Times and Palatino font support and citation in chapters fixed

.gitignore

@@ -22,3 +22,4 @@
 *.ind
 *cookie*
 thesis.ps
+*#

Chapter1/chapter1.tex

@@ -7,7 +7,7 @@
 %********************************** %First Section  **************************************
 \section{What is Loren Ipsum? Title with Math \texorpdfstring{$\sigma$}{[sigma]}} %Section - 1.1 
 
-Lorem Ipsum is simply dummy text of the printing and typesetting industry~\cref{section1.3}. Lorem Ipsum\citep{Aup91,Ancey1996} has been the industry's standard dummy text ever since the 1500s, when an unknown printer took a galley of type and scrambled it to make a type specimen book. It has survived not only five centuries, but also the leap into electronic typesetting, remaining essentially unchanged. It was popularised in the 1960s with the release of Letraset sheets containing Lorem Ipsum passages, and more recently with desktop publishing software like Aldus PageMaker including versions of Lorem Ipsum~\citep{AAB95,Con90,LM65}.
+Lorem Ipsum is simply dummy text of the printing and typesetting industry~\cref{section1.3}. Lorem Ipsum\citep{Aup91} has been the industry's standard dummy text ever since the 1500s, when an unknown printer took a galley of type and scrambled it to make a type specimen book. It has survived not only five centuries, but also the leap into electronic typesetting, remaining essentially unchanged. It was popularised in the 1960s with the release of Letraset sheets containing Lorem Ipsum passages, and more recently with desktop publishing software like Aldus PageMaker including versions of Lorem Ipsum~\citep{AAB95,Con90,LM65}.
 
 The most famous equation in the world: $E^2 = (m_0c^2)^2 + (pc)^2$, which is known as the \textbf{energy-mass-momentum} relation as an in-line equation.
 

Chapter2/chapter2.tex

@@ -1,7 +1,7 @@
 \chapter{My Second Chapter}
 \section[Short title]{Reasonably Long Section Title}
 
-If you have trouble viewing the document please contact Krishna \href{mailto:kks32@cam.ac.uk}{kks32@cam.ac.uk}. The SI Units for dynamic viscosity is \si{\newton\second\per\metre\squared}. I'm going to randomly include a picture~\cref{fig:minion}
+Email ID of Krishna Kumar \href{mailto:kks32@cam.ac.uk}{kks32@cam.ac.uk}. The SI Units for dynamic viscosity is \si{\newton\second\per\metre\squared}. I'm going to randomly include a picture~\cref{fig:minion}
 
 
 \begin{figure}[htbp!] 
@@ -57,7 +57,7 @@ Etiam elementum tristique lacus, sit amet eleifend nibh eleifend sed \footnote{M
 \begin{landscape}
 
 \section*{Subplots}
-I can cite Wall-E (see Fig.~\ref{fig:WallE}) and Minions in despicable me (~\ref{fig:Minnion}) or I can cite the whole figure as (Fig.~\ref{fig:animations})
+I can cite Wall-E (see ~\cref{fig:WallE}) and Minions in despicable me (~\cref{fig:Minnion}) or I can cite the whole figure as ~\cref{fig:animations}
 
 
 \begin{figure}

Chapter3/chapter3.tex

@@ -6,25 +6,25 @@ And now I begin my third chapter here \dots
 
 And now to cite some more people~\citet{Rea85}
 
-\subsection{first subsection in the First Section}
+\subsection{First Subsection in the First Section}
 \dots and some more 
 
-\subsection{second subsection in the First Section}
+\subsection{Second Subsection in the First Section}
 \dots and some more \dots
 
-\subsubsection{first subsub section in the second subsection}
+\subsubsection{First subsub section in the second subsection}
 \dots and some more in the first subsub section otherwise it all looks the same
 doesn't it? well we can add some text to it \dots
 
-\subsection{third subsection in the First Section}
+\subsection{Third Subsection in the First Section}
 \dots and some more \dots
 
-\subsubsection{first subsub section in the third subsection}
+\subsubsection{First subsub section in the third subsection}
 \dots and some more in the first subsub section otherwise it all looks the same
 doesn't it? well we can add some text to it and some more and some more and
 some more and some more and some more and some more and some more \dots
 
-\subsubsection{second subsub section in the third subsection}
+\subsubsection{Second subsub section in the third subsection}
 \dots and some more in the first subsub section otherwise it all looks the same
 doesn't it? well we can add some text to it \dots
 

Classes/PhDThesisPSnPDF.cls

@@ -33,6 +33,10 @@
 \newif\ifCU@index\CU@indexfalse
 \DeclareOption{index}{\CU@indextrue}
 
+% ************************** Font Option *************************
+\newif\ifCU@times\CU@timesfalse % Times with Math Support
+\DeclareOption{times}{\CU@timestrue}
+
 \ProcessOptions\relax%
 
 \ifCU@bookmode
@@ -177,6 +181,14 @@
 \RequirePackage{textcomp}
 \RequirePackage[ansinew]{inputenc}
 \RequirePackage[T1]{fontenc}
+
+% Times
+\ifCU@times
+\RequirePackage{mathptmx}  % times roman, including math (where possible)
+\else
+\RequirePackage{mathpazo}  % palatino, including math (where possible)
+\fi
+
 \input{glyphtounicode}
 \pdfglyphtounicode{f_f}{FB00}
 \pdfglyphtounicode{f_i}{FB01}
@@ -228,7 +240,7 @@
 \fancyfoot{}
 
 
-\setlength{\headheight}{14pt}
+\setlength{\headheight}{14.5pt}
 %\renewcommand{\headrulewidth}{0.5pt}
 %\renewcommand{\footrulewidth}{0pt}
 \fancypagestyle{plain}{

Preamble/preamble.tex

@@ -42,9 +42,9 @@
 
 % *****************************************************************************
 % ******************* Fonts (like different typewriter fonts etc.)*************
-%\RequirePackage[scaled=.87]{couriers}
 %\renewcommand\rmdefault{psb}
-\usepackage{libertine}
+% \usepackage{libertine} % Linux Libertine Font - no Math support
+
 
 
 % *****************************************************************************

README.md

@@ -51,8 +51,6 @@ It also supports some custom options:
 
 *   `twoside` or `oneside`: This is especially useful for printing double side (twoside) or single side.
 
-*   `10pt` or `11pt` or `12pt`: Font Size. Default set as `11pt`.
-
 *   `printmode`: Supports PrintMode and Online Version with different page margins and hyperlink styles.
     Use `printmode` in the options to activate Print Version with appropriate margins and page layout and view    styles. Leaving the options field blank will activate Online version.
 
@@ -62,6 +60,14 @@ It also supports some custom options:
 
     _Note_: the package `makeidx` is used to create the index.
 
+### Choosing the Fonts:
+
+`PhDThesisPSnPDF` currently supports two fonts `Times` and `Palatino (default)`.
+
+*   `times`: Specifying times option in the document class will use `mathptpx` or `Times` font with Math Support.
+
+*   `default (empty)`: When no font is specified, `Palatino` is used as default font with Math Support.
+
 ## Custom Settings
 
 *   The depth of table of contents can be set using: 
@@ -138,6 +144,4 @@ You can run the following command:
 
 *   Support custom margins
 
-*   Support non-free fonts! 
+*   Headheight should be fixed according to the fontsize used!
-
-*   Title page on twoside requires tweaking for College name and degreedate at the bottom

thesis.tex

@@ -1,4 +1,4 @@
-\documentclass[a4paper,11pt,twoside,printmode,index]{Classes/PhDThesisPSnPDF}
+\documentclass[a4paper,times,12pt,twoside,printmode,index]{Classes/PhDThesisPSnPDF}
 
 % ********************************* Preamble **********************************
 % Preamble: Contains packages and user-defined commands and settings