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Revision 2463 - (show annotations)
Tue Jun 9 03:51:23 2009 UTC (10 years, 4 months ago) by jfenwick
Original Path: trunk/doc/user/guide_defs.tex
File MIME type: application/x-tex
File size: 15731 byte(s)
Added an svn-ignore, added changes and references section 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 physicists
23 % see http://www.ams.org/tex/amslatex.html
24 \usepackage{alltt} % handy verbatim stuff
25
26
27 % define some handy commands for escript stuff
28 \newcommand{\LINUX}{{\it Linux}\xspace}
29 \newcommand{\WINDOWS}{{\it MS Windows}\xspace}
30 \newcommand{\PYTHON}{{\it python}\xspace}
31 % \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
32 \newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace}
33 \newcommand{\escript}{\module{esys.escript}\xspace}
34 \newcommand{\finley}{\module{esys.finley}\xspace}
35 \newcommand{\esys}{\module{esys}\xspace}
36 \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
37 \newcommand{\pycad}{\module{esys.pycad}\xspace}
38 \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
39 \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
40 \newcommand{\env}[1]{\textbf{\mbox{#1}}\index{Environment!#1}}
41 % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\cite{MPI}\xspace}
42 % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\cite{OPENMP}\xspace}
43 \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\xspace}
44 \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\xspace}
45 \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
46 \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
47 \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
48 \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
49 \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
50 \newcommand{\esysxml}{{\it esysxml}}
51
52 \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
53 \newcommand{\Poisson}{\class{Poisson}\xspace}
54 \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
55 \newcommand{\Lame}{\class{Lame}\xspace}
56 \newcommand{\Data}{\class{Data}\xspace}
57 \newcommand{\EmptyData}{empty \class{Data}\index{empty Data}\xspace}
58 \newcommand{\Domain}{\class{Domain}\xspace}
59 %\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
60 \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
61 \newcommand{\mayavi}{{\it mayavi}\index{visualization!mayavi}\index{mayavi}}
62 \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
63 \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
64 \newcommand{\False}{\constant{False}\xspace}
65 \newcommand{\True}{\constant{True}\xspace}
66 \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
67 \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
68 \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
69 \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
70 \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
71 \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
72 \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
73 \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
74 \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
75 \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}
76 \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
77 \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
78
79 \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
80 \newcommand{\Operator}{\class{Operator}\xspace}
81 \newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace}
82 \newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace}
83 \newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace}
84 \newcommand{\Function}{general \class{FunctionSpace}\xspace}
85 \newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace}
86 \newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace}
87 \newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace}
88 \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
89 \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
90 \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
91 \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
92 \newcommand{\Tensor}{{tensor \Data object}\xspace}
93 \newcommand{\Vector}{{vector \Data object}\xspace}
94 \newcommand{\Scalar}{{scalar \Data object}\xspace}
95 \newcommand{\DataSample}{{data sample}\index{data sample}\xspace}
96 \newcommand{\DataSamplePoints}{{data sample points}\index{data sample!points}\xspace}
97 \newcommand{\numarray}{\module{numarray}\xspace}
98 \newcommand{\numarrayNA}{\module{numarray}.\class{NumArray}\xspace}
99 \newcommand{\numpy}{\module{numpy}\xspace}
100 \newcommand{\numpyNDA}{\module{numpy.\class{ndarray}\xspace}}
101
102 \newcommand{\Shape}{shape\xspace\index{shape}}
103 \newcommand{\Rank}{rank\xspace\index{shape}}
104 \newcommand{\ExampleDirectory}{example directory\xspace}
105 \newcommand{\ReferenceGuide}{\url{http://esys.esscc.uq.edu.au/docs.html}\xspace}
106 \newcommand{\Point}{\class{Point} \xspace}
107 \newcommand{\PropertySet}{\class{PropertySet} \xspace}
108 \newcommand{\Design}{\class{Design} \xspace}
109 \newcommand{\TagMap}{\class{TagMap} \xspace}
110 \newcommand{\ManifoldOneD}{\class{Manifold1D} \xspace}
111 \newcommand{\ManifoldTwoD}{\class{Manifold2D} \xspace}
112 \newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace}
113
114 % handy commands for pyvisi
115 \newcommand{\VTK}{{\it VTK} \xspace}
116 \newcommand{\VTKUrl}{\url{http://www.vtk.org/}\xspace}
117 \newcommand{\Scene}{\class{Scene}\xspace}
118 \newcommand{\Camera}{\class{Camera}\xspace}
119 \newcommand{\Light}{\class{Light}\xspace}
120 \newcommand{\DataCollector}{\class{DataCollector}\xspace}
121 \newcommand{\ImageReader}{\class{ImageReader}\xspace}
122 \newcommand{\TextTwoD}{\class{Text2D}\xspace}
123 \newcommand{\ActorTwoD}{\class{Actor2D}\xspace}
124 \newcommand{\ActorThreeD}{\class{Actor3D}\xspace}
125 \newcommand{\Transform}{\class{Transform}\xspace}
126 \newcommand{\Clipper}{\class{Clipper}\xspace}
127 \newcommand{\Map}{\class{Map}\xspace}
128 \newcommand{\MapOnPlaneCut}{\class{MapOnPlaneCut}\xspace}
129 \newcommand{\MapOnPlaneClip}{\class{MapOnPlaneClip}\xspace}
130 \newcommand{\MapOnScalarClip}{\class{MapOnScalarClip}\xspace}
131 \newcommand{\MapOnScalarClipWithRotation}{\class{MapOnScalarClipWithRotation}\xspace}
132 \newcommand{\GlyphThreeD}{\class{Glyph3D}\xspace}
133 \newcommand{\MaskPoints}{\class{MaskPoints}\xspace}
134 \newcommand{\Velocity}{\class{Velocity}\xspace}
135 \newcommand{\VelocityOnPlaneCut}{\class{VelocityOnPlaneCut}\xspace}
136 \newcommand{\VelocityOnPlaneClip}{\class{VelocityOnPlaneClip}\xspace}
137 \newcommand{\Sphere}{\class{Sphere}\xspace}
138 \newcommand{\TensorGlyph}{\class{TensorGlyph}\xspace}
139 \newcommand{\Ellipsoid}{\class{Ellipsoid}\xspace}
140 \newcommand{\EllipsoidOnPlaneCut}{\class{EllipsoidOnPlaneCut}\xspace}
141 \newcommand{\EllipsoidOnPlaneClip}{\class{EllipsoidOnPlaneClip}\xspace}
142 \newcommand{\ContourModule}{\class{ContourModule}\xspace}
143 \newcommand{\Contour}{\class{Contour}\xspace}
144 \newcommand{\ContourOnPlaneCut}{\class{ContourOnPlaneCut}\xspace}
145 \newcommand{\ContourOnPlaneClip}{\class{ContourOnPlaneClip}\xspace}
146 \newcommand{\PointSource}{\class{PointSource}\xspace}
147 \newcommand{\StreamLineModule}{\class{StreamLineModule}\xspace}
148 \newcommand{\Tube}{\class{Tube}\xspace}
149 \newcommand{\StreamLine}{\class{StreamLine}\xspace}
150 \newcommand{\Warp}{\class{Warp}\xspace}
151 \newcommand{\Carpet}{\class{Carpet}\xspace}
152 \newcommand{\PlaneSource}{\class{PlaneSource}\xspace}
153 \newcommand{\Image}{\class{Image}\xspace}
154 \newcommand{\Logo}{\class{Logo}\xspace}
155 \newcommand{\ImageReslice}{\class{ImageReslice}\xspace}
156 \newcommand{\Position}{\class{Position}\xspace}
157 \newcommand{\DataSetMapper}{\class{DataSetMapper}\xspace}
158 \newcommand{\Legend}{\class{Legend}\xspace}
159 \newcommand{\ScalarBar}{\class{ScalarBar}\xspace}
160 \newcommand{\Movie}{\class{Movie}\xspace}
161 \newcommand{\CubeSource}{\class{CubeSource}\xspace}
162 \newcommand{\Rectangle}{\class{Rectangle}\xspace}
163 \newcommand{\LocalPosition}{\class{LocalPosition}\xspace}
164 \newcommand{\GlobalPosition}{\class{GlobalPosition}\xspace}
165 \newcommand{\Rotation}{\class{Rotation}\xspace}
166 \newcommand{\thumbnailwidth}{50mm}
167
168 % default width for figures
169 \newcommand{\figwidth}{100mm}
170 % commands useful in cross-referencing
171 \newcommand {\Ref}[1] {Reference~\cite{#1}}
172 \newcommand {\Sec}[1] {Section~\ref{#1}}
173 \newcommand {\App}[1] {Appendix~\ref{#1}}
174 \newcommand {\Chap}[1] {Chapter~\ref{#1}}
175 \newcommand {\etal} {\emph{~et~al.}}
176 \newcommand {\fig}[1] {Figure~\ref{#1}}
177 \newcommand {\eqn}[1] {Equation~(\ref{#1})}
178 \newcommand {\tab}[1] {Table~\ref{#1}}
179
180 % this stops one figure taking up a whole page and lets more text onto
181 % the one page when a figure exists
182 \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
183
184 % improved version of caption handling
185 \usepackage{ccaption}
186 \captionnamefont{\scshape}
187 \captionstyle{}
188 \makeatletter
189 \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
190 \renewcommand{\@makecaption}[2]{%
191 \vskip\abovecaptionskip
192 \sbox\@tempboxa{#1: #2}%
193 \ifdim \wd\@tempboxa >\hsize
194 \def\baselinestretch{1}\@normalsize
195 #1: #2\par
196 \def\baselinestretch{1.5}\@normalsize
197 \else
198 \global \@minipagefalse
199 \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
200 \fi
201 \vskip\belowcaptionskip}
202 \makeatother
203
204 % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
205 %%% this code grabbed from the PyScript docs
206 %%% pyscript.sourceforge.net
207
208 % --------------------------------------------------------------
209 % Code format within \Verb
210 % --------------------------------------------------------------
211
212 % \definecolor{pycolor}{rgb}{0,0.4,0}
213
214 %% \DefineVerbatimEnvironment{python}{Verbatim}
215 %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
216 %% formatcom=\color{pycolor}\small,fontshape=rm}
217
218 %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
219
220 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
221
222 %%% end of grabbed code
223
224 % this is for when one uses pdflatex and therefore needs to load pdf
225 % figures into \includegraphics
226 \ifpdf
227 \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
228 \pdfcompresslevel=9 % 0: no compression, 9: highest compression
229 % or, set compress_level 9 in file pdftex.cfg
230 \else
231 \DeclareGraphicsExtensions{.eps}
232 \fi
233
234 % defines the colour for the background of code examples
235 \definecolor{LightGrey}{gray}{0.9}
236
237 % add the listings package to pretty print the code output
238 \usepackage{listings}
239
240
241 %Some colour definitions added to keep pdflatex happy
242 %I make no claim that these values are particularly good
243 \definecolor{Purple}{rgb}{0.7, 0, 0.6}
244 \definecolor{Tan}{rgb}{0.5,0.5,0.5}
245 \definecolor{BrickRed}{rgb}{0.7, 0.2, 0.2}
246 \definecolor{Black}{rgb}{0, 0, 0}
247
248 % All the \color{x} used to be \color[named]{x}
249 %end color defs
250
251 \lstdefinestyle{myC++}{%
252 %\lstset{%
253 language=C++,
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 morekeywords={,complex,}%
263 frame=none,%
264 backgroundcolor=\color{LightGrey}%
265 }
266
267 \lstdefinestyle{myMatlab}{%
268 %\lstset{%
269 language=Matlab,
270 showstringspaces=false,
271 basicstyle=\small\ttfamily,
272 commentstyle=\color{BrickRed}\ttfamily,
273 keywordstyle=\color{Purple}\ttfamily,
274 %identifierstyle=\color{Blue}\ttfamily,
275 %functionstyle=\color{Blue}\ttfamily,
276 %typestyle=\color{ForestGreen}\ttfamily,
277 stringstyle=\color{Tan}\ttfamily,%
278 frame=none,%
279 backgroundcolor=\color{LightGrey}%
280 }
281
282 \lstdefinestyle{myScilab}{%
283 %\lstset{%
284 language=Scilab,
285 showstringspaces=false,
286 basicstyle=\small\ttfamily,
287 commentstyle=\color{BrickRed}\ttfamily,
288 keywordstyle=\color{Purple}\ttfamily,
289 %identifierstyle=\color{Blue}\ttfamily,
290 %functionstyle=\color{Blue}\ttfamily,
291 %typestyle=\color{ForestGreen}\ttfamily,
292 stringstyle=\color{Tan}\ttfamily,%
293 frame=none,%
294 backgroundcolor=\color{LightGrey}%
295 }
296
297 \lstdefinestyle{myShell}{%
298 %\lstset{%
299 language=ksh,
300 showstringspaces=false,
301 basicstyle=\small\ttfamily,
302 commentstyle=\color{Black}\ttfamily,
303 keywordstyle=\color{Black}\ttfamily,
304 %identifierstyle=\color{Blue}\ttfamily,
305 %functionstyle=\color{Blue}\ttfamily,
306 %typestyle=\color{ForestGreen}\ttfamily,
307 stringstyle=\color{Black}\ttfamily,%
308 frame=none,%
309 backgroundcolor=\color{LightGrey}%
310 }
311
312 \lstdefinestyle{myPython}{%
313 %\lstset{%
314 language=python,
315 showstringspaces=false,
316 basicstyle=\small\ttfamily,
317 commentstyle=\color{BrickRed}\ttfamily,
318 keywordstyle=\color{Purple}\ttfamily,
319 %identifierstyle=\color{Blue}\ttfamily,
320 %functionstyle=\color{Blue}\ttfamily,
321 %typestyle=\color{ForestGreen}\ttfamily,
322 stringstyle=\color{Tan}\ttfamily,%
323 frame=none,%
324 %backgroundcolor=\color{LightGrey}%
325 }
326
327 \lstdefinestyle{myhtml}{%
328 %\lstset{%
329 language=xml,
330 showstringspaces=false,
331 basicstyle=\small\ttfamily,
332 commentstyle=\color{BrickRed}\ttfamily,
333 keywordstyle=\color{Purple}\ttfamily,
334 %identifierstyle=\color{Blue}\ttfamily,
335 %functionstyle=\color{Blue}\ttfamily,
336 %typestyle=\color{ForestGreen}\ttfamily,
337 stringstyle=\color{Tan}\ttfamily,
338 morekeywords={,simulation,prop_dim,error_check,stochastic,%
339 globals,field,dimensions,lattice,domains,samples,vector,%
340 components,fourier_space,sequence,integrate,algorithm,%
341 interval,k_operators,constant,operator_names,vectors,%
342 output,filename,group,sampling,moments,benchmark,use_double,%
343 use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
344 default_value,argv,arg,iterations,cross_propagation,%
345 use_mpi,paths,seed,noises,author,description,name,type,%
346 }
347 frame=none,%
348 %framerule=2pt,%
349 backgroundcolor=\color{LightGrey}%
350 }
351
352 % this implements producing nice code blocks
353 % it also saves time, typing and
354 % *should* reduce errors in the text by removing doubling up of code
355 \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
356
357 % this implements nicely formatted shell code
358 \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
359
360 % this implements nicely formatted Perl code
361 \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
362
363 % this implements nicely formatted Python code
364 \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
365
366 % this implements nicely formatted C++ code
367 \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
368
369 % this implements nicely formatted matlab code
370 \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
371
372 % this implements nicely formatted scilab code
373 \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
374
375 %Ensures that latex doesn't have an error if we don't specify the version
376 \providecommand{\RepVersion}{Unknown\xspace}
377 % to set this value use:
378 % (pdf)latex '\newcommand{\RepVersion}{version\xspace}\input{guide.tex}'
379 % as your command-line

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