git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13617 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/pair_srp.html

@@ -36,7 +36,7 @@ pair_coeff 1 1 dpd 60.0 4.5 1.0
 pair_coeff 1 2 none 
 pair_coeff 2 2 srp 100.0 0.8 
 </PRE>
-<PRE>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 min exclude yes
+<PRE>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
 pair_coeff 1 1 dpd 60.0 50 1.0 
 pair_coeff 1 2 none 
 pair_coeff 2 2 srp 40.0 
@@ -62,7 +62,9 @@ bond-pairwise potential, such that the force on bond <I>i</I> due to bond
 <CENTER><IMG SRC = "Eqs/pair_srp1.jpg">
 </CENTER>
 <P>where <I>r</I> and <I>rij</I> are the distance and unit vector between the two
-bonds. The <I>mid</I> option computes <I>r</I> and <I>rij</I> from the midpoint
+bonds. The bondtype can also be specified as an asterisk (*) and then
+this interaction applied to all bonds.
+The <I>mid</I> option computes <I>r</I> and <I>rij</I> from the midpoint
 distance between bonds. The <I>min</I> option computes <I>r</I> and <I>rij</I> from
 the minimum distance between bonds. The force acting on a bond is
 mapped onto the two bond atoms according to the lever rule,

doc/pair_srp.txt

@@ -27,7 +27,7 @@ pair_coeff 1 1 dpd 60.0 4.5 1.0
 pair_coeff 1 2 none 
 pair_coeff 2 2 srp 100.0 0.8 :pre
 
-pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 min exclude yes
+pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes
 pair_coeff 1 1 dpd 60.0 50 1.0 
 pair_coeff 1 2 none 
 pair_coeff 2 2 srp 40.0 :pre 
@@ -53,7 +53,9 @@ bond-pairwise potential, such that the force on bond {i} due to bond
 :c,image(Eqs/pair_srp1.jpg)
 
 where {r} and {rij} are the distance and unit vector between the two
-bonds. The {mid} option computes {r} and {rij} from the midpoint
+bonds. The bondtype can also be specified as an asterisk (*) and then
+this interaction applied to all bonds.
+The {mid} option computes {r} and {rij} from the midpoint
 distance between bonds. The {min} option computes {r} and {rij} from
 the minimum distance between bonds. The force acting on a bond is
 mapped onto the two bond atoms according to the lever rule,

doc/special_bonds.html

@@ -195,7 +195,7 @@ topology of the system).  If new bonds are created (or molecules added
 containing atoms with more special neighbors), the size of this list
 needs to grow.  Note that adding a single bond always adds a new 1st
 neighbor but may also induce *many* new 2nd and 3rd neighbors,
-depending on the molecular topology of your syste.  Using the <I>extra</I>
+depending on the molecular topology of your system.  Using the <I>extra</I>
 keyword leaves empty space in the list for this N additional 1st, 2nd,
 or 3rd neighbors to be added.  If you do not do this, you may get an
 error when bonds (or molecules) are added.

doc/special_bonds.txt

@@ -189,7 +189,7 @@ topology of the system).  If new bonds are created (or molecules added
 containing atoms with more special neighbors), the size of this list
 needs to grow.  Note that adding a single bond always adds a new 1st
 neighbor but may also induce *many* new 2nd and 3rd neighbors,
-depending on the molecular topology of your syste.  Using the {extra}
+depending on the molecular topology of your system.  Using the {extra}
 keyword leaves empty space in the list for this N additional 1st, 2nd,
 or 3rd neighbors to be added.  If you do not do this, you may get an
 error when bonds (or molecules) are added.

doc/variable.html

@@ -123,13 +123,13 @@ per-atom values from a file rather than from a formula.  Variables can
 be hooked to Python functions using code you provide, so that the
 variable gets its value from the evaluation of the Python code.
 </P>
-<P>IMPORTANT NOTE: As discussed in <A HREF = "Section_commands.html#cmd_2">Section
-3.2</A> of the manual, an input script can
-use "immediate" variables, specified as $(formula) with parenthesis,
-where the formula has the same syntax as equal-style variables
-described on this page.  This is a way to evaluate a formula
-immediately without using the variable command to define a named
-variable.
+<P>IMPORTANT NOTE: As discussed in <A HREF = "Section_commands.html#cmd_2">Section 3.2</A>
+of the manual, an input script can use "immediate" variables, specified
+as $(formula) with parenthesis, where the formula has the same syntax
+as equal-style variables described on this page.  This is a convenient
+way to evaluate a formula immediately without using the variable command
+to define a named variable and then evaluate that variable. See below
+for a more detailed discussion of this feature.
 </P>
 <P>In the discussion that follows, the "name" of the variable is the
 arbitrary string that is the 1st argument in the variable command.
@@ -144,10 +144,12 @@ simulation.
 </P>
 <P>IMPORTANT NOTE: When the input script line is encountered that defines
 a variable of style <I>equal</I> or <I>atom</I> or <I>python</I> that contains a
-formula or Python code, the formula is NOT immediately evaluated and
-the result stored.  See the discussion below about "Immediate
-Evaluation of Variables" if you want to do this.  This is also true of
-the <I>format</I> style variable since it evaluates another variable when
+formula or Python code, the formula is NOT immediately evaluated.
+It will be evaluated every time when the variable is <B>used</B> 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 <I>format</I> style variable since it evaluates another variable when
 it is invoked.
 </P>
 <P>IMPORTANT NOTE: Variables of style <I>equal</I> and <I>atom</I> can be used as
@@ -161,14 +163,6 @@ can also use such a python-style variable.  This means that when the
 LAMMPS command evaluates the variable, the Python function will be
 executed.
 </P>
-<P>When the input script line is encountered that defines
-a variable of style <I>equal</I> or <I>atom</I> or <I>python</I> that contains a
-formula or Python code, the formula is NOT immediately evaluated and
-the result stored.  See the discussion below about "Immediate
-Evaluation of Variables" if you want to do this.  This is also true of
-the <I>format</I> style variable since it evaluates another variable when
-it is invoked.
-</P>
 <P>IMPORTANT NOTE: When a variable command is encountered in the input
 script and the variable name has already been specified, the command
 is ignored.  This means variables can NOT be re-defined in an input

doc/variable.txt

@@ -117,13 +117,13 @@ per-atom values from a file rather than from a formula.  Variables can
 be hooked to Python functions using code you provide, so that the
 variable gets its value from the evaluation of the Python code.
 
-IMPORTANT NOTE: As discussed in "Section
-3.2"_Section_commands.html#cmd_2 of the manual, an input script can
-use "immediate" variables, specified as $(formula) with parenthesis,
-where the formula has the same syntax as equal-style variables
-described on this page.  This is a way to evaluate a formula
-immediately without using the variable command to define a named
-variable.
+IMPORTANT NOTE: As discussed in "Section 3.2"_Section_commands.html#cmd_2
+of the manual, an input script can use "immediate" variables, specified
+as $(formula) with parenthesis, where the formula has the same syntax
+as equal-style variables described on this page.  This is a convenient
+way to evaluate a formula immediately without using the variable command
+to define a named variable and then evaluate that variable. See below
+for a more detailed discussion of this feature.
 
 In the discussion that follows, the "name" of the variable is the
 arbitrary string that is the 1st argument in the variable command.
@@ -138,10 +138,12 @@ simulation.
 
 IMPORTANT NOTE: When the input script line is encountered that defines
 a variable of style {equal} or {atom} or {python} that contains a
-formula or Python code, the formula is NOT immediately evaluated and
-the result stored.  See the discussion below about "Immediate
-Evaluation of Variables" if you want to do this.  This is also true of
-the {format} style variable since it evaluates another variable when
+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.
 
 IMPORTANT NOTE: Variables of style {equal} and {atom} can be used as
@@ -155,14 +157,6 @@ can also use such a python-style variable.  This means that when the
 LAMMPS command evaluates the variable, the Python function will be
 executed.
 
-When the input script line is encountered that defines
-a variable of style {equal} or {atom} or {python} that contains a
-formula or Python code, the formula is NOT immediately evaluated and
-the result stored.  See the discussion below about "Immediate
-Evaluation of Variables" if you want to do this.  This is also true of
-the {format} style variable since it evaluates another variable when
-it is invoked.
-
 IMPORTANT NOTE: When a variable command is encountered in the input
 script and the variable name has already been specified, the command
 is ignored.  This means variables can NOT be re-defined in an input