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Revision 879 - (show annotations)
Wed Oct 25 03:56:34 2006 UTC (13 years, 1 month ago) by jongui
Original Path: trunk/doc/user/guide_defs.tex
File MIME type: application/x-tex
File size: 12564 byte(s)
First prototype of pyvisi is almost done (testing to be done). 
Added all the epydocs and latex files.

1 % $Id$
2 %
3 % Copyright © 2006 by ACcESS MNRF
4 % \url{http://www.access.edu.au
5 % Primary Business: Queensland, Australia.
6 % Licensed under the Open Software License version 3.0
7 % http://www.opensource.org/licenses/osl-3.0.php
8 %
9
10
11 \usepackage{epsfig}
12 \usepackage{graphicx,color}
13 \usepackage{makeidx} % handle the index properly
14 \usepackage{xspace} % handle spaces after commands more nicely
15 % use the ams math stuff, as it makes the maths easier to code, and
16 % nicer output than the standard LaTeX stuff
17 \usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physicists
18 % see http://www.ams.org/tex/amslatex.html
19 \usepackage{alltt} % handy verbatim stuff
20
21
22 % define some handy commands for escript stuff
23 \newcommand{\LINUX}{{\it Linux}\xspace}
24 \newcommand{\escript}{\module{esys.escript}\xspace}
25 \newcommand{\finley}{\module{esys.finley}\xspace}
26 \newcommand{\bruce}{\module{esys.bruce}\xspace}
27 \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
28
29 \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
30 \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
31 \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
32 \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
33 \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
34
35 \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
36 \newcommand{\Poisson}{\class{Poisson}\xspace}
37 \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
38 \newcommand{\Lame}{\class{Lame}\xspace}
39 \newcommand{\Data}{\class{Data}\xspace}
40 \newcommand{\EmptyData}{empty \class{Data} \index{empty Data}\xspace}
41 \newcommand{\Domain}{\class{Domain}\xspace}
42 \newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
43 \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
44 \newcommand{\mayavi}{{\it mayavi} \index{visualization!mayavi}\index{mayavi}}
45 \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
46 \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
47 \newcommand{\False}{\constant{False}\xspace}
48 \newcommand{\True}{\constant{True}\xspace}
49 \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
50 \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
51 \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
52 \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
53 \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
54 \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
55 \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
56 \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
57 \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
58 \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}
59 \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
60 \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
61
62 \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
63 \newcommand{\Operator}{\class{Operator}\xspace}
64 \newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace}
65 \newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace}
66 \newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace}
67 \newcommand{\Function}{general \class{FunctionSpace}\xspace}
68 \newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace}
69 \newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace}
70 \newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace}
71 \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
72 \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
73 \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
74 \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
75 \newcommand{\Tensor}{{tensor \Data object}\xspace}
76 \newcommand{\Vector}{{vector \Data object}\xspace}
77 \newcommand{\Scalar}{{scalar \Data object}\xspace}
78 \newcommand{\DataSample}{{data sample} \index{data sample}\xspace}
79 \newcommand{\DataSamplePoints}{{data sample points} \index{data sample!points}\xspace}
80 \newcommand{\numarray}{\module{numarray}\xspace}
81 \newcommand{\Shape}{shape\xspace\index{shape}}
82 \newcommand{\Rank}{rank\xspace\index{shape}}
83 \newcommand{\ExampleDirectory}{example directory\xspace}
84 \newcommand{\ReferenceGuide}{\url{http://www.iservo.edu.au/esys/epydoc/index.html}}
85
86
87 % handy commands for pyvisi
88 \newcommand{\Scene}{\class{Scene}\xspace}
89 \newcommand{\DataCollector}{\class{DataCollector}\xspace}
90 \newcommand{\Camera}{\class{Camera}\xspace}
91 \newcommand{\Map}{\class{Map}\xspace}
92 \newcommand{\MapOnPlane}{\class{MapOnPlane}\xspace}
93 \newcommand{\MapOnClip}{\class{MapOnClip}\xspace}
94 \newcommand{\Contour}{\class{Contour}\xspace}
95 \newcommand{\ContourOnPlane}{\class{ContourOnPlane}\xspace}
96 \newcommand{\ContourOnClip}{\class{ContourOnClip}\xspace}
97 \newcommand{\Arrows}{\class{Arrows}\xspace}
98 \newcommand{\ArrowsOnPlane}{\class{ArrowsOnPlane}\xspace}
99 \newcommand{\ArrowsOnClip}{\class{ArrowsOnClip}\xspace}
100 \newcommand{\TensorC}{\class{Tensor}\xspace}
101 \newcommand{\TensorOnPlane}{\class{TensorOnPlane}\xspace}
102 \newcommand{\TensorOnClip}{\class{TensorOnClip}\xspace}
103 \newcommand{\Carpet}{\class{Carpet}\xspace}
104 \newcommand{\IsoSurface}{\class{IsoSurface}\xspace}
105 \newcommand{\IsoSurfaceOnPlane}{\class{IsoSurfaceOnPlane}\xspace}
106 \newcommand{\IsoSurfaceOnClip}{\class{IsoSurfaceOnClip}\xspace}
107 \newcommand{\StreamLines}{\class{StreamLines}\xspace}
108 \newcommand{\Image}{\class{Image}\xspace}
109 \newcommand{\Text}{\class{Text}\xspace}
110 \newcommand{\Position}{\class{Position}\xspace}
111 \newcommand{\Transform}{\class{Transform}\xspace}
112 \newcommand{\Style}{\class{Style}\xspace}
113 \newcommand{\BlueToRed}{\class{BlueToRed}\xspace}
114 \newcommand{\RedToBlue}{\class{RedToBlue}\xspace}
115
116
117 % default width for figures
118 \newcommand{\figwidth}{100mm}
119 % commands useful in cross-referencing
120 \newcommand {\Ref}[1] {Reference~\cite{#1}}
121 \newcommand {\Sec}[1] {Section~\ref{#1}}
122 \newcommand {\App}[1] {Appendix~\ref{#1}}
123 \newcommand {\Chap}[1] {Chapter~\ref{#1}}
124 \newcommand {\etal} {\emph{~et~al.}}
125 \newcommand {\fig}[1] {Figure~\ref{#1}}
126 \newcommand {\eqn}[1] {Equation~(\ref{#1})}
127 \newcommand {\tab}[1] {Table~\ref{#1}}
128
129 % this stops one figure taking up a whole page and lets more text onto
130 % the one page when a figure exists
131 \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
132
133 % improved version of caption handling
134 \usepackage{ccaption}
135 \captionnamefont{\scshape}
136 \captionstyle{}
137 \makeatletter
138 \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
139 \renewcommand{\@makecaption}[2]{%
140 \vskip\abovecaptionskip
141 \sbox\@tempboxa{#1: #2}%
142 \ifdim \wd\@tempboxa >\hsize
143 \def\baselinestretch{1}\@normalsize
144 #1: #2\par
145 \def\baselinestretch{1.5}\@normalsize
146 \else
147 \global \@minipagefalse
148 \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
149 \fi
150 \vskip\belowcaptionskip}
151 \makeatother
152
153 % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
154 %%% this code grabbed from the PyScript docs
155 %%% pyscript.sourceforge.net
156
157 % --------------------------------------------------------------
158 % Code format within \Verb
159 % --------------------------------------------------------------
160
161 % \definecolor{pycolor}{rgb}{0,0.4,0}
162
163 %% \DefineVerbatimEnvironment{python}{Verbatim}
164 %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
165 %% formatcom=\color{pycolor}\small,fontshape=rm}
166
167 %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
168
169 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
170
171 %%% end of grabbed code
172
173 % this is for when one uses pdflatex and therefore needs to load pdf
174 % figures into \includegraphics
175 \ifpdf
176 \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
177 \pdfcompresslevel=9 % 0: no compression, 9: highest compression
178 % or, set compress_level 9 in file pdftex.cfg
179 \else
180 \DeclareGraphicsExtensions{.eps}
181 \fi
182
183 % defines the colour for the background of code examples
184 \definecolor{LightGrey}{gray}{0.9}
185
186 % add the listings package to pretty print the code output
187 \usepackage{listings}
188
189 \lstdefinestyle{myC++}{%
190 %\lstset{%
191 language=C++,
192 showstringspaces=false,
193 basicstyle=\small\ttfamily,
194 commentstyle=\color[named]{BrickRed}\ttfamily,
195 keywordstyle=\color[named]{Purple}\ttfamily,
196 %identifierstyle=\color[named]{Blue}\ttfamily,
197 %functionstyle=\color[named]{Blue}\ttfamily,
198 %typestyle=\color[named]{ForestGreen}\ttfamily,
199 stringstyle=\color[named]{Tan}\ttfamily,%
200 morekeywords={,complex,}%
201 frame=none,%
202 backgroundcolor=\color{LightGrey}%
203 }
204
205 \lstdefinestyle{myMatlab}{%
206 %\lstset{%
207 language=Matlab,
208 showstringspaces=false,
209 basicstyle=\small\ttfamily,
210 commentstyle=\color[named]{BrickRed}\ttfamily,
211 keywordstyle=\color[named]{Purple}\ttfamily,
212 %identifierstyle=\color[named]{Blue}\ttfamily,
213 %functionstyle=\color[named]{Blue}\ttfamily,
214 %typestyle=\color[named]{ForestGreen}\ttfamily,
215 stringstyle=\color[named]{Tan}\ttfamily,%
216 frame=none,%
217 backgroundcolor=\color{LightGrey}%
218 }
219
220 \lstdefinestyle{myScilab}{%
221 %\lstset{%
222 language=Scilab,
223 showstringspaces=false,
224 basicstyle=\small\ttfamily,
225 commentstyle=\color[named]{BrickRed}\ttfamily,
226 keywordstyle=\color[named]{Purple}\ttfamily,
227 %identifierstyle=\color[named]{Blue}\ttfamily,
228 %functionstyle=\color[named]{Blue}\ttfamily,
229 %typestyle=\color[named]{ForestGreen}\ttfamily,
230 stringstyle=\color[named]{Tan}\ttfamily,%
231 frame=none,%
232 backgroundcolor=\color{LightGrey}%
233 }
234
235 \lstdefinestyle{myShell}{%
236 %\lstset{%
237 language=ksh,
238 showstringspaces=false,
239 basicstyle=\small\ttfamily,
240 commentstyle=\color[named]{Black}\ttfamily,
241 keywordstyle=\color[named]{Black}\ttfamily,
242 %identifierstyle=\color[named]{Blue}\ttfamily,
243 %functionstyle=\color[named]{Blue}\ttfamily,
244 %typestyle=\color[named]{ForestGreen}\ttfamily,
245 stringstyle=\color[named]{Black}\ttfamily,%
246 frame=none,%
247 backgroundcolor=\color{LightGrey}%
248 }
249
250 \lstdefinestyle{myPython}{%
251 %\lstset{%
252 language=python,
253 showstringspaces=false,
254 basicstyle=\small\ttfamily,
255 commentstyle=\color[named]{BrickRed}\ttfamily,
256 keywordstyle=\color[named]{Purple}\ttfamily,
257 %identifierstyle=\color[named]{Blue}\ttfamily,
258 %functionstyle=\color[named]{Blue}\ttfamily,
259 %typestyle=\color[named]{ForestGreen}\ttfamily,
260 stringstyle=\color[named]{Tan}\ttfamily,%
261 frame=none,%
262 %backgroundcolor=\color{LightGrey}%
263 }
264
265 \lstdefinestyle{myhtml}{%
266 %\lstset{%
267 language=xml,
268 showstringspaces=false,
269 basicstyle=\small\ttfamily,
270 commentstyle=\color[named]{BrickRed}\ttfamily,
271 keywordstyle=\color[named]{Purple}\ttfamily,
272 %identifierstyle=\color[named]{Blue}\ttfamily,
273 %functionstyle=\color[named]{Blue}\ttfamily,
274 %typestyle=\color[named]{ForestGreen}\ttfamily,
275 stringstyle=\color[named]{Tan}\ttfamily,
276 morekeywords={,simulation,prop_dim,error_check,stochastic,%
277 globals,field,dimensions,lattice,domains,samples,vector,%
278 components,fourier_space,sequence,integrate,algorithm,%
279 interval,k_operators,constant,operator_names,vectors,%
280 output,filename,group,sampling,moments,benchmark,use_double,%
281 use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
282 default_value,argv,arg,iterations,cross_propagation,%
283 use_mpi,paths,seed,noises,author,description,name,type,%
284 }
285 frame=none,%
286 %framerule=2pt,%
287 backgroundcolor=\color{LightGrey}%
288 }
289
290 % this implements producing nice code blocks
291 % it also saves time, typing and
292 % *should* reduce errors in the text by removing doubling up of code
293 \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
294
295 % this implements nicely formatted shell code
296 \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
297
298 % this implements nicely formatted Perl code
299 \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
300
301 % this implements nicely formatted Python code
302 \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
303
304 % this implements nicely formatted C++ code
305 \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
306
307 % this implements nicely formatted matlab code
308 \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
309
310 % this implements nicely formatted scilab code
311 \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
312

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