/[escript]/trunk/doc/cookbook/cookbook_defs.tex
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Revision 2495 - (show annotations)
Fri Jun 26 03:39:21 2009 UTC (10 years, 3 months ago) by ahallam
Original Path: trunk/doc/cookbook/TEXT/cookbook_defs.tex
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File size: 14310 byte(s)
Many revisions to Head Diff Documentation, One grammar correction to user guide.
1
2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3 %
4 % Copyright (c) 2003-2008 by University of Queensland
5 % Earth Systems Science Computational Center (ESSCC)
6 % http://www.uq.edu.au/esscc
7 %
8 % Primary Business: Queensland, Australia
9 % Licensed under the Open Software License version 3.0
10 % http://www.opensource.org/licenses/osl-3.0.php
11 %
12 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
13
14
15 \usepackage{subfigure}
16 \usepackage{epsfig}
17 \usepackage{graphicx,color}
18 \usepackage{makeidx} % handle the index properly
19 \usepackage{xspace} % handle spaces after commands more nicely
20 % use the ams math stuff, as it makes the maths easier to code, and
21 % nicer output than the standard LaTeX stuff
22 \usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physici % see http://www.ams.org/tex/amslatex.html
23 \usepackage{alltt} % handy verbatim stuff
24 \usepackage{textcomp}
25
26 %Tony's Commands
27 \newcommand{\editor}[1] {\textit{EDITORIAL: {#1}}}
28 %\newcommand{\eqref}[1] {(\ref{#1})}
29 \newcommand{\esc}{\module{escript}\xspace}
30 \newcommand{\fileex}[1]{\module{\textbackslash examples\textbackslash {#1}}\xspace}
31 \newcommand{\TODO}[1]{\textbf{TODO}:\xspace\textit{#1} }
32 \newcommand{\ESCRIPT}{\textit{escript}\xspace}
33 \newcommand{\ESYS}{\textit{esys}\xspace}
34 \newcommand{\FINLEY}{\textit{finley}\xspace}
35
36 %referencing
37 \newcommand{\reffig}[1]{(Figure \ref{#1})}
38 \newcommand{\refeq}[1]{equation \ref{#1}}
39 \newcommand{\refEq}[1]{Equation \ref{#1}}
40
41 %modules
42 \newcommand{\modesys}{\module{esys}\xspace}
43 \newcommand{\modescript}{\module{esys.escript}\xspace}
44 \newcommand{\modfinley}{\module{esys.finley}\xspace}
45 \newcommand{\modpycad}{\module{esys.pycad}\xspace}
46 \newcommand{\modvtk}{\module{vtk}\xspace}
47 \newcommand{\modnumpy}{\module{numpy}\xspace}
48 \newcommand{\modmpl}{\module{matplotlib}\xspace}
49
50 % % define some handy commands for escript stuff
51 % \newcommand{\LINUX}{{\it Linux}\xspace}
52 % \newcommand{\WINDOWS}{{\it MS Windows}\xspace}
53 % \newcommand{\PYTHON}{{\it python}\xspace}
54 % % \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
55 % \newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace}
56 % \newcommand{\escript}{\module{esys.escript}\xspace}
57 % \newcommand{\finley}{\module{esys.finley}\xspace}
58 % \newcommand{\esys}{\module{esys}\xspace}
59 % \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
60 % \newcommand{\pycad}{\module{esys.pycad}\xspace}
61 % \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
62 % \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
63 % \newcommand{\env}[1]{\textbf{\mbox{#1}}\index{Environment!#1}}
64 % % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\cite{MPI}\xspace}
65 % % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\cite{OPENMP}\xspace}
66 % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\xspace}
67 % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\xspace}
68 % \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
69 % \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
70 % \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
71 % \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
72 % \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
73 % \newcommand{\esysxml}{{\it esysxml}}
74 %
75 % \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
76 % \newcommand{\Poisson}{\class{Poisson}\xspace}
77 % \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
78 % \newcommand{\Lame}{\class{Lame}\xspace}
79 % \newcommand{\Data}{\class{Data}\xspace}
80 % \newcommand{\EmptyData}{empty \class{Data}\index{empty Data}\xspace}
81 % \newcommand{\Domain}{\class{Domain}\xspace}
82 % %\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
83 % \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
84 % \newcommand{\mayavi}{{\it mayavi}\index{visualization!mayavi}\index{mayavi}}
85 % \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
86 % \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
87 % \newcommand{\False}{\constant{False}\xspace}
88 % \newcommand{\True}{\constant{True}\xspace}
89 % \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
90 % \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
91 % \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
92 % \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
93 % \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
94 % \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
95 % \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
96 % \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
97 % \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
98 % \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}
99 % \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
100 % \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
101 %
102 % \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
103 % \newcommand{\Operator}{\class{Operator}\xspace}
104 % \newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace}
105 % \newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace}
106 % \newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace}
107 % \newcommand{\Function}{general \class{FunctionSpace}\xspace}
108 % \newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace}
109 % \newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace}
110 % \newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace}
111 % \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
112 % \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
113 % \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
114 % \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
115 % \newcommand{\Tensor}{{tensor \Data object}\xspace}
116 % \newcommand{\Vector}{{vector \Data object}\xspace}
117 % \newcommand{\Scalar}{{scalar \Data object}\xspace}
118 % \newcommand{\DataSample}{{data sample}\index{data sample}\xspace}
119 % \newcommand{\DataSamplePoints}{{data sample points}\index{data sample!points}\xspace}
120 % \newcommand{\numarray}{\module{numarray}\xspace}
121 % \newcommand{\numarrayNA}{\module{numarray}.\class{NumArray}\xspace}
122 % \newcommand{\Shape}{shape\xspace\index{shape}}
123 % \newcommand{\Rank}{rank\xspace\index{shape}}
124 % \newcommand{\ExampleDirectory}{example directory\xspace}
125 % \newcommand{\ReferenceGuide}{\url{http://shake200.esscc.uq.edu.au/esys/docs.html}\xspace}
126 % \newcommand{\Point}{\class{Point} \xspace}
127 % \newcommand{\PropertySet}{\class{PropertySet} \xspace}
128 % \newcommand{\Design}{\class{Design} \xspace}
129 % \newcommand{\TagMap}{\class{TagMap} \xspace}
130 % \newcommand{\ManifoldOneD}{\class{Manifold1D} \xspace}
131 % \newcommand{\ManifoldTwoD}{\class{Manifold2D} \xspace}
132 % \newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace}
133 %
134 % % default width for figures
135 % \newcommand{\figwidth}{100mm}
136 % % commands useful in cross-referencing
137 % \newcommand {\Ref}[1] {Reference~\cite{#1}}
138 % \newcommand {\Sec}[1] {Section~\ref{#1}}
139 % \newcommand {\App}[1] {Appendix~\ref{#1}}
140 % \newcommand {\Chap}[1] {Chapter~\ref{#1}}
141 % \newcommand {\etal} {\emph{~et~al.}}
142 % \newcommand {\fig}[1] {Figure~\ref{#1}}
143 % \newcommand {\eqn}[1] {Equation~(\ref{#1})}
144 % \newcommand {\tab}[1] {Table~\ref{#1}}
145 %
146 % % this stops one figure taking up a whole page and lets more text onto
147 % % the one page when a figure exists
148 % \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
149 %
150 % % improved version of caption handling
151 % \usepackage{ccaption}
152 % \captionnamefont{\scshape}
153 % \captionstyle{}
154 % \makeatletter
155 % \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
156 % \renewcommand{\@makecaption}[2]{%
157 % \vskip\abovecaptionskip
158 % \sbox\@tempboxa{#1: #2}%
159 % \ifdim \wd\@tempboxa >\hsize
160 % \def\baselinestretch{1}\@normalsize
161 % #1: #2\par
162 % \def\baselinestretch{1.5}\@normalsize
163 % \else
164 % \global \@minipagefalse
165 % \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
166 % \fi
167 % \vskip\belowcaptionskip}
168 % \makeatother
169 %
170 % % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
171 % %%% this code grabbed from the PyScript docs
172 % %%% pyscript.sourceforge.net
173
174 % --------------------------------------------------------------
175 % Code format within \Verb
176 % --------------------------------------------------------------
177
178 % \definecolor{pycolor}{rgb}{0,0.4,0}
179
180 %% \DefineVerbatimEnvironment{python}{Verbatim}
181 %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
182 %% formatcom=\color{pycolor}\small,fontshape=rm}
183
184 %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
185
186 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
187
188 %%% end of grabbed code
189
190 % this is for when one uses pdflatex and therefore needs to load pdf
191 % figures into \includegraphics
192 % \ifpdf
193 % \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
194 % \pdfcompresslevel=9 % 0: no compression, 9: highest compression
195 % % or, set compress_level 9 in file pdftex.cfg
196 % \else
197 % \DeclareGraphicsExtensions{.eps}
198 % \fi
199 %
200 % % defines the colour for the background of code examples
201 % \definecolor{LightGrey}{gray}{0.9}
202 %
203 % % add the listings package to pretty print the code output
204 % \usepackage{listings}
205 %
206 %
207 % %Some colour definitions added to keep pdflatex happy
208 % %I make no claim that these values are particularly good
209 % \definecolor{Purple}{rgb}{0.7, 0, 0.6}
210 % \definecolor{Tan}{rgb}{0.5,0.5,0.5}
211 % \definecolor{BrickRed}{rgb}{0.7, 0.2, 0.2}
212 %
213 % % All the \color{x} used to be \color[named]{x}
214 % %end color defs
215 %
216 % \lstdefinestyle{myC++}{%
217 % %\lstset{%
218 % language=C++,
219 % showstringspaces=false,
220 % basicstyle=\small\ttfamily,
221 % commentstyle=\color{BrickRed}\ttfamily,
222 % keywordstyle=\color{Purple}\ttfamily,
223 % %identifierstyle=\color{Blue}\ttfamily,
224 % %functionstyle=\color{Blue}\ttfamily,
225 % %typestyle=\color{ForestGreen}\ttfamily,
226 % stringstyle=\color{Tan}\ttfamily,%
227 % morekeywords={,complex,}%
228 % frame=none,%
229 % backgroundcolor=\color{LightGrey}%
230 % }
231 %
232 % \lstdefinestyle{myMatlab}{%
233 % %\lstset{%
234 % language=Matlab,
235 % showstringspaces=false,
236 % basicstyle=\small\ttfamily,
237 % commentstyle=\color{BrickRed}\ttfamily,
238 % keywordstyle=\color{Purple}\ttfamily,
239 % %identifierstyle=\color{Blue}\ttfamily,
240 % %functionstyle=\color{Blue}\ttfamily,
241 % %typestyle=\color{ForestGreen}\ttfamily,
242 % stringstyle=\color{Tan}\ttfamily,%
243 % frame=none,%
244 % backgroundcolor=\color{LightGrey}%
245 % }
246 %
247 % \lstdefinestyle{myScilab}{%
248 % %\lstset{%
249 % language=Scilab,
250 % showstringspaces=false,
251 % basicstyle=\small\ttfamily,
252 % commentstyle=\color{BrickRed}\ttfamily,
253 % keywordstyle=\color{Purple}\ttfamily,
254 % %identifierstyle=\color{Blue}\ttfamily,
255 % %functionstyle=\color{Blue}\ttfamily,
256 % %typestyle=\color{ForestGreen}\ttfamily,
257 % stringstyle=\color{Tan}\ttfamily,%
258 % frame=none,%
259 % backgroundcolor=\color{LightGrey}%
260 % }
261 %
262 % \lstdefinestyle{myShell}{%
263 % %\lstset{%
264 % language=ksh,
265 % showstringspaces=false,
266 % basicstyle=\small\ttfamily,
267 % commentstyle=\color{Black}\ttfamily,
268 % keywordstyle=\color{Black}\ttfamily,
269 % %identifierstyle=\color{Blue}\ttfamily,
270 % %functionstyle=\color{Blue}\ttfamily,
271 % %typestyle=\color{ForestGreen}\ttfamily,
272 % stringstyle=\color{Black}\ttfamily,%
273 % frame=none,%
274 % backgroundcolor=\color{LightGrey}%
275 % }
276 %
277 % \lstdefinestyle{myPython}{%
278 % %\lstset{%
279 % language=python,
280 % showstringspaces=false,
281 % basicstyle=\small\ttfamily,
282 % commentstyle=\color{BrickRed}\ttfamily,
283 % keywordstyle=\color{Purple}\ttfamily,
284 % %identifierstyle=\color{Blue}\ttfamily,
285 % %functionstyle=\color{Blue}\ttfamily,
286 % %typestyle=\color{ForestGreen}\ttfamily,
287 % stringstyle=\color{Tan}\ttfamily,%
288 % frame=none,%
289 % %backgroundcolor=\color{LightGrey}%
290 % }
291 %
292 % \lstdefinestyle{myhtml}{%
293 % %\lstset{%
294 % language=xml,
295 % showstringspaces=false,
296 % basicstyle=\small\ttfamily,
297 % commentstyle=\color{BrickRed}\ttfamily,
298 % keywordstyle=\color{Purple}\ttfamily,
299 % %identifierstyle=\color{Blue}\ttfamily,
300 % %functionstyle=\color{Blue}\ttfamily,
301 % %typestyle=\color{ForestGreen}\ttfamily,
302 % stringstyle=\color{Tan}\ttfamily,
303 % morekeywords={,simulation,prop_dim,error_check,stochastic,%
304 % globals,field,dimensions,lattice,domains,samples,vector,%
305 % components,fourier_space,sequence,integrate,algorithm,%
306 % interval,k_operators,constant,operator_names,vectors,%
307 % output,filename,group,sampling,moments,benchmark,use_double,%
308 % use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
309 % default_value,argv,arg,iterations,cross_propagation,%
310 % use_mpi,paths,seed,noises,author,description,name,type,%
311 % }
312 % frame=none,%
313 % %framerule=2pt,%
314 % backgroundcolor=\color{LightGrey}%
315 % }
316 %
317 % % this implements producing nice code blocks
318 % % it also saves time, typing and
319 % % *should* reduce errors in the text by removing doubling up of code
320 % \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
321 %
322 % % this implements nicely formatted shell code
323 % \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
324 %
325 % % this implements nicely formatted Perl code
326 % \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
327 %
328 % % this implements nicely formatted Python code
329 % \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
330 %
331 % % this implements nicely formatted C++ code
332 % \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
333 %
334 % % this implements nicely formatted matlab code
335 % \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
336 %
337 % % this implements nicely formatted scilab code
338 % \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
339 %
340 % %Ensures that latex doesn't have an error if we don't specify the version
341 % \providecommand{\RepVersion}{Unknown\xspace}
342 % to set this value use:
343 % (pdf)latex '\newcommand{\RepVersion}{version\xspace}\input{guide.tex}'
344 % as your command-line

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