src/local_cmmds.tex

   1 % Fourier Transform to angular momentum space
   2 \newcommand{\Four}[1]{\ensuremath{{\mathcal F}\left\{ {#1} \right\}}}
   3 % Fourier Transform to frequency space
   4 \newcommand{\Fourf}[1]{\ensuremath{{\mathcal F}_f\left\{ {#1} \right\}}}
   5
   6 % Symbol denoting the Langevin function
   7 \newcommand{\Langevin}{\ensuremath{\mathcal{L}}}
   8
   9 % Integral from #1 to #2 of #4 with respect to #3
  10 \newcommand{\integral}[4]{\ensuremath{\int_{#1}^{#2} {#4} \dd{#3}}}
  11 % Integral from -infty to +infty of #2 with respect to #1
  12 \newcommand{\iInfInf}[2]{\integral{-\infty}{\infty}{#1}{#2}}
  13 % Integral from 0 to +infty of #2 with respect to #1
  14 % note that the second char in the name is a capital o, not a 0
  15 % because ?Latex doesn't allow digits in command names
  16 \newcommand{\iOInf}[2]{\integral{0}{\infty}{#1}{#2}}
  17 % #3 evaluated at #2 and #1
  18 \newcommand{\evaluated}[3]{\ensuremath{\left.{#3}\right|_{#1}^{#2}}}
  19 % #2 evaluated at #1
  20 \newcommand{\eval}[2]{\ensuremath{\left.{#2}\right|_{#1}}}
  21 % evaluated at infty and -infty
  22 \newcommand{\eInfInf}[1]{\evaluated{-\infty}{\infty}{#1}}
  23 % evaluated at infty and 0
  24 \newcommand{\eOInf}[1]{\evaluated{0}{\infty}{#1}}
  25
  26 % we do a lot of lim t_T -> infty, so macro that out
  27 % lim as #1 -> infty
  28 \newcommand{\limInf}[1]{\ensuremath{\lim_{{#1}\rightarrow \infty}}}
  29 \newcommand{\limT}{\limInf{t_T}}
  30 \newcommand{\normLimT}{\limT \frac{1}{t_T}\ } % '\ ' for a normal space
  31 % lim as t_T -> infty of integral from -t_T/2 to t_T/2 of #1 with respect to t
  32 \newcommand{\iLimT}[1]{\normLimT \integral{-t_T/2}{t_T/2}{t}{#1}}
  33
  34 \newcommand{\magSq}[1]{\ensuremath{\left|{#1}\right|^2}}
  35 \newcommand{\PSD}{\ensuremath{\operatorname{PSD}}}
  36
  37 % complex conjugate
  38 \newcommand{\conj}[1]{\ensuremath{\overline{#1}}}
  39
  40 % Symbol denoting the contour C
  41 \newcommand{\C}{\ensuremath{\mathcal{C}}}
  42 % Integral about contour C of #1 with respect to z
  43 \newcommand{\iC}[1]{\integral{\C}{}{z}{#1}}
  44 \newcommand{\Reals}{\ensuremath{\mathds{R}}}
  45 \newcommand{\Imags}{\ensuremath{\mathds{I}}}
  46 \newcommand{\Real}{\ensuremath{\operatorname{Re}}}
  47 \newcommand{\Imag}{\ensuremath{\operatorname{Im}}}
  48 \newcommand{\ResX}[3]{\operatorname{Res}\left({{#1}={#2}},{#3}\right)}
  49 \newcommand{\Res}[2]{\ResX{z}{#1}{#2}}
  50 \newcommand{\limX}[2]{\lim_{{#1} \rightarrow {#2}}}
  51 \newcommand{\limZ}[1]{\limX{z}{#1}}
  52 \newcommand{\limZp}{\limZ{z_p}}
  53 \newcommand{\CPV}{\ensuremath{\mathds{P}}}
  54
  55 \newcommand{\supScript}[1]{\ensuremath{^{\text{#1}}}}
  56 \newcommand{\st}{\supScript{st}}
  57 \newcommand{\nd}{\supScript{nd}}
  58 \newcommand{\rd}{\supScript{rd}}
  59 \newcommand{\sth}{\supScript{th}} % th, TH already taken
  60
  61 \newcommand{\colA}[1]{\textcolor{red}{#1}}
  62 \newcommand{\colB}[1]{\textcolor{blue}{#1}}
  63 \definecolor{purple}{rgb}{0.8, 0, 0.8}
  64 \newcommand{\colAB}[1]{\textcolor{purple}{#1}}
  65 \newcommand{\colC}[1]{\textcolor{green}{#1}}
  66
  67 \newcommand{\ie}{\emph{i.e.}} % "id est" or "in other words"
  68 \newcommand{\insilico}{\emph{in silico}} % quasi latin for "on a computer"
  69 \newcommand{\invitro}{\emph{in vitro}}   % latin for "in glass"
  70 \newcommand{\invivo}{\emph{in vivo}}     % latin for "in living organisms"
  71
  72 \newcommand{\ensuretext}[1]{\ensuremath{\text{#1}}}
  73 % Hyeon and Thirumalai equation number #1
  74 \newcommand{\HTeq}[1]{\ensuretext{\emph{H\&T eq.\ {#1}}}}
  75 \newcommand{\kT}{\ensuremath{k_B T}}
  76 \newcommand{\bt}{\ensuremath{\beta}}
  77 \newcommand{\fs}{\ensuremath{f^*}}
  78 \newcommand{\dx}{\ensuremath{\Delta x(\fs)}}
  79 \newcommand{\dxs}[1]{\ensuremath{\Delta x_{#1}(\fs)}} % for subscripting
  80 \newcommand{\FO}{\ensuremath{\Delta F_0^\ddagger(\fs)}}
  81 \newcommand{\vD}{\ensuremath{\nu_D(\fs)}}
  82 \newcommand{\vDs}[1]{\ensuremath{\nu_{D{#1}}(\fs)}}
  83 \newcommand{\kexp}{\ensuremath{\vD e^{-\bt \FO}}}
  84 \newcommand{\kexps}[1]{\ensuremath{\vDs{#1} e^{-\bt_{#1} \FO_{#1}}}}
  85 \newcommand{\kf}{\ensuremath{k(\fs)}}
  86 \newcommand{\kfs}[1]{\ensuremath{k_{#1}(\fs)}}
  87 %\newcommand{\avg}[1]{\ensuremath{\left\langle {#1} \right\rangle}}
  88 \newcommand{\abs}[1]{\ensuremath{\lvert {#1} \rvert}}
  89 \newcommand{\logp}[1]{\ensuremath{\log\!\!\left( {#1} \right)}}
  90 % \! is a negative thin space to get the paren closer to the log
  91 %\renewcommand{\r}{\ensuremath{r_f}}
  92 %\newcommand{\rs}[1]{\ensuremath{r_{f{#1}}}}% to avoid double-subscripting
  93 \newcommand{\ep}{\varepsilon}
  94
  95 \newcommand{\species}[1]{\emph{#1}} % \species{Homo sapiens}
  96
  97 % Chemicals
  98 \newcommand{\diNaHPO}{Na\textsubscript{2}HPO\textsubscript{4}}
  99 \newcommand{\NadiHPO}{NaH\textsubscript{2}PO\textsubscript{4}}
 100
 101 % Workaround for inline minted markup
 102 %   http://code.google.com/p/minted/issues/detail?id=15
 103 % usage: \imint{language}|value|
 104 \NewDocumentCommand\imint{mv}{\texttt{#2}}
 105
 106 % Aliases for citations
 107 \defcitealias{calibcant}{calibcant}
 108 \defcitealias{comedi}{Comedi}
 109 \defcitealias{cygwin}{Cygwin}
 110 \defcitealias{cython}{Cython}
 111 \defcitealias{epics}{EPICS}
 112 \defcitealias{gentoo}{Gentoo}
 113 \defcitealias{h5config}{h5config}
 114 \defcitealias{hdf5}{HDF5}
 115 \defcitealias{interix}{Interix}
 116 \defcitealias{king10}{sawsim}
 117 \defcitealias{labview}{LabVIEW}
 118 \defcitealias{prefix}{Gentoo Prefix}
 119 \defcitealias{pyafm}{pyafm}
 120 \defcitealias{pycomedi}{pycomedi}
 121 \defcitealias{pymodbus}{pymodbus}
 122 \defcitealias{pymol}{PyMol}
 123 \defcitealias{pypid}{pypid}
 124 \defcitealias{pypiezo}{pypiezo}
 125 \defcitealias{sandal09}{Hooke}
 126 \defcitealias{stepper}{stepper}
 127 \defcitealias{beazley96}{SWIG}
 128 \defcitealias{unfold-protein}{unfold-protein}
 129 \defcitealias{wavemetrics-igor}{IGOR Pro}
 130 \defcitealias{xcode}{Xcode}
 131 \defcitealias{yaml}{YAML}
 132
 133 \newcommand{\Comedi}{\citetalias{comedi}}
 134 \newcommand{\Hooke}{\citetalias{sandal09}}
 135 \newcommand{\calibcant}{\citetalias{calibcant}}
 136 \newcommand{\hFconfig}{\citetalias{h5config}}
 137 \newcommand{\pyafm}{\citetalias{pyafm}}
 138 \newcommand{\pypid}{\citetalias{pypid}}
 139 \newcommand{\pypiezo}{\citetalias{pypiezo}}
 140 \newcommand{\pycomedi}{\citetalias{pycomedi}}
 141 \newcommand{\pysawsim}{\texttt{pysawsim}}
 142 \newcommand{\sawsim}{\citetalias{king10}}
 143 \newcommand{\stepper}{\citetalias{stepper}}
 144 \newcommand{\unfoldprotein}{\citetalias{unfold-protein}}