manual/macros.tex

   1 %
   2 % This file is part of the GROMACS molecular simulation package.
   3 %
   4 % Copyright (c) 2013, by the GROMACS development team, led by
   5 % Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6 % and including many others, as listed in the AUTHORS file in the
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  17 % Lesser General Public License for more details.
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  28 % derived work must not be called official GROMACS. Details are found
  29 % in the README & COPYING files - if they are missing, get the
  30 % official version at http://www.gromacs.org.
  31 %
  32 % To help us fund GROMACS development, we humbly ask that you cite
  33 % the research papers on the package. Check out http://www.gromacs.org.
  34
  35 \setlength {\parindent}{0.0cm}
  36 \setlength {\parskip}{1ex}
  37 \newcommand{\ve}[1]{\mbox{\boldmath ${#1}$}}
  38   % defines bold italic vectors. To be used in text or math mode.
  39   % Example: \ve{F}
  40 \newcommand{\de}{\mbox{d}}
  41   % defines a straight d for derivatives.
  42 \newcommand{\intel}{Intel {\em i\/}860}
  43 \newcommand{\gromacs}{GROMACS}
  44 \newcommand{\gromosv}[1]{GROMOS-#1}
  45 \newcommand{\gromos}{GROMOS}
  46 \newcommand{\dline}{\hline\hline}
  47 \newcommand{\etal}{{\em et al.}}
  48 \newcommand{\beq}{\begin{equation}}
  49 \newcommand{\eeq}{\end{equation}}
  50 \newcommand{\bea}{\begin{eqnarray}}
  51 \newcommand{\eea}{\end{eqnarray}}
  52 \newcommand{\Dt}{{\Delta t}}
  53 \newcommand{\half}{\frac{1}{2}}
  54 \newcommand{\hDt}{\half \Dt}
  55 \newcommand{\rvi}{\ve{r}_i}
  56 \newcommand{\rvj}{\ve{r}_j}
  57 \newcommand{\rvk}{\ve{r}_k}
  58 \newcommand{\rij}{r_{ij}}
  59 \newcommand{\rvij}{\ve{r}_{ij}}
  60 \newcommand{\rnorm}{\frac{\rvij}{\rij}}
  61 \newcommand{\Fvi}{\ve{F}_i}
  62 \newcommand{\Fvj}{\ve{F}_j}
  63 \newcommand{\Fvk}{\ve{F}_k}
  64 \newcommand{\Fvij}{\ve{F}_{ij}}
  65 \newcommand{\Fvji}{\ve{F}_{ji}}
  66 \newcommand{\vvi}{\ve{v}_i}
  67 \newcommand{\al}{\alpha}
  68 \newcommand{\be}{\beta}
  69 \newcommand{\ab}{\alpha\beta}
  70 \newcommand{\rnij}{\ve{r}_{ij}^n}
  71 \newcommand{\rni}{\ve{r}_i^n}
  72 \newcommand{\hdt}{\frac{\Delta t}{2}}
  73 %\newcommand{\type}[1]{\\ {\tt \% #1}\\}
  74 \newcommand{\normindex}[1]{#1{\index{#1}}}
  75 \newcommand{\seeindexquiet}[2]{\index{#1|see{#2}}}
  76 \newcommand{\seeindex}[2]{#1{\seeindexquiet{#1}{#2}}}
  77 \newcommand{\swapindexquiet}[2]{{\index{#1 #2}}{\seeindexquiet{#2, #1}{#1 #2}}}
  78 \newcommand{\swapindex}[2]{{\normindex{#1 #2}}{\seeindexquiet{#2, #1}{#1 #2}}}
  79 \newcommand{\swapindexthreequiet}[3]{{\index{#1 #2 #3}}{\seeindexquiet{#2!#3!#1}{#1 #2 #3}}}
  80 \newcommand{\swapindexthree}[3]{{\normindex{#1 #2 #3}}{\seeindexquiet{#2!#3!#1}{#1 #2 #3}}}
  81 \newcommand{\pawsindexquiet}[2]{{\seeindexquiet{#1 #2}{#2, #1}}{\index{#2, #1}}}
  82 \newcommand{\pawsindex}[2]{#1 #2{\pawsindexquiet{#1}{#2}}}
  83 \newcommand{\boldindex}[1]{#1\index{#1@\textbf{#1}}}
  84 \newcommand{\eg}{\em e.g.\@}
  85 \newcommand{\ie}{\em i.e.\@}
  86 \newcommand{\mc}[3]{\multicolumn{#1}{#2}{#3}}
  87
  88 % Commands for correct spacing in tables
  89 %       TeX and TUG News, Vol.2, No.3, p10, 1993.
  90 %
  91 \newcommand\T{\rule{0pt}{2.6ex}}         % Top strut
  92 \newcommand\B{\rule[-1.2ex]{0pt}{0pt}}   % Bottom strut
  93 \newcommand{\Ts}{\rule{0pt}{2.4ex}}      % Smaller top strut (To be used in
  94                                          % math mode in \frac, together with
  95                                          % \displaystyle
  96
  97 \newcommand{\captspace}{\vspace{2mm}}
  98
  99 \newif\ifpdfman
 100 \ifx\pdfoutput\undefined
 101   \pdfmanfalse % not using pdflatex
 102 \else
 103   \pdfoutput=1 % using pdflatex
 104   \pdfmantrue
 105 \fi
 106
 107 \ifpdfman
 108   \usepackage[pdftex]{graphicx}
 109   \usepackage[pdftex,plainpages=false,pdfpagelabels,colorlinks=true,urlcolor=blue,citecolor=blue,pdfstartview=FitV]{hyperref}
 110 \else
 111   \usepackage{graphicx}
 112   \usepackage[plainpages=false,colorlinks=true,urlcolor=blue,citecolor=blue]{hyperref}
 113 \fi
 114
 115 % Work-arounds to allow unescaped underscores in text.
 116 % These \usepackage commands should come late in the
 117 % list of packages, and in this order.
 118 \newcommand{\UnderscoreCommands}{\do\index}
 119 \usepackage[strings]{underscore}
 120 \usepackage[english]{babel}
 121
 122 % Slightly darker colors print better on b/w printers
 123 \usepackage{color}
 124 \definecolor{blue}{rgb}{0,0,0.5}
 125 \definecolor{red}{rgb}{0.5,0,0}
 126
 127 \makeindex
 128 % The total a4 paper width is 210 mm, and the margins are defined
 129 % relative to the standard margin of 1 inch.
 130 \setlength{\textwidth}{15cm}
 131 \setlength{\oddsidemargin}{9.6mm}  %35mm-1inch
 132 \setlength{\evensidemargin}{-0.4mm} %25mm-1inch
 133 \setlength{\topmargin}{-4.4mm} % 21mm top margin
 134 \setlength{\textheight}{22cm}
 135
 136 \renewcommand{\textfraction}{0.0}
 137 \newcommand{\qtw}{3.75cm}  % 1/4 of the textwidth
 138 \newcommand{\ttw}{4.33cm}  % 1/3 of the textwidth
 139 \newcommand{\htw}{7.5cm}  % 1/2 of the textwidth
 140 \newcommand{\ntw}{13cm} % 0.9 of the textwidth
 141 \newcommand{\gmxver}{@PROJECT_VERSION@}
 142 \newcommand{\gmxyear}{\the\year}
 143 \newcommand{\figref}[1]{Fig.~\ref{fig:#1}}
 144 \newcommand{\figsref}[2]{Figs.~\ref{fig:#1} and ~\ref{fig:#2}}
 145 \newcommand{\tabref}[1]{Table~\ref{tab:#1}}
 146 \newcommand{\eqnref}[1]{eqn.~\ref{eqn:#1}}
 147 \newcommand{\eqnsref}[2]{eqns.~\ref{eqn:#1} and \ref{eqn:#2}}
 148 \newcommand{\secref}[1]{sec.~\ref{sec:#1}}
 149 \newcommand{\tsecref}[1]{\ref{sec:#1}}
 150 \newcommand{\ssecref}[1]{\ref{subsec:#1}}
 151 \newcommand{\sssecref}[1]{\ref{subsubsec:#1}}
 152 \newcommand{\chref}[1]{chapter~\ref{ch:#1}}
 153 \newcommand{\appref}[1]{Appendix~\ref{app:#1}}
 154 \newcommand{\wwwpage}{\href{http://www.gromacs.org}{www.gromacs.org}}
 155 \newcommand{\gerritpage}{\href{http://gerrit.gromacs.org}{gerrit.gromacs.org}}
 156 \newcommand{\redminepage}{\href{http://redmine.gromacs.org}{redmine.gromacs.org}}
 157 % NOTE: \wwwpage is explicitly included in the 'verbatim' citing instructions!
 158 \newcommand{\mcc}[2]{\multicolumn{#1}{c|}{#2}}
 159 \newcommand{\mcl}[2]{\multicolumn{#1}{l}{#2}}
 160 \setlength{\headwidth}{\textwidth}
 161 \setlength{\headheight}{1.0cm}
 162
 163 % LocalWords:  GROMOS et al ij ji rgb eqn eqns GROMACS