git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12351 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_bond_create.html

@@ -155,13 +155,16 @@ data file with no atoms can be used if you wish to add unbonded atoms
 via the <A HREF = "create_atoms.html">create atoms</A> command, e.g. for a
 percolation simulation.
 </P>
-<P>IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a
-list of 1st, 2nd, and 3rd neighbors of each atom (within the bond
+<P>IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
+list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
 topology of the system) for use in weighting pairwise interactions for
-bonded atoms.  Adding a bond adds a single entry to this list.  The
-"extra special per atom" parameter must typically be set to allow for
-it.  There are 3 ways to do this.  See the <A HREF = "read_data.html">read_data</A>
-or <A HREF = "create_box.html">create_box</A> or "special_bonds extra" commands for
+bonded atoms.  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 system.  The "extra
+special per atom" parameter must typically be set to allow for the new
+maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list.
+There are 3 ways to do this.  See the <A HREF = "read_data.html">read_data</A> or
+<A HREF = "create_box.html">create_box</A> or "special_bonds extra" commands for
 details.
 </P>
 <P>IMPORTANT NOTE: Even if you do not use the <I>atype</I>, <I>dtype</I>, or

doc/fix_bond_create.txt

@@ -143,13 +143,16 @@ data file with no atoms can be used if you wish to add unbonded atoms
 via the "create atoms"_create_atoms.html command, e.g. for a
 percolation simulation.
 
-IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a
-list of 1st, 2nd, and 3rd neighbors of each atom (within the bond
+IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
+list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
 topology of the system) for use in weighting pairwise interactions for
-bonded atoms.  Adding a bond adds a single entry to this list.  The
-"extra special per atom" parameter must typically be set to allow for
-it.  There are 3 ways to do this.  See the "read_data"_read_data.html
-or "create_box"_create_box.html or "special_bonds extra" commands for
+bonded atoms.  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 system.  The "extra
+special per atom" parameter must typically be set to allow for the new
+maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list.
+There are 3 ways to do this.  See the "read_data"_read_data.html or
+"create_box"_create_box.html or "special_bonds extra" commands for
 details.
 
 IMPORTANT NOTE: Even if you do not use the {atype}, {dtype}, or

doc/fix_oneway.html

@@ -13,7 +13,7 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>fix ID group-ID N oneway region-ID direction 
+<PRE>fix ID group-ID oneway N region-ID direction 
 </PRE>
 <UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command 
 
@@ -29,9 +29,9 @@
 </UL>
 <P><B>Examples:</B>
 </P>
-<PRE>fix ions 10 oneway semi -x
-fix all 1 oneway left -z
-fix all 1 oneway right z 
+<PRE>fix ions oneway 10 semi -x
+fix all oneway 1 left -z
+fix all oneway 1 right z 
 </PRE>
 <P><B>Description:</B>
 </P>

doc/fix_oneway.txt

@@ -10,7 +10,7 @@ fix oneway command :h3
 
 [Syntax:]
 
-fix ID group-ID N oneway region-ID direction :pre
+fix ID group-ID oneway N region-ID direction :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 oneway = style name of this fix command :l
@@ -21,9 +21,9 @@ direction = {x} or {-x} or {y} or {-y} or {z} or {-z} = coordinate and direction
 
 [Examples:]
 
-fix ions 10 oneway semi -x
-fix all 1 oneway left -z
-fix all 1 oneway right z :pre
+fix ions oneway 10 semi -x
+fix all oneway 1 left -z
+fix all oneway 1 right z :pre
 
 [Description:]
 

doc/special_bonds.html

@@ -171,18 +171,24 @@ interaction between atoms 2 and 5 will be unaffected (full weighting
 of 1.0).  If the <I>dihedral</I> keyword is specified as <I>no</I> which is the
 default, then the 2,5 interaction will also be weighted by 0.5.
 </P>
-<P>The <I>extra</I> keyword is used when additional bonds will be created
+<P>The <I>extra</I> keyword can be used when additional bonds will be created
 during a simulation run, e.g. by the <A HREF = "fix_bond_create.html">fix
 bond/create</A> command.  It can also be used if
 molecules will be added to the system, e.g. via the <A HREF = "fix_deposit.html">fix
 deposit</A>, or <A HREF = "fix_pour.html">fix pour</A> commands, which
 will have atoms with more special neighbors than any atom in the
-current system has.  A list of 1-2,1-3,1-4 neighbors for each atom is
-calculated and stored by LAMMPS.  If new bonds are created (or
-molecules added with atoms with more special neighbors), the list
-needs to grow.  Using the <I>extra</I> keyword leaves empty space in the
-list for N additional bonds to be added.  If you do not do this, you
-may get an error when bonds (or molecules) are added.
+current system has.  
+</P>
+<P>IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
+list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
+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>
+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.
 </P>
 <P>IMPORTANT NOTE: If you reuse this command in an input script, you
 should set all the options you need each time.  This command cannot be

doc/special_bonds.txt

@@ -165,18 +165,24 @@ interaction between atoms 2 and 5 will be unaffected (full weighting
 of 1.0).  If the {dihedral} keyword is specified as {no} which is the
 default, then the 2,5 interaction will also be weighted by 0.5.
 
-The {extra} keyword is used when additional bonds will be created
+The {extra} keyword can be used when additional bonds will be created
 during a simulation run, e.g. by the "fix
 bond/create"_fix_bond_create.html command.  It can also be used if
 molecules will be added to the system, e.g. via the "fix
 deposit"_fix_deposit.html, or "fix pour"_fix_pour.html commands, which
 will have atoms with more special neighbors than any atom in the
-current system has.  A list of 1-2,1-3,1-4 neighbors for each atom is
-calculated and stored by LAMMPS.  If new bonds are created (or
-molecules added with atoms with more special neighbors), the list
-needs to grow.  Using the {extra} keyword leaves empty space in the
-list for N additional bonds to be added.  If you do not do this, you
-may get an error when bonds (or molecules) are added.
+current system has.  
+
+IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
+list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
+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}
+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.
 
 IMPORTANT NOTE: If you reuse this command in an input script, you
 should set all the options you need each time.  This command cannot be