Minor formatting

Author: rayhem

chapters/Coding_style.tex

@@ -45,8 +45,8 @@
     If a function does not fit in its entirety on a single screen, it is too long---split it up.
     Don't worry about the overhead of calling a function.
     If you use optimization flags like \texttt{-O3}, the compiler will try to inline them anyway.
-  \item\textbf{Modules}---\marginnote{It's also a good idea to put all physical parameters (number of particles, $\pi$, $c$, $k_B$, etc.) into their own module, even if they're just constant numbers. You can then ``load'' the parameters into your subroutines with the \keyword{use} statement instead of having absurdly long lists of arguments, or worse, global variables.}Separate your program into logical units.
-    Combine related functions and subroutines into modules.
+  \item\textbf{Modules}---Separate your program into logical units.
+    Combine related functions and subroutines into modules\footnote{It's also convenient to put all physical parameters (number of particles, $\pi$, $c$, $k_B$, etc.) into their own module, even if they're just constant numbers. You can then ``load'' the parameters into your subroutines with the \keyword{use} statement instead of having absurdly long lists of arguments, or worse, global variables.}.
     For example, a single module with function integrators, or ODE solvers. 
     If you use the object-oriented features of Fortran, it is also good practice to create separate modules for classes, \eg, a sparse-matrix object.
   \item\textbf{Comments}---Comments are kind of a double-edged sword.

chapters/Optimization.tex

@@ -79,7 +79,7 @@ \section{Some optimizations you are allowed to use}
         i & j & k & l
     \end{bmatrix}
     \end{equation*}
-    is actually stored in memory\footnote{Notice, column-major ordering means the leftmost index moves the fastest as one traverses consecutive memory entries. Predictably, row-major ordering means the same for the rightmost index.} as $\left[a,e,i,b,f,j,c,g,k,d,h,l\right]$.
+    is actually stored in memory as $\left[a,e,i,b,f,j,c,g,k,d,h,l\right]$.
     Because of this, operations within a single column are much faster than operations within a single row; the processor can easily load a whole column into the cache, but not a whole row.
     It is therefore important to carefully consider your array layout.
     For example, if you have an array containing the coordinates of many particles, then a $3\times n$ layout will be more efficient than $n\times 3$.

chapters/Structuring_your_code.tex

@@ -31,7 +31,7 @@ \section{Functions and subroutines}
 Fortran subroutines are invoked with the keyword \keyword{call} followed by the name of the routine and an optional list of parameters in parentheses.
 The code for the subroutine itself appears after the keyword \keyword{contains}.
 We don't have to type \keyword{implicit none} again, since that's inherited from the program.
-\marginnote{A \textbf{big} fortran gotcha involves initializing local variables while declaring them (\ie\ \lstinline$real :: x = 10.0$). Variables like this have an implicit \keyword{save}\index{Fortran!save@\keyword{save}} statement, meaning they retain their value through subsequent calls to the subroutine. It's best to either mark these variables with the \keyword{save} attribute explicitly \emph{or} separate initialization from declaration within subroutines and functions.}
+\marginnote{A \textbf{big} fortran gotcha involves initializing local variables while declaring them (\ie\ \lstinline$real :: x = 10.0$). Variables like this have an implicit \keyword{save}\index{Fortran!save@\keyword{save}} statement, meaning they retain their value through subsequent calls to the subroutine. It's a good idea to either mark these variables with the \keyword{save} attribute explicitly \emph{or} separate initialization from declaration within subroutines and functions.}
 When declaring the parameters, we need to specify not only the type, but also how we're going to use them, \ie, the \emph{intent}.\index{Fortran!intent(in/out)@\keyword{intent} (\keyword{in}/\keyword{out})}
 For input and output parameters, we use \texttt{\keyword{intent}(\keyword{in})} and \texttt{\keyword{intent}(\keyword{out})}, respectively.
 For parameters functioning as both, we use \texttt{\keyword{intent}(\keyword{inout})}.