@@ -2290,7 +2290,7 @@ \subsubsection{System preparation}
22902290These lines are used to define the most basic parameters, including the
22912291atom, bond, and angle styles, as well as interaction
22922292potential. Here, \lmpcmd {lj/cut/tip4p/long} imposes a Lennard-Jones potential with
2293- a cut-off at $ 12 \, \text {$ \text { \ AA {}} $ }$ and a long-range Coulomb potential.
2293+ a cut-off at $ 12 \, \text {\ AA {}}$ and a long-range Coulomb potential.
22942294
22952295So far, the commands are relatively similar to those in the previous tutorial,
22962296\hyperref [all-atom-label]{Polymer in water}, with two major differences: the use
@@ -2301,7 +2301,7 @@ \subsubsection{System preparation}
23012301LAMMPS automatically creates a four-point water molecule, assigning type O
23022302atoms as oxygen and type H atoms as hydrogen. The fourth massless atom (M) of the
23032303TIP4P water molecule does not have to be defined explicitly, and the value of
2304- $ 0.1546 \, \text {$ \text { \ AA {}} $ }$ corresponds to the O-M distance of the
2304+ $ 0.1546 \, \text {\ AA {}}$ corresponds to the O-M distance of the
23052305TIP4P-2005 water model~\cite {abascal2005general }. All other atoms in the simulation
23062306are treated as usual, with long-range Coulomb interactions. Another novelty, here, is
23072307the use of \lmpcmd {kspace\_ modify slab 3.0} that is combined with the non-periodic
@@ -3457,7 +3457,7 @@ \subsubsection{Adding water}
34573457not critical since TIP4P/2005 is a rigid water model.
34583458
34593459The water molecule template called \href {\filepath tutorial6/H2O.mol}{\dwlcmd {H2O.mol}}
3460- must be downloaded and located next to \flecmd {gcmc.lmp}
3460+ must be downloaded and located next to \flecmd {gcmc.lmp}.
34613461
34623462Before going further, we need to make a few changes to our data file.
34633463Currently, the \flecmd {cracking.data} file includes only two atom types, but we require four.
@@ -3606,10 +3606,10 @@ \subsubsection{Adding water}
36063606freedom. Here, 100 insertion and deletion attemps are made every 100 steps.
36073607
36083608\begin {note }
3609- At a pressure of $ p = 100 \ \text {bar}$ , the chemical potential of water vapor at $ T = 300 \ \text {K}$
3609+ At a pressure of $ p = 100 \, \text {bar}$ , the chemical potential of water vapor at $ T = 300 \, \text {K}$
36103610can be calculated using as $ \mu = \mu _0 + RT \ln (\frac {p}{p_0}),$ where $ \mu _0 $ is the standard
3611- chemical potential (typically taken at a pressure $ p_0 = 1 \, \text {bar}$ ), \( R = 8.314\ \text {J/mol·K}\)
3612- is the gas constant, \( T = 300\ \text {K}\) is the temperature.
3611+ chemical potential (typically taken at a pressure $ p_0 = 1 \, \text {bar}$ ), $ R = 8.314 \, \text {J/mol·K}$
3612+ is the gas constant, $ T = 300 \, \text {K}$ is the temperature.
36133613\end {note }
36143614
36153615Finally, let us print some information and run for 25\, ps:
@@ -4285,7 +4285,7 @@ \subsubsection{Simulating the reaction}
42854285 extra/improper/per/atom 25 &
42864286 extra/special/per/atom 25
42874287\end {lstlisting }
4288- Here, the \lmpcmd {read$ \_ $ data } command is used to import the
4288+ Here, the \lmpcmd {read\_ data } command is used to import the
42894289previously generated \flecmd {mixing.data} file. All other commands
42904290have been introduced in earlier parts of the tutorial.
42914291
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