> command.  Thus it can increase
 the cost of the PPPM calculation if it is needed on a large fraction
-of the simulation timesteps.  Thie <A HREF = "PDF/kspace.pdf">document</A> describes
+of the simulation timesteps.  
-how the long-range per-atom energy calculation is performed.
 </P>
 <P>Various fixes can contribute to the total potential energy of the
 system.  See the doc pages for <A HREF = "fix.html">individual fixes</A> for

doc/compute_pe.txt

@@ -41,8 +41,7 @@ The Kspace contribution requires 1 extra FFT each timestep the
 per-atom energy is calculated, if using the PPPM solver via the
 "kspace_style pppm"_kspace_style.html command.  Thus it can increase
 the cost of the PPPM calculation if it is needed on a large fraction
-of the simulation timesteps.  Thie "document"_PDF/kspace.pdf describes
+of the simulation timesteps.  
-how the long-range per-atom energy calculation is performed.
 
 Various fixes can contribute to the total potential energy of the
 system.  See the doc pages for "individual fixes"_fix.html for

doc/compute_pe_atom.html

@@ -55,7 +55,8 @@ these terms is included in the pair energy, not the dihedral energy.
 <A HREF = "#Heyes">(Heyes)</A> for the Ewald method and a related method for PPPM,
 as specified by the <A HREF = "kspace_style.html">kspace_style pppm</A> command.
 For PPPM, the calcluation requires 1 extra FFT each timestep that
-per-atom stress is calculated.
+per-atom energy is calculated.  Thie <A HREF = "PDF/kspace.pdf">document</A>
+describes how the long-range per-atom energy calculation is performed.
 </P>
 <P>As an example of per-atom potential energy compared to total potential
 energy, these lines in an input script should yield the same result

doc/compute_pe_atom.txt

@@ -52,7 +52,8 @@ The KSpace contribution is calculated using the method in
 "(Heyes)"_#Heyes for the Ewald method and a related method for PPPM,
 as specified by the "kspace_style pppm"_kspace_style.html command.
 For PPPM, the calcluation requires 1 extra FFT each timestep that
-per-atom stress is calculated.
+per-atom energy is calculated.  Thie "document"_PDF/kspace.pdf
+describes how the long-range per-atom energy calculation is performed.
 
 As an example of per-atom potential energy compared to total potential
 energy, these lines in an input script should yield the same result

doc/dump_modify.html

@@ -358,14 +358,14 @@ In this case, the variable is evaluated at the beginning of a run to
 determine the next timestep at which a dump snapshot will be written
 out.  On that timestep, the variable will be evaluated again to
 determine the next timestep, etc.  Thus the variable should return
-timestep values.  See the stagger() and logfreq() math functions for
+timestep values.  See the stagger() and logfreq() and stride() math
-<A HREF = "variable.html">equal-style variables</A>, as examples of useful functions
+functions for <A HREF = "variable.html">equal-style variables</A>, as examples of
-to use in this context.  Other similar math functions could easily be
+useful functions to use in this context.  Other similar math functions
-added as options for <A HREF = "variable.html">equal-style variables</A>.  When
+could easily be added as options for <A HREF = "variable.html">equal-style
-using the variable option with the <I>every</I> keyword, you also need to
+variables</A>.  When using the variable option with the
-use the <I>first</I> option if you want an initial snapshot written to the
+<I>every</I> keyword, you also need to use the <I>first</I> option if you want
-dump file.  The <I>every</I> keyword cannot be used with the dump <I>dcd</I>
+an initial snapshot written to the dump file.  The <I>every</I> keyword
-style.
+cannot be used with the dump <I>dcd</I> style.
 </P>
 <P>For example, the following commands will
 write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:

doc/thermo_modify.html

@@ -153,11 +153,12 @@ the beginning of a run to determine the next timestep at which a dump
 snapshot will be written out.  On that timestep, the variable will be
 evaluated again to determine the next timestep, etc.  Thus the
 variable should return timestep values.  See the stagger() and
-logfreq() math functions for <A HREF = "variable.html">equal-style variables</A>, as
+logfreq() and stride() math functions for <A HREF = "variable.html">equal-style
-examples of useful functions to use in this context.  Other similar
+variables</A>, as examples of useful functions to use in
-math functions could easily be added as options for <A HREF = "variable.html">equal-style
+this context.  Other similar math functions could easily be added as
-variables</A>.  In addition, thermodynamic output will
+options for <A HREF = "variable.html">equal-style variables</A>.  In addition,
-always occur on the first and last timestep of each run.
+thermodynamic output will always occur on the first and last timestep
+of each run.
 </P>
 <P>For example, the following commands will output thermodynamic info at
 timesteps 0,10,20,30,100,200,300,1000,2000,etc: