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author | Norbert Preining <norbert@preining.info> | 2019-09-02 13:46:59 +0900 |
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committer | Norbert Preining <norbert@preining.info> | 2019-09-02 13:46:59 +0900 |
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tree | 60335e10d2f4354b0674ec22d7b53f0f8abee672 /macros/latex/contrib/endiagram/endiagram_en.tex |
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diff --git a/macros/latex/contrib/endiagram/endiagram_en.tex b/macros/latex/contrib/endiagram/endiagram_en.tex new file mode 100644 index 0000000000..74be547af9 --- /dev/null +++ b/macros/latex/contrib/endiagram/endiagram_en.tex @@ -0,0 +1,1306 @@ +% 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} |