git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2003 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/bond_fene.html

@@ -48,6 +48,10 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
 "molecular" package (which it is by default).  See the <A HREF = "Section_start.html#2_3">Making
 LAMMPS</A> section for more info on packages.
 </P>
+<P>You typically should specify <A HREF = "special_bonds.html">special_bonds 0 1 1</A>
+to use this bond style.  LAMMPS will issue a warning it that's not the
+case.
+</P>
 <P><B>Related commands:</B>
 </P>
 <P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>

doc/bond_fene.txt

@@ -45,6 +45,10 @@ This bond style can only be used if LAMMPS was built with the
 "molecular" package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
+You typically should specify "special_bonds 0 1 1"_special_bonds.html
+to use this bond style.  LAMMPS will issue a warning it that's not the
+case.
+
 [Related commands:]
 
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html

doc/bond_fene_expand.html

@@ -53,6 +53,10 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
 "molecular" package (which it is by default).  See the <A HREF = "Section_start.html#2_3">Making
 LAMMPS</A> section for more info on packages.
 </P>
+<P>You typically should specify <A HREF = "special_bonds.html">special_bonds 0 1 1</A>
+to use this bond style.  LAMMPS will issue a warning it that's not the
+case.
+</P>
 <P><B>Related commands:</B>
 </P>
 <P><A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "delete_bonds.html">delete_bonds</A>

doc/bond_fene_expand.txt

@@ -50,6 +50,10 @@ This bond style can only be used if LAMMPS was built with the
 "molecular" package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#2_3 section for more info on packages.
 
+You typically should specify "special_bonds 0 1 1"_special_bonds.html
+to use this bond style.  LAMMPS will issue a warning it that's not the
+case.
+
 [Related commands:]
 
 "bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html

doc/fix_bond_swap.html

@@ -23,7 +23,7 @@
 </UL>
 <P><B>Examples:</B>
 </P>
-<PRE>fix 1 all bond/swap 0.5 1.5 598934 
+<PRE>fix 1 all bond/swap 0.5 1.3 598934 
 </PRE>
 <P><B>Description:</B>
 </P>

doc/fix_bond_swap.txt

@@ -20,7 +20,7 @@ seed = random # seed (positive integer) :ul
 
 [Examples:]
 
-fix 1 all bond/swap 0.5 1.5 598934 :pre
+fix 1 all bond/swap 0.5 1.3 598934 :pre
 
 [Description:]
 

doc/special_bonds.html

@@ -24,7 +24,7 @@ special_bonds c1 c2 c3 c4 c5 c6
 </P>
 <PRE>special_bonds charmm
 special_bonds amber
-special_bonds 0.0 0.0 1.0
+special_bonds 0 1 1
 special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 
 </PRE>
 <P><B>Description:</B>
@@ -65,6 +65,9 @@ interactions and to 0.0 0.0 0.833 for Coulombic interactions, which is
 the default for a particular version of the AMBER force field, where
 the last value is 5/6.
 </P>
+<P>For a <A HREF = "units.html">lj units</A> system with <A HREF = "bond_fene.html">FENE bonds</A> a
+setting of special bonds 0 1 1 should be used.
+</P>
 <P>A special_bonds command with 3 coefficients sets the 1-2, 1-3, and 1-4
 coefficients for both LJ and Coulombic terms to those values.
 </P>

doc/special_bonds.txt

@@ -21,7 +21,7 @@ Examples:
 
 special_bonds charmm
 special_bonds amber
-special_bonds 0.0 0.0 1.0
+special_bonds 0 1 1
 special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 :pre
 
 [Description:]
@@ -62,6 +62,9 @@ interactions and to 0.0 0.0 0.833 for Coulombic interactions, which is
 the default for a particular version of the AMBER force field, where
 the last value is 5/6.
 
+For a "lj units"_units.html system with "FENE bonds"_bond_fene.html a
+setting of special bonds 0 1 1 should be used.
+
 A special_bonds command with 3 coefficients sets the 1-2, 1-3, and 1-4
 coefficients for both LJ and Coulombic terms to those values.