consistent acronym reset

appendix.tex

@@ -16,7 +16,7 @@ \chapter{List of Gregory-Newton Contact Graphs}
 %\end{figure}
 
 \footnotesize{\begin{longtable}{lll}
-    \caption{List of all GN polyhedral graphs. The ordinal numbers $\omega$ in the first column
+    \caption{List of all \acs{GN} polyhedral graphs. The ordinal numbers $\omega$ in the first column
     can be used to identify the individual polyhedral graphs.
     $|E|$ is the number of edges, and the pairs of numbers refer to edges deleted
     incident vertices $(k,l)$ as defined in the icosahedral graph
@@ -773,7 +773,7 @@ \chapter{List of Gregory-Newton Contact Graphs}
 
 
 \footnotesize{\begin{longtable}{l@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 4pt}r@{\hskip 8pt}r}
-    \caption{GN polyhedron grouped by vertex and face degrees. $|N_n|$ is the
+    \caption{\acs{GN} polyhedron grouped by vertex and face degrees. $|N_n|$ is the
     number of vertices of degree $n$, $|F_n|$ the number of $n$-gonal faces.
     The ordinal numbers $\omega$ in the last column identify the polyhedral
     graphs shown in table~\ref{tab:icosubgraphs}.}\\

introduction.tex

@@ -1,5 +1,5 @@
 %Introduction
-
+\acresetall
 \chapter{Introduction}
 \label{sec:introduction}
 

methods.tex

@@ -1,5 +1,7 @@
 %methods
 
+\acresetall
+
 \part{Methods}
 \label{sec:methods}
 
@@ -12,7 +14,7 @@ \chapter{Program Package \textsc{Spheres}}
 coordinates of cluster structures with respect to a two-body potential was
 required to be created. The optimisation routine needed to be flexible in the
 way that it would be easy to implement different two-body potentials like
-\ac{LJ} or \ac{eLJ}. Furthermore, the program needed to be able to analyse the
+\acf{LJ} or \acf{eLJ}. Furthermore, the program needed to be able to analyse the
 results regarding structure, energy and the matrix of second derivatives. The
 resulting program was written in \Cpp with standard library version 11 and was
 tested to compile in a Linux environment with the \texttt{clang++} compiler
@@ -110,7 +112,7 @@ \subsection{Optimisation of Input Structures}
 \textit{libconfig}.\autocite{Lindner_libconfiglibraryprocessing_2018} For
 example, the optimisation can be controlled using the \texttt{opt} group. In
 this group, the optimisation model can be chosen with the \texttt{name} setting,
-which currently can be set to either \texttt{BFGS} for the \ac{BFGS} algorithm
+which currently can be set to either \texttt{BFGS} for the \acf{BFGS} algorithm
 or \texttt{CG} for the conjugate gradient method. The optimiser uses the machine
 learning library dlib\autocite{King_DlibmlMachineLearning_2009} as a back-end,
 which allows for the implementation of additional optimisation models with

results.tex

@@ -1,5 +1,7 @@
 %results
 
+\acresetall
+
 \part{Results}
 \label{sec:results}
 
@@ -1113,8 +1115,7 @@ \section{Conclusion}
 icosahedral \ce{Au12},
 drastically.\autocite{Pyykko_IcosahedralWAu12Predicted_2002}
 
-
-
+\acresetall
 
 \chapter[From Sticky-Hard-Sphere to Lennard-Jones-Type Clusters]{From
     Sticky-Hard-Sphere to Lennard-Jones-Type clusters\footnote{This chapter is
@@ -1199,7 +1200,7 @@ \section{Introduction}
 %
 Using the Gregory-Newton argument results in $f(N)=6$, however, a tighter upper
 bound has been published more recently by
-\citeauthor{Bezdek-2013}\autocite{Bezdek-2013}.
+\citeauthor{Bezdek-2013}\autocite{Bezdek-2013}
 %
 \begin{equation}
     f(N)=6N-3(18)^{1/3}\pi^{-2/3}N^{2/3}.
@@ -1247,10 +1248,11 @@ \section{Introduction}
 %
 \begin{figure}[htb]\centering
     \includegraphics[width=0.8\columnwidth]{kslj/exampleLJ.pdf}
-    \caption{Lennard-Jones potentials for different exponents $(m,n)$ with
-    fixed $n=2m$. As the exponents grow larger, the well of attraction becomes narrower 
-    and its shape approaches the \acs{SHS} potential. The dashed line
-    shows the extended LJ potential for the xenon dimer \autocite{Jerabek_relativisticcoupledclusterinteraction_2017}.}
+    \caption{Lennard-Jones potentials for different exponents $(m,n)$ with fixed
+    $n=2m$. As the exponents grow larger, the well of attraction becomes
+    narrower and its shape approaches the \acs{SHS} potential. The dashed line
+    shows the extended Lennard-Jones potential for the xenon dimer
+    \autocite{Jerabek_relativisticcoupledclusterinteraction_2017}.}
     \label{fig:LJ}
 \end{figure}
 %
@@ -1758,8 +1760,8 @@ \section{(6,12)-Lennard-Jones Clusters from Basin-Hopping}
 \begin{table}[htb]\centering
     \begin{threeparttable}
     \caption{Number of missing structures after optimisation belonging to the
-    same "seed" (figure~\ref{fig:seeds}). $N=8$ is excluded because all LJ minima were
-    found starting from the \acs{SHS} model.}
+    same "seed" (figure~\ref{fig:seeds}). $N=8$ is excluded because all \acs{LJ}
+    minima were found starting from the \acs{SHS} model.}
     \label{tab:seeds}
     \begin{tabular}{llllll}\toprule
         seed      & $N=9$   & $N=10$  & $N=11$  & $N=12$  & $N=13$  \\ \midrule
@@ -1796,8 +1798,8 @@ \section{(6,12)-Lennard-Jones Clusters from Basin-Hopping}
     \subfloat[$N=13$]{\includegraphics[width=.5\textwidth]{kslj/lj13var.pdf}}
     \caption{Histograms of the difference between the longest and shortest bond
     distances $d_\Delta=d_\text{max}-d_\text{min}$ for the complete set of
-    distinct LJ minima $\mathcal{M}_\text{LJ}(N)$ for $N=\{11,12,13\}$. Orange
-    bars give the number of distinct structures not contained in
+    distinct \acs{LJ} minima $\mathcal{M}_\text{LJ}(N)$ for $N=\{11,12,13\}$.
+    Orange bars give the number of distinct structures not contained in
     $\mathcal{M}_\mathrm{LJ}$ as obtained from the basin-hopping algorithm.}
     \label{fig:bondlength-variance}
 \end{figure}%
@@ -1812,10 +1814,13 @@ \section{(6,12)-Lennard-Jones Clusters from Basin-Hopping}
 \ac{SHS} boundary conditions are not satisfied. The data in
 table~\ref{tab:energies} shows that the unmatched (UM) structures for a specific
 $N$ value have much higher energies compared to the one of the global minimum
-(which is set to zero, i.e. $E_0=0$).
-%
+(which is set to zero, i.e. $E_0=0$). They are always positioned in the upper
+half of the energy spectrum, making them energetically unfavourable. However, no
+correlation between $d_\Delta$ and the energetic position of the \ac{LJ}
+clusters was found.
+
 \begin{table}[htb]\centering
-    \caption{Range $[E_0,E_\text{max}]$ of the energy spectrum of all LJ
+    \caption{Range $[E_0,E_\text{max}]$ of the energy spectrum of all \acs{LJ}
     minima, position of the second lowest minimum structure $E_1$ and position
     of the first unmatched (UM) structure $E_0^\text{UM}$ relative to the
     respective global minimum (in reduced units and $E_0=0$).}
@@ -1830,10 +1835,6 @@ \section{(6,12)-Lennard-Jones Clusters from Basin-Hopping}
         13  & 9.26   & 2.85    & 6.14        \\\bottomrule
         \end{tabular}
 \end{table}%
-%
-They are always positioned in the upper half of the energy spectrum, making them
-energetically unfavourable. However, no correlation between $d_\Delta$ and the
-energetic position of the \ac{LJ} clusters was found.
 
 Last, the geometries of the missing structures were investigated in more detail.
 As it turns out, almost all of the missing stable \ac{LJ} clusters can be
@@ -1930,6 +1931,7 @@ \section{Conclusion}
 However, that would require a considerable amount of programming as the current
 program was developed with only two-body forces in mind.
 
+\acresetall
 
 \chapter[The Gregory-Newton Clusters]{The Gregory-Newton Clusters\footnote{This
     chapter is composed of sections previously published in the articles
@@ -2293,11 +2295,11 @@ \section{Rigid Gregory-Newton Clusters and Corresponding Graphs}
     \centering
     \subfloat[hcp, $|E|=24, \omega =1$.\label{subfig:hcpgraph}]{\includegraphics[width=0.43\columnwidth]{gregory-newton/hcp-new.pdf}\hspace{0.03\textwidth}\includegraphics[width=.37\columnwidth]{gregory-newton/hcp.png}}\\
     \subfloat[fcc, $|E|=24, \omega =2$.\label{subfig:fccgraph}]{\includegraphics[width=0.43\columnwidth]{gregory-newton/fcc-new.pdf}\hspace{0.03\textwidth}\includegraphics[width=.37\columnwidth]{gregory-newton/fcc.png}}
-    \caption{GN hcp (triangular orthobicupola) and fcc (cuboctahedron) graphs
-    (central sphere removed) as sub-graphs of the icosahedral graph and
-    corresponding rigid \acs{GNC}s.  Red lines indicate the edges that were removed to
-    create the GN graph. The ordinal numbers $\omega$ refer to
-    Table~\ref{tab:icosubgraphs} in the appendix.}
+    \caption{\acs{GN} \acs{hcp} (triangular orthobicupola) and \acs{fcc}
+    (cuboctahedron) graphs (central sphere removed) as sub-graphs of the
+    icosahedral graph and corresponding rigid \acsp{GNC}.  Red lines indicate
+    the edges that were removed to create the \acs{GN} graph. The ordinal
+    numbers $\omega$ refer to Table~\ref{tab:icosubgraphs} in the appendix.}
     \label{fig:GNshellgraphs}
 \end{figure}
 
@@ -2334,9 +2336,9 @@ \section{Rigid Gregory-Newton Clusters and Corresponding Graphs}
 \begin{figure}[htb]
     \centering
     \includegraphics[width=.8\columnwidth]{gregory-newton/plane.png}
-    \caption{Illustration of one zig-zag path (light blue spheres) that needs
-    to be deformed such that it aligns with the triangular plane (shown in
-    grey) of the fcc crystal.}
+    \caption{Illustration of one zig-zag path (light blue spheres) that needs to
+    be deformed such that it aligns with the triangular plane (shown in grey) of
+    the \acs{fcc} crystal.}
     \label{fig:ico-fcc-trans}
 \end{figure}
 %
@@ -2363,11 +2365,12 @@ \section{Rigid Gregory-Newton Clusters and Corresponding Graphs}
     \centering
     \subfloat[icosahedral motif, $|E|=22, \omega =4$.\label{subfig:ico4graph}]{\includegraphics[width=0.47\columnwidth]{gregory-newton/4-22-new.pdf}\hspace{0.03\textwidth}\includegraphics[width=.3\columnwidth]{gregory-newton/GNico4-22}}\\
     \subfloat[icosahedral motif, $|E|=22, \omega =7$.\label{subfig:ico7graph}]{\includegraphics[width=0.47\columnwidth]{gregory-newton/7-22-new.pdf}\hspace{0.03\textwidth}\includegraphics[width=.3\columnwidth]{gregory-newton/GNico7-22.png}}
-    \caption{Representative GN graphs (central sphere removed) with $|F_3|=10$
-    as sub-graphs of the icosahedral graph and corresponding rigid \acs{GNC}s. The
-    icosahedral motif in the 3D embedding is clearly visible.  Red lines
-    indicate the edges that were removed to create the GN graph. The ordinal
-    numbers $\omega$ refer to Table~\ref{tab:icosubgraphs} in the appendix.}
+    \caption{Representative \acs{GN} graphs (central sphere removed) with
+    $|F_3|=10$ as sub-graphs of the icosahedral graph and corresponding rigid
+    \acsp{GNC}. The icosahedral motif in the 3D embedding is clearly visible.
+    Red lines indicate the edges that were removed to create the \acs{GN} graph.
+    The ordinal numbers $\omega$ refer to Table~\ref{tab:icosubgraphs} in the
+    appendix.}
     \label{fig:GNicographs}
 \end{figure}
 
@@ -2377,11 +2380,11 @@ \section{Rigid Gregory-Newton Clusters and Corresponding Graphs}
 \begin{figure}[htb]
     \centering
     \subfloat[Distorted elongated pentagonal bipyramid (Johnson solid $J_{16}$), $|E|=23, \omega =3$.\label{subfig:johnsongraph}]{\includegraphics[width=0.47\columnwidth]{gregory-newton/johnson-new.pdf}\hspace{0.03\textwidth}\includegraphics[width=.3\columnwidth]{gregory-newton/johnson.png}}
-    \caption{GN graph (central sphere removed) as sub-graphs of the icosahedral
-    graph and corresponding GN Johnson-like solid (with edges removed). Red
-    lines indicate the edges that were removed from the icosahedral graph to
-    create the GN graph. The ordinal number $\omega$ refers to
-    Table~\ref{tab:icosubgraphs} in the appendix.}
+    \caption{\acs{GN} graph (central sphere removed) as sub-graphs of the
+    icosahedral graph and corresponding \acs{GN} Johnson-like solid (with edges
+    removed). Red lines indicate the edges that were removed from the
+    icosahedral graph to create the \acs{GN} graph. The ordinal number $\omega$
+    refers to Table~\ref{tab:icosubgraphs} in the appendix.}
     \label{fig:GNJohnsongraph}
 \end{figure}
 %
@@ -2425,7 +2428,7 @@ \section{Symmetry-Broken Lennard-Jones Gregory-Newton Clusters}
 \begin{figure}[htb]\centering
     \includegraphics[width=.8\columnwidth]{gregory-newton/ico-2d.pdf}
     \caption{Number of unique structures resulting from an optimisation with a
-    LJ$(a,b)$ potential. The lowest contour line shows the point where more
+    $(a,b)$-\acs{LJ} potential. The lowest contour line shows the point where more
     than one structure results from the optimisation and the distance between
     contour lines is 1.}
     \label{fig:ico-2d}
@@ -2446,7 +2449,7 @@ \section{Symmetry-Broken Lennard-Jones Gregory-Newton Clusters}
 \begin{figure}[htb]\centering
     \includegraphics[width=.8\columnwidth]{gregory-newton/no-ico.pdf}
     \caption{Different types of energy landscapes arising from combinations of
-    the LJ $(a,b)$ exponents. (1) One single (icosahedral) minimum, (2) more
+    the $(a,b)$-\acs{LJ}  exponents. (1) One single (icosahedral) minimum, (2) more
     than one minimum with the icosahedron as the global minimum, (3) more than
     one minimum with the icosahedron becoming a local (and not global) minimum,
     (4) the icosahedral motif disappears completely. The unshaded small area
@@ -2474,11 +2477,11 @@ \section{Symmetry-Broken Lennard-Jones Gregory-Newton Clusters}
 %
 \begin{figure}[htb]\centering
     \includegraphics[width=.8\columnwidth]{gregory-newton/compareLJ.pdf}
-    \caption{Comparison of different shapes of LJ potentials at the phase
+    \caption{Comparison of different shapes of \acs{LJ} potentials at the phase
     transition lines shown in figure~\ref{fig:no-ico} with the traditional
-    LJ(6,12) potential (black solid line). Dashed lines refer to potentials
-    with low $a$ values (left side of figure~\ref{fig:no-ico}), while solid lines
-    refer to potentials with high $a$ values (right side of
+    (6,12)-\acs{LJ} potential (black solid line). Dashed lines refer to
+    potentials with low $a$ values (left side of figure~\ref{fig:no-ico}), while
+    solid lines refer to potentials with high $a$ values (right side of
     figure~\ref{fig:no-ico}).}
     \label{fig:compareLJ}
 \end{figure}
@@ -2501,7 +2504,7 @@ \section{Symmetry-Broken Lennard-Jones Gregory-Newton Clusters}
 %
 \begin{figure}[htb]\centering
     \includegraphics[width=.8\columnwidth]{gregory-newton/sigma.pdf}
-    \caption{Hard-sphere radii $\sigma$ in reduced units for the LJ$(a,b)$
+    \caption{Hard-sphere radii $\sigma$ in reduced units for the $(a,b)$-\acs{LJ}
     potentials on the transition lines shown in figure~\ref{fig:no-ico}.}
     \label{fig:hardsphere}
 \end{figure}

theory.tex

@@ -3,6 +3,8 @@
 \part{Theoretical Background}
 \label{sec:theory}
 
+\acresetall
+
 \chapter{Graph Theory}
 \label{sec:graphtheory}
 
@@ -616,7 +618,7 @@ \section{Graph Matching}
 version included in the \textit{boost graph
 library}\autocite{Siek_BoostGraphLibrary_2002} utilised in this thesis.
 
-
+\acresetall
 
 \chapter{Quantum Chemistry}
 \label{sec:basicsofQC}
@@ -1448,6 +1450,8 @@ \subsection{Projector-Augmented Wave Method}
 which implies that the projector functions must be orthonormal to the pseudo
 partial wave functions $\widetilde{\phi}_i$.
 
+\acresetall
+
 \chapter{Geometry Optimisation}
 \label{sec:geometryoptimisation}
 
@@ -1965,7 +1969,7 @@ \section{Implementation for Two-Body Interaction Potentials}
 three-dimensional space that interact via a given potential some modifications
 have to be made to use the previously described methods. In the following
 paragraphs the mathematical background for the implementation of potentials
-that only depend on the distance between two objects like \ac{LJ} and \ac{eLJ}
+that only depend on the distance between two objects like \acf{LJ} and \acf{eLJ}
 for the program \textsc{Spheres} (chapter~\ref{sec:theprogramspheres}) is
 explained. The physical objects in this case are called spheres and the
 optimisation procedure tries to locate the minimiser corresponding to the
@@ -2258,6 +2262,7 @@ \subsection{Algorithms}
 \ac{PES}. Other algorithms that can be used to solve the problem at hand are,
 for example, the particle swarm algorithm or the ant colony optimisation method.
 
+\acresetall
 
 \chapter{Interaction Potentials}
 \label{sec:energylandscapes}
@@ -2470,7 +2475,7 @@ \subsection{Equation of State from the Partition Function}
 \section{Lennard-Jones Potential}
 \label{sec:LennardJones}
 
-One of the most widely used interaction potentials today is the \ac{LJ}
+One of the most widely used interaction potentials today is the \acf{LJ}
 potential. It was first introduced by
 \citeauthor{Jones_DeterminationMolecularFields_1924} (later Lennard-Jones) on
 April 22, 1924\autocite{Jones_DeterminationMolecularFields_1924}, however, the
@@ -2599,7 +2604,7 @@ \subsection{Lennard-Jones Clusters}
 atoms due to dispersive forces, which are approximated well by the \ac{LJ}
 potential.
 
-The hypersurface upon which the particles move, also called a \ac{PES} or energy
+The hypersurface upon which the particles move, also called a \acf{PES} or energy
 landscape, has been explored extensively for the \ac{LJ} potential.
 \autocite{Tsai_Useeigenmodemethod_1993,Ball_Dynamicsstatisticalsamples_1999,Doye_Saddlepointsdynamics_2002} \citeauthor{Doye_Saddlepointsdynamics_2002}\autocite{Doye_Saddlepointsdynamics_2002}
 employed the eigenvector following method (section~\ref{sec:GOAlgorithms}) to