git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11120 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/thermo_modify.html

@@ -17,8 +17,9 @@
 </PRE>
 <UL><LI>one or more keyword/value pairs may be listed 
 
-<PRE>keyword = <I>lost</I> or <I>norm</I> or <I>flush</I> or <I>line</I> or <I>format</I> or <I>temp</I> or <I>press</I>:l
+<PRE>keyword = <I>lost</I> or <I>lost/bond</I> or <I>norm</I> or <I>flush</I> or <I>line</I> or <I>format</I> or <I>temp</I> or <I>press</I>:l
   <I>lost</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
+  <I>lost/bond</I> value = <I>error</I> or <I>warn</I> or <I>ignore</I>
   <I>norm</I> value = <I>yes</I> or <I>no</I>
   <I>flush</I> value = <I>yes</I> or <I>no</I>
   <I>line</I> value = <I>one</I> or <I>multi</I>
@@ -62,6 +63,16 @@ an error and continue with a warning.  A warning will only be issued
 once, the first time an atom is lost.  This can be a useful debugging
 option.
 </P>
+<P>The <I>lost/bond</I> keyword determines whether LAMMPS throws an error or
+not if an atom in a bonded interaction (bond, angle, etc) cannot be
+found when it creates bonded neighbor lists.  By default this is a
+fatal error.  However in some scenarios it may be desirable to only
+issue a warning or ignore it and skip the computation of the missing
+bond, angle, etc.  An example would be when gas molecules in a vapor
+are drifting out of the box through a fixed boundary condition (see
+the <A HREF = "boundary.html">boundary</A> command).  In this case one atom may be
+deleted before the rest of the molecule is, on a later timestep.
+</P>
 <P>The <I>norm</I> keyword determines whether various thermodynamic output
 values are normalized by the number of atoms or not, depending on
 whether it is set to <I>yes</I> or <I>no</I>.  Different unit styles have

doc/thermo_modify.txt

@@ -13,8 +13,9 @@ thermo_modify command :h3
 thermo_modify keyword value ... :pre
 
 one or more keyword/value pairs may be listed :ulb,l
-keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press}:l
+keyword = {lost} or {lost/bond} or {norm} or {flush} or {line} or {format} or {temp} or {press}:l
   {lost} value = {error} or {warn} or {ignore}
+  {lost/bond} value = {error} or {warn} or {ignore}
   {norm} value = {yes} or {no}
   {flush} value = {yes} or {no}
   {line} value = {one} or {multi}
@@ -57,6 +58,16 @@ an error and continue with a warning.  A warning will only be issued
 once, the first time an atom is lost.  This can be a useful debugging
 option.
 
+The {lost/bond} keyword determines whether LAMMPS throws an error or
+not if an atom in a bonded interaction (bond, angle, etc) cannot be
+found when it creates bonded neighbor lists.  By default this is a
+fatal error.  However in some scenarios it may be desirable to only
+issue a warning or ignore it and skip the computation of the missing
+bond, angle, etc.  An example would be when gas molecules in a vapor
+are drifting out of the box through a fixed boundary condition (see
+the "boundary"_boundary.html command).  In this case one atom may be
+deleted before the rest of the molecule is, on a later timestep.
+
 The {norm} keyword determines whether various thermodynamic output
 values are normalized by the number of atoms or not, depending on
 whether it is set to {yes} or {no}.  Different unit styles have