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

doc/html/_sources/compute_heat_flux.txt

@@ -39,9 +39,15 @@ subtracted to a group of atoms.
 The compute takes three arguments which are IDs of other
 :doc:`computes <compute>`.  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
+third calcualtes per-atom stress (\ *stress-ID*\ ).
-defined for the same group used by compute heat/flux, though LAMMPS
+
-does not check for this.
+.. 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/html/_sources/create_atoms.txt

@@ -212,7 +212,7 @@ 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
 :doc:`internal-style variables <variable>` 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.
@@ -220,9 +220,7 @@ 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
+it is non-zero, the atom is created.
-formulas defined for all of the *set* variables are restored to their
-original strings.
 
 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/html/_sources/variable.txt

@@ -124,7 +124,7 @@ 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::
 
@@ -149,29 +149,26 @@ simulation.
 
 .. note::
 
-   When the input script line is encountered that defines a
+   When an input script line is encountered that defines a variable
-   variable of style *equal* or *vector* or *atom* or *python* that
+   of style *equal* or *vector* or *atom* or *python* that contains a
-   contains a formula or Python code, the formula is NOT immediately
+   formula or Python code, the formula is NOT immediately evaluated.  It
-   evaluated.  It will be evaluated every time when the variable is
+   will be evaluated every time when the variable is **used** instead.  If
-   **used** instead.  If you simply want to evaluate a formula in place you
+   you simply want to evaluate a formula in place you can use as
-   can use as so-called. See the section below about "Immediate
+   so-called. See the section below about "Immediate Evaluation of
-   Evaluation of Variables" for more details on the topic.  This is also
+   Variables" for more details on the topic.  This is also true of a
-   true of a *format* style variable since it evaluates another variable
+   *format* style variable since it evaluates another variable when it is
-   when it is invoked.
+   invoked.
 
-.. note::
+Variables of style *equal* and *vector* and *atom* can be used as
-
+inputs to various other commands which evaluate their formulas as
-   Variables of style *equal* and *vector* and *atom* can be used
+needed, e.g. at different timesteps during a :doc:`run <run>`.
-   as inputs to various other LAMMPS commands which evaluate their
-   formulas as needed, e.g. at different timesteps during a
-   :doc:`run <run>`.
 
 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, except by commands that set the value stored by the
-variable.  Thus any command that states it can use an equal-style
+internal-style variable.  Thus any command that states it can use an
-variable as an argument, can also use an internal-style variable.
+equal-style variable as an argument, can also use an internal-style
-This means that when the LAMMPS command evaluates the variable, it
+variable.  This means that when the command evaluates the variable, it
-will use the value set (internally) by another LAMMPS command.
+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
@@ -194,7 +191,7 @@ executed.
    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

doc/html/compute_heat_flux.html

@@ -158,9 +158,15 @@ subtracted to a group of atoms.</p>
 <p>The compute takes three arguments which are IDs of other
 <a class="reference internal" href="compute.html"><span class="doc">computes</span></a>.  One calculates per-atom kinetic energy
 (<em>ke-ID</em>), one calculates per-atom potential energy (<em>pe-ID)</em>, and the
-third calcualtes per-atom stress (<em>stress-ID</em>).  These should be
+third calcualtes per-atom stress (<em>stress-ID</em>).</p>
-defined for the same group used by compute heat/flux, though LAMMPS
+<div class="admonition note">
-does not check for this.</p>
+<p class="first admonition-title">Note</p>
+<p class="last">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 &#8220;all&#8221;
+(or any group whose atoms are superset of the atoms in this compute&#8217;s
+group).  LAMMPS does not check for this.</p>
+</div>
 <p>The Green-Kubo formulas relate the ensemble average of the
 auto-correlation of the heat flux J to the thermal conductivity kappa:</p>
 <img alt="_images/heat_flux_J.jpg" class="align-center" src="_images/heat_flux_J.jpg" />

doc/html/create_atoms.html

@@ -312,16 +312,14 @@ 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
 <a class="reference internal" href="variable.html"><span class="doc">internal-style variables</span></a> 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 <em>set</em> 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.</p>
 <p>When an atom is created, its x,y,z coordinates become the values for
 any <em>set</em> variable that is defined.  The <em>var</em> 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
+it is non-zero, the atom is created.</p>
-formulas defined for all of the <em>set</em> variables are restored to their
-original strings.</p>
 <p>As an example, these commands can be used in a 2d simulation, to
 create a sinusoidal surface.  Note that the surface is &#8220;rough&#8221; due to
 individual lattice points being &#8220;above&#8221; or &#8220;below&#8221; the mathematical

doc/html/variable.html

@@ -242,7 +242,7 @@ per-atom values from a file rather than from a formula.  Variables of
 style <em>python</em> 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 <em>internal</em> are used by a few
-commands in LAMMPS which set their value directly.</p>
+commands which set their value directly.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">As discussed in <a class="reference internal" href="Section_commands.html#cmd-2"><span class="std std-ref">Section 3.2</span></a> of the
@@ -265,29 +265,25 @@ different values when it is evaluated at different times during a
 simulation.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
-<p class="last">When the input script line is encountered that defines a
+<p class="last">When an input script line is encountered that defines a variable
-variable of style <em>equal</em> or <em>vector</em> or <em>atom</em> or <em>python</em> that
+of style <em>equal</em> or <em>vector</em> or <em>atom</em> or <em>python</em> that contains a
-contains a formula or Python code, the formula is NOT immediately
+formula or Python code, the formula is NOT immediately evaluated.  It
-evaluated.  It will be evaluated every time when the variable is
+will be evaluated every time when the variable is <strong>used</strong> instead.  If
-<strong>used</strong> instead.  If you simply want to evaluate a formula in place you
+you simply want to evaluate a formula in place you can use as
-can use as so-called. See the section below about &#8220;Immediate
+so-called. See the section below about &#8220;Immediate Evaluation of
-Evaluation of Variables&#8221; for more details on the topic.  This is also
+Variables&#8221; for more details on the topic.  This is also true of a
-true of a <em>format</em> style variable since it evaluates another variable
+<em>format</em> style variable since it evaluates another variable when it is
-when it is invoked.</p>
+invoked.</p>
-</div>
-<div class="admonition note">
-<p class="first admonition-title">Note</p>
-<p class="last">Variables of style <em>equal</em> and <em>vector</em> and <em>atom</em> can be used
-as inputs to various other LAMMPS commands which evaluate their
-formulas as needed, e.g. at different timesteps during a
-<a class="reference internal" href="run.html"><span class="doc">run</span></a>.</p>
 </div>
+<p>Variables of style <em>equal</em> and <em>vector</em> and <em>atom</em> can be used as
+inputs to various other commands which evaluate their formulas as
+needed, e.g. at different timesteps during a <a class="reference internal" href="run.html"><span class="doc">run</span></a>.</p>
 <p>Variables of style <em>internal</em> can be used in place of an equal-style
-variable, except by commands that set the value in the internal-style
+variable, except by commands that set the value stored by the
-variable.  Thus any command that states it can use an equal-style
+internal-style variable.  Thus any command that states it can use an
-variable as an argument, can also use an internal-style variable.
+equal-style variable as an argument, can also use an internal-style
-This means that when the LAMMPS command evaluates the variable, it
+variable.  This means that when the command evaluates the variable, it
-will use the value set (internally) by another LAMMPS command.</p>
+will use the value set (internally) by another command.</p>
 <p>Variables of style <em>python</em> can be used in place of an equal-style
 variable so long as the associated Python function, as defined by the
 <a class="reference internal" href="python.html"><span class="doc">python</span></a> command, returns a numeric value.  Thus any
@@ -308,7 +304,7 @@ will override a corresponding index variable setting in the input
 script.</p>
 </div>
 <p>There are two exceptions to this rule.  First, variables of style
-<em>string</em>, <em>getenv</em>, <em>equal</em>, <em>vector</em>, <em>atom</em>, <em>internal</em>, and
+<em>string</em>, <em>getenv</em>, <em>internal</em>, <em>equal</em>, <em>vector</em>, <em>atom</em>, and
 <em>python</em> 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

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
+third calcualtes per-atom stress ({stress-ID}).  
-defined for the same group used by compute heat/flux, though LAMMPS
+
-does not check for this.
+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
+it is non-zero, the atom is created.
-formulas defined for all of the {set} variables are restored to their
-original strings.
 
 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
+NOTE: When an input script line is encountered that defines a variable
-variable of style {equal} or {vector} or {atom} or {python} that
+of style {equal} or {vector} or {atom} or {python} that contains a
-contains a formula or Python code, the formula is NOT immediately
+formula or Python code, the formula is NOT immediately evaluated.  It
-evaluated.  It will be evaluated every time when the variable is
+will be evaluated every time when the variable is [used] instead.  If
-[used] instead.  If you simply want to evaluate a formula in place you
+you simply want to evaluate a formula in place you can use as
-can use as so-called. See the section below about "Immediate
+so-called. See the section below about "Immediate Evaluation of
-Evaluation of Variables" for more details on the topic.  This is also
+Variables" for more details on the topic.  This is also true of a
-true of a {format} style variable since it evaluates another variable
+{format} style variable since it evaluates another variable when it is
-when it is invoked.
+invoked.
 
-NOTE: Variables of style {equal} and {vector} and {atom} can be used
+Variables of style {equal} and {vector} and {atom} can be used as
-as inputs to various other LAMMPS commands which evaluate their
+inputs to various other commands which evaluate their formulas as
-formulas as needed, e.g. at different timesteps during a
+needed, e.g. at different timesteps during a "run"_run.html.
-"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, except by commands that set the value stored by the
-variable.  Thus any command that states it can use an equal-style
+internal-style variable.  Thus any command that states it can use an
-variable as an argument, can also use an internal-style variable.
+equal-style variable as an argument, can also use an internal-style
-This means that when the LAMMPS command evaluates the variable, it
+variable.  This means that when the command evaluates the variable, it
-will use the value set (internally) by another LAMMPS command.
+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