fixed broken links

Author: simongravelle

journal-article.bib

@@ -682,7 +682,7 @@ @article{ovito_paper
 
 @misc{flatpak_home,
   title = {{Flatpak} Homepage},
-  howpublished = {\url{https://www.flatpak.org}},
+  howpublished = {\url{https://flatpak.org}},
   note = {Accessed: 2024-08-09}
 }
 

lammps-tutorials.pdf

@@ -1721,8 +1721,8 @@ \subsubsection{Breakable bonds}
 energy $E$ is initially increasing with the deformation.  When bonds
 break, the energy relaxes abruptly, as can be seen near $t=32~\text{ps}$
 in Fig.~\ref{fig:CNT-breakable-energy-stress}\,a.  Using a similar
-script as previously, i.e.,~\href{\filepath
-  tutorial2/unbreakable-yaml-reader.py}{\dwlcmd{unbreakable-yaml-reader.py}},
+script as previously,
+i.e.,~\href{\filepath tutorial2/unbreakable-yaml-reader.py}{\dwlcmd{unbreakable-yaml-reader.py}},
 import the data into Python and generate the stress-strain curve
 (Fig.~\ref{fig:CNT-breakable-energy-stress}\,b).  The stress-strain
 curve reveals a linear (elastic) regime where
@@ -4051,8 +4051,8 @@ \subsubsection{Method 2: Umbrella sampling}
 \item the values of $x_\text{des}$,
 \item the values of $k$.
 \end{itemize}
-Download the \href{\filepath
-  tutorial7/umbrella-sampling.meta}{\dwlcmd{umbrella-sampling.meta}}
+Download the
+\href{\filepath tutorial7/umbrella-sampling.meta}{\dwlcmd{umbrella-sampling.meta}}
 file and save it next to \flecmd{umbrella-sampling.lmp}.  Then, run the
 WHAM algorithm by typing the following command in the terminal:
 \begin{lstlisting}
@@ -4245,14 +4245,14 @@ \subsubsection{Reaction templates}
 \end{itemize}
 The second reaction uses the prefix `M-P',
 \begin{itemize}
-\item \href{\filepath tutorial8/M-P_pre.lmpmol}{\dwlcmd{M-P$\_$pre.mol}},
-\item \href{\filepath tutorial8/M-P_post.lmpmol}{\dwlcmd{M-P$\_$post.mol}},
+\item \href{\filepath tutorial8/M-P_pre.mol}{\dwlcmd{M-P$\_$pre.mol}},
+\item \href{\filepath tutorial8/M-P_post.mol}{\dwlcmd{M-P$\_$post.mol}},
 \item \href{\filepath tutorial8/M-P.rxnmap}{\dwlcmd{M-P.rxnmap}}.
 \end{itemize}
 The third reaction uses the prefix `P-P',
 \begin{itemize}
-\item \href{\filepath tutorial8/P-P_pre.lmpmol}{\dwlcmd{P-P$\_$pre.mol}},
-\item \href{\filepath tutorial8/P-P_post.lmpmol}{\dwlcmd{P-P$\_$post.mol}},
+\item \href{\filepath tutorial8/P-P_pre.mol}{\dwlcmd{P-P$\_$pre.mol}},
+\item \href{\filepath tutorial8/P-P_post.mol}{\dwlcmd{P-P$\_$post.mol}},
 \item \href{\filepath tutorial8/P-P.rxnmap}{\dwlcmd{P-P.rxnmap}}.
 \end{itemize}
 Here, the file names for each reaction use the abbreviation `M' for monomer and `P'