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lammps-tutorials.tex

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@@ -350,7 +350,7 @@ \subsection{Background knowledge}
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\cite{barrat2003basic}, as well as \textit{Theory of Simple Liquids:
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with Applications to Soft Matter} by Jean-Pierre Hansen and Ian Ranald
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McDonald~\cite{hansen2013theory}. For more resources, the SklogWiki
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platform provies a wide range of information on statistical mechanics
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platform provides a wide range of information on statistical mechanics
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and molecular simulations~\cite{sklogwiki_main_page}.
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\subsection{Software/system requirements}
@@ -359,11 +359,11 @@ \subsection{Software/system requirements}
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and the matching \lammpsgui{} software {\color{blue}version 1.7.0} are required to
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follow the tutorials, as they include features that were first
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introduced in these versions. For Linux (x86\_64 CPU), macOS (BigSur or
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later), and Windows (10 and 11) you can download a precompiled LAMMPS
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later), and Windows (10 and 11) you can download a pre-compiled LAMMPS
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package from the LAMMPS release page on
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GitHub~\cite{lammps_github_release}. Select a package with `GUI' in the
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file name, which includes both, \lammpsgui{} and the LAMMPS command-line
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executable. These precompiled packages are designed to be portable, and
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executable. These pre-compiled packages are designed to be portable, and
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therefore omit support for parallel execution with MPI. Instructions
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for installing \lammpsgui{} and using its most relevant features for the
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tutorials are provided in
@@ -450,7 +450,7 @@ \subsection{Tutorial 1: Lennard-Jones fluid}
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\includegraphics[width=0.65\linewidth]{LJ-avatar}
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\caption{The binary mixture simulated in
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\hyperref[lennard-jones-label]{Tutorial 1}, with the atoms of type 1
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represented as small green spheres and lge atoms of type 2 as large
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represented as small green spheres and the atoms of type 2 as large
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blue spheres.}
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\label{fig:LJ-avatar}
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\end{figure}
@@ -1160,8 +1160,8 @@ \subsubsection{Improving the script}
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compute sumcoor12 grp_t1 reduce ave c_coor12
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\end{lstlisting}
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The \lmpcmd{compute reduce ave} command is used to average the per-atom
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coordination number calculated by the \lmpcmd{coord/atom}
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compute command. {\color{blue}Compute commands do not print or output
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coordination number calculated by the \lmpcmd{compute coord/atom}
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command. {\color{blue}Compute commands do not print or output
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anything by themselves, nor are they automatically executed;} they
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require a ``consumer'' command that references the compute. In this case, the
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first compute is referenced by the second, and we reference the second
@@ -1435,9 +1435,9 @@ \subsubsection{Unbreakable bonds}
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\begin{note}
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{\color{blue}
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Bonds, angles, dihedrals, and impropers in LAMMPS are assigned types and IDs, just like atoms.
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The ID uniquely identifies each instance, while the type determines which parameters
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The ID uniquely identifies each interaction instance, while the type determines which parameters
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(from the \lmpcmd{bond\_coeff}, \lmpcmd{angle\_coeff}, etc. commands) are applied.
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In this tutorial, these types and IDs are specified in the \lmpcmd{.data} file
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In this tutorial, these types and IDs are specified in the \lmpcmd{.data} file and
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read by the \lmpcmd{read\_data} command.}
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\end{note}
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@@ -1487,8 +1487,8 @@ \subsubsection{Unbreakable bonds}
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incorporate it using the \lmpcmd{include} command. Using \lmpcmd{include} allows
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us to conveniently reuse the parameter settings
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in other inputs or switch them with others. This will become more general
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when using type labels, which is shown in the next
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tutorial~\cite{gissinger2024type}.
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when using type labels~\cite{gissinger2024type}, which is shown in the next
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tutorial.
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\end{note}
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\paragraph{Prepare the initial state}
@@ -4699,7 +4699,7 @@ \subsubsection{Simulating the reaction}
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% of it may be redundant with the note, but I would still leave it as the reader
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% will have the full information.
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With the \lmpcmd{stabilization} keyword, the \lmpcmd{fix bond/react} command will
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stabilize the atoms involved in the reaction using the \lmpcmd{nve/limit}
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stabilize the atoms involved in the reaction using the \lmpcmd{fix nve/limit}
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command with a maximum displacement of $0.03\,\mathrm{\AA{}}$.
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{\color{blue}The \lmpcmd{fix nve/limit} command functions similar to
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\lmpcmd{fix nve}, but restricts how far atoms can move in a single time step, even with
@@ -4807,7 +4807,7 @@ \section{Using \lammpsgui{}}
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\subsection{Installation}
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Precompiled versions of \lammpsgui{} are available for Linux, {macOS},
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Pre-compiled versions of \lammpsgui{} are available for Linux, {macOS},
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and Windows on the LAMMPS GitHub Release
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page~\cite{lammps_github_release}. The Linux version is provided in two
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formats: as compressed tar archive (.tar.gz) and as a Flatpak

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