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diff --git a/Master/texmf-dist/doc/latex/chemformula/chemformula-manual.tex b/Master/texmf-dist/doc/latex/chemformula/chemformula-manual.tex new file mode 100644 index 00000000000..6ceb89003d8 --- /dev/null +++ b/Master/texmf-dist/doc/latex/chemformula/chemformula-manual.tex @@ -0,0 +1,1626 @@ +% !arara: pdflatex +% !arara: biber +% arara: pdflatex +% arara: pdflatex +% -------------------------------------------------------------------------- +% the CHEMFORMULA package +% +% typeset chemical compounds and reactions +% +% -------------------------------------------------------------------------- +% Clemens Niederberger +% -------------------------------------------------------------------------- +% https://github.com/cgnieder/chemformula/ +% contact@mychemistry.eu +% -------------------------------------------------------------------------- +% If you have any ideas, questions, suggestions or bugs to report, please +% feel free to contact me. +% -------------------------------------------------------------------------- +% Copyright 2011--2020 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. +% -------------------------------------------------------------------------- +\documentclass{chemformula-manual} + +\addbibresource{cnltx.bib} + +\chemsetup{ + greek = newtx , + modules = {redox,reactions,units} , + formula = chemformula , + chemformula/format = \libertineLF +} + +\usepackage[accsupp]{acro} +\acsetup{ + long-format = \scshape , + short-format = \scshape +} +\DeclareAcronym{iupac}{ + short = iupac , + long = International Union of Pure and Applied Chemistry , + pdfstring = IUPAC , + accsupp = IUPAC +} + +\sisetup{ + detect-mode=false, + mode=text, + text-rm=\libertineLF +} + +\usepackage{filecontents} + +\defbibheading{bibliography}{\section{References}} +\addbibresource{\jobname.bib} +\begin{filecontents*}{\jobname.bib} +@book{iupac:greenbook, + author = {E. Richard Cohan and Tomislav Cvita\v{s} and Jeremy G. Frey and + Bertil Holmstr\"om and Kozo Kuchitsu and Roberto Marquardt and Ian Mills and + Franco Pavese and Martin Quack and J\"urgen Stohner and Herbert L. Strauss and + Michio Takami and Anders J Thor} , + title = {``Quantities, Symbols and Units in Physical Chemistry'', \acs{iupac} + Green Book} , + sorttitle = {Quantities, Symbols and Units in Physical Chemistry} , + indexsorttitle = {Quantities, Symbols and Units in Physical Chemistry} , + edition = {3rd Edition. 2nd Printing} , + year = {2008} , + publisher = {\acs{iupac} \&\ RSC Publishing, Cambridge} +} +\end{filecontents*} + +\DeclareInstance{xfrac}{chemformula-text-frac}{text} + { + scale-factor = 1 , + denominator-bot-sep = -.2ex , + denominator-format = \scriptsize #1 , + numerator-top-sep = -.2ex , + numerator-format = \scriptsize #1 , + slash-right-kern = .05em , + slash-left-kern = .05em + } + +\newpackagename\chemmacros{chemmacros} + +\newidxcmd\manual{\textsf{#1}}[\ (manual)] +\newidxcmd\arrowtype{\code{#1}}[\ (arrow type)] + +\makeatletter +\newcommand*\cf@arrow{% + \@ifstar + {\cf@arrow@star} + {\cf@arrow@nostar}% +} +\newrobustcmd*\cf@arrow@star[1]{% + \@ifnextchar[ + {\cf@arrow@star@opt{#1}} + {\cf@arrow@star@opt{#1}[]}% +} +\newrobustcmd*\cf@arrow@nostar[1]{% + \@ifnextchar[ + {\cf@arrow@nostar@opt{#1}} + {\cf@arrow@nostar@opt{#1}[]}% +} +\def\cf@arrow@star@opt#1[#2]{% + \ifblank{#2} + {\item\arrowtype*{#1}} + {\item\arrowtype*{#1}#2}% + \cnltx@checkdefault{\hfill\newline}% +} +\def\cf@arrow@nostar@opt#1[#2]{% + \ifblank{#2} + {\item\arrowtype{#1}} + {\item\arrowtype{#1}#2}% + \cnltx@checkdefault{\hfill\newline}% +} + +\newenvironment{codedesc} + {% + \def\Code##1{\item\code{##1}\hfill\newline}% + \cnltxlist + } + {\endcnltxlist} + +\newenvironment{arrows} + {% + \let\arrow\cf@arrow + \cnltxlist + } + {\endcnltxlist} +\makeatother + +\renewcommand*\AmS{\hologo{AmS}} + +\newcommand*\TikZ{Ti\textit{k}Z} + +\newname\hensel{Martin Hensel} + +\begin{document} + +\section{Introduction} +Probably every chemist using \LaTeXe\ is aware of the great \pkg{mhchem} +package by \hensel. There have always been some difficulties intertwining it +with the \chemmacros\ package, though. Also, some other minor points in +\pkg{mhchem} always bothered me, but they hardly seemed enough for a new +package. They weren't even enough for a feature request to the \pkg{mhchem} +author. The challenge and the fun of creating a new package and the wish for +a highly customizable alternative led to \chemformula\ after all. + +\chemformula\ works very similar to \pkg{mhchem} but is more strict as to how +compounds, stoichiometric factors and arrows are input. In the same time +\chemformula\ offers \emph{many} possibilities to customize the output. + +\section{Licence and Requirements} +\license + +The \chemformula\ package needs and thus loads the packages +\bnd{l3kernel}~\cite{bnd:l3kernel}, \pkg{xparse}, \pkg{l3keys2e} and +\pkg{xfrac} (all three are part of the \bnd{l3packages} +bundle~\cite{bnd:l3packages}), +\pkg{tikz}\footnote{\CTANurl[graphics]{pgf}}~\cite{pkg:pgf}, +\pkg{amstext}~\cite{pkg:amstext}, \pkg{nicefrac}~\cite{pkg:nicefrac} and +\pkg{scrlfile} (from the \KOMAScript\footnote{\CTANurl{koma-script}} +bundle~\cite{bnd:koma-script}). + +\section{Setup} + +If you're using \chemformula\ as a standalone package options are set up with +the following command: +\begin{commands} + \command{setchemformula}[\marg{options}] + Set up \chemformula. +\end{commands} + +\chemformula\ is tightly intertwined with the \chemmacros\ package. If both +packages are loaded together, \chemformula\ is integrated into the +\chemmacros\ package. Then all of \chemformula's options belong to +\chemmacros' module \module{chemformula}. This means if you load it via +\chemmacros\ or in addition to \chemmacros\ they can be setup with +\begin{commands} + \command{chemsetup}[\Oarg{chemformula}\marg{options}] + Set up options for \chemformula\ exclusively, or + \command{chemsetup}[\Marg{chemformula/\meta{option1},chemformula/\meta{option2}}] + Set up options for \chemformula\ together with others of \chemmacros' + options. +\end{commands} + +\section{The Basic Principle} +\chemformula\ offers one main command. +\begin{commands} + \command{ch}[\oarg{options}\marg{input}] + \chemformula's main command. +\end{commands} +The usage will seem very familiar to you if you're familiar with \pkg{mhchem}: +\begin{example}[side-by-side] + \ch{H2O} \par + \ch{Sb2O3} \par + \ch{H+} \par + \ch{CrO4^2-} \par + \ch{AgCl2-} \par + \ch{[AgCl2]-} \par + \ch{Y^{99}+} \par + \ch{Y^{99+}} \par + \ch{H2_{(aq)}} \par + \ch{NO3-} \par + \ch{(NH4)2S} \par + \ch{^{227}_{90}Th+} \par + $V_{\ch{H2O}}$ \par + \ch{Ce^{IV}} \par + \ch{KCr(SO4)2 * 12 H2O} +\end{example} + +However, there are differences. The most notable one: \chemformula\ +distinguishes between different types of input. These different parts +\emph{have} to be separated with blanks: +\begin{commands} + \command{ch}[\Marg{part1 part2 part3 part4}] +\end{commands} +A blank in the input \emph{never} is a blank in the output. This role of the +blank strictly holds and disregarding it can have unexpected results and even +lead to errors. + +The most visible differences regard spacing and the shapes of the default +arrows: +\begin{example}[side-by-side] + \ch{A + B ->[a] C} \par + \ce{A + B ->[a] C} +\end{example} + +This means that \cs{ch}\Marg{2H2O} is recognized as a \emph{single} part, +which in this case is recognized as a compound. +\begin{example}[side-by-side] + \ch{2H2O} \par + \ch{2 H2O} +\end{example} +This also means, that a part cannot contain a blank since this will +automatically divide it into two parts. If you need an extra blank in the +output you need to use \verbcode+~+ or \cs*{~}. However, since commands +in most cases gobble a space after them a input like +\cs{ch}\Marg{\cs*{command} ABC} will be treated as a single part. If you want +or need to divide them you need to add an empty group: +\cs{ch}\Marg{\cs*{command}\marg{} ABC}. The different input types are +described in the following sections. + +\section{Stoichiometric Factors} +A stoichiometric factor may only contain of numbers and the signs +\verbcode+.,_/()+ +\begin{example}[side-by-side] + \ch{2} \par + \ch{12} + + % decimals: + \ch{.5} \par + \ch{5,75} + + % fractions: + \ch{3/2} \par + \ch{1_1/2} + + % ``iupac'': + \ch{(1/2)} +\end{example} + +As you can see if you input decimal numbers a missing leading zero is added. + +You have to be a little bit careful with the right syntax but I believe it is +rather intuitive. +\begin{sourcecode} + this won't work but will result in an error: \ch{1/1_1} +\end{sourcecode} + +If stoichiometric factors are enclosed with parentheses the fractions are not +recognized and missing leading zeros are not added. What's inside the +parentheses is typeset as is. +\begin{example} + \ch{(1/2) H2O} \ch{1/2 H2O} \ch{0.5 H2O} +\end{example} +You can find many examples like the following for stoichiometric factors in +parentheses in the \acs{iupac} Green Book~\cite{iupac:greenbook}: +\begin{reaction*} + (1/5) K "\ox{7,Mn}" O4 + (8/5) HCl == (1/5) "\ox{2,Mn}" Cl2 + (1/2) Cl2 + (1/5) KCl + (4/5) H2O +\end{reaction*} + +There are a few possibilities to customize the output. +\begin{options} + \keyval{decimal-marker}{marker}\Default{.} + The symbol to indicate the decimal. + \keychoice{frac-style}{math,xfrac,nicefrac}\Default{math} + Determines how fractions are displayed. + \keyval{frac-math-cmd}{command sequence}\Default{\cs*{frac}} + \sinceversion{4.1}Allows you to choose which command is used with + \keyis{frac-style}{math}. This needs to be a command sequence that takes + two arguments that are set in math mode. + \keyval{stoich-space}{skip}\Default{.1667em plus .0333em minus .0117em} + The space that is placed after the stoichiometric factor. A rubber + length. + \keybool{stoich-paren-parse}\Default{false} + If set to true stoichiometric factors enclosed by parentheses also are + parsed. + \keyval{stoich-print}{cs}\Default{\cs{chstoich}} + This option allows to redefine the macro that prints the stoichiometric + factors. \meta{cs} should be a macro that takes one mandatory argument. + \emph{Please note that using this option will disable \chemformula's + stoichiometric parsing as that is done by the default command + \cs{chstoich}.} +\end{options} + +\begin{example} + \ch[decimal-marker={,}]{3.5} \ch[decimal-marker={$\cdot$}]{3,5} +\end{example} + +The option \keyis{frac-style}{xfrac} uses the \cs*{sfrac} command of the +\pkg{xfrac} package. The output strongly depends on the font you use. +\begin{example} + \ch[frac-style=xfrac]{3/2} \ch[frac-style=xfrac]{1_1/2} +\end{example} +\chemformula\ defines the instance \code{chemformula-text-frac} which you can +redefine to your needs. See the \pkg{xfrac} documentation for further +information. The default definition is this: +\begin{sourcecode} + \DeclareInstance{xfrac}{chemformula-text-frac}{text} + { + slash-left-kern = -.15em , + slash-right-kern = -.15em + } +\end{sourcecode} +This document uses the font Linux Libertine~O and the following definition: +\begin{sourcecode} + \DeclareInstance{xfrac}{chemformula-text-frac}{text} + { + scale-factor = 1 , + denominator-bot-sep = -.2ex , + denominator-format = \scriptsize #1 , + numerator-top-sep = -.2ex , + numerator-format = \scriptsize #1 , + slash-right-kern = .05em , + slash-left-kern = .05em + } +\end{sourcecode} + +The option \keyis{frac-style}{nicefrac} uses the \cs*{nicefrac} command of the +\pkg{nicefrac} package. +\begin{example} + \ch[frac-style=nicefrac]{3/2} \ch[frac-style=nicefrac]{1_1/2} +\end{example} + +The option \option{stoich-space} allows you to customize the space between +stoichiometric factor and the group following after it. +\begin{example}[side-by-side] + \ch{2 H2O} \par + \ch[stoich-space=.3em]{2 H2O} +\end{example} + +\section{Compounds}\label{ssec:compounds} +\chemformula\ determines compounds as the type that ``doesn't fit in anywhere +else.'' This point will become more clear when you know what the other types +are. +\begin{example}[side-by-side] + \ch{H2SO4} \par + \ch{[Cu(NH3)4]^2+} +\end{example} + +\subsection{Adducts} +\chemformula\ has two identifiers which will create adducts. +\begin{commands} + \command{ch}[\Marg{A.B}] \ch{A.B} + \command{ch}[\Marg{A*B}] \ch{A*B} +\end{commands} +\begin{example}[side-by-side] + \ch{CaSO4.H2O} \par + \ch{CaSO4*H2O} +\end{example} +Since numbers in a compound always are treated as subscripts (see +section~\ref{ssec:subscripts}) you sometimes need to introduce stoichiometric +factors for the right output: +\begin{example}[side-by-side] + \ch{Na3PO4*12H2O} \par + \ch{Na3PO4* 12 H2O} \par + \ch{Na3PO4 * 12 H2O} +\end{example} + +\subsection{Subscripts}\label{ssec:subscripts} +\emph{All} numbers in a compound are treated as subscripts. +\begin{example}[side-by-side] + \ch{H2SO4} +\end{example} +If you want a letter to be a subscript you can use the math syntax: +\begin{example}[side-by-side] + \ch{A_nB_m} +\end{example} +The subscript recognizes groups. You can also use math inside it. +\begin{example}[side-by-side] + \ch{A_{$n$}B_{$m$}} \par + \ch{NaCl_{(aq)}} +\end{example} + +\subsection{Commands} +Commands are allowed in a compound: +\begin{example}[side-by-side] + \ch{\textbf{A2}B3} \ch{A2\color{red}B3} +\end{example} + +However, if the commands demand numbers as argument, \eg, space commands or +\chemmacros' \verbcode+\ox+ command the direct use will fail. This is +because the numbers are treated as subscripts \emph{before} the command +expands. +\begin{sourcecode} + \ch{A\hspace{2mm}B} will raise an error because \hspace sees something like + this: \hspace{$_2$mm}. Actually not at all like this but equally bad\ldots +\end{sourcecode} +See section~\ref{ssec:text} for a way around this. + +Please also note that formulas are placed inside a group! +\begin{example}[side-by-side] + \ch{A2\color{red}B3 C4} +\end{example} + +\subsection{Charges and Other Superscripts} +\paragraph{Basics} +If a compound \emph{ends} with a plus or minus sign it will be treated as +charge sign and typeset as superscript. In other places a plus is treated as +a triple bond and a dash will be used as a single bond, see +section~\ref{ssec:bonds}. +\begin{example}[side-by-side] + \ch{A+B} \ch{AB+} \par + \ch{A-B} \ch{AB-} +\end{example} + +For longer charge groups or other superscripts you can use the math syntax. +It recognizes groups and you can use math inside them. Inside these groups +neither \code{+} nor \code{-} are treated as bonds. If a dot \code{.} is +inside a superscript it is treated as indicator for a radical. A \code{*} +gives the excited state. +\begin{example}[side-by-side] + \ch{A^{x-}} \par + \ch{A^x-} \par + \ch{A^{x}-} \par + \ch{A^{$x-$}} \par + \ch{RNO2^{-.}} \par + \ch{^31H} \par + \ch{^{14}6C} \par + \ch{^{58}_{26}Fe} \par + \ch{NO^*} +\end{example} + +Actually\changedversion{4.5a} a dot \code{.} is not always treated as +indicator for a radical: if the dot in the superscript is followed by a number +it is interpreted as a decimal sign. It is typeset according to the option +\option{decimal-marker}. This may be a good place to mention that a comma +\code{,} in a superscript is also typeset according to +\option{decimal-marker}. + +\begin{example}[side-by-side] + \ch{^{22,98}_{11}Na} + \ch{^{22.98}_{11}Na}\par + \setchemformula{decimal-marker={,}} + \ch{^{22,98}_{11}Na} + \ch{^{22.98}_{11}Na} +\end{example} + +Ions and ion composites with more than one charge can be typeset quite as +easy: +\begin{example}[side-by-side] + \ch{SO4^2-} \ch{Ca^2+ SO4^2-} +\end{example} + +\paragraph{Charge Commands} +You don't need to use \cs{mch} and related commands inside \cs{ch}. Indeed, +you \emph{shouldn't} use them as they might mess with the subscript and +superscript alignment. The \chemmacros\ option \code{circled} is obeyed by +\cs{ch}. +\begin{example} + \chemsetup[charges]{circled=all} + \ch{H+ + OH- <=> H2O} +\end{example} + +\chemformula\ knows the options \option{circled} and \option{circletype} also +on its own. + +\begin{example} + \setchemformula{circled=all} + \ch{H+ + OH- <=> H2O} +\end{example} + +These options are coupled with \chemmacros\ options, \ie, setting \chemmacros' +options will also set \chemformula's equivalents. The other way around the +options act independently: setting \chemformula's options will \emph{not} set +\chemmacros' options. +\begin{options} + \keychoice{circled}{formal,\default{all},none}\Default{formal} + \chemformula\ uses two different kinds of charges which indicate the usage + of real ($+/-$) and formal (\fplus/\fminus) charges. The choice + \code{formal} distinguishes between them, choice \code{none} displays them + all without circle, choice \code{all} circles all. + % circletype + \keychoice{circletype}{\default{chem},math}\Default{chem} + This option switches between two kinds of circled charge symbols: + \cs{fplus} \fplus\ and \verbcode+$\oplus$+ $\oplus$. +\end{options} + +\paragraph{Behaviour} +The supercripts behave differently depending on their position in a compound, +if there are super- and subscripts following each other directly. +\begin{example} + \ch{^33B} \ch{{}^33B} \ch{3^3B} \ch{B^3} \ch{B3^3} \par + \ch{^{23}_{123}B} \ch{{}^{23}_{123}B} \ch{_{123}^{23}B} + \ch{B^{23}} \ch{B_{123}^{23}} \par + \ch{^{123}_{23}B} \ch{{}^{123}_{23}B} \ch{_{23}^{123}B} + \ch{B^{123}} \ch{B23^{123}} +\end{example} +\begin{itemize} + \item If a compound \emph{starts} with a sub- or superscript both sub- and + superscript are aligned to the \emph{right} else to the \emph{left}. + \item If a compound \emph{does not start} with a sub- or superscript and + there is both a sub- and a superscript, the superscript is shifted + additionally by a length determined from the option + \key{charge-hshift}{dim}, also see page~\pageref{desc:charge-hshift}f. +\end{itemize} +The second point follows \ac{iupac}'s recommendations: +\begin{cnltxquote}[{\acs{iupac} Green Book {\cite[][p.\,51]{iupac:greenbook}}}] + In writing the formula for a complex ion, spacing for charge number can be + added (staggered arrangement), as well as parentheses: + \ch[charge-hshift=full]{SO4^2-}, \ch{(SO4)^2-}. The staggered arrangement + is now recommended. +\end{cnltxquote} + +\subsection{Bonds}\label{ssec:bonds} +\subsubsection{Native Bonds} +There are three kinds of what I will call ``native bonds'': +\begin{example}[side-by-side] + single: \ch{CH3-CH3} \par + double: \ch{CH2=CH2} \par + triple: \ch{CH+CH} +\end{example} + +\subsubsection{Flexible Bonds} +\paragraph{Predefined Bonds} +In addition to the three native bonds there are a few more which can be called +by +\begin{commands} + \command{bond}[\marg{bond name}] + Prints the bond type specified by \meta{bond name}. +\end{commands} +The predefined bond types are shown in table~\vref{tab:bond_types}. + +\begin{table} + \centering + \caption{Bonds available with \cs*{bond}.} + \label{tab:bond_types} + \begin{tabular}{lcl} + \toprule + \bfseries name & \bfseries appearance & \bfseries aliases \\ + \midrule + \code{single} & \bond{single} & \code{normal}, \code{sb} \\ + \code{double} & \bond{double} & \code{db} \\ + \code{triple} & \bond{triple} & \code{tp} \\ + \code{dotted} & \bond{dotted} & \code{semisingle} \\ + \code{deloc} & \bond{deloc} & \code{semidouble} \\ + \code{tdeloc} & \bond{tdeloc} & \code{semitriple} \\ + \code{co>} & \bond{co>} & \code{coordright} \\ + \code{<co} & \bond{<co} & \code{coordleft} \\ + \bottomrule + \end{tabular} +\end{table} + +\begin{example} + \ch{C\bond{sb}C\bond{db}C\bond{tp}C\bond{deloc}C\bond{tdeloc}C\bond{co>}C\bond{<co}C} +\end{example} + +\paragraph{Own Bonds} +\chemformula{} offers commands to define own bond types: +\begin{commands} + \command{NewChemBond}[\marg{name}\marg{code}] + \sinceversion{4.3}Define the new bond type \meta{name}. Issue an error if + a bond \meta{name} already exists. + \command{DeclareChemBond}[\marg{name}\marg{code}] + Define the new bond type \meta{name} or overwrite it if it already + exists. + \command{RenewChemBond}[\marg{name}\marg{code}] + Redefine the existing bond type \meta{name}. Issue an error if a bond + \meta{name} doesn't exist. + \command{ProvideChemBond}[\marg{name}\marg{code}] + \sinceversion{4.12a}Define the new bond type \meta{name} only if it + doesn't exist yet. + \command{NewChemBondAlias}[\marg{new name}\marg{old name}] + \sinceversion{4.3}Declare the bond type \meta{new name} to be an alias of + \meta{old name}. Issue an error if a bond \meta{new name} already + exists. + \command{DeclareChemBondAlias}[\marg{new name}\marg{old name}] + Declare the bond type \meta{new name} to be an alias of \meta{old name}. + \command{ShowChemBond}[\marg{name}] + Print the definition of bond type \meta{name}. +\end{commands} +The usage is best described with an example. So let's see how the +\code{single} bond and the \code{co>} bond are defined: +\begin{sourcecode} + \NewChemBond{single} + { \draw[chembond] (chemformula-bond-start) -- (chemformula-bond-end) ; } + \NewChemBond{coordright} + { + \draw[chembond,butt cap->] + (chemformula-bond-start) -- (chemformula-bond-end) ; + } + \NewChemBondAlias{co>}{coordright} +\end{sourcecode} +Two points are important: the names of the starting and the ending +coordinates, \code{chemformula-bond-start} and \code{chemformula-bond-end}, +and the \TikZ\ style of the bonds \code{chembond}. + +So, let's say you want to define a special kind of dashed bond. You could do +this: +\begin{example} + \usetikzlibrary{decorations.pathreplacing} + \makeatletter + \NewChemBond{dashed} + { + \draw[ + chembond, + decorate, + decoration={ + ticks, + segment length=\chemformula@bondlength/10,amplitude=1.5pt + }] + (chemformula-bond-start) -- (chemformula-bond-end) ; + } + \makeatother + \setchemformula{bond-length=2ex} + \ch{C\bond{dashed}C} +\end{example} + +The last example showed you another macro: \verbcode+\chemformula@bondlength+. +It only exists so you can use it to access the bond length as set with +\option{bond-length} directly. + +\subsection{Customization}\label{ssec:compounds:customization} +These options allow you to customize the ouptut of the compounds: +\begin{options} + \keyval{subscript-vshift}{dim}\Default{0pt} + Extra vertical shift of the subscripts. + \keychoice{subscript-style}{text,math}\Default{text} + Style that is used to typeset the subscripts. + \keyval{charge-hshift}{dim}\Default{.25em} + Shift of superscripts when following a subscript.\label{desc:charge-hshift} + \keyval{charge-vshift}{dim}\Default{0pt} + Extra vertical shift of the superscripts. + \keychoice{charge-style}{text,math}\Default{text} + Style that is used to typeset the superscripts. + \keychoice{circled}{formal,\default{all},none}\Default{formal} + \sinceversion{4.6}Like \chemmacros' package option but local to + \chemformula's \cs{ch}. That is: since \chemmacros' macros use + \chemformula's mechanism this is effectively an alias. + \keychoice{circletype}{\default{chem},math}\Default{chem} + \sinceversion{4.6}Like \chemmacros' package option but local to + \chemformula's \cs{ch}. That is: since \chemmacros' macros use + \chemformula's mechanism this is effectively an alias. + \keyval{adduct-space}{dim}\Default{.1333em} + Space to the left and the right of the adduct point. + \keyval{adduct-penalty}{num}\Default{300} + The\sinceversion{4.14} penalty inserted after the adduct point for + (dis-)allowing line breaks. + \keyval{bond-length}{dim}\Default{.5833em} + The length of the bonds. + \keyval{bond-offset}{dim}\Default{.07em} + Space between bond and atoms. + \keyval{bond-style}{\TikZ}\Default + \TikZ\ options for the bonds. + \keyval{bond-penalty}{num}\Default{10000} + \sinceversion{4.0a}The penalty that is inserted after a bond for + (dis-)allowing line breaks. + \keyval{radical-style}{\TikZ}\Default + \TikZ\ options for the radical point. + \keyval{radical-radius}{dim}\Default{.2ex} + The radius of the radical point. + \keyval{radical-hshift}{dim}\Default{.15em} + Horizontal shift before the radical point is drawn. + \keyval{radical-vshift}{dim}\Default{.5ex} + Vertical shift relative to the current baseline. + \keyval{radical-space}{dim}\Default{.15em} + Horizontal shift after the radical point is drawn. +\end{options} + +Maybe you have noticed that charges of certain ions are shifted to the +right. +\begin{example}[side-by-side] + \ch{SO4^2-} \ch{NH4+} \ch{Na+} +\end{example} +They are shifted if they \emph{follow} a subscript which follows \ac{iupac} +recommendations~\cite[][p.\,51]{iupac:greenbook}. The amount of the shift can +be set with the option \option{charge-hshift}. +\begin{example} + \ch{SO4^2-} \ch{NH4+} \ch{Na+} \par + \setchemformula{charge-hshift=.5ex} + \ch{SO4^2-} \ch{NH4+} \ch{Na+} \par + \setchemformula{charge-hshift=.5pt} + \ch{SO4^2-} \ch{NH4+} \ch{Na+} +\end{example} + +Despite \ac{iupac}'s recommendation \chemformula\ does not make fully staggered +arrangements in the default setting as I find it hard to read in some cases +and ugly in others. Since this is a subjective decision \chemformula\ not only +let's you define the absolute amount of the shift but also provides a +possibility for full staggered arrangements. For this you have to use +\keyis{charge-hshift}{full}. +\begin{example} + \ch[charge-hshift=0pt]{C5H11+} \ch[charge-hshift=0pt]{SO4^2-} \par + \ch{C5H11+} \ch{SO4^2-} \par + \ch[charge-hshift=1ex]{C5H11+} \ch[charge-hshift=1ex]{SO4^2-} \par + \ch[charge-hshift=full]{C5H11+} \ch[charge-hshift=full]{SO4^2-} +\end{example} + +If you don't want the charges to be typeset in text mode you can switch to +math mode: +\begin{example} + \ch{M^x+} \ch{SO4^2-} \par + \setchemformula{charge-style = math} + \ch{M^x+} \ch{SO4^2-} +\end{example} + +The option \option{subscript-vshift} can be used to adjust the vertical shift +of the subscripts: +\begin{example} + \ch{H2SO4} \ch{Na3PO4} \par + \setchemformula{subscript-vshift=.5ex} + \ch{H2SO4} \ch{Na3PO4} \par + \setchemformula{subscript-vshift=-.2ex} + \ch{H2SO4} \ch{Na3PO4} +\end{example} + +You can choose the mode subscripts are typeset in the same way as it is +possible for the charges: +\begin{example} + \ch{A_nB_m} \ch{H2SO4} \par + \setchemformula{subscript-style = math} + \ch{A_nB_m} \ch{H2SO4} +\end{example} + +The option \option{adduct-space} sets the space left and right to the adduct +symbol $\cdot$. +\begin{example} + \ch{Na3PO3*H2O} \par + \setchemformula{adduct-space=.2em} + \ch{Na3PO3*H2O} +\end{example} + +Changing the length of the bonds: +\begin{example} + \setchemformula{bond-length=4mm}% + single: \ch{CH3-CH3} \par + double: \ch{CH2=CH2} \par + triple: \ch{CH+CH} +\end{example} + +You can change the distance between bond and atom, too: +\begin{example} + \ch{H-H + N+N + O=O} \par + \ch[bond-offset=1pt]{H-H + N+N + O=O} +\end{example} + +\subsection{Standalone Formulae} +\chemformula\sinceversion{4.0} offers a command that \emph{only accepts} the +\enquote{compound} input type: +\begin{commands} + \command{chcpd}[\oarg{options}\marg{compound}] + Typeset single compounds. +\end{commands} + +\subsection{Extend Compound Properties}\label{sec:extend-comp-prop} + +It\sinceversion{4.10} is possible to extend the range of special input symbols +within compounds. In the default setting those are \verbcode|*.-=+'| and +arabic numerals. Others can be added or the existing ones be changed with one +of the following commmands: +\begin{commands} + \command{NewChemCompoundProperty}[\marg{token}\marg{replacement}] + \meta{token} will be replaced by \meta{replacement} within compounds. The + property is only added if \meta{token} is not yet part the compounds' + property list. Otherwise an error is issued. + \command{ProvideChemCompoundProperty}[\marg{token}\marg{replacement}] + \meta{token}\sinceversion{4.12a} will be replaced by \meta{replacement} + within compounds. The property is only added if \meta{token} is not yet + part the compounds' property list. + \command{RenewChemCompoundProperty}[\marg{token}\marg{replacement}] + \meta{token} will be replaced by \meta{replacement} within compounds. The + property is only added if \meta{token} is already part the compounds' + property list. Otherwise an error is issued. + \command{DeclareChemCompoundProperty}[\marg{token}\marg{replacement}] + \meta{token} will be replaced by \meta{replacement} within compounds. The + property silently overwrites any previously set \meta{replacement} for + \meta{token} if \meta{token} is already part the compounds' property + list. + \command{RemoveChemCompoundProperty}[\marg{token}] + Removes \meta{token} from the compounds' property list. +\end{commands} + +For example you can use +\begin{sourcecode} + \NewChemCompoundProperty{\}{\slash} +\end{sourcecode} +to allow line breaks after slashes in compounds. + +\section{Special Input Types} +There are some \enquote{special type} input groups. + +\subsection{Single Token Groups} +The first kind are groups which consist of only one token. They are again +divided into two groups, \enquote{addition symbols} and \enquote{symbols}. + +\subsubsection{Addition Symbols}\label{sec:addition-symbols} +\begin{commands} + \command{ch}[\Marg{ + } \ch{ + }] + Creates the plus sign between compounds with space around it:\\ + \cs{ch}\Marg{2 Na + Cl2} \ch{2 Na + Cl2} + \command{ch}[\Marg{ - } \ch{ - }] + \sinceversion{4.3a}Creates the minus sign between compounds with space + around it:\\ + \cs{ch}\Marg{M - H} \ch{M - H} +\end{commands} +Addition symbols are surrounded with space which can be customized according +to options explained in a bit. There is also some penalty prohibiting a line +break after them which also can be customized with an option. + +You can define/redefine your own addition symbols: +\begin{commands} + \command{NewChemAdditionSymbol}[\marg{name}\marg{input}\marg{output}] + Defines\sinceversion{4.11} the addition symbol \meta{name} with input + symbol \meta{input} and output \meta{output}. + \command{ProvideChemAdditionSymbol}[\marg{name}\marg{input}\marg{output}] + Defines\sinceversion{4.12a} the addition symbol \meta{name} with input + symbol \meta{input} and output \meta{output} only no addition symbol with + then name \meta{name} doesn't exist. + \command{RenewChemAdditionSymbol}[\marg{name}\marg{input}\marg{output}] + Redefines\sinceversion{4.11} the addition symbol \meta{name} with input + symbol \meta{input} and output \meta{output}. + \command{DeclareChemAdditionSymbol}[\marg{name}\marg{input}\marg{output}] + (Re-)Defines\sinceversion{4.11} the addition symbol \meta{name} with input + symbol \meta{input} and output \meta{output} without checking if the + symbol exists or not. +\end{commands} + +The space left and right of the plus and the minus sign and the signs +themselves can be set with the following options: +\begin{options} + \keyval{plus-space}{skip}\Default{.3em plus .1em minus .1em} + A rubber length. + \keyval{plus-penalty}{num}\Default{700} + \sinceversion{4.0a}The penalty that is inserted after the plus sign for + (dis-)allowing line breaks. + \keyval{plus-output-symbol}{code}\Default{+} + \sinceversion{4.9}The \meta{code} that is used for the plus sign. + \keyval{minus-space}{skip}\Default{.3em plus .1em minus .1em} + \sinceversion{4.9}A rubber length. + \keyval{minus-penalty}{num}\Default{700} + \sinceversion{4.9}The penalty that is inserted after the minus sign for + (dis-)allowing line breaks. + \keyval{minus-output-symbol}{code}\Default{\$-\$} + \sinceversion{4.9}The \meta{code} that is used for the minus sign. +\end{options} +The corresponding three options are defined when \cs{NewChemAdditionSymbol} +or one of the variants is used, \code{\meta{name}-space} and +\code{\meta{name}-penalty} both with the same defaults as above, and +\code{\meta{name}-output-symbol}. + +\begin{example}[side-by-side] + \ch{A + B}\par + \ch[plus-space=4pt]{A + B} +\end{example} + +\subsubsection{Symbols}\label{sec:symbols} +\begin{commands} + \command{ch}[\Marg{ v } \ch{ v }] + Sign for precipitate: \cs{ch}\Marg{BaSO4 v} \ch{BaSO4 v} + \command{ch}[\Marg{ \textasciicircum\ } \ch{ ^ }] + Sign for escaping gas\footnotemark: \cs{ch}\Marg{H2 \textasciicircum} + \ch{H2 ^} +\end{commands} +\footnotetext{Is this the correct English term? Please correct me if it isn't.} + +You can define/redefine your own symbols: +\begin{commands} + \command{NewChemSymbol}[\marg{input}\marg{output}] + Defines\sinceversion{4.11} the addition symbol with input \meta{input} and + output \meta{output}. + \command{ProvideChemSymbol}[\marg{input}\marg{output}] + Defines\sinceversion{4.12a} the addition symbol with input \meta{input} and + output \meta{output} only if no symbol with input \meta{input} exists. + \command{RenewChemSymbol}[\marg{input}\marg{output}] + Redefines\sinceversion{4.11} the addition symbol with input \meta{input} + and output \meta{output}. + \command{DeclareChemSymbol}[\marg{input}\marg{output}] + (Re-)Defines\sinceversion{4.11} the addition symbol with input + \meta{input} and output \meta{output} without checking if the symbol + exists or not. +\end{commands} + +\subsection{Option Input} +Sometimes you might want to apply an option only to a part of a, say, +reaction. Of course you have the possibility to use \cs{ch} several times. +\begin{example} + \ch{H2O +}\textcolor{red}{\ch{H2SO4}}\ch{-> H3O+ + HSO4-} \par + \ch{H2O +}\ch[subscript-vshift=2pt]{H2SO4}\ch{-> H3O+ + HSO4-} +\end{example} +This, however, interrupts the input in your source and \emph{may} mess with +the spacing. That's why there is an alternative: +\begin{commands} + \command{ch}[\Marg{ @\marg{options} }] + The options specified this way will be valid \emph{only} until the next + compound is set. +\end{commands} +\begin{example} + \ch{H2O +}\textcolor{red}{\ch{H2SO4}}\ch{-> H3O+ + HSO4-} \par + \ch{H2O + @{format=\color{red}} H2SO4 -> H3O+ + HSO4-} \par + or of course:\par + \ch{H2O + \textcolor{red}{H2SO4} -> H3O+ + HSO4-}\par\bigskip + \ch{H2O +}\ch[subscript-vshift=2pt]{H2SO4}\ch{-> H3O+ + HSO4-} \par + \ch{H2O + @{subscript-vshift=2pt} H2SO4 -> H3O+ + HSO4-} +\end{example} + +\section{Escaped Input} +In some cases it may be desirable to prevent \chemformula\ from parsing the +input. This can be done in two ways. + +\subsection{Text}\label{ssec:text} +If you put something between \verbcode+" "+ or \verbcode+' '+ then the input +will be treated as normal text, except that spaces are not allowed and have to +be input with \verbcode+~+. +\begin{commands} + \command{ch}[\Marg{ "\meta{escaped text}" }] + One of two possibilities to \emph{escape} \chemformula's parsing. + \command{ch}[\Marg{ \textquotesingle\meta{escaped text}\textquotesingle\ }] + The second of two possibilities to \emph{escape} \chemformula's parsing. +\end{commands} +\begin{example}[add-sourcecode-options={literate=}] + \ch{"\ox{2,Ca}" O} \par + \ch{"\ldots\," Na + "\ldots\," Cl2 -> "\ldots\," NaCl} \par + \ch{'A~->~B'} +\end{example} +In many cases you won't need to escape the input. But when you get into +trouble when using a command inside \cs{ch} try hiding it. + +\subsection{Math} +If you especially want to input math you just enclose it with \verbcode+$ $+. +This output is different from the escaped text as it is followed by a space. +The reasoning behind this is that I assume math will mostly be used to replace +stoichiometric factors. +\begin{commands} + \command{ch}[\Marg{ \string$\meta{escaped math}\string$ }] + One of two possibilities to \emph{escape} \chemformula's parsing into math + mode. + \command{ch}[\Marg{ \string\(\meta{escaped math}\string\) }] + The second of two possibilities to \emph{escape} \chemformula's parsing + into math mode. +\end{commands} +\begin{example}[side-by-side] + escaped text: \ch{"$x$" H2O} \par + escaped math: \ch{$x$ H2O} \par + also escaped math: \ch{\(x\) H2O} \par + \ch{$2n$ Na + $n$ Cl2 -> $2n$ NaCl} +\end{example} + +The space that is inserted after a math group can be edited: +\begin{options} + \keyval{math-space}{skip}\Default{.1667em plus .0333em minus .0117em} + A rubber length. +\end{options} +\begin{example} + \ch{$2n$ Na + $n$ Cl2 -> $2n$ NaCl} \par + \setchemformula{math-space=.25em} + \ch{$2n$ Na + $n$ Cl2 -> $2n$ NaCl} \par + \ch{$A->B$} +\end{example} + +\section{Arrows}\label{sec:arrows} +\subsection{Arrow types} +Arrows are input in the same intuitive way they are with \pkg{mhchem}. +There are various different types: +\begin{arrows} + \arrow{->}[ \charrow{->}] + standard right arrow + \arrow{<-}[ \charrow{<-}] + standard left arrow + \arrow{-/>}[ \charrow{-/>}] + does not react (right) + \arrow{</-}[ \charrow{</-}] + does not react (left) + \arrow{<->}[ \charrow{<->}] + resonance arrow + \arrow{<>}[ \charrow{<>}] + reaction in both directions + \arrow{==}[ \charrow{==}] + stoichiometric equation + \arrow{<=>}[ \charrow{<=>}] + equilibrium arrow + \arrow{>=<}[ \charrow{>=<}] + \sinceversion{4.5}reversed equilibrium arrow + \arrow{<=>{}>}[ \charrow{<=>>}] + unbalanced equilibrium arrow to the right + \arrow{>=<{}<}[ \charrow{>=<<}] + \sinceversion{4.5}reversed unbalanced equilibrium arrow to the right + \arrow{<{}<=>}[ \charrow{<<=>}] + unbalanced equilibrium arrow to the left + \arrow{>{}>=<}[ \charrow{>>=<}] + \sinceversion{4.5}reversed unbalanced equilibrium arrow to the left + \arrow{<=o>}[ \charrow{<=o>}] + \sinceversion{4.15}quasi equilibrium arrow + \arrow{<=o>{}>}[ \charrow{<=o>>}] + \sinceversion{4.15}unbalanced quasi equilibrium arrow to the right + \arrow{<{}<=o>}[ \charrow{<<=o>}] + \sinceversion{4.15}unbalanced quasi equilibrium arrow to the left + \arrow{<o>}[ \charrow{<o>}] + isolobal arrow + \arrow{<==>}[ \charrow{<==>}] + \sinceversion{4.5}I've seen this one used. I'm not sure it actually has a + meaning in chemical equations. If you have some official reference for + this arrow type please feel free to contact me. +\end{arrows} +All these arrows are drawn with \TikZ. +\begin{example} + \ch{H2 + Cl2 -> 2 HCl} \par + \ch{H2O + CO3^2- <=> OH- + HCO3-} \par + \ch{A <- B} \par + \ch{\{[CH2=CH-CH2]- <-> {}[CH2-CH=CH2]- \}} \par + \ch{A <> B} \par + \ch{H+ + OH- <=>> H2O} \par + \ch{2 NO2 <<=> N2O4} +\end{example} + +\subsection{Labels} +The arrows take two optional arguments to label them. +\begin{arrows} + \arrow*{->\oarg{above}\oarg{below}} + Add text above or under an arrow. +\end{arrows} +\begin{example}[side-by-side] + \ch{A ->[a] B} \par + \ch{A ->[a][b] B} \par + \ch{A ->[\SI{100}{\celsius}] B} +\end{example} +The label text can be parsed seperately from the arrow. The recipe is easy: +leave blanks. +\begin{example}[side-by-side] + \ch{A ->[H2O] B} \par + \ch{A ->[ H2O ] B} \par + \ch{A ->[ "\ox{2,Ca}" F2 ] B} \par + \ch{A ->[ $\Delta$,~ [ H+ ]] B} +\end{example} + +If you leave the blanks \chemformula\ treats the groups inside the square +brackets as seperated input types. The arrow reads its arguments +\emph{afterwards}. As you can see the arrows \enquote{grow} with the length +of the labels. What stays constant is the part that protrudes the labels. +\begin{example} + \ch{A ->[a] B} \par + \ch{A ->[ab] B} \par + \ch{A ->[abc] B} \par + \ch{A ->[abc~abc] B} \par + % needs the `chemfig' package: + \setchemfig{atom sep =15pt} + \ch{A ->[ "\chemfig{-[:30]-[:-30]OH}" ] B} \par +\end{example} + +\subsection{Customization} +These are the options which enable you to customize the arrows: +\begin{options} + \keyval{arrow-offset}{dim}\Default{.75em} + This is the length that an arrow protrudes a label on both sides. This + means an empty arrow's length is two times \code{arrow-offset}. + \keyval{arrow-min-length}{dim}\Default{0pt} + \sinceversion{3.6b}The minimal length an error must have unless two times + \option{arrow-offset} plus the width of the label is larger. + \keyval{arrow-yshift}{dim}\Default{0pt} + Shifts an arrow up (positive value) or down (negative value). + \keyval{arrow-ratio}{<factor>}\Default{.6} + The ratio of the arrow lengths of the unbalanced equilibrium. \code{.4} + would mean that the length of the shorter arrow is $0.4\times$ the length + of the longer arrow. + \keyval{compound-sep}{dim}\Default{.5em} + The space between compounds and the arrows. + \keyval{label-offset}{dim}\Default{2pt} + The space between the labels and the arrows. + \keyval{label-style}{font command}\Default{\cs*{footnotesize}} + The relative font size of the labels. + \keyval{arrow-penalty}{num}\Default{0} + \sinceversion{4.0a}The penalty that is inserted after an arrow for + (dis-)allowing line breaks. + \keyval{arrow-style}{\TikZ}\Default + \sinceversion{4.1a}Additonal \TikZ\ keys for formatting the arrows. +\end{options} + +The following code shows the effect of the different options on the \verbcode+<=>>+ +arrow: +\begin{example} + standard: \ch{A <=>>[x][y] B} \par + longer: \ch[arrow-offset=12pt]{A <=>>[x][y] B} \par + higher: \ch[arrow-yshift=2pt]{A <=>>[x][y] B} \par + more balanced: \ch[arrow-ratio=.8]{A <=>>[x][y] B} \par + labels further away: \ch[label-offset=4pt]{A <=>>[x][y] B} \par + larger distance to compounds: \ch[compound-sep=2ex]{A <=>>[x][y] B} \par + smaller labels: \ch[label-style=\tiny]{A <=>[x][y] B} +\end{example} + +If you want to have different arrow tips\sinceversion{4.7} there is an easy +way to use existing arrow tips (as defined by \TikZ). \chemformula\ uses +three different arrow tips: \code{cf}, \code{left cf} and \code{right cf}. If +you want them to match those of \pkg{chemfig}~\cite{pkg:chemfig} for example +you could do: +\begin{sourcecode} + \pgfkeys{ + cf /.tip = {CF@full} , + left cf /.tip = {CF@half} + } +\end{sourcecode} +\pkg{chemfig} has no equivalent of \code{right cf}. This mechanism relies on +\TikZ\ version~3.0.0 and the new \code{arrows.meta} library. + +\subsection{Modify Arrow Types}\label{sec:arrows_modify} +The arrows are defined with the commands +\begin{commands} + \command{NewChemArrow}[\marg{type}\marg{\TikZ}] + Define the new arrow type \meta{type}. Issue an error if an arrow type + \meta{type} already exists. + \command{ProvideChemArrow}[\marg{type}\marg{\TikZ}] + Define\sinceversion{4.12a} the new arrow type \meta{type} only if it + doesn't exist, yet. + \command{DeclareChemArrow}[\marg{type}\marg{\TikZ}] + Define the new arrow type \meta{type} or overwrite it if it already + exists. + \command{RenewChemArrow}[\marg{type}\marg{\TikZ}] + Redefine the arrow type \meta{type}. Issue an error if an arrow type + \meta{type} doesn't exist. + \command{ShowChemArrow}[\marg{type}] + Print out the current definition of the arrow type \meta{type}. +\end{commands} +\meta{type} is the sequence of tokens that is replaced with the actual arrow +code. For example the basic arrow is defined via +\begin{sourcecode} + \NewChemArrow{->}{ + \draw[chemarrow,-cf] (cf_arrow_start) -- (cf_arrow_end) ; + } +\end{sourcecode} +In order to define arrows yourself you need to know the basics of +\TikZ\footnote{Please see the \manual{pgfmanual} for details.}. The +predefined arrows use the arrow tips \code{cf}, \code{left cf} and \code{right + cf}. They also all except the net reaction arrow \code{==} use the +\TikZ-style \code{chemarrow} that you should use, too, if you want the option +\option{arrow-style} to have an effect. + +There are some predefined coordinates you can and should use. For +completeness' sake the arrow tips and the \TikZ-style are also listed: +\begin{codedesc} + \Code{(cf\_arrow\_start)} + The beginning of the arrow. + \Code{(cf\_arrow\_end)} + The end of the arrow. + \Code{(cf\_arrow\_mid)} + The mid of the arrow. + \Code{(cf\_arrow\_mid\_start)} + The beginning of the shorter arrow in types like \verbcode+<=>>+. + \Code{(cf\_arrow\_mid\_end)} + The end of the shorter arrow in types like \verbcode+<=>>+. + \Code{cf} + A double-sided arrow tip. + \Code{left cf} + A left-sided arrow tip. + \Code{right cf} + A right-sided arrow tip. + \Code{chemarrow} + \chemformula's \TikZ-style that is applied to the arrows and set with + \option{arrow-style} +\end{codedesc} +\begin{example} + \NewChemArrow{.>}{ + \draw[chemarrow,-cf,dotted,red] (cf_arrow_start) -- (cf_arrow_end); + } + \NewChemArrow{n>}{ + \draw[chemarrow,-cf] + (cf_arrow_start) + .. controls ([yshift=3ex]cf_arrow_mid) .. + (cf_arrow_end); + } + \ch{A .> B} \ch{A .>[a][b] B} \ch{A n> B} +\end{example} + +\begin{example} + \texttt{\ShowChemArrow{->}} \par + \RenewChemArrow{->}{\draw[chemarrow,->,red] (cf_arrow_start) -- (cf_arrow_end) ;} + \texttt{\ShowChemArrow{->}} \par + \ch{A -> B} +\end{example} + +\subsection{Standalone Arrows} +\chemformula\ offers\sinceversion{4.0} a command that \emph{only accepts} the +\enquote{arrow} input type: +\begin{commands} + \command{charrow}[\marg{type}\oarg{above}\oarg{below}] + Print the arrow type \meta{type}. +\end{commands} +This command is internally used for the arrows, too, when \cs{ch} is parsed. + +\section{Names} +\subsection{Syntax} +\chemformula\ has a built-in syntax to write text under a compound. In a way +it works very similar to the arrows. +\begin{commands} + \command{ch}[\Marg{ !(\meta{text})( \meta{formula} ) }] + Writes \meta{text} below \meta{formula}. +\end{commands} +If an exclamation mark is followed by a pair of parentheses \chemformula\ will +parse it this way: +\begin{example} + \ch{!(ethanol)( CH3CH2OH )} +\end{example} +The same what's true for the arrows arguments holds for these arguments: if +you leave blanks the different parts will be treated according to their input +type before the text is set below the formula. +\begin{example} + \ch{!(water)(H2O)} \quad + \ch{!( "\textcolor{blue}{water}" )( H2O )} \quad + \ch{!( $2n-1$ )( H2O )} \quad + \ch{!( H2O )( H2O )} \quad + \ch{!(oxonium)( H3O+ )} +\end{example} +If for some reason you want to insert an exclamation mark \emph{without} it +creating a name you only have to make sure it isn't followed by parentheses. +\begin{example}[side-by-side] + \ch{H2O~(!)} \par + \ch{A!{}()} +\end{example} + +\subsection{Customization} +\chemformula\ provides two options to customize the output of the names: +\begin{options} + \keyval{name-format}{commands}\Default{\cs*{scriptsize}\cs*{centering}} + The format of the name. This can be arbitrary input. + \keychoice{name-width}{\meta{dim},auto}\Default{auto} + The width of the box where the label is put into. \code{auto} will detect + the width of the name and set the box to this width. +\end{options} +\begin{example} + \ch{!(acid)( H2SO4 ) -> B} \par + \ch[name-format=\sffamily\small]{!(acid)( H2SO4 ) -> B} \par + \ch[name-format=\scriptsize N:~]{!(acid)( H2SO4 ) -> B} \par + \ch[name-width=3em,name-format=\scriptsize\raggedright]{!(acid)( H2SO4 ) -> B} +\end{example} + +\subsection{Standalone Names} +\chemformula\ offers a command\sinceversion{4.0} that allows the usage of the +\enquote{name} syntax in normal text. This is the command that a bang is +replaced with in \chemformula's formulas, actually. Both arguments are +mandatory. +\begin{commands} + \command{chname}[\darg{text~1}\darg{text~2}] + The command that is useed internally for placing \meta{text~1} below of + \meta{text~2}. +\end{commands} + +\section{Format and Font}\label{sec:format} +In the standard setting \chemformula\ doesn't make any default changes to the +font of the formula output. Let's take a look at a nonsense input which shows +all features: +\begin{example}[pre-output={\biolinumLF\libertineLF\setchemformula{format=}}] + \newcommand*\sample{% + \ch{H2C-C+C-CH=CH+ + CrO4^2- + <=>[x][y] + 2.5 Cl^{-.} + 3_1/2 Na*OH_{(aq)} + !(name)( A^n ) "\LaTeXe"} + } + \sample +\end{example} +\newcommand*\sample{% + \ch{H2C-C+C-CH=CH+ + CrO4^2- + <=>[x][y] + 2.5 Cl^{-.} + 3_1/2 Na*OH_{(aq)} + !(name)( A^n ) "\LaTeXe"} +} + +Now we're going to change different aspects of the font a look what happens: +\begin{example}[pre-output={\biolinumLF\libertineLF\setchemformula{format=}}] + \sffamily Hallo \sample \\ + \ttfamily Hallo \sample \normalfont \\ + \bfseries Hallo \sample \normalfont \\ + \itshape Hallo \sample +\end{example} +As you can see most features adapt to the surrounding font. + +If you want to change the default format you need to use this option: +\begin{options} + \keyval{format}{code}\Default + Adds \meta{code} before the output of \cs{ch}. + \keyval{atom-format}{code}\Default + This\sinceversion{4.13} adds \meta{code} before each formula. This + allows to specify a format for the chemical formulas only and have a + different format for the rest of the chemical equation. +\end{options} +\begin{example}[pre-output={\biolinumLF\libertineLF\setchemformula{format=}}] + \definecolor{newblue}{rgb}{.1,.1,.5} + \setchemformula{format=\color{newblue}\sffamily} + \sffamily Hallo \sample \\ + \ttfamily Hallo \sample \normalfont \\ + \bfseries Hallo \sample \normalfont \\ + \itshape Hallo \sample +\end{example} + +You can also specifically change the fontfamily, fontseries and fontshape of +the output. +\begin{options} + \keyval{font-family}{family}\Default + Changes the fontfamily of the output with \cs*{fontfamily}\marg{family}. + \keyval{font-series}{series}\Default + Changes the fontseries of the output with \cs*{fontseries}\marg{series}. + \keyval{font-shape}{shape}\Default + Changes the fontshape of the output with \cs*{fontshape}\marg{shape}. +\end{options} +\begin{example}[pre-output={\biolinumLF\libertineLF\setchemformula{format=}}] + \setchemformula{font-series=bx} + Hallo \sample \par + \sffamily Hallo \sample \normalfont \par + \setchemformula{font-family=lmss,font-series=m} Hallo \sample + \normalfont \par + \itshape Hallo \sample +\end{example} + +If you're using \XeLaTeX\ or \LuaLaTeX\ and have loaded \pkg{fontspec} you +have the possibilty to set the font with it: +\begin{options} + \keyval{font-spec}{font}\Default + Use font \meta{font} for \chemformula's formulas. +\end{options} +or with options +\begin{options} + \keychoice{font-spec}{\Marg{[\meta{options}]\meta{font}}} + Use font \meta{font} with options \meta{options} for \chemformula's + formulas. +\end{options} +Since this document is typeset with \pdfLaTeX\ the option cannot be +demonstrated here. + +\section{Usage In Math Equations} +The \cs{ch} command can be used inside math equations. It recognizes +\verbcode+\\+ and \verbcode+&+ and passes them on. However, you can't use the +optional arguments of \verbcode+\\+ inside \cs{ch}. +\begin{example} + \begin{align} + \ch{ + H2O & ->[a] H2SO4 \\ + Cl2 & ->[x][y] CH4 + } + \end{align} + \begin{align*} + \ch{ + RNO2 &<=>[ + e- ] RNO2^{-.} \\ + RNO2^{-.} &<=>[ + e- ] RNO2^2- + } + \end{align*} +\end{example} + +\section{Usage with \TikZ\ or \pkg*{pgfplots} and externalization} +Since \chemformula\ uses\sinceversion{4.1} \TikZ\ to draw reaction arrows +and bonds they would be externalized, too, if you use that facility with +\TikZ\ or \needpackage{pgfplots}~\cite{pkg:pgfplots}. This may not be +desirable since they are very small pictures maybe containing of a single +line. This is why \chemformula's default behaviour is to disable +externalization for it's bonds and arrows. This can be turned on and off +through the following option: +\begin{options} + \keybool{tikz-external-disable}\Default{true} + dis- or enable \TikZ' externalization mechanism for \chemformula's arrows + and bonds. +\end{options} + +If you should be using a formula that contains bonds or arrows inside of a +\code{tikzpicture} that is externalized you should locally enable it for +\chemformula, too: + +\begin{sourcecode} + \begin{tikzpicture} + \setchemformula{tikz-external-disable=false} + \begin{axis}[xlabel={\ch{2 H+ + 2 e- -> H2}}] + \addplot ... ; + \end{axis} + \end{tikzpicture} +\end{sourcecode} + +\section{Lewis Formulae}\label{sec:lewis-formulae} +\chemformula\ offers\sinceversion{4.2} a command to typeset Lewis formulae. +This does not mean Lewis structures! Those can be achieved using the +\pkg{chemfig} package~\cite{pkg:chemfig}. \chemformula\ provides the +possibility to draw electrons as dots and pairs of dots or a line around an +atom. + +\begin{commands} + \command{chlewis}[\oarg{options}\marg{electron spec}\marg{atom}] + Draws electrons around the \meta{atom} according to \meta{electron spec}. +\end{commands} + +Electrons are specified by the angle to the horizontal in the couter-clockwise +direction. The default appearance is a pair of electrons drawn as a pair of +dots. Other specifications can be chosen. The specification follows the +pattern \meta{angle}\meta{separator}. \meta{angle} is a positiv or negativ +integer denoting the angle counter clockwise to the horizontal where the +electrons should be drawn. \meta{separator} is either a dot (\code{.}, single +electron), a colon (\code{:}, electron pair), a vertical line (\code{|}, +electron pair), an o (\code{o}, empty pair), or a comma (\code{,} default +spec). + +\begin{commands} + \command{chlewis}[\Marg{\meta{angle1}\meta{type1}\meta{angle2}\meta{type2}}% + \marg{atom}] + For example: \cs{chlewis}\Marg{0,180}\Marg{O} gives \chlewis{0,180}{O} and + \cs{chlewis}\Marg{0.90.180.270.}\Marg{C} gives + \chlewis{0.90.180.270.}{C}. +\end{commands} + +The appearance can be influenced by a number of options: +\begin{options} + \keychoice{lewis-default}{.,:,|,o,single,pair,pair (dotted),pair + (line),empty}\Default{pair} + Sets the default type that is used when no type is given in \meta{electron + spec}. + \keyval{lewis-distance}{dim}\Default{1ex} + The distance of two electrons in a pair. + \keyval{lewis-line-length}{dim}\Default{1.5ex} + The length of the line representing an electron pair. + \keyval{lewis-line-width}{dim}\Default{1pt} + The thickness of a line representing an electron pair. + \keyval{lewis-offset}{dim}\Default{.5ex} + The distance of the symbols from the atom. +\end{options} +The dots are drawn according to the \option{radical-radius} option mentioned +in section~\ref{ssec:compounds:customization}. + +The basic usage should be more or less self-explaining: +\begin{example}[side-by-side] + \chlewis{0:90|180.270}{O} + \quad + \chlewis{45,135}{O} + \quad + \chlewis{0o}{Na} +\end{example} + +The next example shows the effect of some of the options: +\begin{example} + \chlewis[lewis-default=.]{23,68,113,158,203,248,293,338}{X} + \quad + \chlewis{0,90,180,270}{X} + \quad + \chlewis[lewis-distance=1.25ex]{0,90,180,270}{X} + \quad + \chlewis[lewis-distance=.75ex,radical-radius=.5pt]{0,90,180,270}{X} + \quad + \chlewis[ + radical-radius=.5pt, + lewis-default=. + ]{23,68,113,158,203,248,293,338}{X} +\end{example} + +\begin{example} + \ch{ + !($1s^22s^1$)( "\chlewis{180.}{Li}" ) + + !($1s^22s^22p^5$)( "\chlewis{0.90,180,270}{F}" ) + -> + !($1s^2$)( Li+ ) + !($1s^22s^22p^6$)( "\chlewis{0,90,180,270}{F}" {}- ) + } +\end{example} + +\section{Kröger-Vink Notation}\label{sec:kroger-vink-notation} + +\chemformula\ also supports the Kröger-Vink notation\sinceversion{4.5}. +\begin{options} + \keybool{kroeger-vink}\Default{false} + Enable the Kröger-Vink notation. As most options this can be enabled + globally via the setup command or locally as option to \cs{ch}. +\end{options} + +With this option enabled several changes come into effect: \verbcode|'| +produces a prime, a \code{x} in a superscript produces $\times$, and both a +\code{.} and a \code{*} produce a little filled circle. In the Kröger-Vink +notation a prime denotes a negative relative charge, the circle a positive +relative charge, and the cross denotes a neutral relative charge. + +\begin{example}[side-by-side,add-sourcecode-options={literate=}] + \setchemformula{kroeger-vink=true} + \ch{Al_{Al}^'} + \ch{Al_{Al}'}\par + \ch{Ni_{Cu}^{x}}\par + \ch{V_{Cl}^.} + \ch{V_{Cl}^*}\par + \ch{Ca_i^{..}}\par + \ch{e^'}\par + \ch{Cl_i^'} + \ch{Cl_i'}\par + \ch{O_i^{''}} + \ch{O_i''} +\end{example} + +There are a number of options for customizations: +\begin{options} + \keyval{kv-positive-style}{\TikZ}\Default + \TikZ\ code for positive charge dot. + \keyval{kv-positive-radius}{dim}\Default{.3ex} + Radius of positive charge dot + \keyval{kv-positive-hshift}{dim}\Default{.15em} + Horizontal shift of positive charge dot + \keyval{kv-positive-vshift}{dim}\Default{.5ex} + Vertical shift positive charge dot + \keyval{kv-positive-offset}{dim}\Default{.4em} + The offset of two consecutive positive charge dots + \keyval{kv-neutral-symbol}{\TeX\ code}\Default{\$\cs*{times}\$} + Symbol for neutral particles. +\end{options} + +\appendix +\newenvironment{changes}[2][]{% + \subsection*{Version #2\ifblank{#1}{}{ (#1)}} + \itemize\let\change\item +}{\enditemize} + +\section{History Since Version~4.0} + +\begin{changes}{4.0} + \change Since version 4.0\sinceversion{4.0}, the \chemformula\ package is + distributed independently from \chemmacros. +\end{changes} + +\begin{changes}{4.1} + \change New option \option{tikz-external-disable}. + \change New option \option{frac-math-cmd}. +\end{changes} + +\begin{changes}{4.2} + \change New option \option{arrow-style}. + \change New command \cs{chlewis} that allows to add Lewis electrons to an + atom, see section~\ref{sec:lewis-formulae}. +\end{changes} + +\begin{changes}{4.3} + \change New option \option{stoich-print}. + \change New command \cs{chstoich}. + \change The commands \cs*{DeclareChem\meta{...}} now don't give an error any + more if the command already exists. This is more consistent with \LaTeX's + \cs*{DeclareRobustCommand}. For all those commands a version + \cs*{NewChem\meta{...}} is introduced that \emph{does} give an error if + the new command is already defined. +\end{changes} + +\begin{changes}{4.4} + \change A single dash \code{-} in \cs{ch} is now treated as a minus sign. + This is consistent with the behaviour of a \code{+}. +\end{changes} + +\begin{changes}{4.5} + \change New arrow types \arrowtype{>=<}, \arrowtype{>=<{}<}, \arrowtype{>{}>=<} + and \arrowtype{<==>}. + \change Internal changes to \cs{ch} allow usage of optional arguments of + \cs*{\textbackslash} and \cs*{label} in \chemmacros' \env*{reactions} + environment. +\end{changes} + +\begin{changes}{4.6} + \change New options \option{circled} and \option{circletype}. this allows to + set the behaviour as described on \chemmacros' manual for a specific usage + of \cs{ch}. +\end{changes} + +\begin{changes}{4.7} + \change Dependency change: \chemformula\ now requires the \TikZ\ library + \code{arrows.meta} instead of the library \code{arrows}. This requires + \TikZ\ version~3.0.0. +\end{changes} + +\begin{changes}{4.8} + \change The \chemformula\ package now is no longer part of the \chemmacros\ + bundle but is distributed as a package of it's own. +\end{changes} + +\begin{changes}{4.9} + \change New options \option{minus-space} and \option{minus-penalty} equivalent + to the existing \option{plus-space} and \option{plus-penalty} + \change New options \option{plus-output-symbol} and + \option{minus-output-symbol} for customizing the plus and minus signs in + the output. +\end{changes} + +\begin{changes}{4.10} + \change New macro set \cs{NewChemCompoundProperty}, see + section~\ref{sec:extend-comp-prop} for a description. +\end{changes} + +\begin{changes}{4.11} + \change New macro set \cs{NewChemAdditionSymbol}, see + section~\ref{sec:addition-symbols}. + \change New macro set \cs{NewChemSymbol}, see section~\ref{sec:symbols}. +\end{changes} + +\begin{changes}{4.12} + \change Change package requirement: \chemformula\ now not loads complete + \pkg{amsmath} but only \pkg{amstext}. +\end{changes} + +\begin{changes}{4.13} + \change Check for blank input parts and don't process them. + \change Drop support for \cs*{[} and \cs*{]} as replacement for \code{[} and + \code{]} inside arrow captions. + \change New option \option{atom-format}. +\end{changes} + +\begin{changes}{4.14} + \change New option \option{adduct-penalty}. +\end{changes} + +\begin{changes}{4.15} + \change The order of arrow definitions doesn't matter any more. + \change New quasi equilibria arrows. + \change Require \pkg{amsmath}. + \change Allow \option{name-format} to end with a macro that takes an + argument. + \change Various bug fixes. +\end{changes} + +\end{document} |