path: root/Master/texmf-dist/doc/latex/endiagram/endiagram_en.tex

% arara: pdflatex
% arara: biber
% arara: pdflatex
% arara: pdflatex
% --------------------------------------------------------------------------
% the ENdiagram package
%
%   easy creation of potential energy curve diagrams
%
% --------------------------------------------------------------------------
% Clemens Niederberger
% Web:    https://www.bitbucket.org/cgnieder/endiagram
% E-Mail: contact@mychemistry.eu
% --------------------------------------------------------------------------
% If you have any ideas, questions, suggestions or bugs to report, please
% feel free to contact me.
% --------------------------------------------------------------------------
% Copyright 2011--2013 Clemens Niederberger
%
% This work may be distributed and/or modified under the
% conditions of the LaTeX Project Public License, either version 1.3
% of this license or (at your option) any later version.
% The latest version of this license is in
%   http://www.latex-project.org/lppl.txt
% and version 1.3 or later is part of all distributions of LaTeX
% version 2005/12/01 or later.
%
% This work has the LPPL maintenance status `maintained'.
%
% The Current Maintainer of this work is Clemens Niederberger.
%
% This work consists of the files endiagram.sty, endiagram_en.tex,
% README and the derived file endiagram_en.pdf.
% --------------------------------------------------------------------------
\documentclass[load-preamble+]{cnltx-doc}
\usepackage[utf8]{inputenc}
\usepackage{endiagram}

\setcnltx{
  package = endiagram ,
  title   = \ENdiagram ,
  authors = Clemens Niederberger ,
  email   = contact@mychemistry.eu ,
  url     = https://bitbucket.org/cgnieder/endiagram/ ,
  add-cmds = {
    AddAxisLabel, 
    ENcurve, ENsetup,
    MakeOrigin,  ShowEa, ShowGain,
    ShowNiveaus
  } ,
  add-envs = { MOdiagram } ,
  add-silent-cmds = {
    arrow,
    calory, ch, chemfig, chemsetup, color, command,
    DeclareChemIUPAC, draw,
    fontfamily,
    iso,
    joule,
    kilo,
    lewis, libertineLF,
    mole,
    node,
    per,
    schemestart, schemestop, selectfont, setatomsep, sisetup,
    tert, tikz, transitionstatesymbol
  }
}

\newpackagename\ENdiagram{endiagram}

\defbibheading{bibliography}{\addsec{References}}

\usepackage{chemmacros,chemfig,ragged2e}

\usepackage{acro}
\acsetup{short-format=\scshape}
\DeclareAcronym{su}{
  short = su ,
  long  = standard unit
}
\DeclareAcronym{CTAN}{
  short = ctan ,
  long  = Comprehensive \TeX{} Archive Network
}
\DeclareAcronym{MWE}{
  short = mwe ,
  long  = minimal working example
}

\begin{filecontents}{\jobname.bib}
@book{brueckner,
  author    = {Reinhard Br\"uckner},
  title     = {Reaktionsmechanismen},
  publisher = {Springer-Verlag Berlin Heidelberg},
  edition   = {3.\,Auflage, 2.\,korrigierter Nachdruck},
  year      = {2009},
  isbn      = {978-3-8274-1579-0}
}
@package{pkg:tikz,
  author    = {Till Tantau and Mark Wibrow and Christian Feuersänger},
  title     = {Ti\textbf{\textit{k}}Z/pgf},
  sorttitle = {TikZ},
  version   = {2.10},
  date      = {2010-20-25},
  url       = {http://sourceforge.net/projects/pgf/},
  urldate   = {2013-04-18}
}
@package{pkg:siunitx,
  author    = {Joseph Wright},
  title     = {siunitx},
  version   = {2.5q},
  date      = {2013-03-11},
  url       = {mirror.ctan.org/macros/latex/contrib/siunitx/}
}
\end{filecontents}

% \setlength{\marginparwidth}{1.5\marginparwidth}

\newcommand*\TikZ{Ti\textit{k}Z}

\begin{document}

\section{Licence and Requirements}
\license

\ENdiagram\ needs the \bnd{l3kernel}~\cite{bnd:l3kernel} and the package
\pkg{xparse}. \pkg{xparse} is part of the
\bnd{l3packages}~\cite{bnd:l3packages} bundle. \ENdiagram\ also needs
\TikZ~\cite{pkg:pgf} and \pkg{siunitx}~\cite{pkg:siunitx}.

Basic knowledge of \TikZ/pgf is recommended.

\section{Caveat}
This package is in an experimental state.  There is lots of code to clean up
and there are many loose ends to be tied together until I'll be satisfied to
publish this package as stable.  However, as the unofficial release on my blog
has gotten quite some interest\footnote{$\ge 400$ downloads} I decided to
publish this experimental version on the \CTAN{} nonetheless.

If you detect any bugs -- and I guess you will -- please write me a short email
with a \ac{MWE} showing the undesired behaviour or report on issue on
\url{https://www.bitbucket.org/cgnieder/endiagram}.

\section{Setup}

There are two kinds of options: choice options where you can choose one of the
values separated with \code{|}; an underlined value is a default value that is
used, if no value is given.  The others need a value of a certain type like a
number (\meta{num}), arbitrary input (\meta{text}), \TikZ\ options
(\meta{tikz}) \etc.

As a rule commands are only defined inside the \env{endiagram} environment.

Options can also be set up with this command:
\begin{commands}
  \command{ENsetup}[\oarg{module}\marg{options}]
    The setup command.
\end{commands}

\begin{sourcecode}
  \ENsetup{option1 = value1, option2 = value2}
  \ENsetup{module/option = value}
  \ENsetup[module]{option = value}
\end{sourcecode}

Options that belong to a module are specific to a command.  The command
\cs*{command} they belong to can \emph{only} have the options marked with
\module*{command} in his argument \oarg{options}.

All other options can also be set globally as package options.  These are
options which do \emph{not} belong to a module like for example the
\option{draft} option (see page~\pageref{key:debug}):
\begin{sourcecode}
  \usepackage[draft]{endiagram}
\end{sourcecode}

\section{The Curve --  \cs*{ENcurve}}
The potential energy curves are drawn inside the \env{endiagram}
environment using the command \cs{ENcurve}.
\begin{environments}
  \environment{endiagram}[\oarg{options}]
    The basic environment for the potential energy curves
\end{environments}
\begin{commands}
  \command{ENcurve}[\oarg{options}\Marg{\meta{level1},\meta{level2},\meta{level3}}]
    The basic command for drawing the actual curve.
\end{commands}
The command needs a comma separated list of relative energy levels.
\cs{ENcurve}\Marg{1,4,0} means the maximum is four times higher above the end
level than the starting level.

\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

\cs{ENcurve} can read any number of values but needs \emph{at least three}.
Less values will cause an error.
\begin{example}
  \begin{endiagram}
    \ENcurve{1,5,2.5,4,0}
  \end{endiagram}
  \quad
  \begin{endiagram}[scale=.7]
    \ENcurve{1,7,2.5,6,3,4,0}
  \end{endiagram}
\end{example}

\subsection{Properties}
\subsubsection{Scaling}

Values given to \cs{ENcurve} are multiples of \ENdiagram's \ac{su}.  As a default
it is set to \SI{.5}{cm} but can be changed using an option.  There are other ways
to influence the size of the diagram, too.
\begin{options}
 \keyval{unit}{length}\Default{.5cm}
   The standard unit for \cs{ENcurve} and some other commands.  This document
   refers to it with \ac{su}. \label{key:unit}
 \keyval{scale}{factor}\Default{1}
   A scaling factor that allows scaling the diagram.
\end{options}

A changed \ac{su}:
\begin{example}[side-by-side]
  \begin{endiagram}[unit=2em]
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

Scaled by the factor \code{1.5}:
\begin{example}[side-by-side]
  \begin{endiagram}[scale=1.5]
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

\subsubsection{Influencing the position relative to the axes}

The \option{offset} options control the length and position of the horizontal
axis relative to the curve.
\begin{options}
  \keyval{offset}{num}\Default{0}
    \meta{num} is a multiple of the \ac{su} (see page~\pageref{key:unit}).
  \keyval{r-offset}{num}\Default{0}
    \meta{num} is a multiple of the \ac{su}.
  \keyval{l-offset}{num}\Default{0}
    \meta{num} is a multiple of the \ac{su}.
\end{options}

The default behaviour for comparison:
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

\option{l-offset} controls the distance of the start of the $x$ axis to the
start of the curve:
\begin{example}[side-by-side]
  closer to the $y$ axis:\par
  \begin{endiagram}[l-offset=-1]
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

\option{r-offset} controls the ``protruding'' of the $x$ axis after the curve:
\begin{example}[side-by-side]
  $x$ axis extended to the right:\par
  \begin{endiagram}[r-offset=1]
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

\option{offset} changes both values equally:
\begin{example}[side-by-side]
  $x$ extended to the left and the right:\par
  \begin{endiagram}[offset=1]
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

\subsubsection{Increment between the levels}

With the option \option{step} the default increment between the levels can be
changed:
\begin{options}
  \keyval{step}{num}\Module{ENcurve}\Default{2}
    \meta{num} is a multiple of the \ac{su} (see page~\pageref{key:unit}).
\end{options}

\begin{example}
  \begin{endiagram}
    \ENcurve{1,4,0}
  \end{endiagram}
  \quad
  \begin{endiagram}
    \ENcurve[step=3]{1,4,0}
  \end{endiagram}
\end{example}

Sometimes a certain level should be shifted against the others.  This is
possible using an optional argument to the value of that level:
\begin{commands}
  \command{ENcurve}[\Marg{\meta{level}\oarg{offset},...}]
    \meta{offset} is a multiple of the \ac{su} (see page~\pageref{key:unit})
    and is set to \code{0} as default. The level will be shifted to the right
    (positive values) or left (negative values).
\end{commands}
\begin{example}
  \begin{endiagram}
    \ENcurve{1,4,0}
  \end{endiagram}
  \quad
  \begin{endiagram}
    \ENcurve{1,4[.5],0}
  \end{endiagram}
  \quad
  \begin{endiagram}
    \ENcurve{1,4[-.5],0}
  \end{endiagram}
\end{example}

\subsubsection{The shape}

The option \option{looseness} changes the shape of the curve:
\begin{options}
  \keyval{looseness}{value}\Module{ENcurve}\Default{.5}
     should be a number between \code{0} and \code{1}.
\end{options}

\begin{example}
  \begin{endiagram}
    \ENcurve[looseness=0]{0,3,1}
  \end{endiagram}
  \quad
  \begin{endiagram}
    \ENcurve{0,3,1}% corresponds looseness=.5
  \end{endiagram}
  \quad
  \begin{endiagram}
    \ENcurve[looseness=1]{0,3,1}
  \end{endiagram}
\end{example}

\subsubsection{Ending minima}

Sometimes potential energy curves are drawn with local minima at the start and
the end of the cuve.  The option \option{minima} en- or disables them:
\begin{options}
  \keybool{minima}\Module{ENcurve}\Default{false}
    Draw local minima at the ends of the curve.
\end{options}

\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve[minima]{1,4,0}
  \end{endiagram}
\end{example}

\subsubsection{\TikZ{} style}

The style of the curve can be changed using \TikZ{} options:
\begin{options}
  \keyval{tikz}{tikz}\Module{ENcurve}\Default
     Valid are options that can be used with \cs*{draw}.
\end{options}
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve[tikz={red,dotted}]{0,3,1}
  \end{endiagram}
\end{example}

\subsection{The Axes}

There are also possibilities to customize the axes.
\begin{options}
  \keychoice{axes}{xy,y,y-l,y-r,x,all,false}\Default{xy}
    Number and type of axes.
  \keyval{x-axis}{tikz}\Default
    \TikZ{} options to the $x$ axis.
  \keyval{y-axis}{tikz}\Default
    \TikZ{} options to the $y$ axis.
  \keychoice{x-label}{below,right}\Default{below}
    Position of the $x$ axis label.
  \keychoice{y-label}{above,left}\Default{left}
    Position of the $y$ axis label.
  \keyval{x-label-pos}{value}\Default{.5}
    Position of the $x$ axis label when \keyis{x-label}{below} is set.
  \keyval{y-label-pos}{value}\Default{.5}
    Position of the $y$ axis label when \keyis{y-label}{left} is set.
  \keyval{x-label-offset}{length}\Default{0pt}
    Distance between label and $x$ axis.
  \keyval{y-label-offset}{length}\Default{0pt}
    Distance between label and $y$ axis.
  \keyval{x-label-angle}{angle}\Default{0}
    Angle which rotates the $x$ axis label counter clockwise.
  \keyval{y-label-angle}{angle}\Default{0}
    Angle which rotates the $y$ axis label counter clockwise.
  \keyval{x-label-text}{text}\Default{\$\cs*{xi}\$}
    $x$ axis label.
  \keyval{y-label-text}{text}\Default{\$E\$}
   $y$ axis label.
\end{options}

No axes:
\begin{example}[side-by-side]
  \begin{endiagram}[axes=false]
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

All axes:
\begin{example}[side-by-side]
  \begin{endiagram}[axes=all]
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

Only the $x$ axis:
\begin{example}[side-by-side]
  \begin{endiagram}[axes=x]
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

Changed labels:
\begin{example}[side-by-side]
  \begin{endiagram}[x-label-text=\footnotesize reaction coordinate]
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

Different positions of the labels:
\begin{example}
  \begin{endiagram}[
     x-label=right,
     y-label=above]
    \ENcurve{1,4,0}
  \end{endiagram}
  \quad
  \begin{endiagram}[
     x-label-pos=.7,
     y-label-pos=.7,
     y-label-angle=-90,
     y-label-offset=5pt]
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

Crazy setup:
\begin{example}[side-by-side]
  \begin{endiagram}[x-axis={draw=blue,dashed,font=\color{green}}]
    \ENcurve{1,4,0}
  \end{endiagram}
\end{example}

\subsection{Debugging Information}

For precise adjustments of details -- particularly with the options and
commands described in the next sections -- some information is useful that is
hidden normally.  These options enable access:
\begin{options}
  \keybool{debug}\Default{false}
    Enable debug mode of \ENdiagram. \label{key:debug}
  \keybool{draft}\Default{false}
    An alias to \option{debug}.
  \keybool{final}\Default{true}
    The opposite of \option{draft}.
\end{options}

\begin{example}
  \begin{endiagram}[debug]
    \ENcurve{1,4,0}
  \end{endiagram}
  \quad
  \begin{endiagram}[debug,unit=2em]
    \ENcurve[step=3,minima]{1,4,0}
  \end{endiagram}
\end{example}
Shown are a grid, the origin and the coordinates and names of the levels.
Depending on the commands you're using you get more information.  It is
described with the commands they belong to.

\section{The Levels}
\subsection{The \cs*{ShowNiveaus} Command}
The command \cs{ShowNiveaus} draws horizontal lines to the levels:
\begin{commands}
  \command{ShowNiveaus}[\oarg{options}]
    Draw a visual hint of the different niveaus.
\end{commands}

\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowNiveaus
  \end{endiagram}
\end{example}

\subsection{Customization}

A number of options allow fine-tuning:
\begin{options}
  \keyval{length}{num}\Module{ShowNiveaus}\Default{1}
    The length of the lines. \meta{num} is a multiple of the \ac{su} (see
    page~\pageref{key:unit}).
  \keyval{shift}{num}\Module{ShowNiveaus}\Default{0}
    Shift to the right (positive values) or the left (negative values).
    \meta{num} is a multiple of the \ac{su}.
  \keyval{tikz}{tikz}\Module{ShowNiveaus}\Default
    \TikZ options to modify the style of the lines.
\end{options}

Longer lines:
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowNiveaus[length=2]
  \end{endiagram}
\end{example}

Without option \option{shift} the lines are centered to the extrema , \ie,
they protrude by half of the value specified with option \option{length}.
\begin{example}
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowNiveaus[shift=.5]
  \end{endiagram}
  \quad
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowNiveaus[length=2,shift=1]
  \end{endiagram}
\end{example}
Maybe the examples in the next section will make it more clear why option
\option{shift} can be useful.

\subsection{Choose Levels Explicitly}

If you don't want to draw a line to every level you can use this option:
\begin{options}
  \keychoice{niveau}{\Marg{\meta{id1},\meta{id2}}}\Module{ShowNiveaus}
    The \meta{id} is the name of the level as shown by the \option{debug}
    option, see page~\pageref{key:debug}.
\end{options}

The debug information helps in choosing the right level.  The names of the
levels follow the scheme \code{N-\meta{number of curve}-\meta{number of
    level}}.
\begin{example}
  \begin{endiagram}[debug]
    \ENcurve{3,4,0}
  \end{endiagram}
  \quad
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowNiveaus[niveau=N1-2]
  \end{endiagram}
\end{example}

Every level can have a different color, length and shift:
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowNiveaus[length=2,tikz=red,niveau=N1-2]
    \ShowNiveaus[niveau=N1-1,shift=-.5]
    \ShowNiveaus[niveau=N1-3,shift=.5]
  \end{endiagram}
\end{example}

\section{The Energy Gain}
\subsection{The \cs*{ShowGain} Command}

The command \cs{ShowGain} enables you the show the energy gain or loss of the
reaction.  It is always the difference between the first and the last level.
\begin{commands}
  \command{ShowGain}[\oarg{options}]
    Draw a visual hint of the energy gain.
\end{commands}

\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowGain
  \end{endiagram}
\end{example}

\subsection{Customization}

The command has options to modify the appearance.
\begin{options}
  \keyval{tikz}{tikz}\Module{ShowGain}\Default{<->}
    \TikZ{} options for the vertical line.
  \keyval{connect}{tikz}\Module{ShowGain}\Default{dashed,help lines}
    \TikZ{} options for the connecting line.
  \keybool{connect-from-line}\Module{ShowGain}\Default{false}
    The connecting line starts either at the maximum/minimum or at the line
    drawn by \cs{ShowNiveaus}.  This option works with the default values but
    otherwise can lead to unwanted results.  To avoid that you can either set
    \cs{ShowGain} \emph{before} \cs{ShowNiveaus} or you need to choose another
    way.
  \keyval{offset}{num}\Module{ShowGain}\Default{0}
    Shifts the vertical line to the right (positive value) or the left
    (negative value).  \meta{num} is a multiple of \ac{su} (see
    page~\pageref{key:unit}).
  \keychoice{label}{\default{true},false,\meta{text}}\Module{ShowGain}\Default{false}
    Use the default label (\code{true}) or an own label
    (\meta{text}).\label{key:showgain_label}
  \keychoice{label-side}{right,left}\Module{ShowGain}\Default{right}
    The side of the vertical line on which the label should be placed.
  \keyval{label-pos}{<value>}\Module{ShowGain}\Default{.5}
    Position at the line. \code{0} means at the height of $H_1$, \ie, the
    starting level, \code{1} means at the height of $H_2$, \ie, the ending
    level.
  \keyval{label-tikz}{<tikz>}\Module{ShowGain}\Default
    \TikZ{} options for the label.
\end{options}

\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowGain[connect={dotted,red},offset=2]
  \end{endiagram}
\end{example}

Using the \option{label} option:
\begin{example}
  \begin{endiagram}
    \ENcurve{3,4,0}
     \ShowGain[label]
  \end{endiagram}
  \begin{endiagram}
    \ENcurve{0,4,3}
    \ShowGain[label]
  \end{endiagram}
\end{example}

\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowGain[label=exothermic]
  \end{endiagram}
\end{example}

Connecting lines and levels are overlapping:
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowNiveaus
    \ShowGain[connect=red]
  \end{endiagram}
\end{example}

A possible solution:
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowNiveaus
    \ShowGain[connect-from-line,connect=red]
  \end{endiagram}
\end{example}

Better would be to set \cs{ShowNiveaus} \emph{after} \cs{ShowGain},
particularly if you're not using the default settings.
\begin{example}
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowNiveaus[niveau=N1-1]
    \ShowGain[connect={red,dotted}]
  \end{endiagram}
  \begin{endiagram}
    \ENcurve{3,4,0}
    \ShowGain[connect={red,dotted}]
    \ShowNiveaus[niveau=N1-1]
  \end{endiagram}
\end{example}

\subsection{Debugging Information}
Using the \option{debug} option (see page~\pageref{key:debug}) gives you
further information:
\begin{example}[side-by-side]
  \begin{endiagram}[debug]
    \ENcurve{3,4,0}
    \ShowGain
  \end{endiagram}
\end{example}

\section{The Activation Energy}
\subsection{The \cs*{ShowEa} Command}
This command is similar to the commands \cs{ShowNiveaus} and \cs{ShowGain}.
\begin{commands}
  \command{ShowEa}[\oarg{options}]
    Draw a visual hint af the activation energy.
\end{commands}

It enables to show the activation energy:
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{2,4,0}
    \ShowEa
  \end{endiagram}
\end{example}

The default behaviour shows the difference between the \emph{first} maximum
after a \emph{previous} minimum to that minimum:
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{2,0,4}
    \ShowEa
  \end{endiagram}
\end{example}

This also holds if there is more than one maximum.  How you choose a different
one is described in the next section.
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{1,5,2.5,4,0}
    \ShowEa
  \end{endiagram}
\end{example}

\subsection{Choose Level Explicitly}
The default behaviour is all right if there is only one maximum.  If there are
more one might want to choose a different one.  The following options allow
that.
\begin{options}
  \keychoice{max}{first,all}\Module{ShowEa}\Default{first}
    Show the difference to the first maximum or to all maxima.
  \keychoice{from}{\Marg{(\meta{coordinate1})to(\meta{coordinate2})}}\Module{ShowEa}
    Specify the coordinates that should be connected.  You can either use the
    coordinates \code{(\meta{x},\meta{y})} or the name \code{(\meta{name})} of
    the node.
\end{options}

Using \keyis{max}{all}:
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{1,5,2.5,4,0}
    \ShowEa[max=all]
  \end{endiagram}
\end{example}

Since in most cases this won't be what you want you can specify the
coordinates yourself.  The option \option{debug} (see
page~\pageref{key:debug}) may help.
\begin{example}
  \begin{endiagram}[debug]
    \ENcurve{1,5,2.5,4,0}
    \ShowEa
  \end{endiagram}
  \quad
   \begin{endiagram}
    \ENcurve{1,5,2.5,4,0}
    \ShowEa[from={(0,1) to (6,4)}]
  \end{endiagram}

  \begin{endiagram}
    \ENcurve{1,5,2.5,4,0}
    \ShowEa[from={(N1-1) to (N1-3)}]
  \end{endiagram}
  \quad
  \begin{endiagram}
    \ENcurve{1,5,2.5,4,0}
    \ShowEa[from={(N1-5) to (N1-4)}]
  \end{endiagram}
\end{example}
In every case the position of the vertical line is determined by the \emph{first}
coordinate.

\subsection{Customization}
Again there are a number of options to customize the appearance.
\begin{options}
  \keyval{tikz}{tikz}\Module{ShowEa}\Default{<->}
    \TikZ{} options for the vertical line.
  \keyval{connect}{tikz}\Module{ShowEa}\Default{dashed,help lines}
    \TikZ{} options for the horizontal line.
  \keychoice{label}{\default{true},false,\meta{text}}\Module{ShowEa}\Default{false}
    Use the default label ($E_{\mathrm{a}}$) or an own
    label.\label{key:showea_label}
  \keychoice{label-side}{right,left}\Module{ShowEa}\Default{right}
    The side of the vertical line where the label should appear.
  \keyval{label-pos}{value}\Module{ShowEa}\Default{.5}
    Determines the vertical position of the label relative to the vertical line.
    \code{0} means at the lower end, \code{1} means at the upper end.
  \keyval{label-tikz}{tikz}\Module{ShowEa}\Default
    \TikZ options for the label.
\end{options}

\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve[step=4]{1,6,0}
    \ShowEa[label,label-pos=.3]
  \end{endiagram}
\end{example}

\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve{1,5,2.5,4,0}
    \ShowEa[
      from    = {(N1-1) to (N1-3)},
      connect = {draw=none},
      label   = endoth.]
    \ShowEa[
      from  = (N1-3) to (N1-5),
      label = exoth.,
      label-pos = .7]
    \ShowGain[label=exoth.] 
  \end{endiagram}
\end{example}

\subsection{Debugging Information}
The \option{debug} option gives you further information.
\begin{example}
  \begin{endiagram}[debug]
    \ENcurve{1,5,2,3,0}
    \ShowEa[max=all]
  \end{endiagram}
  \quad
  \begin{endiagram}[debug]
    \ENcurve{1,5,2,3,0}
    \ShowEa[from={(0,1) to (6,3)}]
  \end{endiagram}
\end{example}

\section{Several Curves in one Diagram}
It's easy to draw several curves.  You only need to use \cs{ENcurve} more than
once.
\begin{example}
  \begin{endiagram}
    \ENcurve[tikz=blue]{1,4,0}
    \ENcurve[tikz=red]{1,2.5,0}
    \draw[blue] (5,5) -- ++(1,0) node[black,right] {without enzyme};
    \draw[red] (5,4) -- ++(1,0) node[black,right] {with enzyme};
  \end{endiagram}
\end{example}

The commands \cs{ShowNiveaus}, \cs{ShowGain} and \cs{ShowEa} always relate to
the curve set at last.  This means you can use them selectively.
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve[tikz=blue]{1,4,0}
    \ShowEa[tikz={blue,<->}]
    \ENcurve[tikz=red]{1,2.5,0}
  \end{endiagram}

  \begin{endiagram}
    \ENcurve[tikz=blue]{1,4,0}
    \ENcurve[tikz=red]{1,2.5,0}
    \ShowEa[tikz={red,<->}]
  \end{endiagram}
\end{example}

Using more than one curves explains the multiple numbering of the level names:
\begin{example}[side-by-side]
  % the names of the levels (N1-1)
  % and (N1-3) are hidden behind
  % (N2-1) and (N2-3), resp.
  \begin{endiagram}[debug]
    \ENcurve{1,4,0}
    \ENcurve{1,2.5,0}
  \end{endiagram}

  \begin{endiagram}
    \ENcurve[tikz=blue]{1,4,0}
    \ENcurve[tikz=red]{1,2.5,0}
    \draw[<->] (N1-2) -- (N2-2) ;
  \end{endiagram}
\end{example}

Of course it's possible to choose different options for different curves.
This means you can use curves with a different number of maxima.
\begin{example}[side-by-side]
  \begin{endiagram}
    \ENcurve[step=4]{1,6,0}
    \ENcurve[
      tikz={densely dotted}]
     {1,4[1],2.5,3[-1],0}
  \end{endiagram}
\end{example}

\section{Usage of \TikZ}
Since the \env{endiagram} environment only is a \env*{tikzpicture} environment
(well, more or less) you can use \TikZ{} commands inside it.  This means you
can easily add additional information to the diagram.
\begin{example}
  % needs the package `chemmacros'
  \begin{endiagram}
    \ENcurve{1,5,2,3,0}
    \ShowNiveaus[length=2,niveau={N1-2,N1-3,N1-4}]
    \node[above,xshift=4pt] at (N1-2) {[\"UZ1]$^{\transitionstatesymbol}$} ;
    \node[below] at (N1-3) {ZZ} ;
    \node[above,xshift=4pt] at (N1-4) {[\"UZ2]$^{\transitionstatesymbol}$} ;
  \end{endiagram}
  \quad
  \begin{endiagram}
    \ENcurve{2,3,0}
    \draw[<-,red] (N1-2) -- ++(2,1) node[right] {transition state} ;
  \end{endiagram}
\end{example}

\subsection{The Origin}
The nodes \code{(origin-l)} and \code{(origin-r)} are set at the end of the
environment.  This means they are \emph{not} available inside the
\env{endiagram} environment.  If you want to use them you either need to look
up their coordinates using the \option{debug} option (see
page~\pageref{key:debug}) \ldots

\begin{example}
  \begin{endiagram}[y-label=above]
    \ENcurve{1,3[.5],0}
    \draw[dashed,help lines]
      (N1-2) -- (N1-2 -| -1.5,-1)
      node[left,black] {max} ;
  \end{endiagram}
\end{example}
\ldots\ or use this option:
\begin{options}
  \keyval{tikz}{tikz}\Default
    \TikZ{} options for the \env{endiagram} environment.
\end{options}
With it you can pass arbitrary \TikZ{} options to the internal \code{tikzpicture}
environment.
\begin{example}[side-by-side]
  \begin{endiagram}[
      y-label = above,
      tikz    = {remember picture}]
    \ENcurve{1,3[.5],0}
  \end{endiagram}
  \tikz[remember picture,overlay]{
    \draw[dashed,help lines]
      (N1-2) -- (N1-2 -| origin-l)
      node[left,black] {max} ;
  }
\end{example}

There is an easier way, though: you can use the following command \emph{after}
drawing all curves:
\begin{commands}
  \command{MakeOrigin}
    Helper command to make the origin of the coordinate system
    known.\label{cmd:makeorigin}
\end{commands}

\begin{example}[side-by-side]
  \begin{endiagram}[y-label = above]
    \ENcurve{1,3[.5],0}
    \MakeOrigin
    \draw[dashed,help lines]
      (N1-2) -- (N1-2 -| origin-l)
      node[left,black] {max} ;
  \end{endiagram}
\end{example}

\section{Axes Ticks and Labels}
\subsection{Automatic Ticks}

The $y$ axes can get ticks automatically.
\begin{options}
  \keychoice{ticks}{y,\default{y-l},y-r,none}\Default{none}
    Adds ticks to the specified axes.
  \keyval{ticks-step}{num}\Default{1}
    \meta{num} is a multiple of the \ac{su}. \keyis{ticks-step}{2} means that
    only every second tick is added.
\end{options}
\ENsetup{
  AddAxisLabel/font=\libertineLF
}

\begin{example}
  \ENsetup{ticks,y-label=above}
  \begin{endiagram}
    \ENcurve{1,5,2.5,4,0}
  \end{endiagram}
  \quad
  \begin{endiagram}[ticks-step=2]
    \ENcurve{1,5,2.5,4,0}
  \end{endiagram}
\end{example}
These ticks obey the \option{energy-unit} option, see
section~\ref{sec:reale_werte}.

\subsection{The \cs*{AddAxisLabel} Command}
% TODO auf Unterschied zwischen den Ticks produziert durch AddAxisLabel und
% Option ticks hinweisen
To be able to add labels to the ticks there is the command
\begin{commands}
  \command{AddAxisLabel}[\oarg{options}\Marg{(\meta{point1})[\meta{opt.\@
      label}];(\meta{point2});...}]
    Add axis labels to points.
  \command{AddAxisLabel}[\sarg\oarg{options}\Marg{\meta{level1}[\meta{opt.\@
      label}];\meta{level2};...}]
    Add axis labels to levels.
\end{commands}
As you can see there are two variants.  The first one awaits a list of
coordinates in the \TikZ{} sense.  The second awaits $y$ values.  Every of
these values has an optional argument with which you can specify the label.

The first variant also draws lines between the points specifiad and the $y$
axis.  Internally this command calls \cs{MakeOrigin}, see
page~\pageref{cmd:makeorigin}, which means it should be used \emph{after}
drawing all curves.

Example for the second variant:
\begin{example}
  \begin{endiagram}[y-label=above]
    \ENcurve{1,3,2}
    \AddAxisLabel*{1;2;3}
  \end{endiagram}
  \begin{endiagram}[y-label=above]
    \ENcurve{1,3,2}
    \AddAxisLabel*{1[10];2[20];3[30]}
  \end{endiagram}
\end{example}

Example for the first variant:
\begin{example}[side-by-side]
  \begin{endiagram}[y-label=above]
    \ENcurve{1,3,2}
    \AddAxisLabel{(N1-1)[$H_1$];(N1-3)[$H_2$]}
  \end{endiagram}
\end{example}

The optional arguments can also get \TikZ{} options. The description should read:
\begin{commands}
  \command{AddAxisLabel}[\oarg{options}\Marg{(\meta{point1})[\meta{opt.\@
      label},\meta{tikz}];(\meta{point2});...}]
    Add axis labels to points.
  \command{AddAxisLabel}[\sarg\oarg{options}\Marg{\meta{level1}[\meta{opt.\@
      label},\meta{tikz}];\meta{level2};...}]
    Add axis labels to levels.
\end{commands}

\begin{example}
  \begin{endiagram}[y-label=above]
    \ENcurve{1,3,2}
    \AddAxisLabel*{1[10];2[20,{draw,fill=green!15}];3[30]}
  \end{endiagram}
  \begin{endiagram}[y-label=above]
    \ENcurve{1,3,2}
    \AddAxisLabel{(N1-1)[$H_1$];(N1-3)[$H_2$,{draw,font=\color{red},fill=green!15}]}
  \end{endiagram}
\end{example}

\subsection{Customization}

You have several options to customize the labels:
\begin{options}
  \keychoice{axis}{y-l,y-r,x}\Module{AddAxisLabel}\Default{y-l}
    Choose which axis gets the labels.
  \keyval{connect}{tikz}\Module{AddAxisLabel}\Default{dashed,help lines}
    Change the style of the lines.
  \keyval{font}{commands}\Module{AddAxisLabel}\Default
    You can add commands like \cs*{footnotesize} and/or \cs*{color}\Marg{red}
    to format the label text.
\end{options}

\begin{example}
  \begin{endiagram}[y-label=above]
    \ENcurve{1,3,2}
    \AddAxisLabel{(2,3)[\"UZ]}
  \end{endiagram}
  \begin{endiagram}[y-label=above,x-label=right]
    \ENcurve{1,3,2}
    \AddAxisLabel[axis=x,connect=dotted]{(2,3)[\"UZ]}
  \end{endiagram}
  \begin{endiagram}[axes=all,y-label=above]
    \ENcurve{1,3,2}
    \AddAxisLabel[axis=y-r,connect=red]{(2,3)[\"UZ]}
  \end{endiagram}
\end{example}

\section{Actual Values}\label{sec:reale_werte}
\subsection{The Basics}

If you want to have a more quantitative diagram or use actual values for the
energies you can use these options:
\begin{options}
  \keyval{energy-unit}{unit}\Default
    The unit of the energy scale.  A unit in the \pkg{siunitx} sense.
  \keyval{energy-step}{num}\Default{1}
    Determines which increment on the energy scale corresponds to the
    \ac{su}.
  \keyval{energy-zero}{num}\Default{0}
    Shifts the origin of the energy scale by \meta{num} in multiples of the
    energy scale.
  \keyval{energy-unit-separator}{anything}\Default{/}
    Separates the $y$ axes label from the unit.
  \keyval{energy-round}{num}\Default{3}
    Rounds the value to this number of figures.
  % \keybool{energy-round-places}\Default{false}
  %   Switch rounding mode to places.
\end{options}
Choosing a unit will add ticks and labels to the $y$ axis automatically and has
an impact on the commands \cs{ShowGain} and \cs{ShowEa}, see
section~\ref{ssec:real_einfluss}.

\begin{example}
  \begin{endiagram}[ticks,y-label=above,energy-step=10]
    \ENcurve{1,3,2}
  \end{endiagram}
  \begin{endiagram}[y-label=above,energy-step=10,energy-zero=30]
    \ENcurve{1,3,2}
    \AddAxisLabel*{1;2;3}
  \end{endiagram}
\end{example}

\begin{example}
  \begin{endiagram}[
      y-label=above,
      energy-step=15,
      energy-zero=30,
      energy-unit=\kilo\joule]
    \ENcurve{1,3,2}
    \AddAxisLabel*{1;2;3}
  \end{endiagram}
  \begin{endiagram}[
      y-label=above,
      energy-step=10,
      energy-unit=\kilo\joule,
      energy-unit-separator={ in }]
    \ENcurve{1,3,2}
    \AddAxisLabel*{1;2;3}
  \end{endiagram}
\end{example}

\begin{example}
  \ENsetup{
    energy-unit=kJ,
    energy-step=10,
    energy-zero=.613,
    y-label-offset=20pt
  }
  \begin{endiagram}
    \ENcurve{1.0613,4.3465,2.9876}
    \ShowGain[label]
  \end{endiagram}
\end{example}
  % \begin{endiagram}% [energy-round-places]
  %   \ENcurve{1.0613,4.3465,2.9876}
  %   \ShowGain[label]
  % \end{endiagram}

\subsection{Impact on Other Commands}\label{ssec:real_einfluss}

Using the option \option{energy-unit} changes the default labels of
\cs{ShowGain} and \cs{ShowEa}.  Now an actual value is shown:
\begin{example}
  % uses \DeclareSIUnit{\calory}{cal}
  \sisetup{per-mode = fraction}
  \ENsetup{
    energy-step           = 100,
    energy-unit           = \kilo\calory\per\mole,
    energy-unit-separator = { in },
    y-label               = above,
    AddAxisLabel/font     = \libertineLF\footnotesize
  }
  \begin{endiagram}[scale=1.5]
    \ENcurve{2.232,4.174,.308}
    \AddAxisLabel*{0;1;2;3;4}
    \ShowEa[label,connect={draw=none}]
    \ShowGain[label]
  \end{endiagram}
\end{example}

This behaviour can be switched off, though:
\begin{options}
  \keybool{calculate}\Default{true}
  Switch the calculating of activation energy and energy gain on or off.
\end{options}
\begin{example}
  % uses \DeclareSIUnit{\calory}{cal}
  \sisetup{per-mode = fraction}
  \ENsetup{
    energy-step           = 100,
    energy-unit           = \kilo\calory\per\mole,
    energy-unit-separator = { in },
    y-label               = above,
    AddAxisLabel/font     = \footnotesize,
  }
  \begin{endiagram}[scale=1.5,calculate=false]
    \ENcurve{2.232,4.174,.308}
    \AddAxisLabel*{0;1;2;3;4}
    \ShowEa[label,connect={draw=none}]
    \ShowGain[label]
  \end{endiagram}
\end{example}

\section{Example}

The illustration of the Bell-Evans-Polanyi principle
(figure~\ref{fig:bell-evans-polanyi}) serves as an example for a more complex
usage. One reaction is coloured as it an exception to the principle. The
figure is a reproduction of a similar figure in~\cite{brueckner}.

\begin{sourcecode}
  % uses the packages `chemmacros', `chemfig' and `libertine'
  \setatomsep{1.5em}
  \DeclareChemIUPAC\iso{\textit{i}}
  \chemsetup[chemformula]{format=\libertineLF}
  \ENsetup{
    ENcurve/minima,
    AddAxisLabel/font=\libertineLF\footnotesize
  }
  \begin{endiagram}[
     tikz         = {yscale=1.5}, scale        = 1.7,
     y-label      = above,        y-label-text = $\Delta H$,
     x-label      = right,        x-label-text = RK,
     energy-step  = 10]
    \ENcurve{0,3.5,1}
    \ENcurve[tikz=red]{0,3.7,.4}
    \ENcurve{0,4.3[.2],2.4}
    \ENcurve{0,4.7[.3],2.7}
    \ENcurve{0,4.9[.35],2.9}
    \ENcurve{0,5.2[.4],3.3}
    \AddAxisLabel*{1;2;3;4;6}
    \AddAxisLabel{
      (N1-1)[0]; (N1-2)[35]; (N2-2)[37]; (N3-2)[43]; (N4-2)[47]; (N5-2)[49];
      (N6-2)[52]
    }
    \draw[right] (N1-3) ++ (1,0)
      node {\small \ch{2 "\chemfig{=_[:30]-[::-60]\lewis{0.,}}~" + N2} } ;
    \draw[right,red] (N2-3) ++ (1,-.3)
      node {\small \ch{2 "\chemfig{[:-60]*6(=-=-(-\lewis{0.,})=-)}~" + N2} } ;
    \draw[right] (N3-3) ++ (1,-.2)
      node {\small \ch{2 "\tert-\lewis{0.,Bu}~" + N2} } ;
    \draw[right] (N4-3) ++ (1,-.1)
      node {\small \ch{2 "\iso-\lewis{0.,Pr}~" + N2} } ;
    \draw[right] (N5-3) ++ (1,0)
      node {\small \ch{2 "\lewis{0.,Et}~" + N2} } ;
    \draw[right] (N6-3) ++ (1,0)
      node {\small \ch{2 "\lewis{0.,Me}~" + N2} } ;
    \draw[above,font=\fontfamily{fxlf}\selectfont\footnotesize]
     (N1-3) node {10} (N2-3) node[red] {4}
     (N3-3) node {24} (N4-3) node {27}
     (N5-3) node {29} (N6-3) node {33} ;
  \end{endiagram}

  \setatomsep{2em}
  \schemestart
    \chemfig{R-[:30]N=N-[:30]R}
    \arrow{->[$\Delta$]}[,2.1]
    \ch{2 "\lewis{0.,R}~" + N2}
  \schemestop
\end{sourcecode}

\begin{figure}
  \centering
  \centering
  \setatomsep{1.5em}
  \DeclareChemIUPAC\iso{\textit{i}}
  \chemsetup[chemformula]{format=\libertineLF}
  \ENsetup{
    ENcurve/minima,
    AddAxisLabel/font=\libertineLF\footnotesize
  }
  \begin{endiagram}[
     tikz         = {yscale=1.5}, scale        = 1.7,
     y-label      = above,        y-label-text = $\Delta H$,
     x-label      = right,        x-label-text = RK,
     energy-step  = 10]
    \ENcurve{0,3.5,1}
    \ENcurve[tikz=red]{0,3.7,.4}
    \ENcurve{0,4.3[.2],2.4}
    \ENcurve{0,4.7[.3],2.7}
    \ENcurve{0,4.9[.35],2.9}
    \ENcurve{0,5.2[.4],3.3}
    \AddAxisLabel*{1;2;3;4;6}
    \AddAxisLabel{
      (N1-1)[0]; (N1-2)[35]; (N2-2)[37]; (N3-2)[43]; (N4-2)[47]; (N5-2)[49];
      (N6-2)[52]
    }
    \draw[right] (N1-3) ++ (1,0)
      node {\small \ch{2 "\chemfig{=_[:30]-[::-60]\lewis{0.,}}~" + N2} } ;
    \draw[right,red] (N2-3) ++ (1,-.3)
      node {\small \ch{2 "\chemfig{[:-60]*6(=-=-(-\lewis{0.,})=-)}~" + N2} } ;
    \draw[right] (N3-3) ++ (1,-.2)
      node {\small \ch{2 "\tert-\lewis{0.,Bu}~" + N2} } ;
    \draw[right] (N4-3) ++ (1,-.1)
      node {\small \ch{2 "\iso-\lewis{0.,Pr}~" + N2} } ;
    \draw[right] (N5-3) ++ (1,0)
      node {\small \ch{2 "\lewis{0.,Et}~" + N2} } ;
    \draw[right] (N6-3) ++ (1,0)
      node {\small \ch{2 "\lewis{0.,Me}~" + N2} } ;
    \draw[above,font=\fontfamily{fxlf}\selectfont\footnotesize]
     (N1-3) node {10} (N2-3) node[red] {4}
     (N3-3) node {24} (N4-3) node {27}
     (N5-3) node {29} (N6-3) node {33} ;
  \end{endiagram}

  \setatomsep{2em}
  \schemestart
    \chemfig{R-[:30]N=N-[:30]R}
    \arrow{->[$\Delta$]}[,2.1]
    \ch{2 "\lewis{0.,R}~" + N2}
  \schemestop
  \caption{\label{fig:bell-evans-polanyi}Enthalpie-Entwicklung
    entlang der Reaktionskoordinate bei einer Serie von Thermolysen
    aliphatischer Azoverbindungen.  Alle Thermolysen dieser Serie -- mit
    Ausnahme der farbig hervorgehobenen -- folgen dem
    Bell-Evans-Polanyi-Prinzip~\cite{brueckner}.}
\end{figure}

\end{document}


\end{document}