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Commit 7d6f493b authored by Benjamin Cumming's avatar Benjamin Cumming
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add latex documentation

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......@@ -32,3 +32,11 @@
*.dot
*.pdf
*.jpg
# latex output
*.aux
*.log
*.out
*.pdf
*.toc
docs/SelfArx.cls 0 → 100644
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% ---------------------------------------------------------------------
% Conference proceedings and article templates for
% personal open-archiving activities
% September 2012
% ---------------------------------------------------------------------
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{SelfArx}[25/01/2012, v1.0]
\RequirePackage{ifthen}
\RequirePackage{calc}
\AtEndOfClass{\RequirePackage{microtype}}
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
\ProcessOptions*
\LoadClass{article}
\RequirePackage{ifpdf} % Needed to pick between latex and pdflatex
%----------------------------------------------------------------------
% FONTS
%----------------------------------------------------------------------
\RequirePackage{times} % Loads the Times-Roman Fonts
\RequirePackage{mathptmx} % Loads the Times-Roman Math Fonts
%----------------------------------------------------------------------
% VARIOUS USEFUL PACKAGES
%----------------------------------------------------------------------
\RequirePackage[utf8]{inputenc}
\RequirePackage{amsmath,amsfonts,amssymb}
\RequirePackage{graphicx,xcolor}
\RequirePackage[english]{babel}
\RequirePackage{booktabs}
%----------------------------------------------------------------------
% MARGINS
%----------------------------------------------------------------------
\RequirePackage[left=2cm,%
right=2cm,%
top=2.25cm,%
bottom=2.25cm,%
headheight=11pt,%
letterpaper]{geometry}%
%----------------------------------------------------------------------
% FIGURES AND TABLES CAPTIONS
%----------------------------------------------------------------------
\RequirePackage[labelfont={bf,sf,small},%
labelsep=period,%
justification=raggedright]{caption}
\setlength{\abovecaptionskip}{0pt}
\setlength{\belowcaptionskip}{0pt}
%----------------------------------------------------------------------
% PAGE HEADER
%----------------------------------------------------------------------
\RequirePackage{fancyhdr} % Needed to define custom headers/footers
\RequirePackage{lastpage} % Number of pages in the document
\pagestyle{fancy} % Enables the custom headers/footers
% Headers
\lhead{}%
\chead{}%
\rhead{\small\sffamily\bfseries\@PaperTitle\ --- \thepage/\pageref{LastPage}}
% Footers
\lfoot{}%
\cfoot{}%
\rfoot{}%
\renewcommand{\headrulewidth}{0pt}% % No header rule
\renewcommand{\footrulewidth}{0pt}% % No footer rule
%----------------------------------------------------------------------
% SECTION/SUBSECTION/PARAGRAPH SET-UP
%----------------------------------------------------------------------
\RequirePackage[explicit]{titlesec}
\titleformat{\section}
{\color{color1}\large\sffamily\bfseries}
{}
{0em}
{\colorbox{color2!10}{\parbox{\dimexpr\linewidth-2\fboxsep\relax}{\centering\arabic{section}. #1}}}
[]
\titleformat{name=\section,numberless}
{\color{color1}\large\sffamily\bfseries}
{}
{0em}
{\colorbox{color2!10}{\parbox{\dimexpr\linewidth-2\fboxsep\relax}{\centering#1}}}
[]
\titleformat{\subsection}
{\color{color1}\sffamily\bfseries}
{\thesubsection}
{0.5em}
{#1}
[]
\titleformat{\subsubsection}
{\sffamily\small\bfseries}
{\thesubsubsection}
{0.5em}
{#1}
[]
\titleformat{\paragraph}[runin]
{\sffamily\small\bfseries}
{}
{0em}
{#1}
\titlespacing*{\section}{0pc}{3ex \@plus4pt \@minus3pt}{5pt}
\titlespacing*{\subsection}{0pc}{2.5ex \@plus3pt \@minus2pt}{0pt}
\titlespacing*{\subsubsection}{0pc}{2ex \@plus2.5pt \@minus1.5pt}{0pt}
\titlespacing*{\paragraph}{0pc}{1.5ex \@plus2pt \@minus1pt}{10pt}
%----------------------------------------------------------------------
% TABLEOFCONTENTS SET-UP
%----------------------------------------------------------------------
\newlength{\tocsep}
\setlength\tocsep{1.5pc} % Sets the indentation of the sections in the table of contents
\setcounter{tocdepth}{3} % Three levels in the table of contents section: sections, subsections and subsubsections
\usepackage{titletoc}
\contentsmargin{0cm}
\titlecontents{section}[\tocsep]
{\addvspace{4pt}\small\bfseries\sffamily}
{\contentslabel[\thecontentslabel]{\tocsep}}
{}
{\hfill\thecontentspage}
[]
\titlecontents{subsection}[\tocsep]
{\addvspace{2pt}\sffamily}
{\contentslabel[\thecontentslabel]{\tocsep}}
{}
{\ \titlerule*[.5pc]{.}\ \thecontentspage}
[]
\titlecontents*{subsubsection}[\tocsep]
{\footnotesize\sffamily}
{}
{}
{}
[\ \textbullet\ ]
%----------------------------------------------------------------------
% MULTIPLE AUTHOR SET
%----------------------------------------------------------------------
\newcount\@authcnt
\newcount\@tmpcnt\@tmpcnt\z@
\def\@affiliation{%
\ifnum\@tmpcnt<\@authcnt
\global\advance\@tmpcnt1
\raggedright \csname @auth\romannumeral\the\@tmpcnt\endcsname\hfill\\%
\let\next\@affiliation \vskip1pt
\else
\let\next\relax
\fi
\next}
\newcommand{\affiliation}[1]{%
\global\advance\@authcnt1
\expandafter\gdef\csname @auth\romannumeral\the\@authcnt\endcsname
{#1}}
%----------------------------------------------------------------------
% LIST CONTROL
%----------------------------------------------------------------------
\RequirePackage{enumitem}
%\setlist{nolistsep} % Uncomment to remove spacing between items in lists (enumerate, itemize)
%----------------------------------------------------------------------
% ABSTRACT+AUTHOR FRAME
%----------------------------------------------------------------------
\newcommand{\PaperTitle}[1]{\def\@PaperTitle{#1}}
\newcommand{\Archive}[1]{\def\@Archive{#1}}
\newcommand{\Authors}[1]{\def\@Authors{#1}}
\newcommand{\JournalInfo}[1]{\def\@JournalInfo{#1}}
\newcommand{\Abstract}[1]{\def\@Abstract{#1}}
\newcommand{\Keywords}[1]{\def\@Keywords{#1}}
% ---------------------------------------------------------------------
\renewcommand{\@maketitle}{%
\twocolumn[
{%
\thispagestyle{empty}%
\vskip-36pt%
{\raggedleft\small\sffamily\bfseries\@JournalInfo\\\@Archive\par}%
\vskip20pt%
{\raggedright\color{color1}\sffamily\bfseries\fontsize{20}{25}\selectfont \@PaperTitle\par}%
\vskip10pt%
%{\raggedright\color{color1}\sffamily\fontsize{12}{16}\selectfont \@Authors\par}%
\vskip18pt%
%\fcolorbox{color1}{white}{%
%\parbox{\textwidth-2\fboxsep-2\fboxrule}{\centering%
%\colorbox{color2!10}{%
%\parbox{\textwidth-4\fboxsep-2\fboxrule}{%
%\ifx\@Keywords\@empty%
%\sffamily\textbf{\abstractname}\\\@Abstract%
%\else%
%\sffamily\textbf{\abstractname}\\\@Abstract\\[4pt]%
%\textbf{\keywordname}\\\@Keywords%
%\fi%
%}%
%}%
%\vskip4pt%
%\begingroup%
%\raggedright\sffamily\small%
%\footnotesize\@affiliation\par%
%\endgroup%%
%}%
%}%
%\vskip25pt
}
]%
}%
%----------------------------------------------------------------------
% REFERENCES
%----------------------------------------------------------------------
% Remove brackets from numbering in List of References
\renewcommand{\@biblabel}[1]{\bfseries\color{color1}\textsuperscript{[#1]}}
%\setlength{\bibitemsep}{0cm}
\let\oldbibliography\thebibliography
\renewcommand{\thebibliography}[1]{%
\addcontentsline{toc}{section}{\refname}%
\oldbibliography{#1}%
\setlength\itemsep{0pt}}%
docs/formulation.tex 0 → 100644
+ 14
− 0
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\section*{Introduction}
The cable equation is a nonlinear parabolic PDE that can be written in the form
\begin{equation}
c_m \pder{V}{t} = \frac{1}{2ar_{L}} \pder{}{x} \left( a^2 \pder{V}{x} \right) - i_m + i_e,
\end{equation}
where
\begin{itemize}
\item $V$ is the potential relative to the ECM $[mV]$
\item $a$ is the cable radius \todo{units}
\item $c_m$ is the {specific membrane capacitance}, approximately the same for all neurons $\approx 10~nF/mm^2$. Related to \emph{membrane capacitance} $C_m$ by the relationship $C_m=c_{m}A$, where $A$ is the surface area of the cell.
\item $i_m$ is the membrane current \todo{units}
\item $r_L$ is intracellular resistivity, typical value $1~k\Omega$
\end{itemize}
docs/makefile 0 → 100644
+ 12
− 0
View file @ 7d6f493b
report.pdf : *.tex
pdflatex report.tex
force : report.pdf
pdflatex report.tex
clean :
rm -f *.pdf
rm -f *.log
rm -f *.out
rm -f *.aux
rm -f *.toc
docs/report.tex 0 → 100644
+ 108
− 0
View file @ 7d6f493b
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Stylish Article
% LaTeX Template
% Version 2.0 (13/4/14)
%
% This template has been downloaded from:
% http://www.LaTeXTemplates.com
%
% Original author:
% Mathias Legrand (legrand.mathias@gmail.com)
%
% License:
% CC BY-NC-SA 3.0 (http://creativecommons.org/licenses/by-nc-sa/3.0/)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%----------------------------------------------------------------------------------------
% PACKAGES AND OTHER DOCUMENT CONFIGURATIONS
%----------------------------------------------------------------------------------------
\documentclass[fleqn,10pt]{SelfArx} % Document font size and equations flushed left
\usepackage{xspace}
\usepackage{color}
%----------------------------------------------------------------------------------------
% COLUMNS
%----------------------------------------------------------------------------------------
\setlength{\columnsep}{0.55cm} % Distance between the two columns of text
\setlength{\fboxrule}{0.75pt} % Width of the border around the abstract
%----------------------------------------------------------------------------------------
% COLORS
%----------------------------------------------------------------------------------------
\definecolor{color1}{RGB}{0,0,90} % Color of the article title and sections
\definecolor{color2}{RGB}{0,20,20} % Color of the boxes behind the abstract and headings
%----------------------------------------------------------------------------------------
% PLOTTING and DRAWING
%----------------------------------------------------------------------------------------
\usepackage{tikz}
\usetikzlibrary{positioning}
\usetikzlibrary{shapes,arrows,backgrounds,fit,shapes.geometric,calc}
\usetikzlibrary{pgfplots.groupplots}
\usepackage{pgfplots}
\usepackage{pgfplotstable}
%----------------------------------------------------------------------------------------
% HYPERLINKS
%----------------------------------------------------------------------------------------
\usepackage{hyperref} % Required for hyperlinks
\hypersetup{hidelinks,colorlinks,breaklinks=true,urlcolor=color2,citecolor=color1,linkcolor=color1,bookmarksopen=false,pdftitle={Title},pdfauthor={Author}}
%----------------------------------------------------------------------------------------
% CUSTOM COMMANDS
%----------------------------------------------------------------------------------------
\newcommand{\HWtwelve}{HW12\xspace}
\newcommand{\HWtwelves}{HW12$^*$\xspace}
\newcommand{\HWeight}{HW8\xspace}
\newcommand{\HWsix}{HW6\xspace}
\newcommand{\HWfour}{HW4\xspace}
\newcommand{\SBeight}{SB8\xspace}
\newcommand{\HWtwelvecode}{E5-2690v3\xspace}
\newcommand{\HWtwelvescode}{E5-2680v3\xspace}
\newcommand{\HWeightcode}{E5-1660v3\xspace}
\newcommand{\HWsixcode}{E5-1650v3\xspace}
\newcommand{\HWfourcode}{E5-1620v3\xspace}
\newcommand{\SBeightcode}{E5-2670\xspace}
\newcommand{\todo}[1]{\textbf{\textcolor{blue}{TODO: #1}}} % add a comment to the article
\newcommand{\tbl}[1]{\textbf{Table \ref{#1}}\xspace}
\newcommand{\fig}[1]{\textbf{Figure \ref{#1}}\xspace}
\newcommand{\eq}[1]{\textbf{(\ref{#1})}\xspace}
\newcommand{\ssec}[1]{\textbf{\S\ref{#1}}\xspace}
\newcommand{\pder}[2]{\frac{\partial{#1}}{\partial{#2}}}
%----------------------------------------------------------------------------------------
% ARTICLE INFORMATION
%----------------------------------------------------------------------------------------
\JournalInfo{CSCS} % name of "journal" on upper right corner
\Archive{working document}
\PaperTitle{Cable Equation}
%===============================================================================
\begin{document}
\flushbottom % Makes all text pages the same height
\maketitle % Print the title and authors
\tableofcontents
\thispagestyle{empty} % Removes page numbering from the first page
%------------------------------------------------
\input{formulation.tex}
\end{document}
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