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initial add for sisl-analysis
Signed-off-by: Nick Papior <nickpapior@gmail.com>
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‎presentations/03/siesta.tex‎

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\section{Analysing Siesta output}
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\begin{frame}
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\frametitle{Analysing Siesta output}
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\tableofcontents[currentsection]
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\end{frame}
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\subsection{Siesta utilities}
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\begin{frame}
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\frametitle{Analysing Siesta output}
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\framesubtitle{Siesta utilities}
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\begin{block}{Siesta}
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\siesta\ calculates \emph{many} quantities and writes out a large number of auxiliary
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files which may be used for post-processing.
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Among the output one finds:
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\begin{itemize}
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\item Real-space quantities
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\item Eigenspectrum
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\item Sparse matrices
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\begin{itemize}
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\item Density matrix
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\item Hamiltonian
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\item Overlap
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\end{itemize}
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\item Basis set information
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\item Wavefunction coefficients
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\end{itemize}
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\end{block}
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\end{frame}
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\begin{frame}
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\frametitle{Analysing Siesta output}
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\framesubtitle{Siesta utilities}
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\footnotesize
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\begin{tabular}{lcll}
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File & Utility & fdf & Content
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\\
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\hline
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EIG & Eig2DOS & \texttt{kgrid.MonkhorstPack} & Eigenvalue spectrum
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\\
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bands & gnubands & \texttt{kgrid.MonkhorstPack} & Band-structure eigenvalues
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\\
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VH & grid2cube & \texttt{SaveElectrostaticPotential} & Electrostatic potential
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\\
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VT & grid2cube & \texttt{SaveTotalPotential} & Total potential
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\\
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RHO & grid2cube & \texttt{SaveRho} & Electronic charge
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\\
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\dots & \dots & \texttt{Save}\dots & Real-space quantities in many variants
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\\
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PDOS & \texttt{pdosxml} & \texttt{ProjectedDensityOfStates} & Projected Density of States
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\\
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DM & \texttt{denchar} & \texttt{Write.DM} & Density matrix $\to$ real-space charge
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\\
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WFS/WFSX & \texttt{denchar} & \texttt{WriteWaveFunctions} & Wavefunction/Molecular
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orbitals
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\\
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\vdots
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\end{tabular}
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Using a combination of the above tools one can post-process a lot of Siesta output
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However, all utilities are required to be compiled separately and each program has its
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own input. Some utilities (\texttt{pdosxml}) requires a new compilation per different
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analysis, making the entry barrier high.
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\end{frame}
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‎presentations/03/sisl.tex‎

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\section{Using sisl as analysis tool}
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\begin{frame}
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\frametitle{Using sisl as analysis tool}
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\tableofcontents[currentsection]
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\end{frame}
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\subsection{Siesta utilities}
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\begin{frame}
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\frametitle{Using sisl as analysis tool}
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\framesubtitle{Siesta utilities}
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\begin{block}{sisl}
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sisl replaces nearly all utilities in Siesta and thus so with generalised Python
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modules which results in a more powerful analysis tool.
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\end{block}
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\begin{block}{Command line utilities}
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sisl exposes 3 command line utilities:
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\begin{description}
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\item[sgeom] Geometry manipulation, move, extend etc.
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\item[sgrid] Real-space grid manipulation, sum, subtract remove etc
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\item[sdata] Generic command utility for \emph{any} file (a parser per file)
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\end{description}
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\end{block}
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\begin{tabular}{lcll}
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File & Utility & sisl & Content
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\\
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\hline
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EIG & Eig2DOS & \texttt{eigSileSiesta} & Eigenvalue spectrum
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\\
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bands & gnubands & \texttt{bandsSileSiesta} & Band-structure eigenvalues
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\\
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VH & grid2cube & \texttt{gridSileSiesta} & Electrostatic potential
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\\
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VT & grid2cube & \texttt{gridSileSiesta} & Total potential
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\\
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RHO & grid2cube & \texttt{gridSileSiesta} & Electronic charge
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\\
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\dots & \dots & & Real-space quantities in many variants
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\\
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PDOS & \texttt{pdosxml} & \texttt{pdosSileSiesta} & Projected Density of States
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\\
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DM & \texttt{denchar} & \texttt{dmSileSiesta} & Density matrix $\to$ real-space charge
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\\
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WFS/WFSX & \texttt{denchar} & \texttt{Hamiltonian.eigenstate} & Wavefunction/Molecular
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orbitals
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\\
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\vdots
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\end{tabular}
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\end{frame}
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‎presentations/03/talk.tex‎

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\input ../common.tex
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\graphicspath{{fig/}}
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\institute[2018, Nick R. Papior; DTU Nanotech]{\begin{tikzpicture}
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\node[shape=rectangle split,rectangle split parts=2,anchor=base] at (0,0)
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{DTU: sisl, TBtrans and TranSiesta workshop};
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\end{tikzpicture}}
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\date{21. November 2018}
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\title{Siesta and sisl analysis}
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\author{Nick R. Papior}
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\begin{document}
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\begin{frame}
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\titlepage
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\end{frame}
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\begin{frame}
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\frametitle{Outline}
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\tableofcontents
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\end{frame}
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\input siesta.tex
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\input sisl.tex
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\end{document}

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