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