src/local_cmmds.tex

   1 % String comparison for \fref
   2 \makeatletter
   3 \long\def\isequal#1#2{\pdf@strcmp{#1}{#2}}
   4 \makeatother
   5
   6 % An reference index from an unspecified source
   7 % usage: \iref{environment}{value}
   8 % for example: \iref{equation}{75}
   9 \newcommand{\iref}[2]{%
  10   \switch%
  11   \case{\isequal{#1}{equation}}%
  12     ({#2})%
  13   \otherwise%
  14     {#2}%
  15   \endswitch%
  16 }
  17
  18 % A formatted reference from an unspecified source
  19 % usage: \fref{environment}{value}
  20 % for example: \fref{figure}{75}
  21 \newcommand{\fref}[2]{%
  22   \switch%
  23   \case{\isequal{#1}{equation}}%
  24     Eq.~\iref{#1}{#2}%
  25   \case{\isequal{#1}{figure}}%
  26     Fig.~\iref{#1}{#2}%
  27   \case{\isequal{#1}{section}}%
  28     Section~\iref{#1}{#2}%
  29   \otherwise%
  30     \PackageError{fref}{
  31       \MessageBreak
  32       environment value >#2< unknown \MessageBreak
  33     }{possible values are: equation. \MessageBreak}%
  34   \endswitch%
  35 }
  36
  37 % References to external figures, equations, etc.
  38 % usage: \xref{key}{environment}{value}
  39 % for example: \xref{roman12}{figure}{75}
  40 \newcommand{\xref}[3]{\citet{#1} \fref{#2}{#3}}
  41
  42 % Fourier Transform to angular momentum space
  43 \newcommand{\Four}[1]{\ensuremath{{\mathcal F}\left\{ {#1} \right\}}}
  44 % Fourier Transform to frequency space
  45 \newcommand{\Fourf}[1]{\ensuremath{{\mathcal F}_f\left\{ {#1} \right\}}}
  46
  47 % use e^{...} instead of exp ...
  48 \renewcommand{\exp}[1]{\ensuremath{e^{#1}}}
  49
  50 % Symbol denoting the Langevin function
  51 \newcommand{\Langevin}{\ensuremath{\mathcal{L}}}
  52 % Symbol denoting big-O order of #1
  53 \newcommand{\order}[1]{\ensuremath{\mathcal{O}\p({#1})}}
  54
  55 % Integral from #1 to #2 of #4 with respect to #3
  56 \newcommand{\integral}[4]{\ensuremath{\int_{#1}^{#2} {#4} \dd{#3}}}
  57 % Integral from -infty to +infty of #2 with respect to #1
  58 \newcommand{\iInfInf}[2]{\integral{-\infty}{\infty}{#1}{#2}}
  59 % Integral from 0 to +infty of #2 with respect to #1
  60 % note that the second char in the name is a capital o, not a 0
  61 % because ?Latex doesn't allow digits in command names
  62 \newcommand{\iOInf}[2]{\integral{0}{\infty}{#1}{#2}}
  63 % #3 evaluated at #2 and #1
  64 \newcommand{\evaluated}[3]{\ensuremath{\left.{#3}\right|_{#1}^{#2}}}
  65 % #2 evaluated at #1
  66 \newcommand{\eval}[2]{\ensuremath{\left.{#2}\right|_{#1}}}
  67 % evaluated at infty and -infty
  68 \newcommand{\eInfInf}[1]{\evaluated{-\infty}{\infty}{#1}}
  69 % evaluated at infty and 0
  70 \newcommand{\eOInf}[1]{\evaluated{0}{\infty}{#1}}
  71
  72 % we do a lot of lim t_T -> infty, so macro that out
  73 % lim as #1 -> infty
  74 \newcommand{\limInf}[1]{\ensuremath{\lim_{{#1}\rightarrow \infty}}}
  75 \newcommand{\limT}{\limInf{t_T}}
  76 \newcommand{\normLimT}{\limT \frac{1}{t_T}\ } % '\ ' for a normal space
  77 % lim as t_T -> infty of integral from -t_T/2 to t_T/2 of #1 with respect to t
  78 \newcommand{\iLimT}[1]{\normLimT \integral{-t_T/2}{t_T/2}{t}{#1}}
  79
  80 \newcommand{\magSq}[1]{\ensuremath{\left|{#1}\right|^2}}
  81 \newcommand{\PSD}{\ensuremath{\operatorname{PSD}}}
  82
  83 % complex conjugate
  84 \newcommand{\conj}[1]{\ensuremath{\overline{#1}}}
  85
  86 % Symbol denoting the contour C
  87 \newcommand{\C}{\ensuremath{\mathcal{C}}}
  88 % Integral about contour C of #1 with respect to z
  89 \newcommand{\iC}[1]{\integral{\C}{}{z}{#1}}
  90 \newcommand{\Reals}{\ensuremath{\mathds{R}}}
  91 \newcommand{\Imags}{\ensuremath{\mathds{I}}}
  92 \newcommand{\Real}{\ensuremath{\operatorname{Re}}}
  93 \newcommand{\Imag}{\ensuremath{\operatorname{Im}}}
  94 \newcommand{\ResX}[3]{\operatorname{Res}\left({{#1}={#2}},{#3}\right)}
  95 \newcommand{\Res}[2]{\ResX{z}{#1}{#2}}
  96 \newcommand{\limX}[2]{\lim_{{#1} \rightarrow {#2}}}
  97 \newcommand{\limZ}[1]{\limX{z}{#1}}
  98 \newcommand{\limZp}{\limZ{z_p}}
  99 \newcommand{\CPV}{\ensuremath{\mathds{P}}}
 100
 101 \newcommand{\supScript}[1]{\ensuremath{^{\text{#1}}}}
 102 \newcommand{\st}{\supScript{st}}
 103 \newcommand{\nd}{\supScript{nd}}
 104 \newcommand{\rd}{\supScript{rd}}
 105 \newcommand{\sth}{\supScript{th}} % th, TH already taken
 106
 107 \newcommand{\colA}[1]{\textcolor{red}{#1}}
 108 \newcommand{\colB}[1]{\textcolor{blue}{#1}}
 109 \definecolor{purple}{rgb}{0.8, 0, 0.8}
 110 \newcommand{\colAB}[1]{\textcolor{purple}{#1}}
 111 \newcommand{\colC}[1]{\textcolor{green}{#1}}
 112
 113 \newcommand{\cf}{\emph{cf.}} % "confer" or "bring together" / "compare"
 114 \newcommand{\ie}{\emph{i.e.}} % "id est" or "in other words"
 115 \newcommand{\insilico}{\emph{in silico}} % quasi latin for "on a computer"
 116 \newcommand{\invitro}{\emph{in vitro}}   % latin for "in glass"
 117 \newcommand{\invivo}{\emph{in vivo}}     % latin for "in living organisms"
 118
 119 \newcommand{\ensuretext}[1]{\ensuremath{\text{#1}}}
 120 % Hyeon and Thirumalai equation number #1
 121 \newcommand{\HTeq}[1]{\ensuretext{\emph{H\&T eq.\ {#1}}}}
 122 \newcommand{\kT}{\ensuremath{k_B T}}
 123 \newcommand{\bt}{\ensuremath{\beta}}
 124 \newcommand{\fs}{\ensuremath{f^*}}
 125 \newcommand{\dx}{\ensuremath{\Delta x(\fs)}}
 126 \newcommand{\dxs}[1]{\ensuremath{\Delta x_{#1}(\fs)}} % for subscripting
 127 \newcommand{\FO}{\ensuremath{\Delta F_0^\ddagger(\fs)}}
 128 \newcommand{\vD}{\ensuremath{\nu_D(\fs)}}
 129 \newcommand{\vDs}[1]{\ensuremath{\nu_{D{#1}}(\fs)}}
 130 \newcommand{\kexp}{\ensuremath{\vD e^{-\bt \FO}}}
 131 \newcommand{\kexps}[1]{\ensuremath{\vDs{#1} e^{-\bt_{#1} \FO_{#1}}}}
 132 \newcommand{\kf}{\ensuremath{k(\fs)}}
 133 \newcommand{\kfs}[1]{\ensuremath{k_{#1}(\fs)}}
 134 %\newcommand{\avg}[1]{\ensuremath{\left\langle {#1} \right\rangle}}
 135 \newcommand{\abs}[1]{\ensuremath{\lvert {#1} \rvert}}
 136 \newcommand{\logp}[1]{\ensuremath{\log\!\!\left( {#1} \right)}}
 137 % \! is a negative thin space to get the paren closer to the log
 138 %\renewcommand{\r}{\ensuremath{r_f}}
 139 %\newcommand{\rs}[1]{\ensuremath{r_{f{#1}}}}% to avoid double-subscripting
 140 \newcommand{\ep}{\varepsilon}
 141
 142 \newcommand{\species}[1]{\emph{#1}} % \species{Homo sapiens}
 143
 144 % Chemicals
 145 \newcommand{\Ca}{Ca\textsuperscript{2+}}
 146 \newcommand{\CaCl}{CaCl\textsubscript{2}}
 147 \newcommand{\Cl}{Cl\textsuperscript{-}}
 148 \newcommand{\HCl}{HCl}
 149 \newcommand{\Na}{Na\textsuperscript{+}}
 150 \newcommand{\NaCl}{NaCl}
 151 \newcommand{\diNaHPO}{Na\textsubscript{2}HPO\textsubscript{4}}
 152 \newcommand{\NadiHPO}{NaH\textsubscript{2}PO\textsubscript{4}}
 153 \newcommand{\NaOH}{NaOH}
 154
 155 % Workaround for inline minted markup
 156 %   http://code.google.com/p/minted/issues/detail?id=15
 157 % usage: \imint{language}|value|
 158 \NewDocumentCommand\imint{mv}{\texttt{#2}}
 159
 160 % Aliases for citations
 161 \defcitealias{calibcant}{calibcant}
 162 \defcitealias{comedi}{Comedi}
 163 \defcitealias{cygwin}{Cygwin}
 164 \defcitealias{cython}{Cython}
 165 \defcitealias{epics}{EPICS}
 166 \defcitealias{force-robot}{ForceRobot}
 167 \defcitealias{gentoo}{Gentoo}
 168 \defcitealias{h5config}{h5config}
 169 \defcitealias{hdf5}{HDF5}
 170 \defcitealias{interix}{Interix}
 171 \defcitealias{kernighan88}{C}
 172 \defcitealias{king10}{sawsim}
 173 \defcitealias{labview}{LabVIEW}
 174 \defcitealias{picoforce}{PicoForce}
 175 \defcitealias{prefix}{Gentoo Prefix}
 176 \defcitealias{punias}{PUNIAS}
 177 \defcitealias{pyafm}{pyafm}
 178 \defcitealias{pycomedi}{pycomedi}
 179 \defcitealias{pymodbus}{pymodbus}
 180 \defcitealias{pymol}{PyMol}
 181 \defcitealias{pypid}{pypid}
 182 \defcitealias{pypiezo}{pypiezo}
 183 \defcitealias{python}{Python}
 184 \defcitealias{sandal09}{Hooke}
 185 \defcitealias{stepper}{stepper}
 186 \defcitealias{beazley96}{SWIG}
 187 \defcitealias{unfold-protein}{unfold-protein}
 188 \defcitealias{wavemetrics-igor}{IGOR Pro}
 189 \defcitealias{xcode}{Xcode}
 190 \defcitealias{yaml}{YAML}
 191
 192 \newcommand{\Comedi}{\citetalias{comedi}}
 193 \newcommand{\Hooke}{\citetalias{sandal09}}
 194 \newcommand{\calibcant}{\citetalias{calibcant}}
 195 \newcommand{\hFconfig}{\citetalias{h5config}}
 196 \newcommand{\pyafm}{\citetalias{pyafm}}
 197 \newcommand{\pypid}{\citetalias{pypid}}
 198 \newcommand{\pypiezo}{\citetalias{pypiezo}}
 199 \newcommand{\pycomedi}{\citetalias{pycomedi}}
 200 \newcommand{\pysawsim}{\texttt{pysawsim}}
 201 \newcommand{\sawsim}{\citetalias{king10}}
 202 \newcommand{\stepper}{\citetalias{stepper}}
 203 \newcommand{\unfoldprotein}{\citetalias{unfold-protein}}
 204
 205 % draw a line TikZ (useful for captions explaining figures)
 206 % usage: \tikzline{style}
 207 \DeclareRobustCommand{\tikzline}[1]{%
 208   \protect\tikz \draw[#1] (0,0) -- (14pt,6pt);}
 209
 210 \DeclareRobustCommand{\thermocouple}{%
 211   \begin{tikzpicture}
 212     \draw[red] (0,1pt) -- (10pt,1pt);
 213     \draw[purple] (0,3pt) -- (10pt,3pt);
 214     \fill[black!20] (10pt,2pt) circle (2pt);
 215   \end{tikzpicture}
 216 }
 217
 218 % draw a thermometer in TikZ
 219 % usage: \thermometerx{bulb-location}
 220 \newcommand{\thermometerx}[1]{
 221   \draw[blue!20, line width=4pt, cap=round] #1 -- +(0, 12pt);
 222   \fill[blue!20] #1 circle (5pt);
 223   \draw[red, line width=2pt, cap=butt] #1 -- +(0, 8pt);
 224   \fill[red] #1 circle (4pt);
 225 }
 226
 227 \DeclareRobustCommand{\thermometer}{%
 228   \raisebox{-2pt}{%
 229     \resizebox{!}{10pt}{%
 230       \begin{tikzpicture}%
 231         \thermometerx{(0,2.5pt)};%
 232       \end{tikzpicture}%
 233     }%
 234   }%
 235 }
 236
 237 % shared figure between pyafm and calibcant
 238 % usage: \tikzstack{unfold-protein-color}{calibcant-color}
 239 \newcommand{\tikzstack}[2]{%
 240   \begin{tikzpicture}[decoration={
 241       markings,%  switch on markings
 242       mark=%  add a mark for screw threading
 243         between positions 0 and 1 step 1pt
 244         with
 245         {
 246           \draw (0, 2pt) -- (1pt, -2pt);
 247         }
 248       },
 249       bend angle=5
 250       ]
 251     \tikzstyle{every node}=[text depth=0pt, rounded rectangle,
 252       draw=blue!50, very thick, minimum height=1.7em]
 253     % hardware nodes and coordinates
 254     \node[shape=rectangle,draw=none,inner sep=0]
 255       (image) at (0,0) {
 256       \asyinclude{figures/schematic/afm}};
 257     \node[shape=rectangle,draw=black, semithick]
 258       (daq) at ($(image.south west) + (-0.25, -1)$) {DAQ card};
 259     \node[shape=rectangle,draw=black, semithick]
 260       (motor) at ($(image.south) + (0, -1)$) {motor};
 261     \coordinate (thermocouple) at ($(image.west) + (1.4, -4pt)$);
 262     \thermometerx{(thermocouple)}
 263     \coordinate (photodiode) at ($(image.west) + (1, 26pt)$);
 264     \coordinate (piezo) at ($(image.south) + (-6pt, 0)$);
 265     \draw[black!20,dashed] ($(daq.south west) + (-10pt, 0)$) -- +(0, 4);
 266     % software nodes
 267     \node (pycomedi) at ($(daq) + (-6,0)$) {pycomedi};
 268     \node (pypiezo) at ($(pycomedi) + (0,1)$) {pypiezo};
 269     \node (pyafm) at ($(pypiezo) + (0,1)$) {pyafm};
 270     \node[#1] (unfold-protein) at ($(pyafm) + (0,1)$) {unfold-protein};
 271     \node (stepper) at ($(pycomedi) + (2,1)$) {stepper};
 272     \node (pypid) at ($(stepper) + (2,0)$) {pypid};
 273     \node (h5config) at ($(pycomedi) + (-3,0)$) {h5config};
 274     \node[#2] (calibcant) at ($(unfold-protein) + (-3,0)$) {calibcant};
 275     % software connections
 276     \draw (pypiezo) -- (pyafm);
 277     \draw (stepper) -- (pyafm);
 278     \draw (pypid) -- (pyafm);
 279     \draw[#1] (pyafm) -- (unfold-protein);
 280     \draw (h5config) -- (pypiezo);
 281     \draw (h5config) -- (pyafm);
 282     \ifthenelse{\equal{#1}{}}{%  draw unfold-protein in black (the default)
 283       \draw[#2] (pyafm) -- (calibcant);
 284       \draw[#1] (h5config) -- (unfold-protein);%  default path on top
 285       }{%
 286       \draw[#1] (h5config) -- (unfold-protein);
 287       \draw[#2] (pyafm) -- (calibcant);%  default path on top
 288       }
 289     \draw[#2] (h5config) -- (calibcant);
 290     % hardware connections
 291     \begin{pgfonlayer}{background}
 292       \draw[purple, ->] (thermocouple) -- (pypid);
 293     \end{pgfonlayer}
 294     % begin motor screw
 295     \draw[black!20, line width=4pt]
 296       (motor) -- (image.south);   % shaft with decoration threads
 297     \draw[black, decorate, ultra thin]
 298       (motor) -- (image.south);   % shaft with decoration threads
 299     % end motor screw
 300     \draw[red, <->] (pypiezo) -- (pycomedi);
 301     \draw[red, <->] (pycomedi) to [bend left] (daq);
 302     \draw[red, ->] (daq) -- (piezo);
 303     \begin{pgfonlayer}{background}
 304       \draw[red, ->, out=180, in=90] (photodiode) to (daq.north);
 305     \end{pgfonlayer}
 306     \draw[blue, ->] (stepper) -- (pycomedi);
 307     \draw[blue, ->] (pycomedi) to [bend right] (daq);
 308     \draw[blue, ->] (daq) -- (motor);
 309   \end{tikzpicture}
 310 }