git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12159 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/delete_atoms.html

@@ -90,12 +90,13 @@ number of atoms in the system.  This is not done for molecular systems
 has already been assigned.
 </P>
 <P>It the <I>mol</I> keyword is set to <I>yes</I>, then for every atom that is
-deleted, all other atoms in the same molecule (i.e. with the same
+deleted, all other atoms in the same molecule (with the same molecule
-molecule ID) will also be deleted.  This is a way to insure that
+ID) will also be deleted.  This is not done for atoms with molecule ID
-entire molecules are deleted instead of only a subset of atoms in the
+= 0, since it is assumed to flag isolated atoms that are not part of
-molecule which will typically lead to errors because of bond, angle,
+molecules.  This is a way to insure that entire molecules are deleted
-or dihedral interactions stored by remaining atoms which reference
+instead of only a subset of atoms in the molecule which will typically
-deleted atoms.
+lead to errors because of bond, angle, or dihedral interactions stored
+by remaining atoms which reference deleted atoms.
 </P>
 <P>IMPORTANT NOTE: The molecule deletion operation in invoked after all
 individual atoms have been deleted using the rules described above for

doc/delete_atoms.txt

@@ -82,12 +82,13 @@ number of atoms in the system.  This is not done for molecular systems
 has already been assigned.
 
 It the {mol} keyword is set to {yes}, then for every atom that is
-deleted, all other atoms in the same molecule (i.e. with the same
+deleted, all other atoms in the same molecule (with the same molecule
-molecule ID) will also be deleted.  This is a way to insure that
+ID) will also be deleted.  This is not done for atoms with molecule ID
-entire molecules are deleted instead of only a subset of atoms in the
+= 0, since it is assumed to flag isolated atoms that are not part of
-molecule which will typically lead to errors because of bond, angle,
+molecules.  This is a way to insure that entire molecules are deleted
-or dihedral interactions stored by remaining atoms which reference
+instead of only a subset of atoms in the molecule which will typically
-deleted atoms.
+lead to errors because of bond, angle, or dihedral interactions stored
+by remaining atoms which reference deleted atoms.
 
 IMPORTANT NOTE: The molecule deletion operation in invoked after all
 individual atoms have been deleted using the rules described above for

doc/group.html

@@ -176,14 +176,15 @@ variables are current when they are evaluated between runs.
 </P>
 <P>The <I>include</I> style with its arg <I>molecule</I> adds atoms to a group that
 have the same molecule ID as atoms already in the group.  The molecule
-ID = 0 is ignored in this operation, since it assumed to represent
+ID = 0 is ignored in this operation, since it is assumed to flag
-atoms that are not part of molecules.  An example of where this
+isolated atoms that are not part of molecules.  An example of where
-operation is useful is if the <I>region</I> style has been used previously
+this operation is useful is if the <I>region</I> style has been used
-to add atoms to a group that are within a geometric region.  If
+previously to add atoms to a group that are within a geometric region.
-molecules straddle the region boundary, then atoms outside the region
+If molecules straddle the region boundary, then atoms outside the
-that are part of molecules with atoms inside the region will not be in
+region that are part of molecules with atoms inside the region will
-the group.  Using the group command a 2nd time with <I>include molecule</I>
+not be in the group.  Using the group command a 2nd time with <I>include
-will add those atoms that are outside the region to the group.
+molecule</I> will add those atoms that are outside the region to the
+group.
 </P>
 <P>IMPORTANT NOTE: The <I>include molecule</I> operation is relatively
 expensive in a parallel sense.  This is because it requires

doc/group.txt

@@ -172,14 +172,15 @@ variables are current when they are evaluated between runs.
 
 The {include} style with its arg {molecule} adds atoms to a group that
 have the same molecule ID as atoms already in the group.  The molecule
-ID = 0 is ignored in this operation, since it assumed to represent
+ID = 0 is ignored in this operation, since it is assumed to flag
-atoms that are not part of molecules.  An example of where this
+isolated atoms that are not part of molecules.  An example of where
-operation is useful is if the {region} style has been used previously
+this operation is useful is if the {region} style has been used
-to add atoms to a group that are within a geometric region.  If
+previously to add atoms to a group that are within a geometric region.
-molecules straddle the region boundary, then atoms outside the region
+If molecules straddle the region boundary, then atoms outside the
-that are part of molecules with atoms inside the region will not be in
+region that are part of molecules with atoms inside the region will
-the group.  Using the group command a 2nd time with {include molecule}
+not be in the group.  Using the group command a 2nd time with {include
-will add those atoms that are outside the region to the group.
+molecule} will add those atoms that are outside the region to the
+group.
 
 IMPORTANT NOTE: The {include molecule} operation is relatively
 expensive in a parallel sense.  This is because it requires