/[escript]/trunk/doc/user/guide_defs.tex
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revision 3292 by caltinay, Thu Oct 21 00:37:42 2010 UTC revision 3293 by caltinay, Thu Oct 21 23:18:32 2010 UTC
# Line 13  Line 13 
13    
14    
15  \usepackage{subfigure}  \usepackage{subfigure}
16  \usepackage{graphicx,color}  \usepackage{makeidx}
 \usepackage{makeidx}  % handle the index properly  
 \usepackage{xspace}   % handle spaces after commands more nicely  
 % use the ams math stuff, as it makes the maths easier to code, and  
 % nicer output than the standard LaTeX stuff  
 \usepackage{amsmath,amsfonts,amssymb} % see http://www.ams.org/tex/amslatex.html  
 \usepackage{alltt} % handy verbatim stuff  
17    
18  \graphicspath{{figures/}}  \graphicspath{{figures/}}
19    
20    % default width for figures
21    \newcommand{\figwidth}{100mm}
22    
23    % commands useful in cross-referencing
24    \newcommand{\Ref}[1]{Reference~\cite{#1}}
25    \newcommand{\Sec}[1]{Section~\ref{#1}}
26    \newcommand{\App}[1]{Appendix~\ref{#1}}
27    \newcommand{\Chap}[1]{Chapter~\ref{#1}}
28    \newcommand{\etal}{\emph{~et~al.}}
29    \newcommand{\fig}[1]{Figure~\ref{#1}}
30    \newcommand{\eqn}[1]{Equation~(\ref{#1})}
31    \newcommand{\tab}[1]{Table~\ref{#1}}
32    \newcommand{\env}[1]{\textbf{\mbox{#1}}\index{Environment!#1}}
33    
34  % define some handy commands for escript stuff  % define some handy commands for escript stuff
35  \newcommand{\LINUX}{{\it Linux}\xspace}  \newcommand{\LINUX}{{\it Linux}\xspace}
36  \newcommand{\WINDOWS}{{\it MS Windows}\xspace}  \newcommand{\WINDOWS}{{\it MS Windows}\xspace}
37  \newcommand{\PYTHON}{{\it python}\xspace}  \newcommand{\PYTHON}{{\it python}\xspace}
 % \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}  
38  \newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace}  \newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace}
39  \newcommand{\escript}{\module{esys.escript}\xspace}  \newcommand{\escript}{\module{esys.escript}\xspace}
40  \newcommand{\finley}{\module{esys.finley}\xspace}  \newcommand{\finley}{\module{esys.finley}\xspace}
# Line 35  Line 42 
42  \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}  \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
43  \newcommand{\pycad}{\module{esys.pycad}\xspace}  \newcommand{\pycad}{\module{esys.pycad}\xspace}
44  \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}  \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
45  \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}  \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh}\xspace}
46  \newcommand{\SCIPY}{{\it SciPy}\cite{SCIPY}\index{SciPy} \xspace}  \newcommand{\SCIPY}{{\it SciPy}\cite{SCIPY}\index{SciPy}\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}  
47  \newcommand{\MPI}{{\it MPI}\index{Message Passing Interface!MPI}\xspace}  \newcommand{\MPI}{{\it MPI}\index{Message Passing Interface!MPI}\xspace}
48  \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\xspace}  \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\xspace}
49  \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}  \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
50  \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}  \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
51  \newcommand{\modelframe}{\module{esys.modelframe}\xspace}  \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
52  \newcommand{\pdetools}{\module{esys.escript.pdetools}\xspace}  \newcommand{\pdetools}{\module{esys.escript.pdetools}\xspace}
53  \newcommand{\esysxml}{{\it esysxml}}  \newcommand{\False}{\constant{False}\xspace}
54    \newcommand{\True}{\constant{True}\xspace}
55    \newcommand{\warning}[1]{\emph{Warning: #1}}
56    
57  \newcommand{\SolverOptions}{\class{SolverOptions}\xspace}  \newcommand{\SolverOptions}{\class{SolverOptions}\xspace}
58  \newcommand{\Poisson}{\class{Poisson}\xspace}  \newcommand{\Poisson}{\class{Poisson}\xspace}
# Line 55  Line 61 
61  \newcommand{\Data}{\class{Data}\xspace}  \newcommand{\Data}{\class{Data}\xspace}
62  \newcommand{\EmptyData}{empty \class{Data}\index{empty Data}\xspace}  \newcommand{\EmptyData}{empty \class{Data}\index{empty Data}\xspace}
63  \newcommand{\Domain}{\class{Domain}\xspace}  \newcommand{\Domain}{\class{Domain}\xspace}
64  \newcommand{\gnuplot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}  \newcommand{\gnuplot}{{\it gnuplot}\cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
65  \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}  \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
 \newcommand{\False}{\constant{False}\xspace}  
 \newcommand{\True}{\constant{True}\xspace}  
66  \newcommand{\PCG}{\member{SolverOptions.PCG}\xspace\index{linear solver!PCG}\index{PCG}}  \newcommand{\PCG}{\member{SolverOptions.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
67  \newcommand{\BiCGStab}{\member{SolverOptions.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}  \newcommand{\BiCGStab}{\member{SolverOptions.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
68  \newcommand{\Direct}{\member{SolverOptions.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}  \newcommand{\Direct}{\member{SolverOptions.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
# Line 70  Line 74 
74  \newcommand{\RILU}{\member{SolverOptions.RILU}\xspace\index{preconditioner!RILU}\index{RILU}}  \newcommand{\RILU}{\member{SolverOptions.RILU}\xspace\index{preconditioner!RILU}\index{RILU}}
75  \newcommand{\LUMPING}{\member{SolverOptions.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}  \newcommand{\LUMPING}{\member{SolverOptions.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
76  \newcommand{\NOREORDERING}{\member{SolverOptions.NO\hackscore REORDERING}\xspace}  \newcommand{\NOREORDERING}{\member{SolverOptions.NO\hackscore REORDERING}\xspace}
77  \newcommand{\MINIMUMFILLIN}{\member{SolverOptions.MINIMUM\hackscore FILL\hackscore IN}\xspace  \newcommand{\MINIMUMFILLIN}{\member{SolverOptions.MINIMUM\hackscore FILL\hackscore IN\xspace}
78  \index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}  \index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
79  \newcommand{\NESTEDDESCTION}{\member{SolverOptions.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}  \newcommand{\NESTEDDESCTION}{\member{SolverOptions.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
80  \newcommand{\AMG}{\member{SolverOptions.AMG}\xspace\index{linear solver!AMG}\index{algebraic Multi-grid}\index{AMG}}  \newcommand{\AMG}{\member{SolverOptions.AMG}\xspace\index{linear solver!AMG}\index{algebraic Multi-grid}\index{AMG}}
# Line 105  Line 109 
109  \newcommand{\Rank}{rank\xspace\index{shape}}  \newcommand{\Rank}{rank\xspace\index{shape}}
110  \newcommand{\ExampleDirectory}{example directory\xspace}  \newcommand{\ExampleDirectory}{example directory\xspace}
111  \newcommand{\ReferenceGuide}{\url{http://esys.esscc.uq.edu.au/docs.html}\xspace}  \newcommand{\ReferenceGuide}{\url{http://esys.esscc.uq.edu.au/docs.html}\xspace}
112  \newcommand{\Point}{\class{Point} \xspace}  \newcommand{\Point}{\class{Point}\xspace}
113  \newcommand{\PropertySet}{\class{PropertySet} \xspace}  \newcommand{\PropertySet}{\class{PropertySet}\xspace}
114  \newcommand{\Design}{\class{Design} \xspace}  \newcommand{\Design}{\class{Design}\xspace}
115  \newcommand{\TagMap}{\class{TagMap} \xspace}  \newcommand{\TagMap}{\class{TagMap}\xspace}
116  \newcommand{\ManifoldOneD}{\class{Manifold1D} \xspace}  \newcommand{\ManifoldOneD}{\class{Manifold1D}\xspace}
117  \newcommand{\ManifoldTwoD}{\class{Manifold2D} \xspace}  \newcommand{\ManifoldTwoD}{\class{Manifold2D}\xspace}
118  \newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace}  \newcommand{\ManifoldThreeD}{\class{Manifold3D}\xspace}
119    
120  % handy commands related to visualization  % handy commands related to visualization
121  \newcommand{\VTK}{{\it VTK}\index{visualization!VTK}\index{VTK}\xspace}  \newcommand{\VTK}{{\it VTK}\index{visualization!VTK}\index{VTK}\xspace}
# Line 120  Line 124 
124  \newcommand{\VTKUrl}{\url{http://www.vtk.org/}\index{visualization!VTK}\index{VTK}\xspace}  \newcommand{\VTKUrl}{\url{http://www.vtk.org/}\index{visualization!VTK}\index{VTK}\xspace}
125  \newcommand{\VisIt}{{\it VisIt}\index{visualization!VisIt}\index{VisIt}\xspace}  \newcommand{\VisIt}{{\it VisIt}\index{visualization!VisIt}\index{VisIt}\xspace}
126  \newcommand{\mayavi}{{\it mayavi}\index{visualization!mayavi}\index{mayavi}\xspace}  \newcommand{\mayavi}{{\it mayavi}\index{visualization!mayavi}\index{mayavi}\xspace}
127  \newcommand{\OpenDX}{{\it OpenDX} \index{visualization!OpenDX}\index{OpenDX}\cite{OPENDX}\xspace}  \newcommand{\OpenDX}{{\it OpenDX}\index{visualization!OpenDX}\index{OpenDX}\cite{OPENDX}\xspace}
128    
129    % deprecated pyvisi commands
130  \newcommand{\Scene}{\class{Scene}\xspace}  \newcommand{\Scene}{\class{Scene}\xspace}
131  \newcommand{\Camera}{\class{Camera}\xspace}  \newcommand{\Camera}{\class{Camera}\xspace}
132  \newcommand{\Light}{\class{Light}\xspace}  \newcommand{\Light}{\class{Light}\xspace}
# Line 172  Line 177 
177  \newcommand{\GlobalPosition}{\class{GlobalPosition}\xspace}  \newcommand{\GlobalPosition}{\class{GlobalPosition}\xspace}
178  \newcommand{\Rotation}{\class{Rotation}\xspace}  \newcommand{\Rotation}{\class{Rotation}\xspace}
179  \newcommand{\thumbnailwidth}{50mm}  \newcommand{\thumbnailwidth}{50mm}
180    % end of pyvisi commands
 % default width for figures  
 \newcommand{\figwidth}{100mm}  
 % commands useful in cross-referencing  
 \newcommand {\Ref}[1] {Reference~\cite{#1}}  
 \newcommand {\Sec}[1] {Section~\ref{#1}}  
 \newcommand {\App}[1] {Appendix~\ref{#1}}  
 \newcommand {\Chap}[1] {Chapter~\ref{#1}}  
 \newcommand {\etal} {\emph{~et~al.}}  
 \newcommand {\fig}[1] {Figure~\ref{#1}}  
 \newcommand {\eqn}[1] {Equation~(\ref{#1})}  
 \newcommand {\tab}[1] {Table~\ref{#1}}  
181    
182  % this stops one figure taking up a whole page and lets more text onto  % this stops one figure taking up a whole page and lets more text onto
183  % the one page when a figure exists  % the one page when a figure exists
184  \renewcommand{\floatpagefraction}{0.8} %   Default = 0.5  \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
185    
186  % improved version of caption handling  % improved version of caption handling
187  \usepackage{ccaption}  \usepackage{ccaption}
# Line 209  Line 203 
203  \vskip\belowcaptionskip}  \vskip\belowcaptionskip}
204  \makeatother  \makeatother
205    
 % \usepackage{fancyvrb}  % fancy verbatim stuff.  Needed so code below goes  
 %%% this code grabbed from the PyScript docs  
 %%% pyscript.sourceforge.net  
   
 % --------------------------------------------------------------  
 % Code format within \Verb  
 % --------------------------------------------------------------  
   
 % \definecolor{pycolor}{rgb}{0,0.4,0}  
   
 %% \DefineVerbatimEnvironment{python}{Verbatim}  
 %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},  
 %% formatcom=\color{pycolor}\small,fontshape=rm}  
   
 %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}  
   
 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}  
   
 %%% end of grabbed code  
   
206  % this is for when one uses pdflatex and therefore needs to load pdf  % this is for when one uses pdflatex and therefore needs to load pdf
207  % figures into \includegraphics  % figures into \includegraphics
208  \ifpdf  \ifpdf
# Line 242  Line 216 
216  % defines the colour for the background of code examples  % defines the colour for the background of code examples
217  \definecolor{LightGrey}{gray}{0.9}  \definecolor{LightGrey}{gray}{0.9}
218    
 % add the listings package to pretty print the code output  
 \usepackage{listings}  
   
   
219  %Some colour definitions added to keep pdflatex happy  %Some colour definitions added to keep pdflatex happy
220  %I make no claim that these values are particularly good  %I make no claim that these values are particularly good
221  \definecolor{Purple}{rgb}{0.7, 0, 0.6}  \definecolor{Purple}{rgb}{0.7, 0, 0.6}
# Line 257  Line 227 
227  %end color defs  %end color defs
228    
229  \lstdefinestyle{myC++}{%  \lstdefinestyle{myC++}{%
 %\lstset{%  
230  language=C++,  language=C++,
231  showstringspaces=false,  showstringspaces=false,
232  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,
# Line 273  backgroundcolor=\color{LightGrey}% Line 242  backgroundcolor=\color{LightGrey}%
242  }  }
243    
244  \lstdefinestyle{myMatlab}{%  \lstdefinestyle{myMatlab}{%
 %\lstset{%  
245  language=Matlab,  language=Matlab,
246  showstringspaces=false,  showstringspaces=false,
247  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,
# Line 288  backgroundcolor=\color{LightGrey}% Line 256  backgroundcolor=\color{LightGrey}%
256  }  }
257    
258  \lstdefinestyle{myScilab}{%  \lstdefinestyle{myScilab}{%
 %\lstset{%  
259  language=Scilab,  language=Scilab,
260  showstringspaces=false,  showstringspaces=false,
261  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,
# Line 303  backgroundcolor=\color{LightGrey}% Line 270  backgroundcolor=\color{LightGrey}%
270  }  }
271    
272  \lstdefinestyle{myShell}{%  \lstdefinestyle{myShell}{%
 %\lstset{%  
273  language=ksh,  language=ksh,
274  showstringspaces=false,  showstringspaces=false,
275  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,
# Line 318  backgroundcolor=\color{LightGrey}% Line 284  backgroundcolor=\color{LightGrey}%
284  }  }
285    
286  \lstdefinestyle{myPython}{%  \lstdefinestyle{myPython}{%
 %\lstset{%  
287  language=python,  language=python,
288  showstringspaces=false,  showstringspaces=false,
289  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,
# Line 333  frame=none,% Line 298  frame=none,%
298  }  }
299    
300  \lstdefinestyle{myhtml}{%  \lstdefinestyle{myhtml}{%
 %\lstset{%  
301  language=xml,  language=xml,
302  showstringspaces=false,  showstringspaces=false,
303  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,

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