notebook.tex

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Compact Laboratory Book
% LaTeX Template
% Version 1.0 (4/6/12)
%
% This template has been downloaded from:
% http://www.LaTeXTemplates.com
%
% Original author:
% Joan Queralt Gil (http://phobos.xtec.cat/jqueralt) using the labbook class by
% Frank Kuster (http://www.ctan.org/tex-archive/macros/latex/contrib/labbook/)
%
% License:
% CC BY-NC-SA 3.0 (http://creativecommons.org/licenses/by-nc-sa/3.0/)
%
% Important note:
% This template requires the labbook.cls file to be in the same directory as the
% .tex file. The labbook.cls file provides the necessary structure to create the
% lab book.
%
% The \lipsum[#] commands throughout this template generate dummy text
% to fill the template out. These commands should all be removed when 
% writing lab book content.
%
% HOW TO USE THIS TEMPLATE 
% Each day in the lab consists of three main things:
%
% 1. LABDAY: The first thing to put is the \labday{} command with a date in 
% curly brackets, this will make a new section showing that you are working
% on a new day.
%
% 2. EXPERIMENT/SUBEXPERIMENT: Next you need to specify what 
% experiment(s) and subexperiment(s) you are working on with a 
% \experiment{} and \subexperiment{} commands with the experiment 
% shorthand in the curly brackets. The experiment shorthand is defined in the 
% 'DEFINITION OF EXPERIMENTS' section below, this means you can 
% say \experiment{pcr} and the actual text written to the PDF will be what 
% you set the 'pcr' experiment to be. If the experiment is a one off, you can 
% just write it in the bracket without creating a shorthand. Note: if you don't 
% want to have an experiment, just leave this out and it won't be printed.
%
% 3. CONTENT: Following the experiment is the content, i.e. what progress 
% you made on the experiment that day.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%----------------------------------------------------------------------------------------
%	PACKAGES AND OTHER DOCUMENT CONFIGURATIONS
%----------------------------------------------------------------------------------------                               

\documentclass[fontsize=11pt, % Document font size
               paper=a4, % Document paper type
               oneside, % Shifts odd pages to the left for easier reading when printed, can be changed to oneside
               captions=tableheading,
               index=totoc,
               hyperref]{labbook}
 
\usepackage[bottom=10em]{geometry} % Reduces the whitespace at the bottom of the page so more text can fit

\usepackage[english]{babel} % English language
\usepackage{lipsum} % Used for inserting dummy 'Lorem ipsum' text into the template

\usepackage[utf8]{inputenc} % Uses the utf8 input encoding
\usepackage[T1]{fontenc} % Use 8-bit encoding that has 256 glyphs

\usepackage[osf]{mathpazo} % Palatino as the main font
\linespread{1.05}\selectfont % Palatino needs some extra spacing, here 5% extra
\usepackage[scaled=.88]{beramono} % Bera-Monospace
\usepackage[scaled=.86]{berasans} % Bera Sans-Serif

\usepackage{booktabs,array} % Packages for tables

\usepackage{amsmath} % For typesetting math
\usepackage{graphicx} % Required for including images
\usepackage{etoolbox}
\usepackage[norule]{footmisc} % Removes the horizontal rule from footnotes
\usepackage{lastpage} % Counts the number of pages of the document

\graphicspath{{/Users/dsondak/Documents/Research/Notebook/Research-Notebook/figures/2016/}{/h1/dsondak/Research-Notebook/figures/2016/}}

\usepackage{natbib}

\usepackage[dvipsnames]{xcolor}  % Allows the definition of hex colors
\definecolor{titleblue}{rgb}{0.16,0.24,0.64} % Custom color for the title on the title page
\definecolor{linkcolor}{rgb}{0,0,0.42} % Custom color for links - dark blue at the moment

\addtokomafont{title}{\Huge\color{titleblue}} % Titles in custom blue color
\addtokomafont{chapter}{\color{OliveGreen}} % Lab dates in olive green
\addtokomafont{section}{\color{Sepia}} % Sections in sepia
\addtokomafont{pagehead}{\normalfont\sffamily\color{gray}} % Header text in gray and sans serif
\addtokomafont{caption}{\footnotesize\itshape} % Small italic font size for captions
\addtokomafont{captionlabel}{\upshape\bfseries} % Bold for caption labels
\addtokomafont{descriptionlabel}{\rmfamily}
%\setcapwidth[r]{10cm} % Right align caption text
\setkomafont{footnote}{\sffamily} % Footnotes in sans serif

\deffootnote[4cm]{4cm}{1em}{\textsuperscript{\thefootnotemark}} % Indent footnotes to line up with text

\DeclareFixedFont{\textcap}{T1}{phv}{bx}{n}{1.5cm} % Font for main title: Helvetica 1.5 cm
\DeclareFixedFont{\textaut}{T1}{phv}{bx}{n}{0.8cm} % Font for author name: Helvetica 0.8 cm

\usepackage[nouppercase,headsepline]{scrpage2} % Provides headers and footers configuration
\pagestyle{scrheadings} % Print the headers and footers on all pages
\clearscrheadfoot % Clean old definitions if they exist

\automark[chapter]{chapter}
\ohead{\headmark} % Prints outer header

\setlength{\headheight}{25pt} % Makes the header take up a bit of extra space for aesthetics
\setheadsepline{.4pt} % Creates a thin rule under the header
\addtokomafont{headsepline}{\color{lightgray}} % Colors the rule under the header light gray

\ofoot[\normalfont\normalcolor{\thepage\ |\  \pageref{LastPage}}]{\normalfont\normalcolor{\thepage\ |\  \pageref{LastPage}}} % Creates an outer footer of: "current page | total pages"

% These lines make it so each new lab day directly follows the previous one i.e. does not start on a new page - comment them out to separate lab days on new pages
\makeatletter
\patchcmd{\addchap}{\if@openright\cleardoublepage\else\clearpage\fi}{\par}{}{}
\makeatother
\renewcommand*{\chapterpagestyle}{scrheadings}

% These lines make it so every figure and equation in the document is numbered consecutively rather than restarting at 1 for each lab day - comment them out to remove this behavior
\usepackage{chngcntr}
\counterwithout{figure}{labday}
\counterwithout{equation}{labday}

% For color boxes
\usepackage{tcolorbox}

% For chemistry
\usepackage{mhchem}

% Hyperlink configuration
\usepackage[
    pdfauthor={}, % Your name for the author field in the PDF
    pdftitle={Laboratory Journal}, % PDF title
    pdfsubject={}, % PDF subject
    bookmarksopen=true,
    linktocpage=true,
    urlcolor=linkcolor, % Color of URLs
    citecolor=linkcolor, % Color of citations
    linkcolor=linkcolor, % Color of links to other pages/figures
    backref=page,
    pdfpagelabels=true,
    plainpages=false,
    colorlinks=true, % Turn off all coloring by changing this to false
    bookmarks=true,
    pdfview=FitB]{hyperref}

\usepackage[stretch=10]{microtype} % Slightly tweak font spacing for aesthetics

%\setlength\parindent{0pt} % Uncomment to remove all indentation from paragraphs

%----------------------------------------------------------------------------------------
%       NEW COMMANDS
%----------------------------------------------------------------------------------------

\newcommand{\fenics}{FEniCS \ }
\newcommand{\lr}[1]{\left(#1\right)}
\newcommand{\pdeone}[2]{\frac{\partial #1}{\partial #2}}
\newcommand{\pden}[3]{\frac{\partial^{#3} #1}{\partial #2^{#3}}}
\newcommand{\odeone}[2]{\frac{\mathrm{d} #1}{\mathrm{d} #2}}
\newcommand{\nup}[1]{\nu_{#1}^{\prime\prime}}
\newcommand{\nur}[1]{\nu_{#1}^{\prime}}
\newcommand{\frate}[1]{K_{#1}^{\left(f\right)}}
\newcommand{\rrate}[1]{K_{#1}^{\left(r\right)}}

\input{experiment_list}

%----------------------------------------------------------------------------------------

\begin{document}

%----------------------------------------------------------------------------------------
%	TITLE PAGE
%----------------------------------------------------------------------------------------

\title{\textcap{Laboratory Journal \\[1cm]  
%\textaut{Beginning 23-03-2016}
}
}

\author{
    \textaut{David Sondak}\\ \\ % Your name
}
\date{} % No date by default, add \today if you wish to include the publication date

\maketitle % Title page

\printindex
\tableofcontents % Table of contents
\newpage % Start lab look on a new page

%\begin{addmargin}[4cm]{0cm} % Makes the text width much shorter for a compact look

\pagestyle{scrheadings} % Begin using headers

%----------------------------------------------------------------------------------------
%	LAB BOOK CONTENTS
%----------------------------------------------------------------------------------------

%\input{2016/March/notebook_March2016.tex}
%\input{2016/April/notebook_April2016.tex}
%\input{2016/May/notebook_May2016.tex}
%\input{2016/July/notebook_July2016.tex}
%\input{2016/August/notebook_August2016.tex}
\input{2016/September/notebook_September2016.tex}
%-----------------------------------------

\bibliographystyle{plain}
\bibliography{references}

%-----------------------------------------
%\end{addmargin}

\end{document}