--- trunk/doc/user/guide_defs.tex	2008/12/04 03:48:22	2128
+++ trunk/doc/user/guide_defs.tex	2009/03/26 04:33:44	2335
@@ -26,7 +26,10 @@
 
 % define some handy commands for escript stuff
 \newcommand{\LINUX}{{\it Linux}\xspace}
-\newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
+\newcommand{\WINDOWS}{{\it MS Windows}\xspace}
+\newcommand{\PYTHON}{{\it python}\xspace}
+% \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
+\newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace}
 \newcommand{\escript}{\module{esys.escript}\xspace}
 \newcommand{\finley}{\module{esys.finley}\xspace}
 \newcommand{\esys}{\module{esys}\xspace}
@@ -34,13 +37,17 @@
 \newcommand{\pycad}{\module{esys.pycad}\xspace}
 \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
 \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
-
-
+\newcommand{\env}[1]{\textbf{\mbox{#1}}\index{Environment!#1}}
+% \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\cite{MPI}\xspace}
+% \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\cite{OPENMP}\xspace}
+\newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\xspace}
+\newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\xspace}
 \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
 \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
 \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
 \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
 \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
+\newcommand{\esysxml}{{\it esysxml}}
 
 \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
 \newcommand{\Poisson}{\class{Poisson}\xspace}
@@ -227,17 +234,27 @@
 % add the listings package to pretty print the code output
 \usepackage{listings}
 
+
+%Some colour definitions added to keep pdflatex happy
+%I make no claim that these values are particularly good
+\definecolor{Purple}{rgb}{0.7, 0, 0.6}
+\definecolor{Tan}{rgb}{0.5,0.5,0.5}
+\definecolor{BrickRed}{rgb}{0.7, 0.2, 0.2}
+
+% All the \color{x} used to be \color[named]{x}
+%end color defs
+
 \lstdefinestyle{myC++}{%
 %\lstset{%
 language=C++,
 showstringspaces=false,
 basicstyle=\small\ttfamily,
-commentstyle=\color[named]{BrickRed}\ttfamily,
-keywordstyle=\color[named]{Purple}\ttfamily,
-%identifierstyle=\color[named]{Blue}\ttfamily,
-%functionstyle=\color[named]{Blue}\ttfamily,
-%typestyle=\color[named]{ForestGreen}\ttfamily,
-stringstyle=\color[named]{Tan}\ttfamily,%
+commentstyle=\color{BrickRed}\ttfamily,
+keywordstyle=\color{Purple}\ttfamily,
+%identifierstyle=\color{Blue}\ttfamily,
+%functionstyle=\color{Blue}\ttfamily,
+%typestyle=\color{ForestGreen}\ttfamily,
+stringstyle=\color{Tan}\ttfamily,%
 morekeywords={,complex,}%
 frame=none,%
 backgroundcolor=\color{LightGrey}%
@@ -248,12 +265,12 @@
 language=Matlab,
 showstringspaces=false,
 basicstyle=\small\ttfamily,
-commentstyle=\color[named]{BrickRed}\ttfamily,
-keywordstyle=\color[named]{Purple}\ttfamily,
-%identifierstyle=\color[named]{Blue}\ttfamily,
-%functionstyle=\color[named]{Blue}\ttfamily,
-%typestyle=\color[named]{ForestGreen}\ttfamily,
-stringstyle=\color[named]{Tan}\ttfamily,%
+commentstyle=\color{BrickRed}\ttfamily,
+keywordstyle=\color{Purple}\ttfamily,
+%identifierstyle=\color{Blue}\ttfamily,
+%functionstyle=\color{Blue}\ttfamily,
+%typestyle=\color{ForestGreen}\ttfamily,
+stringstyle=\color{Tan}\ttfamily,%
 frame=none,%
 backgroundcolor=\color{LightGrey}%
 }
@@ -263,12 +280,12 @@
 language=Scilab,
 showstringspaces=false,
 basicstyle=\small\ttfamily,
-commentstyle=\color[named]{BrickRed}\ttfamily,
-keywordstyle=\color[named]{Purple}\ttfamily,
-%identifierstyle=\color[named]{Blue}\ttfamily,
-%functionstyle=\color[named]{Blue}\ttfamily,
-%typestyle=\color[named]{ForestGreen}\ttfamily,
-stringstyle=\color[named]{Tan}\ttfamily,%
+commentstyle=\color{BrickRed}\ttfamily,
+keywordstyle=\color{Purple}\ttfamily,
+%identifierstyle=\color{Blue}\ttfamily,
+%functionstyle=\color{Blue}\ttfamily,
+%typestyle=\color{ForestGreen}\ttfamily,
+stringstyle=\color{Tan}\ttfamily,%
 frame=none,%
 backgroundcolor=\color{LightGrey}%
 }
@@ -278,12 +295,12 @@
 language=ksh,
 showstringspaces=false,
 basicstyle=\small\ttfamily,
-commentstyle=\color[named]{Black}\ttfamily,
-keywordstyle=\color[named]{Black}\ttfamily,
-%identifierstyle=\color[named]{Blue}\ttfamily,
-%functionstyle=\color[named]{Blue}\ttfamily,
-%typestyle=\color[named]{ForestGreen}\ttfamily,
-stringstyle=\color[named]{Black}\ttfamily,%
+commentstyle=\color{Black}\ttfamily,
+keywordstyle=\color{Black}\ttfamily,
+%identifierstyle=\color{Blue}\ttfamily,
+%functionstyle=\color{Blue}\ttfamily,
+%typestyle=\color{ForestGreen}\ttfamily,
+stringstyle=\color{Black}\ttfamily,%
 frame=none,%
 backgroundcolor=\color{LightGrey}%
 }
@@ -293,12 +310,12 @@
 language=python,
 showstringspaces=false,
 basicstyle=\small\ttfamily,
-commentstyle=\color[named]{BrickRed}\ttfamily,
-keywordstyle=\color[named]{Purple}\ttfamily,
-%identifierstyle=\color[named]{Blue}\ttfamily,
-%functionstyle=\color[named]{Blue}\ttfamily,
-%typestyle=\color[named]{ForestGreen}\ttfamily,
-stringstyle=\color[named]{Tan}\ttfamily,%
+commentstyle=\color{BrickRed}\ttfamily,
+keywordstyle=\color{Purple}\ttfamily,
+%identifierstyle=\color{Blue}\ttfamily,
+%functionstyle=\color{Blue}\ttfamily,
+%typestyle=\color{ForestGreen}\ttfamily,
+stringstyle=\color{Tan}\ttfamily,%
 frame=none,%
 %backgroundcolor=\color{LightGrey}%
 }
@@ -308,12 +325,12 @@
 language=xml,
 showstringspaces=false,
 basicstyle=\small\ttfamily,
-commentstyle=\color[named]{BrickRed}\ttfamily,
-keywordstyle=\color[named]{Purple}\ttfamily,
-%identifierstyle=\color[named]{Blue}\ttfamily,
-%functionstyle=\color[named]{Blue}\ttfamily,
-%typestyle=\color[named]{ForestGreen}\ttfamily,
-stringstyle=\color[named]{Tan}\ttfamily,
+commentstyle=\color{BrickRed}\ttfamily,
+keywordstyle=\color{Purple}\ttfamily,
+%identifierstyle=\color{Blue}\ttfamily,
+%functionstyle=\color{Blue}\ttfamily,
+%typestyle=\color{ForestGreen}\ttfamily,
+stringstyle=\color{Tan}\ttfamily,
 morekeywords={,simulation,prop_dim,error_check,stochastic,%
   globals,field,dimensions,lattice,domains,samples,vector,%
   components,fourier_space,sequence,integrate,algorithm,%