git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4224 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_evaporate.html

@@ -58,9 +58,9 @@ molecule ID, but does not check for this at the time of deletion.
 <P>If the setting for the <I>molecule</I> keyword is <I>yes</I>, then when an atom
 is chosen for deletion, the entire molecule it is part of is deleted.
 The count of deleted atoms is incremented by the number of atoms in
-the molecule.  If the molecule ID of the chosen atom is 0, then it is
+the molecule, which may make it exceed <I>M</I>.  If the molecule ID of the
-assumed to not be part of a molecule, and just the single atom is
+chosen atom is 0, then it is assumed to not be part of a molecule, and
-deleted.
+just the single atom is deleted.
 </P>
 <P>As an example, if you wish to delete 10 water molecules every <I>N</I>
 steps, you should set <I>M</I> to 30.  If only the water's oxygen atoms

doc/fix_evaporate.txt

@@ -47,9 +47,9 @@ molecule ID, but does not check for this at the time of deletion.
 If the setting for the {molecule} keyword is {yes}, then when an atom
 is chosen for deletion, the entire molecule it is part of is deleted.
 The count of deleted atoms is incremented by the number of atoms in
-the molecule.  If the molecule ID of the chosen atom is 0, then it is
+the molecule, which may make it exceed {M}.  If the molecule ID of the
-assumed to not be part of a molecule, and just the single atom is
+chosen atom is 0, then it is assumed to not be part of a molecule, and
-deleted.
+just the single atom is deleted.
 
 As an example, if you wish to delete 10 water molecules every {N}
 steps, you should set {M} to 30.  If only the water's oxygen atoms

doc/thermo_modify.html

@@ -50,10 +50,17 @@ thermo_modify command after it.
 </P>
 <P>The <I>lost</I> keyword determines whether LAMMPS checks for lost atoms
 each time it computes thermodynamics and what it does if atoms are
-lost.  If the value is <I>ignore</I>, LAMMPS does not check for lost atoms.
+lost.  An atom can be "lost" if it moves across a non-periodic
-If the value is <I>error</I> or <I>warn</I>, LAMMPS checks and either issues an
+simulation box <A HREF = "boundary.html">boundary</A> or if it moves more than a box
-error or warning.  The code will exit with an error and continue with
+length outside the simulation domain (or more than a processor
-a warning.  This can be a useful debugging option.
+sub-domain length) before reneighboring occurs.  The latter case is
+typically due to bad dynamics, e.g. too large a timestep or huge
+forces and velocities.  If the value is <I>ignore</I>, LAMMPS does not
+check for lost atoms.  If the value is <I>error</I> or <I>warn</I>, LAMMPS
+checks and either issues an error or warning.  The code will exit with
+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>norm</I> keyword determines whether various thermodynamic output
 values are normalized by the number of atoms or not, depending on

doc/thermo_modify.txt

@@ -45,10 +45,17 @@ thermo_modify command after it.
 
 The {lost} keyword determines whether LAMMPS checks for lost atoms
 each time it computes thermodynamics and what it does if atoms are
-lost.  If the value is {ignore}, LAMMPS does not check for lost atoms.
+lost.  An atom can be "lost" if it moves across a non-periodic
-If the value is {error} or {warn}, LAMMPS checks and either issues an
+simulation box "boundary"_boundary.html or if it moves more than a box
-error or warning.  The code will exit with an error and continue with
+length outside the simulation domain (or more than a processor
-a warning.  This can be a useful debugging option.
+sub-domain length) before reneighboring occurs.  The latter case is
+typically due to bad dynamics, e.g. too large a timestep or huge
+forces and velocities.  If the value is {ignore}, LAMMPS does not
+check for lost atoms.  If the value is {error} or {warn}, LAMMPS
+checks and either issues an error or warning.  The code will exit with
+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 {norm} keyword determines whether various thermodynamic output
 values are normalized by the number of atoms or not, depending on