/[escript]/trunk/doc/user/guide_defs.tex
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Revision 983 - (show annotations)
Tue Feb 20 02:49:08 2007 UTC (12 years, 2 months ago) by gross
File MIME type: application/x-tex
File size: 12752 byte(s)
full Data object dump and load now available. Tests added.
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{\netCDF}{{\it netCDF}\xspace}
25 \newcommand{\escript}{\module{esys.escript}\xspace}
26 \newcommand{\finley}{\module{esys.finley}\xspace}
27 \newcommand{\bruce}{\module{esys.bruce}\xspace}
28 \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
29
30 \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
31 \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
32 \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
33 \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
34 \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
35
36 \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
37 \newcommand{\Poisson}{\class{Poisson}\xspace}
38 \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
39 \newcommand{\Lame}{\class{Lame}\xspace}
40 \newcommand{\Data}{\class{Data}\xspace}
41 \newcommand{\EmptyData}{empty \class{Data} \index{empty Data}\xspace}
42 \newcommand{\Domain}{\class{Domain}\xspace}
43 \newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
44 \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
45 \newcommand{\mayavi}{{\it mayavi} \index{visualization!mayavi}\index{mayavi}}
46 \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
47 \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
48 \newcommand{\False}{\constant{False}\xspace}
49 \newcommand{\True}{\constant{True}\xspace}
50 \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
51 \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
52 \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
53 \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
54 \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
55 \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
56 \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
57 \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
58 \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
59 \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}
60 \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
61 \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
62
63 \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
64 \newcommand{\Operator}{\class{Operator}\xspace}
65 \newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace}
66 \newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace}
67 \newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace}
68 \newcommand{\Function}{general \class{FunctionSpace}\xspace}
69 \newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace}
70 \newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace}
71 \newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace}
72 \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
73 \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
74 \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
75 \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
76 \newcommand{\Tensor}{{tensor \Data object}\xspace}
77 \newcommand{\Vector}{{vector \Data object}\xspace}
78 \newcommand{\Scalar}{{scalar \Data object}\xspace}
79 \newcommand{\DataSample}{{data sample} \index{data sample}\xspace}
80 \newcommand{\DataSamplePoints}{{data sample points} \index{data sample!points}\xspace}
81 \newcommand{\numarray}{\module{numarray}\xspace}
82 \newcommand{\Shape}{shape\xspace\index{shape}}
83 \newcommand{\Rank}{rank\xspace\index{shape}}
84 \newcommand{\ExampleDirectory}{example directory\xspace}
85 \newcommand{\ReferenceGuide}{\url{http://www.iservo.edu.au/esys/epydoc/index.html}}
86
87
88 % handy commands for pyvisi
89 \newcommand{\Scene}{\class{Scene}\xspace}
90 \newcommand{\Image}{\class{Image}\xspace}
91 \newcommand{\Text}{\class{Text}\xspace}
92 \newcommand{\DataCollector}{\class{DataCollector}\xspace}
93 \newcommand{\Camera}{\class{Camera}\xspace}
94 \newcommand{\Light}{\class{Light}\xspace}
95 \newcommand{\Map}{\class{Map}\xspace}
96 \newcommand{\MapOnPlane}{\class{MapOnPlane}\xspace}
97 \newcommand{\MapOnClip}{\class{MapOnClip}\xspace}
98 \newcommand{\MapOnScalarClip}{\class{MapOnScalarClip}\xspace}
99 \newcommand{\Arrows}{\class{Arrows}\xspace}
100 \newcommand{\ArrowsOnPlane}{\class{ArrowsOnPlane}\xspace}
101 \newcommand{\ArrowsOnClip}{\class{ArrowsOnClip}\xspace}
102 \newcommand{\IsoSurface}{\class{IsoSurface}\xspace}
103 \newcommand{\IsoSurfaceOnPlane}{\class{IsoSurfaceOnPlane}\xspace}
104 \newcommand{\IsoSurfaceOnClip}{\class{IsoSurfaceOnClip}\xspace}
105 \newcommand{\Contour}{\class{Contour}\xspace}
106 \newcommand{\ContourOnPlane}{\class{ContourOnPlane}\xspace}
107 \newcommand{\ContourOnClip}{\class{ContourOnClip}\xspace}
108 \newcommand{\TensorC}{\class{Tensor}\xspace}
109 \newcommand{\TensorOnPlane}{\class{TensorOnPlane}\xspace}
110 \newcommand{\TensorOnClip}{\class{TensorOnClip}\xspace}
111 \newcommand{\StreamLines}{\class{StreamLines}\xspace}
112 \newcommand{\Carpet}{\class{Carpet}\xspace}
113 \newcommand{\Position}{\class{Position}\xspace}
114 \newcommand{\Transform}{\class{Transform}\xspace}
115 \newcommand{\Style}{\class{Style}\xspace}
116 \newcommand{\BlueToRed}{\class{BlueToRed}\xspace}
117 \newcommand{\RedToBlue}{\class{RedToBlue}\xspace}
118 \newcommand{\Plane}{\class{Plane}\xspace}
119
120
121 % default width for figures
122 \newcommand{\figwidth}{100mm}
123 % commands useful in cross-referencing
124 \newcommand {\Ref}[1] {Reference~\cite{#1}}
125 \newcommand {\Sec}[1] {Section~\ref{#1}}
126 \newcommand {\App}[1] {Appendix~\ref{#1}}
127 \newcommand {\Chap}[1] {Chapter~\ref{#1}}
128 \newcommand {\etal} {\emph{~et~al.}}
129 \newcommand {\fig}[1] {Figure~\ref{#1}}
130 \newcommand {\eqn}[1] {Equation~(\ref{#1})}
131 \newcommand {\tab}[1] {Table~\ref{#1}}
132
133 % this stops one figure taking up a whole page and lets more text onto
134 % the one page when a figure exists
135 \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
136
137 % improved version of caption handling
138 \usepackage{ccaption}
139 \captionnamefont{\scshape}
140 \captionstyle{}
141 \makeatletter
142 \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
143 \renewcommand{\@makecaption}[2]{%
144 \vskip\abovecaptionskip
145 \sbox\@tempboxa{#1: #2}%
146 \ifdim \wd\@tempboxa >\hsize
147 \def\baselinestretch{1}\@normalsize
148 #1: #2\par
149 \def\baselinestretch{1.5}\@normalsize
150 \else
151 \global \@minipagefalse
152 \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
153 \fi
154 \vskip\belowcaptionskip}
155 \makeatother
156
157 % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
158 %%% this code grabbed from the PyScript docs
159 %%% pyscript.sourceforge.net
160
161 % --------------------------------------------------------------
162 % Code format within \Verb
163 % --------------------------------------------------------------
164
165 % \definecolor{pycolor}{rgb}{0,0.4,0}
166
167 %% \DefineVerbatimEnvironment{python}{Verbatim}
168 %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
169 %% formatcom=\color{pycolor}\small,fontshape=rm}
170
171 %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
172
173 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
174
175 %%% end of grabbed code
176
177 % this is for when one uses pdflatex and therefore needs to load pdf
178 % figures into \includegraphics
179 \ifpdf
180 \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
181 \pdfcompresslevel=9 % 0: no compression, 9: highest compression
182 % or, set compress_level 9 in file pdftex.cfg
183 \else
184 \DeclareGraphicsExtensions{.eps}
185 \fi
186
187 % defines the colour for the background of code examples
188 \definecolor{LightGrey}{gray}{0.9}
189
190 % add the listings package to pretty print the code output
191 \usepackage{listings}
192
193 \lstdefinestyle{myC++}{%
194 %\lstset{%
195 language=C++,
196 showstringspaces=false,
197 basicstyle=\small\ttfamily,
198 commentstyle=\color[named]{BrickRed}\ttfamily,
199 keywordstyle=\color[named]{Purple}\ttfamily,
200 %identifierstyle=\color[named]{Blue}\ttfamily,
201 %functionstyle=\color[named]{Blue}\ttfamily,
202 %typestyle=\color[named]{ForestGreen}\ttfamily,
203 stringstyle=\color[named]{Tan}\ttfamily,%
204 morekeywords={,complex,}%
205 frame=none,%
206 backgroundcolor=\color{LightGrey}%
207 }
208
209 \lstdefinestyle{myMatlab}{%
210 %\lstset{%
211 language=Matlab,
212 showstringspaces=false,
213 basicstyle=\small\ttfamily,
214 commentstyle=\color[named]{BrickRed}\ttfamily,
215 keywordstyle=\color[named]{Purple}\ttfamily,
216 %identifierstyle=\color[named]{Blue}\ttfamily,
217 %functionstyle=\color[named]{Blue}\ttfamily,
218 %typestyle=\color[named]{ForestGreen}\ttfamily,
219 stringstyle=\color[named]{Tan}\ttfamily,%
220 frame=none,%
221 backgroundcolor=\color{LightGrey}%
222 }
223
224 \lstdefinestyle{myScilab}{%
225 %\lstset{%
226 language=Scilab,
227 showstringspaces=false,
228 basicstyle=\small\ttfamily,
229 commentstyle=\color[named]{BrickRed}\ttfamily,
230 keywordstyle=\color[named]{Purple}\ttfamily,
231 %identifierstyle=\color[named]{Blue}\ttfamily,
232 %functionstyle=\color[named]{Blue}\ttfamily,
233 %typestyle=\color[named]{ForestGreen}\ttfamily,
234 stringstyle=\color[named]{Tan}\ttfamily,%
235 frame=none,%
236 backgroundcolor=\color{LightGrey}%
237 }
238
239 \lstdefinestyle{myShell}{%
240 %\lstset{%
241 language=ksh,
242 showstringspaces=false,
243 basicstyle=\small\ttfamily,
244 commentstyle=\color[named]{Black}\ttfamily,
245 keywordstyle=\color[named]{Black}\ttfamily,
246 %identifierstyle=\color[named]{Blue}\ttfamily,
247 %functionstyle=\color[named]{Blue}\ttfamily,
248 %typestyle=\color[named]{ForestGreen}\ttfamily,
249 stringstyle=\color[named]{Black}\ttfamily,%
250 frame=none,%
251 backgroundcolor=\color{LightGrey}%
252 }
253
254 \lstdefinestyle{myPython}{%
255 %\lstset{%
256 language=python,
257 showstringspaces=false,
258 basicstyle=\small\ttfamily,
259 commentstyle=\color[named]{BrickRed}\ttfamily,
260 keywordstyle=\color[named]{Purple}\ttfamily,
261 %identifierstyle=\color[named]{Blue}\ttfamily,
262 %functionstyle=\color[named]{Blue}\ttfamily,
263 %typestyle=\color[named]{ForestGreen}\ttfamily,
264 stringstyle=\color[named]{Tan}\ttfamily,%
265 frame=none,%
266 %backgroundcolor=\color{LightGrey}%
267 }
268
269 \lstdefinestyle{myhtml}{%
270 %\lstset{%
271 language=xml,
272 showstringspaces=false,
273 basicstyle=\small\ttfamily,
274 commentstyle=\color[named]{BrickRed}\ttfamily,
275 keywordstyle=\color[named]{Purple}\ttfamily,
276 %identifierstyle=\color[named]{Blue}\ttfamily,
277 %functionstyle=\color[named]{Blue}\ttfamily,
278 %typestyle=\color[named]{ForestGreen}\ttfamily,
279 stringstyle=\color[named]{Tan}\ttfamily,
280 morekeywords={,simulation,prop_dim,error_check,stochastic,%
281 globals,field,dimensions,lattice,domains,samples,vector,%
282 components,fourier_space,sequence,integrate,algorithm,%
283 interval,k_operators,constant,operator_names,vectors,%
284 output,filename,group,sampling,moments,benchmark,use_double,%
285 use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
286 default_value,argv,arg,iterations,cross_propagation,%
287 use_mpi,paths,seed,noises,author,description,name,type,%
288 }
289 frame=none,%
290 %framerule=2pt,%
291 backgroundcolor=\color{LightGrey}%
292 }
293
294 % this implements producing nice code blocks
295 % it also saves time, typing and
296 % *should* reduce errors in the text by removing doubling up of code
297 \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
298
299 % this implements nicely formatted shell code
300 \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
301
302 % this implements nicely formatted Perl code
303 \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
304
305 % this implements nicely formatted Python code
306 \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
307
308 % this implements nicely formatted C++ code
309 \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
310
311 % this implements nicely formatted matlab code
312 \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
313
314 % this implements nicely formatted scilab code
315 \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
316

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