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

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Revision 2658 - (show annotations)
Thu Sep 10 02:58:44 2009 UTC (9 years, 10 months ago) by ahallam
File MIME type: application/x-tex
File size: 14947 byte(s)
Updates to all files scripts to support MPI testing proceedure. Updates to cookbook, new section on functino spaces/domains (needs work). Finalising first 3 chapters for editing.
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 \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{\TBA}[1]{\textbf{TO BE ADDED: \begin{enumerate} {#1} \end{enumerate}}}
33 \newcommand{\ESCRIPT}{\textit{escript}\xspace}
34 \newcommand{\ESYS}{\textit{esys}\xspace}
35 \newcommand{\FINLEY}{\textit{finley}\xspac}
36 \newcommand{\exf}{\textit{/doc/examples/cookbook/}\xspace}
37 \newcommand{\mayavi}{\textit{Mayavi2}\xspace}
38
39 %referencing
40 \newcommand{\reffig}[1]{(Figure \ref{#1})}
41 \newcommand{\refeq}[1]{equation \ref{#1}}
42 \newcommand{\refEq}[1]{Equation \ref{#1}}
43 \newcommand{\refCh}[1]{Chapter \ref{#1}}
44
45 %modules
46 \newcommand{\modesys}{\module{esys}\xspace}
47 \newcommand{\modescript}{\module{esys.escript}\xspace}
48 \newcommand{\modLPDE}{\module{esys.escript.LinearPDEs}\xspace}
49 \newcommand{\modfinley}{\module{esys.finley}\xspace}
50 \newcommand{\modpycad}{\module{esys.pycad}\xspace}
51 \newcommand{\modvtk}{\module{vtk}\xspace}
52 \newcommand{\modnumpy}{\module{numpy}\xspace}
53 \newcommand{\modmpl}{\module{matplotlib}\xspace}
54 \newcommand{\pycad}{\module{esys.pycad}\xspace}
55 \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
56 \newcommand{\pylab}{\module{pylab}\xspace}
57 \newcommand{\mpl}{\module{matplotlib}\xspace}
58 \newcommand{\numpy}{\module{numpy}\xspace}
59
60 %list scripts
61 \newcommand{\sslist}[1]{\textit{The scripts referenced in this section are; #1} \newline \newline}
62
63 % % define some handy commands for escript stuff
64 % \newcommand{\LINUX}{{\it Linux}\xspace}
65 % \newcommand{\WINDOWS}{{\it MS Windows}\xspace}
66 % \newcommand{\PYTHON}{{\it python}\xspace}
67 % % \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
68 % \newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace}
69 % \newcommand{\escript}{\module{esys.escript}\xspace}
70 % \newcommand{\finley}{\module{esys.finley}\xspace}
71 % \newcommand{\esys}{\module{esys}\xspace}
72 % \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
73 % \newcommand{\pycad}{\module{esys.pycad}\xspace}
74 % \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
75 % \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
76 % \newcommand{\env}[1]{\textbf{\mbox{#1}}\index{Environment!#1}}
77 % % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\cite{MPI}\xspace}
78 % % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\cite{OPENMP}\xspace}
79 % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\xspace}
80 % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\xspace}
81 % \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
82 % \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
83 % \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
84 % \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
85 % \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
86 % \newcommand{\esysxml}{{\it esysxml}}
87 %
88 % \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
89 % \newcommand{\Poisson}{\class{Poisson}\xspace}
90 % \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
91 % \newcommand{\Lame}{\class{Lame}\xspace}
92 % \newcommand{\Data}{\class{Data}\xspace}
93 % \newcommand{\EmptyData}{empty \class{Data}\index{empty Data}\xspace}
94 % \newcommand{\Domain}{\class{Domain}\xspace}
95 % %\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
96 % \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
97 % \newcommand{\mayavi}{{\it mayavi}\index{visualization!mayavi}\index{mayavi}}
98 % \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
99 % \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
100 % \newcommand{\False}{\constant{False}\xspace}
101 % \newcommand{\True}{\constant{True}\xspace}
102 % \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
103 % \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
104 % \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
105 % \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
106 % \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
107 % \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
108 % \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
109 % \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
110 % \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
111 % \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}
112 % \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
113 % \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
114 %
115 % \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
116 % \newcommand{\Operator}{\class{Operator}\xspace}
117 % \newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace}
118 % \newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace}
119 % \newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace}
120 % \newcommand{\Function}{general \class{FunctionSpace}\xspace}
121 % \newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace}
122 % \newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace}
123 % \newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace}
124 % \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
125 % \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
126 % \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
127 % \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
128 % \newcommand{\Tensor}{{tensor \Data object}\xspace}
129 % \newcommand{\Vector}{{vector \Data object}\xspace}
130 % \newcommand{\Scalar}{{scalar \Data object}\xspace}
131 % \newcommand{\DataSample}{{data sample}\index{data sample}\xspace}
132 % \newcommand{\DataSamplePoints}{{data sample points}\index{data sample!points}\xspace}
133 % \newcommand{\numarray}{\module{numarray}\xspace}
134 % \newcommand{\numarrayNA}{\module{numarray}.\class{NumArray}\xspace}
135 % \newcommand{\Shape}{shape\xspace\index{shape}}
136 % \newcommand{\Rank}{rank\xspace\index{shape}}
137 % \newcommand{\ExampleDirectory}{example directory\xspace}
138 % \newcommand{\ReferenceGuide}{\url{http://shake200.esscc.uq.edu.au/esys/docs.html}\xspace}
139 % \newcommand{\Point}{\class{Point} \xspace}
140 % \newcommand{\PropertySet}{\class{PropertySet} \xspace}
141 % \newcommand{\Design}{\class{Design} \xspace}
142 % \newcommand{\TagMap}{\class{TagMap} \xspace}
143 % \newcommand{\ManifoldOneD}{\class{Manifold1D} \xspace}
144 % \newcommand{\ManifoldTwoD}{\class{Manifold2D} \xspace}
145 % \newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace}
146 %
147 % % default width for figures
148 % \newcommand{\figwidth}{100mm}
149 % % commands useful in cross-referencing
150 % \newcommand {\Ref}[1] {Reference~\cite{#1}}
151 % \newcommand {\Sec}[1] {Section~\ref{#1}}
152 % \newcommand {\App}[1] {Appendix~\ref{#1}}
153 % \newcommand {\Chap}[1] {Chapter~\ref{#1}}
154 % \newcommand {\etal} {\emph{~et~al.}}
155 % \newcommand {\fig}[1] {Figure~\ref{#1}}
156 % \newcommand {\eqn}[1] {Equation~(\ref{#1})}
157 % \newcommand {\tab}[1] {Table~\ref{#1}}
158 %
159 % % this stops one figure taking up a whole page and lets more text onto
160 % % the one page when a figure exists
161 % \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
162 %
163 % % improved version of caption handling
164 % \usepackage{ccaption}
165 % \captionnamefont{\scshape}
166 % \captionstyle{}
167 % \makeatletter
168 % \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
169 % \renewcommand{\@makecaption}[2]{%
170 % \vskip\abovecaptionskip
171 % \sbox\@tempboxa{#1: #2}%
172 % \ifdim \wd\@tempboxa >\hsize
173 % \def\baselinestretch{1}\@normalsize
174 % #1: #2\par
175 % \def\baselinestretch{1.5}\@normalsize
176 % \else
177 % \global \@minipagefalse
178 % \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
179 % \fi
180 % \vskip\belowcaptionskip}
181 % \makeatother
182 %
183 % % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
184 % %%% this code grabbed from the PyScript docs
185 % %%% pyscript.sourceforge.net
186
187 % --------------------------------------------------------------
188 % Code format within \Verb
189 % --------------------------------------------------------------
190
191 % \definecolor{pycolor}{rgb}{0,0.4,0}
192
193 %% \DefineVerbatimEnvironment{python}{Verbatim}
194 %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
195 %% formatcom=\color{pycolor}\small,fontshape=rm}
196
197 %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
198
199 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
200
201 %%% end of grabbed code
202
203 % this is for when one uses pdflatex and therefore needs to load pdf
204 % figures into \includegraphics
205 % \ifpdf
206 % \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
207 % \pdfcompresslevel=9 % 0: no compression, 9: highest compression
208 % % or, set compress_level 9 in file pdftex.cfg
209 % \else
210 % \DeclareGraphicsExtensions{.eps}
211 % \fi
212 %
213 % % defines the colour for the background of code examples
214 % \definecolor{LightGrey}{gray}{0.9}
215 %
216 % % add the listings package to pretty print the code output
217 % \usepackage{listings}
218 %
219 %
220 % %Some colour definitions added to keep pdflatex happy
221 % %I make no claim that these values are particularly good
222 % \definecolor{Purple}{rgb}{0.7, 0, 0.6}
223 % \definecolor{Tan}{rgb}{0.5,0.5,0.5}
224 % \definecolor{BrickRed}{rgb}{0.7, 0.2, 0.2}
225 %
226 % % All the \color{x} used to be \color[named]{x}
227 % %end color defs
228 %
229 % \lstdefinestyle{myC++}{%
230 % %\lstset{%
231 % language=C++,
232 % showstringspaces=false,
233 % basicstyle=\small\ttfamily,
234 % commentstyle=\color{BrickRed}\ttfamily,
235 % keywordstyle=\color{Purple}\ttfamily,
236 % %identifierstyle=\color{Blue}\ttfamily,
237 % %functionstyle=\color{Blue}\ttfamily,
238 % %typestyle=\color{ForestGreen}\ttfamily,
239 % stringstyle=\color{Tan}\ttfamily,%
240 % morekeywords={,complex,}%
241 % frame=none,%
242 % backgroundcolor=\color{LightGrey}%
243 % }
244 %
245 % \lstdefinestyle{myMatlab}{%
246 % %\lstset{%
247 % language=Matlab,
248 % showstringspaces=false,
249 % basicstyle=\small\ttfamily,
250 % commentstyle=\color{BrickRed}\ttfamily,
251 % keywordstyle=\color{Purple}\ttfamily,
252 % %identifierstyle=\color{Blue}\ttfamily,
253 % %functionstyle=\color{Blue}\ttfamily,
254 % %typestyle=\color{ForestGreen}\ttfamily,
255 % stringstyle=\color{Tan}\ttfamily,%
256 % frame=none,%
257 % backgroundcolor=\color{LightGrey}%
258 % }
259 %
260 % \lstdefinestyle{myScilab}{%
261 % %\lstset{%
262 % language=Scilab,
263 % showstringspaces=false,
264 % basicstyle=\small\ttfamily,
265 % commentstyle=\color{BrickRed}\ttfamily,
266 % keywordstyle=\color{Purple}\ttfamily,
267 % %identifierstyle=\color{Blue}\ttfamily,
268 % %functionstyle=\color{Blue}\ttfamily,
269 % %typestyle=\color{ForestGreen}\ttfamily,
270 % stringstyle=\color{Tan}\ttfamily,%
271 % frame=none,%
272 % backgroundcolor=\color{LightGrey}%
273 % }
274 %
275 % \lstdefinestyle{myShell}{%
276 % %\lstset{%
277 % language=ksh,
278 % showstringspaces=false,
279 % basicstyle=\small\ttfamily,
280 % commentstyle=\color{Black}\ttfamily,
281 % keywordstyle=\color{Black}\ttfamily,
282 % %identifierstyle=\color{Blue}\ttfamily,
283 % %functionstyle=\color{Blue}\ttfamily,
284 % %typestyle=\color{ForestGreen}\ttfamily,
285 % stringstyle=\color{Black}\ttfamily,%
286 % frame=none,%
287 % backgroundcolor=\color{LightGrey}%
288 % }
289 %
290 % \lstdefinestyle{myPython}{%
291 % %\lstset{%
292 % language=python,
293 % showstringspaces=false,
294 % basicstyle=\small\ttfamily,
295 % commentstyle=\color{BrickRed}\ttfamily,
296 % keywordstyle=\color{Purple}\ttfamily,
297 % %identifierstyle=\color{Blue}\ttfamily,
298 % %functionstyle=\color{Blue}\ttfamily,
299 % %typestyle=\color{ForestGreen}\ttfamily,
300 % stringstyle=\color{Tan}\ttfamily,%
301 % frame=none,%
302 % %backgroundcolor=\color{LightGrey}%
303 % }
304 %
305 % \lstdefinestyle{myhtml}{%
306 % %\lstset{%
307 % language=xml,
308 % showstringspaces=false,
309 % basicstyle=\small\ttfamily,
310 % commentstyle=\color{BrickRed}\ttfamily,
311 % keywordstyle=\color{Purple}\ttfamily,
312 % %identifierstyle=\color{Blue}\ttfamily,
313 % %functionstyle=\color{Blue}\ttfamily,
314 % %typestyle=\color{ForestGreen}\ttfamily,
315 % stringstyle=\color{Tan}\ttfamily,
316 % morekeywords={,simulation,prop_dim,error_check,stochastic,%
317 % globals,field,dimensions,lattice,domains,samples,vector,%
318 % components,fourier_space,sequence,integrate,algorithm,%
319 % interval,k_operators,constant,operator_names,vectors,%
320 % output,filename,group,sampling,moments,benchmark,use_double,%
321 % use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
322 % default_value,argv,arg,iterations,cross_propagation,%
323 % use_mpi,paths,seed,noises,author,description,name,type,%
324 % }
325 % frame=none,%
326 % %framerule=2pt,%
327 % backgroundcolor=\color{LightGrey}%
328 % }
329 %
330 % % this implements producing nice code blocks
331 % % it also saves time, typing and
332 % % *should* reduce errors in the text by removing doubling up of code
333 % \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
334 %
335 % % this implements nicely formatted shell code
336 % \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
337 %
338 % % this implements nicely formatted Perl code
339 % \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
340 %
341 % % this implements nicely formatted Python code
342 % \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
343 %
344 % % this implements nicely formatted C++ code
345 % \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
346 %
347 % % this implements nicely formatted matlab code
348 % \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
349 %
350 % % this implements nicely formatted scilab code
351 % \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
352 %
353 % %Ensures that latex doesn't have an error if we don't specify the version
354 % \providecommand{\RepVersion}{Unknown\xspace}
355 % to set this value use:
356 % (pdf)latex '\newcommand{\RepVersion}{version\xspace}\input{guide.tex}'
357 % as your command-line

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