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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/modiagram/modiagram_en.tex |
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diff --git a/macros/latex/contrib/modiagram/modiagram_en.tex b/macros/latex/contrib/modiagram/modiagram_en.tex new file mode 100644 index 0000000000..3d5cc900ed --- /dev/null +++ b/macros/latex/contrib/modiagram/modiagram_en.tex @@ -0,0 +1,1282 @@ +% arara: pdflatex +% arara: pdflatex +% -------------------------------------------------------------------------- +% the MODIAGRAM package +% +% easy creation of molecular orbital diagrams +% +% -------------------------------------------------------------------------- +% Clemens Niederberger +% Web: https://www.bitbucket.org/cgnieder/modiagram +% E-Mail: contact@mychemistry.eu +% -------------------------------------------------------------------------- +% If you have any ideas, questions, suggestions or bugs to report, please +% feel free to contact me. +% -------------------------------------------------------------------------- +% Copyright 2011--2015 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 modiagram.sty, modiagram_en.tex, +% README and the derived file modiagram_en.pdf. +% -------------------------------------------------------------------------- +\documentclass[load-preamble+]{cnltx-doc} +\usepackage[utf8]{inputenc} +\usepackage{modiagram} + +\setcnltx{ + package = modiagram , + authors = Clemens Niederberger , + email = contact@mychemistry.eu , + url = https://bitbucket.org/cgnieder/modiagram/ , + add-cmds = { + AO, + atom, + connect, + EnergyAxis, + molecule, + MOsetup + } , + add-envs = { MOdiagram } , + add-silent-cmds = { + ch, + draw, + chlewis, + node, + textcolor, + chemsigma, + chemSigma + } , + abstract = {% + \begin{MOdiagram}[style=fancy,distance=7cm,AO-width=15pt,labels,names] + \atom[N]{left}{ 2p = {0;up,up,up} } + \atom[O]{right}{ 2p = {2;pair,up,up} } + \molecule[NO]{ + 2pMO = {1.8,.4;pair,pair,pair,up}, + color = { 2piy*=red } + } + \end{MOdiagram} + } +} + +\defbibheading{bibliography}{\addsec{References}} + +\usepackage{booktabs} + +\usepackage{acro} +\DeclareAcronym{AO}{ + short = AO , + long = atomic orbital +} +\DeclareAcronym{MO}{ + short = MO , + long = molecular orbital +} + +\expandafter\def\csname libertine@figurestyle\endcsname{LF} +\usepackage[libertine]{newtxmath} +\expandafter\def\csname libertine@figurestyle\endcsname{OsF} + +\usepackage{chemmacros,chemformula} +\chemsetup{ + greek = newtx, + modules = units +} +\setchemformula{format=\libertineLF} + +\NewDocumentCommand \AOinline { o m } + {% + \begingroup + \IfNoValueTF{#1} + {\MOsetup{ style=square,AO-width=8pt }}% + {\MOsetup{ style=square,AO-width=8pt , #1 }}% + \begin{MOdiagram} + \AO{s}{0;#2} + \end{MOdiagram}% + \endgroup + } + +\newcommand*\TikZ{Ti\textit{k}Z} + +\begin{document} + +\section{Licence, Requirements} +\license + +\modiagram\ uses \bnd{l3kernel}~\cite{bnd:l3kernel} and +\bnd{l3packages}~\cite{bnd:l3packages}. It also uses \TikZ~\cite{pkg:pgf} and +the package \pkg{chemgreek}~\cite{pkg:chemgreek} bundle. Additionally the +\TikZ\ libraries \code{calc} and \code{arrows} are loaded. Knowledge of +\TikZ\ is helpful. + +\section{Motivation} +This package has been written as a reaction to a question on +\url{http://tex.stackexchange.com/}. To be more precise: as a reaction to the +question +``\href{http://tex.stackexchange.com/questions/13863/molecular-orbital-diagrams-in-latex}% +{Molecular orbital diagrams in LaTeX}.'' There it says +\begin{cnltxquote} + I'm wondering if anyone has seen a package for drawing (qualitative) + molecular orbital splitting diagrams in \LaTeX? Or if there exist any + packages that can be easily re-purposed to this task? + + Otherwise, I think I'll have a go at it in \TikZ. +\end{cnltxquote} +The problem was solved using \TikZ, since no package existed for that purpose. +For one thing \modiagram\ is intended to fill this gap. I also found it very +tedious, to make all this copying and pasting when I needed a second, third, +\ldots\ diagram. \modiagram\ took care of that. + + +\section{Main Commands} +All molecular orbital (MO) diagrams are created using the environment +\env{MOdiagram}{}. + +\subsection{The \cs*{atom} Command} +\begin{commands} + \command{atom}[\oarg{name}\Marg{\meta{left}|\meta{right}}\marg{AO-spec}] + Place an \acs{AO} in the diagram. \meta{name} is caption of the atom, + \meta{left} and \meta{right} determine the placement in the diagram, + \meta{AO-spec} is the specification of the \ac{AO}. +\end{commands} + +Let's take a look at an example: +\begin{example}[side-by-side] + \begin{MOdiagram} + \atom{right}{ + 1s = { 0; pair} , + 2s = { 1; pair} , + 2p = {1.5; up, down } + } + \end{MOdiagram} +\end{example} + +As you can see, the argument \meta{AO-spec} is essential to create the actual +orbitals and the electrons within. You can use these key/value pairs to specify +what you need: +\begin{options} + \keychoice{1s}{\{\meta{rel-energy}; \meta{el-spec}\}} + Energy level and electron specifications for the 1s orbital. + \keychoice{2s}{\{\meta{rel-energy}; \meta{el-spec}\}} + Energy level and electron specifications for the 2s orbital. + \keychoice{2p}{\{\meta{rel-energy}; \meta{x el-spec}{,} \meta{y el-spec}{,} + \meta{z el-spec}\}} + Energy level and electron specifications for the 2p orbitals. +\end{options} +\meta{el-spec} can have the values \code{pair}, \code{up} and \code{down} or +can be left empty. \meta{rel-energy} actually is the $y$ coordinate and shifts +the \ac{AO} vertically by \meta{rel-energy} \si{\centi\metre}. + +The argument \meta{left}/\meta{right} is important, when p~orbitals are used. +For instance compare the following example to the one before: +\begin{example}[side-by-side] + \begin{MOdiagram} + \atom{left}{ + 1s = { 0; pair} , + 2s = { 1; pair} , + 2p = {1.5; up, down } + } + \end{MOdiagram} +\end{example} + +When both variants are used one can also see, that the right atom is shifted to +the right (hence the naming). The right atom is shifted by \SI{4}{\centi\metre} +per default and can be adjusted individually, see page~\pageref{option:distance}. +\begin{example} + \begin{MOdiagram} + \atom{left}{ + 1s = { 0; pair} , + 2s = { 1; pair} , + 2p = {1.5; up, down } + } + \atom{right}{ + 1s = { 0; pair} , + 2s = { 1; pair} , + 2p = {1.5; up, down } + } + \end{MOdiagram} +\end{example} +With the command \cs{molecule} (section~\ref{ssec:molecule}) the reason for the +shift becomes clear. + +Any of the arguments for the \ac{AO} can be left empty or be omitted. +\begin{example}[side-by-side] + Without argument: default height, full:\par + \begin{MOdiagram} + \atom{left}{1s, 2s, 2p} + \end{MOdiagram} +\end{example} + +\begin{example}[side-by-side] + empty argument: default height, empty:\par + \begin{MOdiagram} + \atom{left}{1s=, 2s=, 2p=} + \end{MOdiagram} +\end{example} + +\begin{example}[side-by-side] + using some values:\par + \begin{MOdiagram} + \atom{left}{1s, 2s=1, 2p={;,up} } + \end{MOdiagram} +\end{example} + +\subsection{The \cs*{molecule} Command}\label{ssec:molecule} +\begin{commands} + \command{molecule}[\oarg{name}\marg{MO-spec}] + Place a \acs{MO} in the diagram. \meta{name} is caption of the molecule, + \meta{MO-spec} is the specification of the \ac{MO}. +\end{commands} + +An example first: +\begin{example}[side-by-side] + \begin{MOdiagram} + \atom{left} { 1s = { 0; up } } + \atom{right}{ 1s = { 0; up } } + \molecule { 1sMO = {.75; pair } } + \end{MOdiagram} +\end{example} +The command \cs{molecule} connects the \acp{AO} with the bonding and +anti-bondung \acp{MO}. \cs{molecule} can only be used \emph{after} one has +set \emph{both} atoms since the orbitals that are to be connected must be +known. + +The argument \meta{MO-spec} accepts a comma separated list of key/value pairs: +\begin{options} + \keychoice{1sMO}{\{\meta{energy gain}/\meta{energy loss}; \meta{s + el-spec}{,} \meta{s* el-spec}\}} + connects the \acp{AO} specified by \option{1s}. + \keychoice{2sMO}{\{\meta{energy gain}/\meta{energy loss}; \meta{s + el-spec}{,} \meta{s* el-spec}\}} + connects the \acp{AO} specified by \option{2s} + \keychoice{2pMO}{\{\meta{s energy gain}/\meta{s energy loss}{,} \meta{p + energy gain}/\meta{p energy loss}; \meta{s el-spec}{,} \meta{py + el-spec}{,} \meta{pz el- spec}{,} \meta{py* el-spec}{,} \meta{pz* + el-spec}{,} \meta{s* el-spec}\}} + connects the \acp{AO} specified by \option{2p}. +\end{options} + +Obviously the regarding \acp{AO} must have been set in order to connect them. +This for example won't work: +\begin{sourcecode} + \begin{MOdiagram} + \atom{left} { 1s = 0 } + \atom{right}{ 1s = 0 } + \molecule { 2sMO = .75 } + \end{MOdiagram} +\end{sourcecode} +The value used in \meta{energy gain} determines how many \si{\centi\metre} the +bonding \ac{MO} lies below the lower \ac{AO} or how many \si{\centi\metre} the +anti-bondung \ac{MO} lies above the higher \ac{AO}. + +\begin{example}[side-by-side] + same level:\par + \begin{MOdiagram} + \atom{left} { 1s = { 0; up } } + \atom{right}{ 1s = { 0; up } } + \molecule { 1sMO = {.75; pair } } + \end{MOdiagram} + + different levels:\par + \begin{MOdiagram} + \atom{left} { 1s = { 0; up } } + \atom{right}{ 1s = { 1; up } } + \molecule { 1sMO = {.25; pair } } + \end{MOdiagram} +\end{example} + +If you specify \meta{energy loss} you can create non-symmetrical splittings. +Then, the first value (\meta{energy gain}) is used for the bonding \ac{MO} and +the second value (\meta{energy loss}) is used for the anti-bonding \ac{MO}. +\begin{example}[side-by-side] + \begin{MOdiagram} + \atom{left} { 1s = { 0; up } } + \atom{right}{ 1s = { 0; up } } + \molecule { 1sMO = {.75/.25; pair } } + \end{MOdiagram} + + \begin{MOdiagram} + \atom{left} { 1s = { 0; up } } + \atom{right}{ 1s = { 1; up } } + \molecule { 1sMO = {.25/.75; pair } } + \end{MOdiagram} +\end{example} + +Please be aware, that you have to specify \emph{two} such values or pairs with +\option{2pMO}: the splitting of the \chemsigma\ orbitals and the splitting of +the \chempi\ orbitals. +\begin{example} + \begin{MOdiagram} + \atom{left} { 2p = { 0; up, up } } + \atom{right}{ 2p = { 1; up, up } } + \molecule { 2pMO = { 1.5, .75; pair, up, up } } + \end{MOdiagram} +\end{example} + +The complete \ac{MO} diagram for triplett dioxygen now could look something +like that: +\begin{example} + \begin{MOdiagram} + \atom{left}{ + 1s, 2s, 2p = {;pair,up,up} + } + \atom{right}{ + 1s, 2s, 2p = {;pair,up,up} + } + \molecule{ + 1sMO, 2sMO, 2pMO = {;pair,pair,pair,up,up} + } + \end{MOdiagram} +\end{example} + +\subsection{The Naming Scheme}\label{Namensgebung} +Since one wants to be able to put labels to the orbitals and since they are +nodes in a \env*{tikzpicture}, the internal naming scheme is important. It +closely follows the function: +\begin{center} + \begin{MOdiagram}[ + distance = 6cm, + AO-width = 20pt, + labels-fs = \ttfamily\footnotesize, + labels-style = {yshift=10pt} + ] + \atom{left}{ + 1s = 0 , + 2s = 2 , + 2p = 5 , + label = { + 1sleft = {1sleft} , + 2sleft = {2sleft} , + 2pxleft = {2pxleft} , + 2pyleft = {2pyleft} , + 2pzleft = {2pzleft} + } + } + \atom{right}{ + 1s = 0 , + 2s = 2 , + 2p = 5 , + label = { + 1sright = {1sright} , + 2sright = {2sright} , + 2pxright = {2pxright} , + 2pyright = {2pyright} , + 2pzright = {2pzright} + } + } + \molecule{ + 1sMO = .5 , + 2sMO = .5 , + 2pMO = {1.5,.5} , + label = { + 1sigma = {1sigma} , + 1sigma* = {1sigma*} , + 2sigma = {2sigma} , + 2sigma* = {2sigma*} , + 2psigma = {2psigma} , + 2psigma* = {2psigma*} , + 2piy = {2piy} , + 2piy* = {2piy*} , + 2piz = {2piz} , + 2piz* = {2piz*} + } + } + \end{MOdiagram} +\end{center} + +With these names it is possible to reference the orbitals with the known \TikZ +commands: +\begin{example}[side-by-side] + \begin{MOdiagram} + \atom{left} { 1s = 0 } + \atom{right}{ 1s = 0 } + \molecule { 1sMO = .75 } + \draw[<->,red,semithick] + (1sigma.center) -- (1sigma*.center) ; + \draw[red] + (1sigma*) ++ (2cm,.5cm) node {splitting} ; + \end{MOdiagram} +\end{example} + +\begin{example} + \begin{MOdiagram} + \atom{left} { 1s = 0 } + \atom{right}{ 1s = 0 } + \molecule { 1sMO = .75 } + \draw[draw=blue,very thick,fill=blue!40,opacity=.5] + (1sigma*) circle (8pt); + \draw[<-,shorten <=8pt,shorten >=15pt,blue] + (1sigma*) --++(2,1) node {anti-bonding MO}; + \end{MOdiagram} +\end{example} + +\subsection{Placing AOs and MOs Arbitrarily}\label{ssec:AO_MO_irgendwo} +The standard orbitals are not always sufficient in order to draw a correct +\ac{MO} diagram. For example in the \ac{MO} diagram of \ch{XeF2} one would +need the part that illustrates the interaction between the bonding and +anti-bonding combination of two p orbitals of Flourine with one p orbital of +Xenon: + +\begin{center} + \begin{MOdiagram}[names] + \atom[\chlewis{0.}{F}\hspace*{5mm}\chlewis{180.}{F}]{left}{ + 1s=.2;up,up-el-pos={1sleft=.5} + } + \atom[Xe]{right}{1s=1.25;pair} + \molecule[\ch{XeF2}]{1sMO={1/.25;pair}} + \AO(1cm){s}{0;up} + \AO(3cm){s}{0;pair} + \connect{ AO1 & AO2 } + \node[right,xshift=4mm] at (1sigma) {\footnotesize bonding}; + \node[above] at (AO2.90) {\footnotesize non-bonding}; + \node[above] at (1sigma*.90) {\footnotesize anti-bonding}; + \end{MOdiagram} +\end{center} + +To create diagrams like this there is the following command, which draws a single +\ac{AO}: +\begin{commands} + \command{AO}[\oarg{name}\darg{xshift}\marg{type}\oarg{options}\Marg{\meta{energy}; + \meta{el-spec}}] + Place an \acs{AO} in the diagram. \meta{<name>} (optional) is the name of + the node; if not specified, \code{AO\#} is used where \code{\#} is a + consecutive number. \meta{xshift} is the vertical position of the orbital(s), + a \TeX\ dimension. \meta{type} can be \code{s} or \code{p}. + \meta{options} is a list of key/value pairs with which the \ac{AO} can be + customized, see section~\ref{ssec:AO_anpassen}. \meta{AO-spec} is the + specification of the \ac{AO}. +\end{commands} + +Depending on the \meta{type} one s or three p orbitals are drawn. +\begin{example}[side-by-side] + \begin{MOdiagram} + \AO{s}{0;} + \AO(-20pt){p}{1;pair,up,down} + \end{MOdiagram} +\end{example} + +If one wants to place such an \ac{AO} at the position of an atom, one has to +know their \meta{xshift}. They have predefined values (also see +section~\ref{orbital-positionen}):\label{xshift} +\begin{itemize} + \item atom left: \SI{1}{\centi\metre} + \item molecule: \SI{3}{\centi\metre} + \item atom right: \SI{5}{\centi\metre} +\end{itemize} + +\begin{example}[side-by-side] + \begin{MOdiagram} + \atom{left} {1s=0} + \atom{right}{1s=0} + \molecule {1sMO=1} + \AO(1cm){s}{2} + \AO(3cm){s}{2} + \AO(5cm){s}{2} + \end{MOdiagram} +\end{example} + +Within the p orbitals there is an additional shift by \SI{20}{pt} per orbital. +This is equivalent to a double shift by the length \code{AO-width} (see +section~\ref{option:AO-width}): +\begin{example} + \begin{MOdiagram} + \atom{left} {2p=0} + \atom{right}{2p=0} + % above the left atom: + \AO(1cm) {s}{ .5} + \AO(1cm-20pt){s}{ 1;up} + \AO(1cm-40pt){s}{1,5;down} + % above the right atom: + \AO(1cm) {s}{ .5} + \AO(5cm+20pt){s}{ 1;up} + \AO(5cm+40pt){s}{1.5;down} + \end{MOdiagram} +\end{example} + +The \acp{AO} created with \cs{AO} also can be connected. For this you can use +the \TikZ\ command \cs*{draw}, of course. You can use the predefined node +names\ldots +\begin{example} + \begin{MOdiagram} + \AO{s}{0} \AO(2cm){s}{1} + \AO{s}{2} \AO(2cm){s}{1.5} + \draw[red] (AO1.0) -- (AO2.180) (AO3.0) -- (AO4.180); + \end{MOdiagram} +\end{example} +\ldots\ or use own node names +\begin{example} + \begin{MOdiagram} + \AO[a]{s}{0} \AO[b](2cm){s}{1} + \AO[c]{s}{2} \AO[d](2cm){s}{1.5} + \draw[red] (a.0) -- (b.180) (c.0) -- (d.180); + \end{MOdiagram} +\end{example} + +The predefined names are \code{AO1}, \code{AO2} \etc for the type \code{s} and +\code{AO1x}, \code{AO1y}, \code{AO1z}, \code{AO2x} \etc\ for the type +\code{p}. Nodes of the type \code{p} get an \code{x}, \code{y} or \code{z} if +you specify your own name, too. +\begin{example} + \begin{MOdiagram} + \AO{p}{0} + \draw[<-,shorten >=5pt] (AO1y.-90) -- ++ (.5,-1) node {y}; + \end{MOdiagram} + and + \begin{MOdiagram} + \AO[A]{p}{0} + \draw[<-,shorten >=5pt] (Ay.-90) -- ++ (.5,-1) node {y}; + \end{MOdiagram} +\end{example} + +However, if you want the lines to be drawn in the same style as the ones +created by \cs{molecule}\footnote{which can be customized, see + page~\pageref{option:lines}}, you should use the command \cs{connect}. +\begin{commands} + \command{connect}[\marg{AO-connect}] + Connects the specified \acp{AO}. \meta{AO-connect} is comma separated + list of node name pairs connected with \code{\&}. +\end{commands} +This command expects a comma separated list of node name pairs that are to be +connected. The names have to be connected with a \code{\&}: +\begin{example}[side-by-side] + \begin{MOdiagram} + \AO{s}{0;} \AO(2cm){s}{1;} + \AO{s}{2;} \AO(2cm){s}{1.5;} + \connect{ AO1 & AO2, AO3 & AO4 } + \end{MOdiagram} +\end{example} + +Some things still need to be said: \cs{connect} adds the anchor \code{east} to +the first name and the anchor \code{west} to the second one. This means a +connection only makes sense from the left to the right. However, you can add +own anchors using the usual \TikZ\ way: +\begin{example} + \begin{tikzpicture} + \draw (0,0) node (a) {a} ++ (1,0) node (b) {b} + ++ (0,1) node (c) {c} ++ (-1,0) node (d) {d} ; + \connect{ a.90 & d.-90, c.180 & d.0 } + \end{tikzpicture} +\end{example} + +\subsection{The Positioning Scheme}\label{orbital-positionen} +The figure below shows the values of the $x$ coordinates of the orbitals +depending on the values of \meta{distance} (\meta{dist}) and \meta{AO-width} +(\meta{AO}). In sections~\ref{option:distance} and \ref{option:AO-width} these +lengths and how they can be changed are discussed. +\begin{center} + \begin{MOdiagram}[ + AO-width = 22pt , + labels-fs = \ttfamily\tiny , + labels-style = {text width=40pt,align=center,yshift=11pt}] + \atom{left}{ + 1s = 0 , + 2s = 2 , + 2p = 5.5 , + label = { + 1sleft = {1cm} , + 2sleft = {1cm} , + 2pxleft = {1cm - 4*\meta{AO}} , + 2pyleft = {1cm - 2*\meta{AO}} , + 2pzleft = {1cm} + }} + \atom{right}{ + 1s = 0 , + 2s = 2 , + 2p = 5.5 , + label = { + 1sright = {1cm + \meta{dist}} , + 2sright = {1cm + \meta{dist}} , + 2pxright = {1cm+ \meta{dist}} , + 2pyright = {1cm + \meta{dist} + 2*\meta{AO}} , + 2pzright = {1cm + \meta{dist} + 4*\meta{AO}} + }} + \molecule{ + 1sMO = .5 , + 2sMO = .5 , + 2pMO = {2,.75} , + label = { + 1sigma = {.5*\meta{dist} + 1cm} , + 1sigma* = {.5*\meta{dist} + 1cm} , + 2sigma = {.5*\meta{dist} + 1cm} , + 2sigma* = {.5*\meta{dist} + 1cm} , + 2psigma = {.5*\meta{dist} + 1cm} , + 2psigma* = {.5*\meta{dist} + 1cm} , + 2piy = {.5*\meta{dist} + 1cm - \meta{AO}} , + 2piy* = {.5*\meta{dist} + 1cm - \meta{AO}} , + 2piz = {.5*\meta{dist} + 1cm + \meta{AO}} , + 2piz* = {.5*\meta{dist} + 1cm + \meta{AO}} + } + } + \end{MOdiagram} +\end{center} + +\subsection{Default Values} +If you leave the arguments (or better: values) for the specification of the +\ac{AO} or \ac{MO} empty or omit them, default values are used. The table below +shows you, which ones. +\begin{center} + \small + \begin{tabular}{l>{\ttfamily}l>{\ttfamily}l>{\ttfamily}l} + \toprule & + \normalfont\bfseries\ac{AO}/\ac{MO} & + \normalfont\bfseries omitted & + \normalfont\bfseries empty \\ + \midrule + syntax: + & & 1s & 1s= \\ + \midrule + & 1s & \{0;pair\} & \{0;\} \\ + & 2s & \{2;pair\} & \{2;\} \\ + & 2p & \{5;pair,pair,pair\} & \{5;,{},\} \\ + \midrule + & 1sMO & \{.5;pair,pair\} & \{.5;,\} \\ + & 2sMO & \{.5;pair,pair\} & \{.5;,\} \\ + & 2pMO & \{1.5,.5;pair,pair,pair,pair,pair,pair\} & \{1.5,.5;{},{},{},{},{},\} \\ + \bottomrule + \end{tabular} +\end{center} + +This is similar for the \cs{AO} command (page~\pageref{ssec:AO_MO_irgendwo}); +it needs a value for \meta{energy}, though. + +\begin{center} + \small + \begin{tabular}{>{\ttfamily}l>{\ttfamily}l>{\ttfamily}l} + \toprule + \bfseries\meta{type} & \bfseries \meta{el-spec} \\ + \midrule + s & pair \\ + p & pair,pair,pair \\ + \bottomrule + \end{tabular} +\end{center} + +Compare these examples: +\begin{example}[side-by-side] + \begin{MOdiagram} + \atom{left} { 1s={0;pair} } + \atom{right}{ 1s } + \end{MOdiagram} + + \hrulefill + + \begin{MOdiagram} + \atom{left}{ 1s=1 } + \atom{right}{ 1s= } + \end{MOdiagram} +\end{example} + +\section{Customization} +The options of the section~\ref{ssec:umgebungs_optionen} can be set global as +package option, \ie, with \cs*{usepackage}\oarg{options}\Marg{modiagram}, or +via the setup command \cs{MOsetup}\marg{options}. + +\subsection{Environment Options}\label{ssec:umgebungs_optionen} +There are some options with which the layout of the \ac{MO} diagrams can be +changed: +\begin{options} + \keyval{style}{type} + change the style of the orbitals and the connecting lines, + section~\ref{option:style}. + \keyval{distance}{dim} + distance betwen left and right atom, + section~\ref{option:distance}. + \keyval{AO-width}{dim} + change the width of orbitals, + section~\ref{option:AO-width}. + \keyval{el-sep}{num} + distance between the electron pair arrows, + section~\ref{option:electrons}. + \keyval{up-el-pos}{num} + position of the spin-up arrow, + section~\ref{option:electrons}. + \keyval{down-el-pos}{num} + position of the spin-down arrow, + section~\ref{option:electrons}. + \keyval{lines}{tikz} + change the \TikZ\ style of the connecting lines, + section~\ref{option:lines}. + \keybool{names} + add captions to the atoms and the molecule, + section~\ref{option:names}. + \keyval{names-style}{tikz} + change the \TikZ\ style of the captions, + section~\ref{option:names_style}. + \keyval{names-style-add}{tikz} + change the \TikZ\ style of the captions, + section~\ref{option:names_style}. + \keybool{labels} + add default labels to the orbitals, + section~\ref{option:labels}. + \keyval{labels-fs}{cs} + change the font size of the labels, + section~\ref{option:labels-fs}. + \keyval{labels-style}{tikz} + change the \TikZ\ style of the labels, + section~\ref{option:labels-style}. +\end{options} +They all are discussed in the following sections. If they're used as options +for the environment, they're set locally and only change that environment. +\begin{sourcecode} + \begin{MOdiagram}[options] + ... + \end{MOdiagram} +\end{sourcecode} + +\subsubsection{Option \option*{style}}\label{option:style} +There are five different styles which can be chosen. +\begin{itemize} + \item\keyis{style}{plain} \AOinline[style=plain]{pair} (default) + \item\keyis{style}{square} \AOinline[style=square]{pair} + \item\keyis{style}{circle} \AOinline[style=circle]{pair} + \item\keyis{style}{round} \AOinline[style=round]{pair} + \item\keyis{style}{fancy} \AOinline[style=fancy]{pair} +\end{itemize} + +Let's take the \ac{MO} diagram of \ch{H2} to illustrate the different styles: +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[style=plain]% default + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[style=square] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[style=circle] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[style=round] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[style=fancy] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\subsubsection{Option \option*{distance}}\label{option:distance} +Depending on labels and captions the \SI{4}{\centi\metre} by which the right +and left atom are separated can be too small. With \key{distance}{dim} the +length can be adjusted. This will change the position of the right atom to +\code{1cm + \meta{dim}} and the position of the molecule is changed to +\code{0.5*(1cm + \meta{dim})}, also see page~\pageref{xshift} and +section~\ref{orbital-positionen}. +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[distance=6cm] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\subsubsection{Option \option*{AO-width}}\label{option:AO-width} +The length \option{AO-width} sets the length of the horizontal line in a +orbital displayed with the \code{plain} style. It's default value is +\SI{10}{pt}. +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[AO-width=15pt] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[style=fancy,AO-width=15pt] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} +By changing the value of \option{AO-width} the positions of the p and the +\chempi\ orbitals also change, see section~\ref{orbital-positionen}. + +\subsubsection{Optionen \option*{el-sep}, \option*{up-el-pos} und + \option*{down-el-pos}} +\label{option:electrons} + +These three options change the horizontal positions of the arrows representing +the electrons in an \ac{AO}/\ac{MO}. The option \key{el-sep}{num} needs a +value between \code{0} and \code{1}. \code{0} means \emph{no} distance between +the arrows and \code{1} \emph{full} distance (with respect to the length +\option{AO-width}, see section~\ref{option:AO-width}). + +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[el-sep=.2]% default + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[el-sep=0] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[el-sep=1] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +The options \key{up-el-pos}{<num>} and \key{down-el-pos}{<num>} can be used +alternatively to place the spin-up and spin-down electron, respectively. +Again they need values between \code{0} and \code{1}. This time \code{0} +means \emph{on the left} and \code{1} means \emph{on the right}. + +\begin{example} + % use package `chemmacros' + \begin{MOdiagram}[up-el-pos=.4,down-el-pos=.6]% default + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\begin{example} + % use package `chemmacros' + \begin{MOdiagram}[up-el-pos=.333,down-el-pos=.667] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\begin{example} + % use package `chemmacros' + \begin{MOdiagram}[up-el-pos=.7,down-el-pos=.3] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\subsubsection{Option \option*{lines}}\label{option:lines} +The option \option{lines} can be used to modify the \TikZ\ style of the +connecting lines: +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[lines={gray,thin}] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\subsubsection{Option \option*{names}}\label{option:names} +If you use the option \option{names} the atoms and the molecule get captions +provided you have used the optional \meta{name} argument of \cs{atom} and/or +\cs{molecule}. +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[names] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\subsubsection{Options \option*{names-style} and \option*{names-style-add}}\label{option:names_style} +These options enable to customize the style of the captions of the atoms and +of the molecule. By default this setting is used: +\key{names-style}{anchor=base}\footnote{Please see ``\TikZ\ and PGF -- Manual + for Version 2.10'' p.\,183 section 16.4.4 (pgfmanual.pdf) for the meaning}. +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[names,names-style={draw=blue}] + \atom[p]{left} { 1s = {;up} } + \atom[b]{right}{ 1s = {;up} } + \molecule[\ch{X2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +With this the default setting is overwritten. As you can see it destroys the +vertical alignment of the nodes. In order to avoid that you can for example +specify \code{text height} and \code{text depth} yourself \ldots +\begin{example} + % use package `chemmacros' + \begin{MOdiagram}[names,names-style={text height=1.5ex, text depth=.25ex, draw=blue}] + \atom[p]{left} { 1s = {;up} } + \atom[b]{right}{ 1s = {;up} } + \molecule[\ch{X2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\ldots, add the \code{anchor} again \ldots +\begin{example} + % use package `chemmacros' + \begin{MOdiagram}[names,names-style={anchor=base, draw=blue}] + \atom[p]{left} { 1s = {;up} } + \atom[b]{right}{ 1s = {;up} } + \molecule[\ch{X2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\ldots\ or use the option \key{names-style-add}. It doesn't overwrite the +current setting but appends the new declaration: +\begin{example} + % use package `chemmacros' + \begin{MOdiagram}[names,names-style-add={draw=blue}] + \atom[p]{left} { 1s = {;up} } + \atom[b]{right}{ 1s = {;up} } + \molecule[\ch{X2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\begin{example} + % use package `chemmacros' + \MOsetup{ + names, + names-style = { + text height = 2.5ex, + text depth = .5ex, + draw = blue!80, + rounded corners + } + } + \begin{MOdiagram} + \atom[p]{left} { 1s = {;up} } + \atom[b]{right}{ 1s = {;up} } + \molecule[\ch{X2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} + \begin{MOdiagram}[names-style-add={fill=blue!20}] + \atom[p]{left} { 1s = {;up} } + \atom[b]{right}{ 1s = {;up} } + \molecule[\ch{X2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\subsubsection{Option \option*{labels}}\label{option:labels} +If you use the option \option{labels} predefined labels are written below the +orbitals. These labels can be changed, see section~\ref{sec:key:label}. +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[labels] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\subsubsection{Option \option*{labels-fs}}\label{option:labels-fs} +Labels are set with the font size \cs*{small}. If you want to change that you +can use the option \option{labels-fs}. +\begin{example} + % use package `chemmacros' + \begin{MOdiagram}[labels,labels-fs=\footnotesize] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +This also allows you to change the font style or font shape of the labels. +\begin{example} + % use package `chemmacros' + \begin{MOdiagram}[labels,labels-fs=\sffamily\footnotesize] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\subsubsection{Option \option*{labels-style}}\label{option:labels-style} +The option \option{labels-style} changes the \TikZ\ style of the nodes within +which the labels are written. +\begin{example} + % use package `chemmacros' + \begin{MOdiagram}[labels,labels-style={blue,yshift=4pt}] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ 1sMO = {.75;pair} } + \end{MOdiagram} +\end{example} + +\subsection{\cs*{atom} and \cs*{molecule} Specific Customizations} +\subsubsection{The \option*{label} Key}\label{sec:key:label} +If you don't want to use the predefined labels, change single labels or use +only one or two labels, you can use the key \option{label}. This option is +used in the \cs{atom} and \cs{molecule} commands in the \meta{AO-spec} or +\meta{MO-spec} argument, respectively. The key awaits a comma separated +key/value list. The names mentioned in section~\ref{Namensgebung} are used as +keys to specify the \ac{AO} that you want to label. +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[labels-fs=\footnotesize] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ + 1sMO = {.75;pair}, + label = { 1sigma = {bonding MO} } + } + \end{MOdiagram} +\end{example} + +\begin{example}[side-by-side] + \begin{MOdiagram}[style=square,distance=6cm] + \atom{left} { 1s = {;up} } + \atom{right}{ 1s = {;up} } + \molecule{ + 1sMO = {.75;pair} , + label = { + 1sigma = \chemsigma, + 1sigma* = \chemsigma$^*$ + } + } + \node[right] at (1sigma.-45) {bonding}; + \node[right] at (1sigma*.45) {anti-bonding}; + \end{MOdiagram} +\end{example} + +If the option is used together with the \option{labels} option +(page~\pageref{option:labels}) single labels are overwritten: +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[labels] + \atom[H]{left} { 1s = {;up} } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ + 1sMO = {.75;pair}, + label = { 1sigma = \textcolor{red}{??} } + } + \end{MOdiagram} +\end{example} + +\subsubsection{The \option*{color} Key}\label{sec:key:color} +Analogous to the \option{label} key the \option{color} key can be used to +display coloured electrons: +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram}[labels-fs=\footnotesize] + \atom[H]{left}{ + 1s, color = { 1sleft = blue } + } + \atom[H]{right}{ + 1s, color = { 1sright = red } + } + \molecule[\ch{H2}]{ + 1sMO, + label = { 1sigma = {bonding MO} }, + color = { 1sigma = green, 1sigma* = cyan } + } + \end{MOdiagram} +\end{example} + +\subsubsection{The \option*{up-el-pos} and \option*{down-el-pos} keys}\label{sec:key:electrons} +The options \option{up-el-pos} and \option{down-el-pos} allow it to shift the +arrows representing the electrons in a single \ac{AO} or \ac{MO} individually. +You need to use values between \code{0} and \code{1}, also see +section~\ref{option:electrons}. +\begin{example}[side-by-side] + % use package `chemmacros' + \begin{MOdiagram} + \atom[H]{left}{ + 1s = {;up}, + up-el-pos = { 1sleft=.5 } + } + \atom[H]{right}{ 1s = {;up} } + \molecule[\ch{H2}]{ + 1sMO = {.75;pair} , + up-el-pos = { 1sigma=.15 } , + down-el-pos = { 1sigma=.85 } + } + \end{MOdiagram} +\end{example} + +\subsection{\cs*{AO} Specific Customizations}\label{ssec:AO_anpassen} +These keys enable to customize orbitals created with \cs{AO}. + +\subsubsection{The \option*{label} Key}\label{key:AO_label} +The key \option{label}\Oarg{\meta{x}/\meta{y}/\meta{z}} allows you to put a +label to the \ac{AO}/\ac{MO}. If you use the type \code{p} you can specify +the orbital you want to label in square brackets: +\begin{example}[side-by-side] + \begin{MOdiagram}[style=square] + \AO{s}[label={s orbital}]{0} + \AO{p}[label[y]=py,label[z]=pz]{1.5} + \end{MOdiagram} +\end{example} + +\subsubsection{The \option*{color} Key}\label{key:AO_color} +Analogous to the \option{label} key there is the key +\option{color}\Oarg{\meta{x}/\meta{y}/\meta{z}} which enables you to choose a +color for the electrons. If you use the type \code{p} you can specify the +orbital in square brackets: +\begin{example}[side-by-side] + \begin{MOdiagram}[style=square] + \AO{s}[color=red]{0} + \AO{p}[color[y]=green,color[z]=cyan]{1.5} + \end{MOdiagram} +\end{example} + +\subsubsection{The \option*{up-el-pos} and \option*{down-el-pos} Keys}\label{key:AO_electrons} +Then there are the keys \option{up-el-pos}\Oarg{\meta{x}/\meta{y}/\meta{z}} +and \option{down-el-pos}\Oarg{\meta{x}/\meta{y}/\meta{z}} with which the +electrons can be shifted horizontally. You can use values between \code{0} +and \code{1}, also see section~\ref{option:electrons}. If you use the type +\code{p} you can specify the orbital in square brackets: +\begin{example}[side-by-side] + \begin{MOdiagram}[style=square] + \AO{s}[up-el-pos=.15]{0} + \AO{p}[up-el-pos[y]=.15,down-el-pos[z]=.15]{1.5} + \end{MOdiagram} +\end{example} + +\subsection{Energy Axis} +Last but not least one might want to add an energy axis to the diagram. For +this there is the command \cs{EnergyAxis}. + +\begin{commands} + \command{EnergyAxis}[\oarg{option}] + Adds an energy axis to the diagram. \meta{options} are key/value pairs to + modify the axis. +\end{commands} + +\begin{example}[side-by-side] + \begin{MOdiagram} + \atom{left} { 1s = {;up} } + \atom{right}{ 1s = {;up} } + \molecule{ 1sMO = {.75;pair} } + \EnergyAxis + \end{MOdiagram} +\end{example} + +For the time being there are two options to modify the axis. +\begin{options} + \keyval{title}{title}\Default{energy} + the axis label. If used without value the default is used. + \keyval{head}{tikz arrow head}\Default{>} + the arrow head; you can use the arrow heads specified in the \TikZ\ library + \code{arrows} (pgfmanual v2.10 pages 256ff.) +\end{options} + +\begin{example}[side-by-side] + \begin{MOdiagram} + \atom{left} { 1s = {;up} } + \atom{right}{ 1s = {;up} } + \molecule{ 1sMO = {.75;pair} } + \EnergyAxis[title] + \end{MOdiagram} +\end{example} + +\begin{example}[side-by-side] + \begin{MOdiagram} + \atom{left} { 1s = {;up} } + \atom{right}{ 1s = {;up} } + \molecule{ 1sMO = {.75;pair} } + \EnergyAxis[title=E,head=stealth] + \end{MOdiagram} +\end{example} + +\section{Examples} +The example from the beginning of section \ref{ssec:AO_MO_irgendwo}. +\begin{example} + % use package `chemmacros' + \begin{MOdiagram}[names] + \atom[\chlewis{0.}{F}\hspace*{5mm}\chlewis{180.}{F}]{left}{ + 1s=.2;up,up-el-pos={1sleft=.5} + } + \atom[Xe]{right}{1s=1.25;pair} + \molecule[\ch{XeF2}]{1sMO={1/.25;pair}} + \AO(1cm){s}{0;up} + \AO(3cm){s}{0;pair} + \connect{ AO1 & AO2 } + \node[right,xshift=4mm] at (1sigma) {\footnotesize bonding}; + \node[above] at (AO2.90) {\footnotesize non-bonding}; + \node[above] at (1sigma*.90) {\footnotesize anti-bonding}; + \end{MOdiagram} +\end{example} + +\begin{example}[outside] + % use package `chemmacros' + \begin{figure}[p] + \centering + \begin{MOdiagram}[style=square,labels,names,AO-width=8pt,labels-fs=\footnotesize] + \atom[\ch{O_a}]{left}{ + 1s, 2s, 2p = {;pair,up,up} + } + \atom[\ch{O_b}]{right}{ + 1s, 2s, 2p = {;pair,up,up} + } + \molecule[\ch{O2}]{ + 1sMO, 2sMO, 2pMO = {;pair,pair,pair,up,up}, + color = { 2piy*=red, 2piz*=red } + } + \EnergyAxis + \end{MOdiagram} + \caption{MO diagram of \ch{^3 "\chemSigma-" O2}.} + \end{figure} +\end{example} + +\begin{example}[outside] + % use package `chemmacros' + \begin{figure}[p] + \centering + \MOsetup{style = fancy, distance = 7cm, AO-width = 15pt, labels} + \begin{MOdiagram} + \atom[N]{left}{ + 2p = {0;up,up,up} + } + \atom[O]{right}{ + 2p = {2;pair,up,up} + } + \molecule[NO]{ + 2pMO = {1.8,.4;pair,pair,pair,up}, + color = { 2piy*=red } + } + \EnergyAxis + \end{MOdiagram} + \caption{Part of the MO diagram of \chlewis{180.}{NO}.} + \end{figure} +\end{example} + +\clearpage + +\end{document} |