/[escript]/trunk/doc/cookbook/cookbook_defs.tex
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Contents of /trunk/doc/cookbook/cookbook_defs.tex

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Revision 2681 - (show annotations)
Thu Sep 24 03:04:04 2009 UTC (9 years, 11 months ago) by ahallam
File MIME type: application/x-tex
File size: 15107 byte(s)
proof reading and review of cookbook, minor changes only + updated depth profiles to cb from last week
1
2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3 %
4 % Copyright (c) 2003-2009 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
18 \usepackage{graphicx,color}
19 % \usepackage[pdftex]{graphicx,color}
20 \usepackage{makeidx} % handle the index properly
21 \usepackage{xspace} % handle spaces after commands more nicely
22 % use the ams math stuff, as it makes the maths easier to code, and
23 % nicer output than the standard LaTeX stuff
24 \usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physici % see http://www.ams.org/tex/amslatex.html
25 \usepackage{alltt} % handy verbatim stuff
26 \usepackage{textcomp}
27
28
29 %Ensures that latex doesn't have an error if we don't specify the version
30 \providecommand{\RepVersion}{Unknown\xspace}
31
32 %Tony's Commands
33 \newcommand{\editor}[1] {\textit{EDITORIAL: {#1}}}
34 %\newcommand{\eqref}[1] {(\ref{#1})}
35 \newcommand{\esc}{\module{escript}\xspace}
36 \newcommand{\fileex}[1]{\module{\textbackslash examples\textbackslash {#1}}\xspace}
37 \newcommand{\TODO}[1]{\textbf{TODO}:\xspace\textit{#1} }
38 \newcommand{\TBA}[1]{\textbf{TO BE ADDED: \begin{enumerate} {#1} \end{enumerate}}}
39 \newcommand{\ESCRIPT}{\textit{escript}\xspace}
40 \newcommand{\ESYS}{\textit{esys}\xspace}
41 \newcommand{\FINLEY}{\textit{finley}\xspac}
42 \newcommand{\exf}{\textit{/doc/examples/cookbook/}\xspace}
43 \newcommand{\mayavi}{\textit{Mayavi2}\xspace}
44
45 %referencing
46 \newcommand{\reffig}[1]{(Figure \ref{#1})}
47 \newcommand{\refeq}[1]{equation \ref{#1}}
48 \newcommand{\refEq}[1]{Equation \ref{#1}}
49 \newcommand{\refCh}[1]{Chapter \ref{#1}}
50
51 %modules
52 \newcommand{\modesys}{\module{esys}\xspace}
53 \newcommand{\modescript}{\module{esys.escript}\xspace}
54 \newcommand{\modLPDE}{\module{esys.escript.LinearPDEs}\xspace}
55 \newcommand{\modfinley}{\module{esys.finley}\xspace}
56 \newcommand{\modpycad}{\module{esys.pycad}\xspace}
57 \newcommand{\modvtk}{\module{vtk}\xspace}
58 \newcommand{\modnumpy}{\module{numpy}\xspace}
59 \newcommand{\modmpl}{\module{matplotlib}\xspace}
60 \newcommand{\pycad}{\module{esys.pycad}\xspace}
61 \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
62 \newcommand{\pylab}{\module{pylab}\xspace}
63 \newcommand{\mpl}{\module{matplotlib}\xspace}
64 \newcommand{\numpy}{\module{numpy}\xspace}
65
66 %list scripts
67 \newcommand{\sslist}[1]{\textit{The scripts referenced in this section are; #1} \newline \newline}
68
69 % % define some handy commands for escript stuff
70 % \newcommand{\LINUX}{{\it Linux}\xspace}
71 % \newcommand{\WINDOWS}{{\it MS Windows}\xspace}
72 % \newcommand{\PYTHON}{{\it python}\xspace}
73 % % \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
74 % \newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace}
75 % \newcommand{\escript}{\module{esys.escript}\xspace}
76 % \newcommand{\finley}{\module{esys.finley}\xspace}
77 % \newcommand{\esys}{\module{esys}\xspace}
78 % \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
79 % \newcommand{\pycad}{\module{esys.pycad}\xspace}
80 % \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
81 % \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
82 % \newcommand{\env}[1]{\textbf{\mbox{#1}}\index{Environment!#1}}
83 % % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\cite{MPI}\xspace}
84 % % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\cite{OPENMP}\xspace}
85 % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\xspace}
86 % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\xspace}
87 % \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
88 % \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
89 % \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
90 % \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
91 % \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
92 % \newcommand{\esysxml}{{\it esysxml}}
93 %
94 % \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
95 % \newcommand{\Poisson}{\class{Poisson}\xspace}
96 % \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
97 % \newcommand{\Lame}{\class{Lame}\xspace}
98 % \newcommand{\Data}{\class{Data}\xspace}
99 % \newcommand{\EmptyData}{empty \class{Data}\index{empty Data}\xspace}
100 % \newcommand{\Domain}{\class{Domain}\xspace}
101 % %\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
102 % \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
103 % \newcommand{\mayavi}{{\it mayavi}\index{visualization!mayavi}\index{mayavi}}
104 % \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
105 % \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
106 % \newcommand{\False}{\constant{False}\xspace}
107 % \newcommand{\True}{\constant{True}\xspace}
108 % \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
109 % \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
110 % \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
111 % \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
112 % \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
113 % \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
114 % \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
115 % \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
116 % \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
117 % \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}
118 % \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
119 % \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
120 %
121 % \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
122 % \newcommand{\Operator}{\class{Operator}\xspace}
123 % \newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace}
124 % \newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace}
125 % \newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace}
126 % \newcommand{\Function}{general \class{FunctionSpace}\xspace}
127 % \newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace}
128 % \newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace}
129 % \newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace}
130 % \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
131 % \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
132 % \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
133 % \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
134 % \newcommand{\Tensor}{{tensor \Data object}\xspace}
135 % \newcommand{\Vector}{{vector \Data object}\xspace}
136 % \newcommand{\Scalar}{{scalar \Data object}\xspace}
137 % \newcommand{\DataSample}{{data sample}\index{data sample}\xspace}
138 % \newcommand{\DataSamplePoints}{{data sample points}\index{data sample!points}\xspace}
139 % \newcommand{\numarray}{\module{numarray}\xspace}
140 % \newcommand{\numarrayNA}{\module{numarray}.\class{NumArray}\xspace}
141 % \newcommand{\Shape}{shape\xspace\index{shape}}
142 % \newcommand{\Rank}{rank\xspace\index{shape}}
143 % \newcommand{\ExampleDirectory}{example directory\xspace}
144 % \newcommand{\ReferenceGuide}{\url{http://shake200.esscc.uq.edu.au/esys/docs.html}\xspace}
145 % \newcommand{\Point}{\class{Point} \xspace}
146 % \newcommand{\PropertySet}{\class{PropertySet} \xspace}
147 % \newcommand{\Design}{\class{Design} \xspace}
148 % \newcommand{\TagMap}{\class{TagMap} \xspace}
149 % \newcommand{\ManifoldOneD}{\class{Manifold1D} \xspace}
150 % \newcommand{\ManifoldTwoD}{\class{Manifold2D} \xspace}
151 % \newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace}
152 %
153 % % default width for figures
154 % \newcommand{\figwidth}{100mm}
155 % % commands useful in cross-referencing
156 % \newcommand {\Ref}[1] {Reference~\cite{#1}}
157 % \newcommand {\Sec}[1] {Section~\ref{#1}}
158 % \newcommand {\App}[1] {Appendix~\ref{#1}}
159 % \newcommand {\Chap}[1] {Chapter~\ref{#1}}
160 % \newcommand {\etal} {\emph{~et~al.}}
161 % \newcommand {\fig}[1] {Figure~\ref{#1}}
162 % \newcommand {\eqn}[1] {Equation~(\ref{#1})}
163 % \newcommand {\tab}[1] {Table~\ref{#1}}
164 %
165 % % this stops one figure taking up a whole page and lets more text onto
166 % % the one page when a figure exists
167 % \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
168 %
169 % % improved version of caption handling
170 % \usepackage{ccaption}
171 % \captionnamefont{\scshape}
172 % \captionstyle{}
173 % \makeatletter
174 % \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
175 % \renewcommand{\@makecaption}[2]{%
176 % \vskip\abovecaptionskip
177 % \sbox\@tempboxa{#1: #2}%
178 % \ifdim \wd\@tempboxa >\hsize
179 % \def\baselinestretch{1}\@normalsize
180 % #1: #2\par
181 % \def\baselinestretch{1.5}\@normalsize
182 % \else
183 % \global \@minipagefalse
184 % \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
185 % \fi
186 % \vskip\belowcaptionskip}
187 % \makeatother
188 %
189 % % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
190 % %%% this code grabbed from the PyScript docs
191 % %%% pyscript.sourceforge.net
192
193 % --------------------------------------------------------------
194 % Code format within \Verb
195 % --------------------------------------------------------------
196
197 % \definecolor{pycolor}{rgb}{0,0.4,0}
198
199 %% \DefineVerbatimEnvironment{python}{Verbatim}
200 %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
201 %% formatcom=\color{pycolor}\small,fontshape=rm}
202
203 %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
204
205 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
206
207 %%% end of grabbed code
208
209 % this is for when one uses pdflatex and therefore needs to load pdf
210 % figures into \includegraphics
211 % \ifpdf
212 % \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
213 % \pdfcompresslevel=9 % 0: no compression, 9: highest compression
214 % % or, set compress_level 9 in file pdftex.cfg
215 % \else
216 % \DeclareGraphicsExtensions{.eps}
217 % \fi
218 %
219 % % defines the colour for the background of code examples
220 % \definecolor{LightGrey}{gray}{0.9}
221 %
222 % % add the listings package to pretty print the code output
223 % \usepackage{listings}
224 %
225 %
226 % %Some colour definitions added to keep pdflatex happy
227 % %I make no claim that these values are particularly good
228 % \definecolor{Purple}{rgb}{0.7, 0, 0.6}
229 % \definecolor{Tan}{rgb}{0.5,0.5,0.5}
230 % \definecolor{BrickRed}{rgb}{0.7, 0.2, 0.2}
231 %
232 % % All the \color{x} used to be \color[named]{x}
233 % %end color defs
234 %
235 % \lstdefinestyle{myC++}{%
236 % %\lstset{%
237 % language=C++,
238 % showstringspaces=false,
239 % basicstyle=\small\ttfamily,
240 % commentstyle=\color{BrickRed}\ttfamily,
241 % keywordstyle=\color{Purple}\ttfamily,
242 % %identifierstyle=\color{Blue}\ttfamily,
243 % %functionstyle=\color{Blue}\ttfamily,
244 % %typestyle=\color{ForestGreen}\ttfamily,
245 % stringstyle=\color{Tan}\ttfamily,%
246 % morekeywords={,complex,}%
247 % frame=none,%
248 % backgroundcolor=\color{LightGrey}%
249 % }
250 %
251 % \lstdefinestyle{myMatlab}{%
252 % %\lstset{%
253 % language=Matlab,
254 % showstringspaces=false,
255 % basicstyle=\small\ttfamily,
256 % commentstyle=\color{BrickRed}\ttfamily,
257 % keywordstyle=\color{Purple}\ttfamily,
258 % %identifierstyle=\color{Blue}\ttfamily,
259 % %functionstyle=\color{Blue}\ttfamily,
260 % %typestyle=\color{ForestGreen}\ttfamily,
261 % stringstyle=\color{Tan}\ttfamily,%
262 % frame=none,%
263 % backgroundcolor=\color{LightGrey}%
264 % }
265 %
266 % \lstdefinestyle{myScilab}{%
267 % %\lstset{%
268 % language=Scilab,
269 % showstringspaces=false,
270 % basicstyle=\small\ttfamily,
271 % commentstyle=\color{BrickRed}\ttfamily,
272 % keywordstyle=\color{Purple}\ttfamily,
273 % %identifierstyle=\color{Blue}\ttfamily,
274 % %functionstyle=\color{Blue}\ttfamily,
275 % %typestyle=\color{ForestGreen}\ttfamily,
276 % stringstyle=\color{Tan}\ttfamily,%
277 % frame=none,%
278 % backgroundcolor=\color{LightGrey}%
279 % }
280 %
281 % \lstdefinestyle{myShell}{%
282 % %\lstset{%
283 % language=ksh,
284 % showstringspaces=false,
285 % basicstyle=\small\ttfamily,
286 % commentstyle=\color{Black}\ttfamily,
287 % keywordstyle=\color{Black}\ttfamily,
288 % %identifierstyle=\color{Blue}\ttfamily,
289 % %functionstyle=\color{Blue}\ttfamily,
290 % %typestyle=\color{ForestGreen}\ttfamily,
291 % stringstyle=\color{Black}\ttfamily,%
292 % frame=none,%
293 % backgroundcolor=\color{LightGrey}%
294 % }
295 %
296 % \lstdefinestyle{myPython}{%
297 % %\lstset{%
298 % language=python,
299 % showstringspaces=false,
300 % basicstyle=\small\ttfamily,
301 % commentstyle=\color{BrickRed}\ttfamily,
302 % keywordstyle=\color{Purple}\ttfamily,
303 % %identifierstyle=\color{Blue}\ttfamily,
304 % %functionstyle=\color{Blue}\ttfamily,
305 % %typestyle=\color{ForestGreen}\ttfamily,
306 % stringstyle=\color{Tan}\ttfamily,%
307 % frame=none,%
308 % %backgroundcolor=\color{LightGrey}%
309 % }
310 %
311 % \lstdefinestyle{myhtml}{%
312 % %\lstset{%
313 % language=xml,
314 % showstringspaces=false,
315 % basicstyle=\small\ttfamily,
316 % commentstyle=\color{BrickRed}\ttfamily,
317 % keywordstyle=\color{Purple}\ttfamily,
318 % %identifierstyle=\color{Blue}\ttfamily,
319 % %functionstyle=\color{Blue}\ttfamily,
320 % %typestyle=\color{ForestGreen}\ttfamily,
321 % stringstyle=\color{Tan}\ttfamily,
322 % morekeywords={,simulation,prop_dim,error_check,stochastic,%
323 % globals,field,dimensions,lattice,domains,samples,vector,%
324 % components,fourier_space,sequence,integrate,algorithm,%
325 % interval,k_operators,constant,operator_names,vectors,%
326 % output,filename,group,sampling,moments,benchmark,use_double,%
327 % use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
328 % default_value,argv,arg,iterations,cross_propagation,%
329 % use_mpi,paths,seed,noises,author,description,name,type,%
330 % }
331 % frame=none,%
332 % %framerule=2pt,%
333 % backgroundcolor=\color{LightGrey}%
334 % }
335 %
336 % % this implements producing nice code blocks
337 % % it also saves time, typing and
338 % % *should* reduce errors in the text by removing doubling up of code
339 % \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
340 %
341 % % this implements nicely formatted shell code
342 % \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
343 %
344 % % this implements nicely formatted Perl code
345 % \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
346 %
347 % % this implements nicely formatted Python code
348 % \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
349 %
350 % % this implements nicely formatted C++ code
351 % \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
352 %
353 % % this implements nicely formatted matlab code
354 % \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
355 %
356 % % this implements nicely formatted scilab code
357 % \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
358 %
359 % %Ensures that latex doesn't have an error if we don't specify the version
360 % \providecommand{\RepVersion}{Unknown\xspace}
361 % to set this value use:
362 % (pdf)latex '\newcommand{\RepVersion}{version\xspace}\input{guide.tex}'
363 % as your command-line

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