git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15450 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/src/compute_heat_flux.txt

@@ -38,9 +38,13 @@ subtracted to a group of atoms.
 The compute takes three arguments which are IDs of other
 "computes"_compute.html.  One calculates per-atom kinetic energy
 ({ke-ID}), one calculates per-atom potential energy ({pe-ID)}, and the
-third calcualtes per-atom stress ({stress-ID}).  These should be
-defined for the same group used by compute heat/flux, though LAMMPS
-does not check for this.
+third calcualtes per-atom stress ({stress-ID}).  
+
+NOTE: These other computes should provide values for all the atoms in
+the group this compute specifies.  That means the other computes could
+use the same group as this compute, or they can just use group "all"
+(or any group whose atoms are superset of the atoms in this compute's
+group).  LAMMPS does not check for this.
 
 The Green-Kubo formulas relate the ensemble average of the
 auto-correlation of the heat flux J to the thermal conductivity kappa:

doc/src/create_atoms.txt

@@ -197,7 +197,7 @@ three variables which will store the x, y, or z coordinates of an atom
 (one variable per coordinate).  If used, these other variables must be
 "internal-style variables"_variable.html defined in the input script;
 their initial numeric value can be anything.  They must be
-internal-style variables, because this command updates their values
+internal-style variables, because this command resets their values
 directly.  The {set} keyword is used to identify the names of these
 other variables, one variable for the x-coordinate of a created atom,
 one for y, and one for z.
@@ -205,9 +205,7 @@ one for y, and one for z.
 When an atom is created, its x,y,z coordinates become the values for
 any {set} variable that is defined.  The {var} variable is then
 evaluated.  If the returned value is 0.0, the atom is not created.  If
-it is non-zero, the atom is created.  After all atoms are created, the
-formulas defined for all of the {set} variables are restored to their
-original strings.
+it is non-zero, the atom is created.
 
 As an example, these commands can be used in a 2d simulation, to
 create a sinusoidal surface.  Note that the surface is "rough" due to

doc/src/variable.txt

@@ -122,7 +122,7 @@ per-atom values from a file rather than from a formula.  Variables of
 style {python} can be hooked to Python functions using code you
 provide, so that the variable gets its value from the evaluation of
 the Python code.  Variables of style {internal} are used by a few
-commands in LAMMPS which set their value directly.
+commands which set their value directly.
 
 NOTE: As discussed in "Section 3.2"_Section_commands.html#cmd_2 of the
 manual, an input script can use "immediate" variables, specified as
@@ -143,27 +143,26 @@ evaluation of the string.  Note that the same string can generate
 different values when it is evaluated at different times during a
 simulation.
 
-NOTE: When the input script line is encountered that defines a
-variable of style {equal} or {vector} or {atom} or {python} that
-contains a formula or Python code, the formula is NOT immediately
-evaluated.  It will be evaluated every time when the variable is
-[used] instead.  If you simply want to evaluate a formula in place you
-can use as so-called. See the section below about "Immediate
-Evaluation of Variables" for more details on the topic.  This is also
-true of a {format} style variable since it evaluates another variable
-when it is invoked.
+NOTE: When an input script line is encountered that defines a variable
+of style {equal} or {vector} or {atom} or {python} that contains a
+formula or Python code, the formula is NOT immediately evaluated.  It
+will be evaluated every time when the variable is [used] instead.  If
+you simply want to evaluate a formula in place you can use as
+so-called. See the section below about "Immediate Evaluation of
+Variables" for more details on the topic.  This is also true of a
+{format} style variable since it evaluates another variable when it is
+invoked.
 
-NOTE: Variables of style {equal} and {vector} and {atom} can be used
-as inputs to various other LAMMPS commands which evaluate their
-formulas as needed, e.g. at different timesteps during a
-"run"_run.html.  
+Variables of style {equal} and {vector} and {atom} can be used as
+inputs to various other commands which evaluate their formulas as
+needed, e.g. at different timesteps during a "run"_run.html.
 
 Variables of style {internal} can be used in place of an equal-style
-variable, except by commands that set the value in the internal-style
-variable.  Thus any command that states it can use an equal-style
-variable as an argument, can also use an internal-style variable.
-This means that when the LAMMPS command evaluates the variable, it
-will use the value set (internally) by another LAMMPS command.
+variable, except by commands that set the value stored by the
+internal-style variable.  Thus any command that states it can use an
+equal-style variable as an argument, can also use an internal-style
+variable.  This means that when the command evaluates the variable, it
+will use the value set (internally) by another command.
 
 Variables of style {python} can be used in place of an equal-style
 variable so long as the associated Python function, as defined by the
@@ -184,7 +183,7 @@ will override a corresponding index variable setting in the input
 script.
 
 There are two exceptions to this rule.  First, variables of style
-{string}, {getenv}, {equal}, {vector}, {atom}, {internal}, and
+{string}, {getenv}, {internal}, {equal}, {vector}, {atom}, and
 {python} ARE redefined each time the command is encountered.  This
 allows these style of variables to be redefined multiple times in an
 input script.  In a loop, this means the formula associated with an