Applied cecimarques comments

Author: simongravelle

lammps-tutorials.tex

@@ -596,25 +596,26 @@ \subsubsection{My first input}
 
 The third line, \lmpcmd{create\_atoms (\dots)}, generates 1500 atoms of
 type 1 at random positions within the \lmpcmd{simbox} region.
-{\color{blue}Each created atom in LAMMPS is automatically assigned a
-  unique atom ID, which serves as a numerical identifier to distinguish
-  individual atoms throughout the simulation.  Atom IDs by default have
-  the range from 1 to the total number of atoms, but this is not
-  enforced.  Deleting atoms, for example, causes ``holes'' in the list
-  of atom IDs.} The integer 34134 is a seed for the internal random
+The integer 34134 is a seed for the internal random
 number generator, which can be changed to produce different sequences of
 random numbers and, consequently, different initial atom positions.  The
 fourth line adds 100 atoms of type 2.  Both \lmpcmd{create\_atoms}
 commands use the optional argument \lmpcmd{overlap 0.3}, which enforces
 a minimum distance of 0.3 {\color{blue}length} units between the
 randomly placed atoms.  This constraint helps avoid ``close contacts''
 between atoms, which can lead to excessively large forces and simulation
-instability.
+instability. {\color{blue}Each created atom in LAMMPS is automatically assigned a
+  unique atom ID, which serves as a numerical identifier to distinguish
+  individual atoms throughout the simulation.  Atom IDs by default have
+  the range from 1 to the total number of atoms, but this is not
+  enforced.  Deleting atoms, for example, causes ``holes'' in the list
+  of atom IDs.}
 
 \begin{note}
   \textcolor{blue}{Another way to define a system in LAMMPS, besides the
     \lmpcmd{create\_atoms} commands, is to import an existing topology
-    with coordinates and other system, force field, and atom properties
+    file containing atomic coordinates as well as, optionally, other
+    attributes such as atomic velocities and the force field parameters
     using the \lmpcmd{read\_data} command, as shown in
     \hyperref[carbon-nanotube-label]{Tutorial 2}.}
 \end{note}
@@ -676,8 +677,7 @@ \subsubsection{My first input}
 \label{fig:LJ}
 \end{figure}
 
-The system is now fully parameterized, and the input is ready to compute
-forces.  Let us complete the two remaining categories,
+The system is now fully parameterized.  Let us complete the two remaining categories,
 \lmpcmd{Monitoring} and \lmpcmd{Run}, by adding the following lines
 to \flecmd{initial.lmp}:
 \begin{lstlisting}