git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11886 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/compute_modify.html

@@ -56,8 +56,8 @@ Only compute styles that compute a temperature use this option.  By
 default, N is assumed to be constant.  If you are adding atoms to the
 system (see the <A HREF = "fix_pour.html">fix pour</A> or <A HREF = "fix_deposit.html">fix
 deposit</A> commands) or expect atoms to be lost
-(e.g. due to evaporation), then this option can be used to insure the
-temperature is correctly normalized.
+(e.g. due to evaporation), then this option should be used to insure
+the temperature is correctly normalized.
 </P>
 <P>The <I>thermo</I> keyword determines whether the potential energy
 contribution calculated by some <A HREF = "fix.html">fixes</A> is added to the

doc/compute_modify.txt

@@ -49,8 +49,8 @@ Only compute styles that compute a temperature use this option.  By
 default, N is assumed to be constant.  If you are adding atoms to the
 system (see the "fix pour"_fix_pour.html or "fix
 deposit"_fix_deposit.html commands) or expect atoms to be lost
-(e.g. due to evaporation), then this option can be used to insure the
-temperature is correctly normalized.
+(e.g. due to evaporation), then this option should be used to insure
+the temperature is correctly normalized.
 
 The {thermo} keyword determines whether the potential energy
 contribution calculated by some "fixes"_fix.html is added to the

doc/fix_bond_break.html

@@ -88,6 +88,11 @@ interaction, that interaction is removed as well.  These changes
 typically affect pairwise interactions between atoms that used to be
 part of bonds, angles, etc.
 </P>
+<P>IMPORTANT NOTE: One data structure that is not updated when a bond
+breaks are the molecule IDs stored by each atom.  Even though
+one molecule becomes two moleclues due to the broken bond, all atoms
+in both new moleclues retain their original molecule IDs.
+</P>
 <P>Computationally, each timestep this fix operates, it loops over all
 the bonds in the system and computes distances between pairs of bonded
 atoms.  It also communicates between neighboring processors to

doc/fix_bond_break.txt

@@ -77,6 +77,11 @@ interaction, that interaction is removed as well.  These changes
 typically affect pairwise interactions between atoms that used to be
 part of bonds, angles, etc.
 
+IMPORTANT NOTE: One data structure that is not updated when a bond
+breaks are the molecule IDs stored by each atom.  Even though
+one molecule becomes two moleclues due to the broken bond, all atoms
+in both new moleclues retain their original molecule IDs.
+
 Computationally, each timestep this fix operates, it loops over all
 the bonds in the system and computes distances between pairs of bonded
 atoms.  It also communicates between neighboring processors to

doc/fix_bond_create.html

@@ -128,6 +128,11 @@ the <I>atype</I>, <I>dtype</I>, and <I>itype</I> keywords.  All of these changes
 typically affect pairwise interactions between atoms that are now part
 of new bonds, angles, etc.
 </P>
+<P>IMPORTANT NOTE: One data structure that is not updated when a bond
+breaks are the molecule IDs stored by each atom.  Even though two
+molecules become one moleclue due to the created bond, all atoms in
+the new moleclue retain their original molecule IDs.
+</P>
 <P>If the <I>atype</I> keyword is used and if an angle potential is defined
 via the <A HREF = "angle.html">angle_style</A> command, then any new 3-body
 interactions inferred by the creation of a bond will create new angles

doc/fix_bond_create.txt

@@ -116,6 +116,11 @@ the {atype}, {dtype}, and {itype} keywords.  All of these changes
 typically affect pairwise interactions between atoms that are now part
 of new bonds, angles, etc.
 
+IMPORTANT NOTE: One data structure that is not updated when a bond
+breaks are the molecule IDs stored by each atom.  Even though two
+molecules become one moleclue due to the created bond, all atoms in
+the new moleclue retain their original molecule IDs.
+
 If the {atype} keyword is used and if an angle potential is defined
 via the "angle_style"_angle.html command, then any new 3-body
 interactions inferred by the creation of a bond will create new angles

doc/fix_thermal_conductivity.html

@@ -44,7 +44,7 @@ fix 1 all thermal/conductivity 50 z 20 swap 2
 paper</A> to exchange kinetic energy between two particles
 in different regions of the simulation box every N steps.  This
 induces a temperature gradient in the system.  As described below this
-enables a thermal conductivity of the fluid to be calculated.  This
+enables the thermal conductivity of a material to be calculated.  This
 algorithm is sometimes called a reverse non-equilibrium MD (reverse
 NEMD) approach to computing thermal conductivity.  This is because the
 usual NEMD approach is to impose a temperature gradient on the system

doc/fix_thermal_conductivity.txt

@@ -34,7 +34,7 @@ Use the Muller-Plathe algorithm described in "this
 paper"_#Muller-Plathe to exchange kinetic energy between two particles
 in different regions of the simulation box every N steps.  This
 induces a temperature gradient in the system.  As described below this
-enables a thermal conductivity of the fluid to be calculated.  This
+enables the thermal conductivity of a material to be calculated.  This
 algorithm is sometimes called a reverse non-equilibrium MD (reverse
 NEMD) approach to computing thermal conductivity.  This is because the
 usual NEMD approach is to impose a temperature gradient on the system

doc/variable.html

@@ -704,9 +704,9 @@ atom with ID = 243.
 evaluating the variable.
 </P>
 <P>The meaning of the different atom values and vectors is mostly
-self-explanatory.  Mol refernces the molecule ID of an atom, and is
-only defined if an <A HREF = "atom_style.html">atom_style</A> is being used
-that defines molecule IDs.
+self-explanatory.  Mol refers to the molecule ID of an atom, and is
+only defined if an <A HREF = "atom_style.html">atom_style</A> is being used that
+defines molecule IDs.
 </P>
 <P>Note that many other atom attributes can be used as inputs to a
 variable by using the <A HREF = "compute_property_atom.html">compute

doc/variable.txt

@@ -704,9 +704,9 @@ Atom vectors generate one value per atom, so that a reference like
 evaluating the variable.
 
 The meaning of the different atom values and vectors is mostly
-self-explanatory.  Mol refernces the molecule ID of an atom, and is
-only defined if an "atom_style"_atom_style.html is being used
-that defines molecule IDs.
+self-explanatory.  Mol refers to the molecule ID of an atom, and is
+only defined if an "atom_style"_atom_style.html is being used that
+defines molecule IDs.
 
 Note that many other atom attributes can be used as inputs to a
 variable by using the "compute