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# start a dune project with information from dune.module

dune_project()

dune_enable_all_packages()

find_package(HDF5 COMPONENTS C REQUIRED)

add_subdirectory("src")

\pgfplotsarraynew\heights{%

  -40\\-20\\-10\\-5\\-2.5\\%

  0\\%

  2.5\\5\\10\\20\\40\\%

}

\def\fnamebase{2d-dip-contours}

\def\fname{rfpitol=100e-7}

\newread\threequakesminread

\openin\threequakesminread=generated/timeframe:min:threequakes:\fname.tex

\read\threequakesminread to \threequakesmin

\closein\threequakesminread

\newread\threequakesmaxread

\openin\threequakesmaxread=generated/timeframe:max:threequakes:\fname.tex

\read\threequakesmaxread to \threequakesmax

\closein\threequakesmaxread

\begin{tikzpicture}[trim axis group left, trim axis group right]

  \begin{groupplot}[

    xmin=\threequakesmin, xmax=\threequakesmax, max space between ticks=40pt,

    x tick label style={ /pgf/number format/1000 sep={} },

    tick label style={font=\footnotesize},

    label style={font=\small},

    group style={

      x descriptions at = edge bottom,

      group size=1 by 4,

      vertical sep=0cm

    },

    width=12cm,

    enlargelimits=false]

    \nextgroupplot[

    semithick,

    height = 6.5cm,

    /pgf/number format/1000 sep={},

    ymax=0.7,

    colormap/jet,

    y tick label style={

      /pgf/number format/.cd,

      fixed, fixed zerofill, precision=2,

      /tikz/.cd

    },

    tick label style={font=\footnotesize},

    label style={font=\small},

    legend style={font=\small,

                  at={(1.05,1)},

                  anchor=north west,

                  fill=none},

    ylabel = distance from trench, y unit = m,

    legend cell align=right,

    contour/labels=false,

    contour prepared]

    \pgfplotsinvokeforeach{1,...,9} { % level 0 and 10 are empty

      \pgfplotscolormapaccess[0:10]{#1}{jet}

      \def\TEMP{\definecolor{mycolor#1}{rgb}}

      \expandafter\TEMP\expandafter{\pgfmathresult}

      \def\fnameX{generated/\fnamebase:\fname:level:%

        \pgfplotsarrayvalueofelem#1\of\heights.tex}

      \addplot[contour prepared={draw color=mycolor#1}, forget plot] table \fnameX;

      \addlegendimage{line legend,color=mycolor#1}

      \addlegendentry{%

         \SI{\pgfplotsarrayvalueofelem#1\of\heights}{\micro\meter}}

    };

    \nextgroupplot[

    semithick,

    height = 3.5cm,

    ylabel style={align=center}, ylabel = time step\\size, y unit = s,

    ytick={1e-3,1e-2,1e-1},

    ymax = 1, ymin = 1e-4,

    ymode = log]

    \addplot[const plot, mark=none] table[col sep=comma, y=timeIncrement]

    {generated/2d-performance:\fname.csv};

    \nextgroupplot[

    semithick,

    height = 3.5cm,

    ylabel style={align=center}, ylabel=fixed-point\\iterations,

    ytick={2,4,6,8},

    ymin=0, ymax=10]

    \addplot[const plot, mark=none] table[col sep=comma, y=fixedPointIterations]

    {generated/2d-performance:\fname.csv};

    \nextgroupplot[

    semithick,

    height = 3.5cm,

    xlabel = time, x unit = s,

    ylabel style={align=center}, ylabel=multigrid\\iterations,

    ytick={5,10,15,20},

    ymin=0, ymax=25]

    \addplot[const plot, mark=none] table[col sep=comma, y=multiGridIterations]

    {generated/2d-performance:\fname.csv};

  \end{groupplot}

\end{tikzpicture}

\def\fnamebase{dip-single-points}

\def\fname{rfpitol=100e-7}

\newread\threequakesminread

\openin\threequakesminread=generated/timeframe:min:threequakes:\fname.tex

\read\threequakesminread to \threequakesmin

\closein\threequakesminread

\newread\threequakesmaxread

\openin\threequakesmaxread=generated/timeframe:max:threequakes:\fname.tex

\read\threequakesmaxread to \threequakesmax

\closein\threequakesmaxread

\begin{tikzpicture}[trim axis left, trim axis right]

  \begin{axis}[

    xmin=\threequakesmin, xmax=\threequakesmax, max space between ticks=40pt,

    /pgf/number format/1000 sep={},

    x tick label style={

      /pgf/number format/.cd,

      1000 sep={},

      /tikz/.cd

    },

    y tick label style={

      /pgf/number format/.cd,

      fixed, fixed zerofill, precision=2,

      /tikz/.cd

    },

    tick label style={font=\footnotesize},

    label style={font=\small},

    legend style={font=\small, at={(1.05,1)},

                  anchor=north west,

                  fill=none},

    legend entries={

      \SI{15}{\centi\meter},

      \SI{30}{\centi\meter},

      \SI{45}{\centi\meter}

    },

    ylabel style={align=center}, ylabel=vertical surface\\displacement, y unit = m,

    change y base, y SI prefix=micro,

    xlabel = time, x unit=s,

    width = 12cm,

    height = 4cm,

    semithick]

    \addplot[width=2pt] table[col sep=comma, x index = 0, y index=1]

      {generated/\fnamebase:\fname.csv};

    \addplot[width=2pt, dashed] table[col sep=comma, x index = 0, y index=2]

      {generated/\fnamebase:\fname.csv};

    \addplot[width=2pt, dotted] table[col sep=comma, x index = 0, y index=3]

      {generated/\fnamebase:\fname.csv};

  \end{axis}

\end{tikzpicture}

\begin{tikzpicture}[trim axis left, trim axis right]

  \begin{axis}[

    semithick,

    width = 12cm,

    height = 4cm,

    xmode=log,

    %ymin = 0,

    % scaled y ticks=base 10:0,

    xlabel = fixed point tolerance,

    ylabel style={align=center}, ylabel = multigrid\\iterations, % (multigrid steps)

    extra x ticks       = 1e-5,

    extra x tick labels = { time-stepping\\tolerance },

    extra x tick style  = { align=center, grid = major, ticklabel pos=right }

    ]

    \addplot[mark=+] table[col sep=comma, y=mg] {generated/fpi-data.csv};

  \end{axis}

\end{tikzpicture}

\pgfplotsarraynew\contourlevels{%

  1\\3\\

  10\\30\\

  100\\300\\

  1000\\3000\\

}

\def\fname{threequakes:rfpitol=100e-7}

\newread\threequakesminread

\openin\threequakesminread=generated/timeframe:min:\fname.tex

\read\threequakesminread to \threequakesmin

\closein\threequakesminread

\newread\threequakesmaxread

\openin\threequakesmaxread=generated/timeframe:max:\fname.tex

\read\threequakesmaxread to \threequakesmax

\closein\threequakesmaxread

\begin{tikzpicture}[trim axis left, trim axis right]

  \begin{axis}[

    xmin=\threequakesmin, xmax=\threequakesmax, max space between ticks=40pt,

    ymax=0.85,

    colormap/jet,

    x tick label style={

      /pgf/number format/.cd,

      1000 sep={},

      /tikz/.cd

    },

    y tick label style={

      /pgf/number format/.cd,

      fixed, fixed zerofill, precision=2,

      /tikz/.cd

    },

    tick label style={font=\footnotesize},

    label style={font=\small},

    legend style={font=\small,

                  at={(1.05,1)},

                  anchor=north west,

                  fill=none},

    ylabel = distance from trench, y unit = m,

    xlabel = time, x unit=s,

    width = 12cm, height = 6.5cm,

    legend cell align=right,

    contour/labels=false,

    enlargelimits=false,

    semithick]

    \pgfplotsinvokeforeach{0,2,4,6} {

      \pgfplotscolormapaccess[0:7]{#1}{jet}

      \def\TEMP{\definecolor{mycolor#1}{rgb}}

      \expandafter\TEMP\expandafter{\pgfmathresult}

      \def\fnameX{generated/2d-velocity-contours:\fname:level:%

        \pgfplotsarrayvalueofelem#1\of\contourlevels.tex}

      \addplot[contour prepared={draw color=mycolor#1}, forget plot] table \fnameX;

      \addlegendimage{line legend,color=mycolor#1}

      \addlegendentry{%

        \SI{\pgfplotsarrayvalueofelem#1\of\contourlevels}{\micro\meter/\second}}

    };

  \end{axis}

\end{tikzpicture}

\pgfplotsarraynew\contourlevels{%

  1\\3\\

  10\\30\\

  100\\300\\

  1000\\3000\\

}

\def\fname{zoom:rfpitol=100e-7}

\begin{tikzpicture}[trim axis left, trim axis right]

  \begin{axis}[

    max space between ticks=40pt,

    ymax=0.7,

    colormap/jet,

    x tick label style={

      /pgf/number format/.cd,

      fixed, fixed zerofill, precision=2,

      1000 sep={},

      /tikz/.cd

    },

    y tick label style={

      /pgf/number format/.cd,

      fixed, fixed zerofill, precision=2,

      /tikz/.cd

    },

    tick label style={font=\footnotesize},

    label style={font=\small},

    legend style={font=\small,

                  at={(1.05,1)},

                  anchor=north west,

                  fill=none},

    ylabel = distance from trench, y unit = m,

    xlabel = time, x unit=s,

    width = 12cm, height = 6.5cm,

    legend cell align=right,

    enlargelimits=false,

    contour/labels=false,

    semithick]

    \pgfplotsinvokeforeach{0,...,6} { % level 7 is empty

      \pgfplotscolormapaccess[0:7]{#1}{jet}

      \def\TEMP{\definecolor{mycolor#1}{rgb}}

      \expandafter\TEMP\expandafter{\pgfmathresult}

      \def\fnameX{generated/2d-velocity-contours:\fname:level:%

        \pgfplotsarrayvalueofelem#1\of\contourlevels.tex}

      \addplot[contour prepared={draw color=mycolor#1}, forget plot] table \fnameX;

      \addlegendimage{line legend,color=mycolor#1}

      \addlegendentry{%

        \SI{\pgfplotsarrayvalueofelem#1\of\contourlevels}{\micro\meter/\second}}

    };

  \end{axis}

\end{tikzpicture}

\def\fname{rtol=1e-5_diam=1e-2}

\newread\threequakesminread

\openin\threequakesminread=generated/timeframe:min:threequakes:\fname.tex

\read\threequakesminread to \threequakesmin

\closein\threequakesminread

\newread\threequakesmaxread

\openin\threequakesmaxread=generated/timeframe:max:threequakes:\fname.tex

\read\threequakesmaxread to \threequakesmax

\closein\threequakesmaxread

\begin{tikzpicture}[trim axis group left, trim axis group right]

  \begin{groupplot}[

    xmin=\threequakesmin, xmax=\threequakesmax,

    max space between ticks=40pt,

    x tick label style={

      /pgf/number format/.cd,

      1000 sep={},

      /tikz/.cd

    },

    tick label style={font=\footnotesize},

    label style={font=\small},

    group style={

      x descriptions at = edge bottom,

      group size=1 by 3,

      vertical sep=0cm

    },

    height=3.5cm, width=12cm,

    enlargelimits=false]

    \nextgroupplot[

    semithick,

    ylabel style={align=center}, ylabel = time step\\size, y unit = s,

    ytick={1e-3,1e-2,1e-1},

    ymax = 1, ymin = 1e-4,

    ymode = log]

    \addplot[const plot, mark=none] table[col sep=comma, y=timeIncrement]

    {generated/3d-performance:\fname.csv};

    \nextgroupplot[

    semithick,

    ylabel style={align=center}, ylabel = fixed-point\\iterations,

    ytick={2,4,6,8},

    ymin=0, ymax=10]

    \addplot[const plot, mark=none] table[col sep=comma, y=fixedPointIterations]

    {generated/3d-performance:\fname.csv};

    \nextgroupplot[

    semithick,

    xlabel = time, x unit = s,

    ylabel style={align=center}, ylabel=multigrid\\iterations,

    ytick={5,10,15,20},

    ymin=0, ymax=25

    ]

    \addplot[const plot, mark=none] table[col sep=comma, y=multiGridIterations]

    {generated/3d-performance:\fname.csv};

  \end{groupplot}

\end{tikzpicture}

\def\fname{generated/3d-velocity-contours:rtol=1e-5_diam=1e-2}

\pgfplotstableread[col sep=comma]{\fname:times.csv}\myloadedtable

\pgfplotsarraynew\contourlevels{%

  1\\2\\3\\5\\%

  10\\20\\30\\50\\%

  100\\200\\300\\500\\%

  1000\\

}

\begin{tikzpicture}[trim axis group left, trim axis group right]

  \begin{groupplot}[

    group style={

      y descriptions at = edge left,

      group size=6 by 1,

      horizontal sep=0cm

    },

    ymin=-0.30, ymax= 0.30,

    enlarge x limits=false,

    colormap/jet,

    y tick label style={

      /pgf/number format/.cd,

      fixed, fixed zerofill, precision=2,

      /tikz/.cd

    },

    ytick = {-0.30,-0.20,-0.10,0.00,0.10,0.20,0.30},

    tick label style={font=\footnotesize},

    label style={font=\small},

    width = 3.5cm, height = 6cm,

    enlargelimits=false,

    contour/labels=false,

    %

    groupplot xlabel={distance from trench [\si{\meter}]},

    ]

    \nextgroupplot[semithick, xlabel = {

      \pgfplotstablegetelem{0}{times}\of\myloadedtable%

      $t_0 \approx

      \SI[round-mode=places,round-precision=0]{\pgfplotsretval}{\second}$

    },

    ylabel = width, y unit = m]

    \draw[color=gray!20] (0.162533,-0.30) -- (0.162533,+0.30);           % X

    \draw[color=gray!20] (0.362533+0.05,-0.30) -- (0.362533-0.05,+0.30); % Y

    \pgfplotsinvokeforeach{0,...,12} {

      \pgfplotscolormapaccess[0:14]{#1}{jet}

      \def\TEMP{\definecolor{mycolor#1}{rgb}}

      \expandafter\TEMP\expandafter{\pgfmathresult}

      \pgfplotstablegetelem{0}{timeSteps}\of\myloadedtable

      \edef\fnameX{\fname:%

        step:\pgfplotsretval:%

        level:\pgfplotsarrayvalueofelem#1\of\contourlevels.tex}

      \addplot[contour prepared={draw color=mycolor#1}] table \fnameX;

    };

    \nextgroupplot[semithick, xlabel = {

      \pgfplotstablegetelem{1}{timeOffsets}\of\myloadedtable%

      $t_0 +

      \SI[round-mode=places,round-precision=2]{\pgfplotsretval}{\second}$

    }]

    \draw[color=gray!20] (0.162533,-0.30) -- (0.162533,+0.30);           % X

    \draw[color=gray!20] (0.362533+0.05,-0.30) -- (0.362533-0.05,+0.30); % Y

    \pgfplotsinvokeforeach{0,...,12} { % level 13 and 14 are empty

      \pgfplotscolormapaccess[0:14]{#1}{jet}

      \def\TEMP{\definecolor{mycolor#1}{rgb}}

      \expandafter\TEMP\expandafter{\pgfmathresult}

      \pgfplotstablegetelem{1}{timeSteps}\of\myloadedtable

      \edef\fnameX{\fname:%

        step:\pgfplotsretval:%

        level:\pgfplotsarrayvalueofelem#1\of\contourlevels.tex}

      \addplot[contour prepared={draw color=mycolor#1}] table \fnameX;

    };

    \nextgroupplot[semithick, xlabel = {

      \pgfplotstablegetelem{2}{timeOffsets}\of\myloadedtable%

      $t_0 +

      \SI[round-mode=places,round-precision=2]{\pgfplotsretval}{\second}$

    }]

    \draw[color=gray!20] (0.162533,-0.30) -- (0.162533,+0.30);           % X

    \draw[color=gray!20] (0.362533+0.05,-0.30) -- (0.362533-0.05,+0.30); % Y

    \pgfplotsinvokeforeach{0,...,12} { % level 13 and 14 are empty

      \pgfplotscolormapaccess[0:14]{#1}{jet}

      \def\TEMP{\definecolor{mycolor#1}{rgb}}

      \expandafter\TEMP\expandafter{\pgfmathresult}

      \pgfplotstablegetelem{2}{timeSteps}\of\myloadedtable

      \edef\fnameX{\fname:%

        step:\pgfplotsretval:%

        level:\pgfplotsarrayvalueofelem#1\of\contourlevels.tex}

      \addplot[contour prepared={draw color=mycolor#1}] table \fnameX;

    };

    \nextgroupplot[semithick, xlabel = {

      \pgfplotstablegetelem{3}{timeOffsets}\of\myloadedtable%

      $t_0 +

      \SI[round-mode=places,round-precision=2]{\pgfplotsretval}{\second}$

    },

    legend columns=4,

    legend cell align=right,

    legend style={font=\small,

                  at={(0,1.05)},

                  anchor=south,

                  fill=none},

    ]

    \draw[color=gray!20] (0.162533,-0.30) -- (0.162533,+0.30);           % X

    \draw[color=gray!20] (0.362533+0.05,-0.30) -- (0.362533-0.05,+0.30); % Y

    \pgfplotsinvokeforeach{0,...,12} { % level 13 and 14 are empty

      \pgfplotscolormapaccess[0:14]{#1}{jet}

      \def\TEMP{\definecolor{mycolor#1}{rgb}}

      \expandafter\TEMP\expandafter{\pgfmathresult}

      \pgfplotstablegetelem{3}{timeSteps}\of\myloadedtable

      \edef\fnameX{\fname:%

        step:\pgfplotsretval:%

        level:\pgfplotsarrayvalueofelem#1\of\contourlevels.tex}

      \addplot[contour prepared={draw color=mycolor#1}, forget plot] table \fnameX;

      \addlegendimage{line legend,color=mycolor#1}

      \addlegendentry{%

        \SI{\pgfplotsarrayvalueofelem#1\of\contourlevels}{\micro\meter/\second}}

    };

    \nextgroupplot[semithick, xlabel = {

      \pgfplotstablegetelem{4}{timeOffsets}\of\myloadedtable%

      $t_0 +

      \SI[round-mode=places,round-precision=2]{\pgfplotsretval}{\second}$

    }]

    \draw[color=gray!20] (0.162533,-0.30) -- (0.162533,+0.30);           % X

    \draw[color=gray!20] (0.362533+0.05,-0.30) -- (0.362533-0.05,+0.30); % Y

    \pgfplotsinvokeforeach{0,...,12} { % level 13 and 14 are empty

      \pgfplotscolormapaccess[0:14]{#1}{jet}

      \def\TEMP{\definecolor{mycolor#1}{rgb}}

      \expandafter\TEMP\expandafter{\pgfmathresult}

      \pgfplotstablegetelem{4}{timeSteps}\of\myloadedtable

      \edef\fnameX{\fname:%

        step:\pgfplotsretval:%

        level:\pgfplotsarrayvalueofelem#1\of\contourlevels.tex}

      \addplot[contour prepared={draw color=mycolor#1}] table \fnameX;

    };

    \nextgroupplot[semithick, xlabel = {

      \pgfplotstablegetelem{5}{timeOffsets}\of\myloadedtable%

      $t_0 +

      \SI[round-mode=places,round-precision=2]{\pgfplotsretval}{\second}$

    }]

    \draw[color=gray!20] (0.162533,-0.30) -- (0.162533,+0.30);           % X

    \draw[color=gray!20] (0.362533+0.05,-0.30) -- (0.362533-0.05,+0.30); % Y

    \pgfplotsinvokeforeach{0,...,12} { % level 13 and 14 are empty

      \pgfplotscolormapaccess[0:14]{#1}{jet}

      \def\TEMP{\definecolor{mycolor#1}{rgb}}

      \expandafter\TEMP\expandafter{\pgfmathresult}

      \pgfplotstablegetelem{5}{timeSteps}\of\myloadedtable

      \edef\fnameX{\fname:%

        step:\pgfplotsretval:%

        level:\pgfplotsarrayvalueofelem#1\of\contourlevels.tex}

      \addplot[contour prepared={draw color=mycolor#1}] table \fnameX;

    };

  \end{groupplot}

\end{tikzpicture}

\def\simulationtag{rfpitol=100e-7}

\begin{tikzpicture}[trim axis group left, trim axis group right]

  \begin{groupplot}[

    tick label style={font=\footnotesize},

    label style={font=\small},

    %

    group style={

      y descriptions at = edge left,

      group size=3 by 1,

      horizontal sep=0.75cm

    },

    height=4cm,

    width=4.5cm,

    %

    ytick={1,2,3},

    yticklabels={experiment, simulation}

    ]

    %

    \nextgroupplot[semithick, xlabel = recurrence time, x unit = s, xmode=log,

    log ticks with fixed point, xtick={5,10,20,40}]

    \addplot[mark=+, boxplot={ box extend = 0.5 }]

    table[y index=0] {generated/boxplot-data:lab:recurrence.tex};

    \addplot[mark=+, boxplot={ box extend = 0.5 }]

    table[y index=0] {generated/boxplot-data:simulation:\simulationtag:recurrence.tex};

    %

    \nextgroupplot[semithick, xlabel = rupture width, x unit=m, xmin=0, xmax=0.4,

    extra x ticks       = 0.2,

    extra x tick labels = ,

    extra x tick style  = { grid = major }

    ]

    \addplot[mark=+, boxplot={ box extend = 0.5 }]

    table[y index=0] {generated/boxplot-data:lab:ruptureWidth.tex};

    \addplot[mark=+, boxplot={ box extend = 0.5 }]

    table[y index=0] {generated/boxplot-data:simulation:\simulationtag:ruptureWidth.tex};

    %

    \nextgroupplot[semithick, xlabel = peak slip, x unit=mm, xmode=log, log ticks with fixed point,

    xtick={0.03, 0.06, 0.12}]

    \addplot[mark=+, boxplot={ box extend = 0.5 }]

    table[y index=0] {generated/boxplot-data:lab:peakSlip.tex};

    \addplot[mark=+, boxplot={ box extend = 0.5 }]

    table[y index=0] {generated/boxplot-data:simulation:\simulationtag:peakSlip.tex};

  \end{groupplot}

\end{tikzpicture}

start,end,peakSlipRate,ruptureWidth

26.75999999999787,26.784999999997865,0.027083990074991897,0.7066604616124774

28.98999999999762,29.049999999997617,0.03226818570782891,0.7066460434893268

31.56499999999734,31.614999999997334,0.042600764506162535,0.7065953907642707

34.18999999999705,34.24499999999704,0.039804029857929246,0.7065001704582403

36.69999999999678,36.75499999999677,0.04534969591160434,0.7063800319864028

39.32999999999648,39.39499999999648,0.038848015455120025,0.7062439809396165

42.71999999999611,42.7699999999961,0.04713727822866609,0.7063968867127027

45.77499999999578,45.83999999999577,0.04896737991925046,0.7064612510276674

48.69499999999545,48.75499999999545,0.04528040064825157,0.7062545440454634

\usepackage{pgfplots}

\pgfplotsset{compat=1.11} % FIXME: 1.12 would be nice; debian:8.7 only has 1.11

\usepackage{pgfplotstable}

\usepgfplotslibrary{groupplots}

\usepgfplotslibrary{statistics}

\usepgfplotslibrary{units}

%% Typeset the mu from '[xy] SI prefix=micro' as an upright mu

%% From https://tex.stackexchange.com/a/224574

\pgfplotsset{

  x SI prefix/micro/.style={/pgfplots/axis base prefix={axis x base 6 prefix \micro}},

  y SI prefix/micro/.style={/pgfplots/axis base prefix={axis y base 6 prefix \micro}},

  z SI prefix/micro/.style={/pgfplots/axis base prefix={axis z base 6 prefix \micro}},

  unit code/.code 2 args={\si{#1#2}},

}

%% Add support for 'groupplot [xy]label'

%% From http://tex.stackexchange.com/a/117935/16940, see also

%% https://sourceforge.net/p/pgfplots/feature-requests/48/

\makeatletter

\pgfplotsset{

    groupplot xlabel/.initial={},

    every groupplot x label/.style={

        at={($({\pgfplots@group@name\space c1r\pgfplots@group@rows.west}|-{\pgfplots@group@name\space c1r\pgfplots@group@rows.outer south})!0.5!({\pgfplots@group@name\space c\pgfplots@group@columns r\pgfplots@group@rows.east}|-{\pgfplots@group@name\space c\pgfplots@group@columns r\pgfplots@group@rows.outer south})$)},

        anchor=north,

    },

    groupplot ylabel/.initial={},

    every groupplot y label/.style={

            rotate=90,

        at={($({\pgfplots@group@name\space c1r1.north}-|{\pgfplots@group@name\space c1r1.outer

west})!0.5!({\pgfplots@group@name\space c1r\pgfplots@group@rows.south}-|{\pgfplots@group@name\space c1r\pgfplots@group@rows.outer west})$)},

        anchor=south

    },

    execute at end groupplot/.code={%

      \node [/pgfplots/every groupplot x label]

{\pgfkeysvalueof{/pgfplots/groupplot xlabel}};

      \node [/pgfplots/every groupplot y label]

{\pgfkeysvalueof{/pgfplots/groupplot ylabel}};

    }

}

\def\endpgfplots@environment@groupplot{%

    \endpgfplots@environment@opt%

    \pgfkeys{/pgfplots/execute at end groupplot}%

    \endgroup%

}

\makeatother

%% Have \includegraphics{} support tikz files

\usepackage{tikzscale}

 No newline at end of file

\documentclass[border={3cm 0cm}]{standalone}

\usepackage{siunitx}

\input{includes}

\begin{document}

\includegraphics{2d-dip-contours-performance.tikz}

\end{document}

\documentclass[border={3cm 0cm}]{standalone}

\usepackage{siunitx}

\input{includes}

\begin{document}

\includegraphics{2d-dip-single-points.tikz}

\end{document}

\documentclass[border={3cm 0cm}]{standalone}

\usepackage{siunitx}

\input{includes}

\begin{document}

\includegraphics{2d-effort-over-tolerance.tikz}

\end{document}

\documentclass[border={3cm 0cm}]{standalone}

\usepackage{siunitx}

\input{includes}

\begin{document}

\includegraphics{2d-velocity-contours-threequakes}

\end{document}

\documentclass[border={3cm 0cm}]{standalone}

\usepackage{siunitx}

\input{includes}

\begin{document}

\includegraphics{2d-velocity-contours-zoom}

\end{document}

\documentclass[border={3cm 0cm}]{standalone}

\usepackage{siunitx}

\input{includes}

\begin{document}

\includegraphics{3d-performance.tikz}

\end{document}

\documentclass[border={3cm 0cm}]{standalone}

\usepackage{siunitx}

\input{includes}

\begin{document}

\includegraphics{3d-velocity-contours.tikz}

\end{document}

PDFs=\

  2d-dip-contours-performance.pdf \

  2d-dip-single-points.pdf \

  2d-effort-over-tolerance.pdf \

  2d-velocity-contours-threequakes.pdf \

  2d-velocity-contours-zoom.pdf \

  3d-performance.pdf \

  3d-velocity-contours.pdf \

  boxplot.pdf

PNGs=$(PDFs:.pdf=.png)

pdf: $(PDFs)

%.pdf: standalone/%.tex

	latexmk -pdf $<

png: $(PNGs)

%.png: %.pdf

	convert -density 300 $< -quality 100 $@

\documentclass[border={3cm 0cm}]{standalone}

\usepackage{siunitx}

\input{includes}

\begin{document}

\input{boxplot.tikz}

\end{document}

source('tools/support/findQuakes.R')

source('tools/support/writeContours.R')

Rcpp::sourceCpp('tools/support/trapezoidal.cpp')

finalTime              <- 1000 # s

specialTrenchDistances <- c(0.15,0.30,0.45) # m

convergenceVelocity    <- 5e-5 # m/s

last      <- function(x) x[[length(x)]]

paste.    <- function(...) paste(..., sep='.')

pasteColon<- function(...) paste(..., sep=':')

directories <- ini::read.ini('config.ini')$directories

dir.create(directories[['output']], recursive=TRUE, showWarnings=FALSE)

for (basedir in c("rfpitol=100e-7")) {

  dir          <- file.path(directories[['simulation']],

                            '2d-lab-fpi-tolerance', basedir)

  h5file       <- h5::h5file(file.path(dir, 'output.h5'), 'r')

  relativeTime <- h5file['relativeTime'][]

  realTime     <- finalTime * relativeTime

  calcMask     <- relativeTime >= 0.7

  calcTime     <- realTime[calcMask]

  calcDuration <- last(calcTime) - calcTime[[1]]

  calcRange    <- range(which(calcMask))

  calcLength   <- sum(calcMask)

  ## We are interested in an enlarged time range around actual events here,

  ## (and no other quantities!) hence we pass a very low velocity here.

  quakes           <- findQuakes(1e-6 + convergenceVelocity,

                                 h5file['/frictionalBoundary/velocity'][,,],

                                 indices = calcRange[1]:calcRange[2])

  quakes$beginning <- realTime[quakes$beginningIndex]

  quakes$ending    <- realTime[quakes$endingIndex]

  quakes$duration  <- quakes$ending - quakes$beginning

  numQuakes        <- nrow(quakes)

  relaxedTime <- extendrange(c(quakes[[numQuakes-2,'beginning']],

                               quakes[[numQuakes,  'ending']]), f=0.02)

  threeQuakeTimeMask <- (realTime > relaxedTime[[1]]) & (realTime < relaxedTime[[2]])

  plotMask   <- threeQuakeTimeMask

  plotTime   <- realTime[plotMask]

  plotRange  <- range(which(plotMask))

  plotLength <- sum(plotMask)

  write(relaxedTime[[1]],

        file.path(directories[['output']],

                  paste.(pasteColon('timeframe', 'min', 'threequakes', basedir),

                         'tex')))

  write(relaxedTime[[2]],

        file.path(directories[['output']],

                  paste.(pasteColon('timeframe', 'max', 'threequakes', basedir),

                         'tex')))

  surfaceCoordinates    <- h5file['/surface/coordinates'][]

  surfaceTrenchDistance <- surfaceCoordinates[,1] / cos(atan(.27))

  perm                  <- order(surfaceTrenchDistance)

  displacement <- h5file['/surface/displacement']

  # This is the displacement imposed through the Dirichlet condition at the last node

  displacementOffset <- displacement[calcRange[1]:calcRange[2],last(perm),1]

  balancedSurfaceDisplacement <- matrix(nrow = plotLength, ncol = displacement@dim[2])

  for (k in 1:displacement@dim[2]) {

    d <- displacement[calcRange[1]:calcRange[2],k,1:2]

    d[,,1] <- d[,,1] - displacementOffset

    # We're in a tilted coordinate system

    dv <- -sin(atan(.27))*d[,,1] + cos(atan(.27))*d[,,2]