/[escript]/trunk/doc/user/guide_defs.tex
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Revision 2446 - (hide annotations)
Fri May 29 04:24:01 2009 UTC (10 years, 5 months ago) by gross
File MIME type: application/x-tex
File size: 15591 byte(s)
same adjustment of nameing
1 ksteube 1811
2     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3 ksteube 1316 %
4 ksteube 1811 % Copyright (c) 2003-2008 by University of Queensland
5     % Earth Systems Science Computational Center (ESSCC)
6     % http://www.uq.edu.au/esscc
7 gross 625 %
8 ksteube 1811 % 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 gross 625 %
12 ksteube 1811 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
13 jgs 82
14 ksteube 1811
15 lgraham 2128 \usepackage{subfigure}
16 jgs 82 \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 gross 565 \newcommand{\LINUX}{{\it Linux}\xspace}
29 gross 2316 \newcommand{\WINDOWS}{{\it MS Windows}\xspace}
30     \newcommand{\PYTHON}{{\it python}\xspace}
31 jfenwick 2331 % \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
32     \newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace}
33 jgs 107 \newcommand{\escript}{\module{esys.escript}\xspace}
34     \newcommand{\finley}{\module{esys.finley}\xspace}
35 gross 999 \newcommand{\esys}{\module{esys}\xspace}
36 gross 565 \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
37 gross 993 \newcommand{\pycad}{\module{esys.pycad}\xspace}
38 gross 999 \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
39     \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
40 gross 2316 \newcommand{\env}[1]{\textbf{\mbox{#1}}\index{Environment!#1}}
41 jfenwick 2331 % \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 gross 565 \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
46 jgs 102 \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
47 jgs 121 \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
48     \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
49     \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
50 jfenwick 2331 \newcommand{\esysxml}{{\it esysxml}}
51 gross 565
52 jgs 102 \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
53     \newcommand{\Poisson}{\class{Poisson}\xspace}
54 gross 568 \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
55 gross 653 \newcommand{\Lame}{\class{Lame}\xspace}
56 jgs 82 \newcommand{\Data}{\class{Data}\xspace}
57 jfenwick 1955 \newcommand{\EmptyData}{empty \class{Data}\index{empty Data}\xspace}
58 jgs 102 \newcommand{\Domain}{\class{Domain}\xspace}
59 jongui 1002 %\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
60 gross 606 \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
61 jfenwick 1955 \newcommand{\mayavi}{{\it mayavi}\index{visualization!mayavi}\index{mayavi}}
62 gross 599 \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
63 jgs 102 \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
64     \newcommand{\False}{\constant{False}\xspace}
65     \newcommand{\True}{\constant{True}\xspace}
66 gross 653 \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 jgs 82
79 jgs 102 \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 gross 565 \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
89 jgs 102 \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
90     \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
91     \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
92 gross 660 \newcommand{\Tensor}{{tensor \Data object}\xspace}
93     \newcommand{\Vector}{{vector \Data object}\xspace}
94 jgs 102 \newcommand{\Scalar}{{scalar \Data object}\xspace}
95 jfenwick 1955 \newcommand{\DataSample}{{data sample}\index{data sample}\xspace}
96     \newcommand{\DataSamplePoints}{{data sample points}\index{data sample!points}\xspace}
97 jgs 102 \newcommand{\numarray}{\module{numarray}\xspace}
98 jfenwick 1957 \newcommand{\numarrayNA}{\module{numarray}.\class{NumArray}\xspace}
99 jgs 102 \newcommand{\Shape}{shape\xspace\index{shape}}
100 gross 565 \newcommand{\Rank}{rank\xspace\index{shape}}
101 jgs 102 \newcommand{\ExampleDirectory}{example directory\xspace}
102 gross 2446 \newcommand{\ReferenceGuide}{\url{http://esys.esscc.uq.edu.au/docs.html}\xspace}
103 gross 999 \newcommand{\Point}{\class{Point} \xspace}
104     \newcommand{\PropertySet}{\class{PropertySet} \xspace}
105     \newcommand{\Design}{\class{Design} \xspace}
106     \newcommand{\TagMap}{\class{TagMap} \xspace}
107     \newcommand{\ManifoldOneD}{\class{Manifold1D} \xspace}
108     \newcommand{\ManifoldTwoD}{\class{Manifold2D} \xspace}
109     \newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace}
110 jgs 102
111 jongui 879 % handy commands for pyvisi
112 jongui 1002 \newcommand{\VTK}{{\it VTK} \xspace}
113     \newcommand{\VTKUrl}{\url{http://www.vtk.org/}\xspace}
114 jongui 879 \newcommand{\Scene}{\class{Scene}\xspace}
115     \newcommand{\Camera}{\class{Camera}\xspace}
116 jongui 886 \newcommand{\Light}{\class{Light}\xspace}
117 jongui 1035 \newcommand{\DataCollector}{\class{DataCollector}\xspace}
118     \newcommand{\ImageReader}{\class{ImageReader}\xspace}
119     \newcommand{\TextTwoD}{\class{Text2D}\xspace}
120     \newcommand{\ActorTwoD}{\class{Actor2D}\xspace}
121     \newcommand{\ActorThreeD}{\class{Actor3D}\xspace}
122     \newcommand{\Transform}{\class{Transform}\xspace}
123     \newcommand{\Clipper}{\class{Clipper}\xspace}
124 jongui 879 \newcommand{\Map}{\class{Map}\xspace}
125 jongui 1035 \newcommand{\MapOnPlaneCut}{\class{MapOnPlaneCut}\xspace}
126     \newcommand{\MapOnPlaneClip}{\class{MapOnPlaneClip}\xspace}
127 jongui 886 \newcommand{\MapOnScalarClip}{\class{MapOnScalarClip}\xspace}
128 jongui 1211 \newcommand{\MapOnScalarClipWithRotation}{\class{MapOnScalarClipWithRotation}\xspace}
129 jongui 1035 \newcommand{\GlyphThreeD}{\class{Glyph3D}\xspace}
130 jongui 1078 \newcommand{\MaskPoints}{\class{MaskPoints}\xspace}
131 jongui 1035 \newcommand{\Velocity}{\class{Velocity}\xspace}
132     \newcommand{\VelocityOnPlaneCut}{\class{VelocityOnPlaneCut}\xspace}
133     \newcommand{\VelocityOnPlaneClip}{\class{VelocityOnPlaneClip}\xspace}
134     \newcommand{\Sphere}{\class{Sphere}\xspace}
135     \newcommand{\TensorGlyph}{\class{TensorGlyph}\xspace}
136     \newcommand{\Ellipsoid}{\class{Ellipsoid}\xspace}
137     \newcommand{\EllipsoidOnPlaneCut}{\class{EllipsoidOnPlaneCut}\xspace}
138     \newcommand{\EllipsoidOnPlaneClip}{\class{EllipsoidOnPlaneClip}\xspace}
139     \newcommand{\ContourModule}{\class{ContourModule}\xspace}
140 jongui 879 \newcommand{\Contour}{\class{Contour}\xspace}
141 jongui 1035 \newcommand{\ContourOnPlaneCut}{\class{ContourOnPlaneCut}\xspace}
142     \newcommand{\ContourOnPlaneClip}{\class{ContourOnPlaneClip}\xspace}
143     \newcommand{\PointSource}{\class{PointSource}\xspace}
144     \newcommand{\StreamLineModule}{\class{StreamLineModule}\xspace}
145     \newcommand{\Tube}{\class{Tube}\xspace}
146     \newcommand{\StreamLine}{\class{StreamLine}\xspace}
147     \newcommand{\Warp}{\class{Warp}\xspace}
148 jongui 879 \newcommand{\Carpet}{\class{Carpet}\xspace}
149 jongui 1035 \newcommand{\PlaneSource}{\class{PlaneSource}\xspace}
150     \newcommand{\Image}{\class{Image}\xspace}
151 jongui 1112 \newcommand{\Logo}{\class{Logo}\xspace}
152     \newcommand{\ImageReslice}{\class{ImageReslice}\xspace}
153 jongui 879 \newcommand{\Position}{\class{Position}\xspace}
154 jongui 1194 \newcommand{\DataSetMapper}{\class{DataSetMapper}\xspace}
155     \newcommand{\Legend}{\class{Legend}\xspace}
156     \newcommand{\ScalarBar}{\class{ScalarBar}\xspace}
157     \newcommand{\Movie}{\class{Movie}\xspace}
158 jongui 1205 \newcommand{\CubeSource}{\class{CubeSource}\xspace}
159     \newcommand{\Rectangle}{\class{Rectangle}\xspace}
160     \newcommand{\LocalPosition}{\class{LocalPosition}\xspace}
161     \newcommand{\GlobalPosition}{\class{GlobalPosition}\xspace}
162 jongui 1211 \newcommand{\Rotation}{\class{Rotation}\xspace}
163 jongui 1081 \newcommand{\thumbnailwidth}{50mm}
164 jgs 102
165 jgs 82 % default width for figures
166     \newcommand{\figwidth}{100mm}
167     % commands useful in cross-referencing
168     \newcommand {\Ref}[1] {Reference~\cite{#1}}
169     \newcommand {\Sec}[1] {Section~\ref{#1}}
170     \newcommand {\App}[1] {Appendix~\ref{#1}}
171     \newcommand {\Chap}[1] {Chapter~\ref{#1}}
172     \newcommand {\etal} {\emph{~et~al.}}
173     \newcommand {\fig}[1] {Figure~\ref{#1}}
174     \newcommand {\eqn}[1] {Equation~(\ref{#1})}
175     \newcommand {\tab}[1] {Table~\ref{#1}}
176    
177 jgs 102 % this stops one figure taking up a whole page and lets more text onto
178     % the one page when a figure exists
179     \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
180    
181 jgs 82 % improved version of caption handling
182     \usepackage{ccaption}
183     \captionnamefont{\scshape}
184     \captionstyle{}
185     \makeatletter
186     \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
187     \renewcommand{\@makecaption}[2]{%
188     \vskip\abovecaptionskip
189     \sbox\@tempboxa{#1: #2}%
190     \ifdim \wd\@tempboxa >\hsize
191     \def\baselinestretch{1}\@normalsize
192     #1: #2\par
193     \def\baselinestretch{1.5}\@normalsize
194     \else
195     \global \@minipagefalse
196     \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
197     \fi
198     \vskip\belowcaptionskip}
199     \makeatother
200    
201 gross 572 % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
202 jgs 82 %%% this code grabbed from the PyScript docs
203     %%% pyscript.sourceforge.net
204    
205     % --------------------------------------------------------------
206     % Code format within \Verb
207     % --------------------------------------------------------------
208    
209 gross 572 % \definecolor{pycolor}{rgb}{0,0.4,0}
210 jgs 82
211 jgs 102 %% \DefineVerbatimEnvironment{python}{Verbatim}
212     %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
213     %% formatcom=\color{pycolor}\small,fontshape=rm}
214 jgs 82
215     %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
216    
217 gross 572 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
218 jgs 82
219     %%% end of grabbed code
220    
221     % this is for when one uses pdflatex and therefore needs to load pdf
222     % figures into \includegraphics
223     \ifpdf
224     \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
225     \pdfcompresslevel=9 % 0: no compression, 9: highest compression
226     % or, set compress_level 9 in file pdftex.cfg
227     \else
228     \DeclareGraphicsExtensions{.eps}
229     \fi
230 jgs 102
231     % defines the colour for the background of code examples
232     \definecolor{LightGrey}{gray}{0.9}
233    
234     % add the listings package to pretty print the code output
235     \usepackage{listings}
236    
237 jfenwick 2335
238     %Some colour definitions added to keep pdflatex happy
239     %I make no claim that these values are particularly good
240     \definecolor{Purple}{rgb}{0.7, 0, 0.6}
241     \definecolor{Tan}{rgb}{0.5,0.5,0.5}
242     \definecolor{BrickRed}{rgb}{0.7, 0.2, 0.2}
243    
244     % All the \color{x} used to be \color[named]{x}
245     %end color defs
246    
247 jgs 102 \lstdefinestyle{myC++}{%
248     %\lstset{%
249     language=C++,
250     showstringspaces=false,
251     basicstyle=\small\ttfamily,
252 jfenwick 2335 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 jgs 102 morekeywords={,complex,}%
259     frame=none,%
260     backgroundcolor=\color{LightGrey}%
261     }
262    
263     \lstdefinestyle{myMatlab}{%
264     %\lstset{%
265     language=Matlab,
266     showstringspaces=false,
267     basicstyle=\small\ttfamily,
268 jfenwick 2335 commentstyle=\color{BrickRed}\ttfamily,
269     keywordstyle=\color{Purple}\ttfamily,
270     %identifierstyle=\color{Blue}\ttfamily,
271     %functionstyle=\color{Blue}\ttfamily,
272     %typestyle=\color{ForestGreen}\ttfamily,
273     stringstyle=\color{Tan}\ttfamily,%
274 jgs 102 frame=none,%
275     backgroundcolor=\color{LightGrey}%
276     }
277    
278     \lstdefinestyle{myScilab}{%
279     %\lstset{%
280     language=Scilab,
281     showstringspaces=false,
282     basicstyle=\small\ttfamily,
283 jfenwick 2335 commentstyle=\color{BrickRed}\ttfamily,
284     keywordstyle=\color{Purple}\ttfamily,
285     %identifierstyle=\color{Blue}\ttfamily,
286     %functionstyle=\color{Blue}\ttfamily,
287     %typestyle=\color{ForestGreen}\ttfamily,
288     stringstyle=\color{Tan}\ttfamily,%
289 jgs 102 frame=none,%
290     backgroundcolor=\color{LightGrey}%
291     }
292    
293     \lstdefinestyle{myShell}{%
294     %\lstset{%
295     language=ksh,
296     showstringspaces=false,
297     basicstyle=\small\ttfamily,
298 jfenwick 2335 commentstyle=\color{Black}\ttfamily,
299     keywordstyle=\color{Black}\ttfamily,
300     %identifierstyle=\color{Blue}\ttfamily,
301     %functionstyle=\color{Blue}\ttfamily,
302     %typestyle=\color{ForestGreen}\ttfamily,
303     stringstyle=\color{Black}\ttfamily,%
304 jgs 102 frame=none,%
305     backgroundcolor=\color{LightGrey}%
306     }
307    
308     \lstdefinestyle{myPython}{%
309     %\lstset{%
310     language=python,
311     showstringspaces=false,
312     basicstyle=\small\ttfamily,
313 jfenwick 2335 commentstyle=\color{BrickRed}\ttfamily,
314     keywordstyle=\color{Purple}\ttfamily,
315     %identifierstyle=\color{Blue}\ttfamily,
316     %functionstyle=\color{Blue}\ttfamily,
317     %typestyle=\color{ForestGreen}\ttfamily,
318     stringstyle=\color{Tan}\ttfamily,%
319 jgs 102 frame=none,%
320     %backgroundcolor=\color{LightGrey}%
321     }
322    
323     \lstdefinestyle{myhtml}{%
324     %\lstset{%
325     language=xml,
326     showstringspaces=false,
327     basicstyle=\small\ttfamily,
328 jfenwick 2335 commentstyle=\color{BrickRed}\ttfamily,
329     keywordstyle=\color{Purple}\ttfamily,
330     %identifierstyle=\color{Blue}\ttfamily,
331     %functionstyle=\color{Blue}\ttfamily,
332     %typestyle=\color{ForestGreen}\ttfamily,
333     stringstyle=\color{Tan}\ttfamily,
334 jgs 102 morekeywords={,simulation,prop_dim,error_check,stochastic,%
335     globals,field,dimensions,lattice,domains,samples,vector,%
336     components,fourier_space,sequence,integrate,algorithm,%
337     interval,k_operators,constant,operator_names,vectors,%
338     output,filename,group,sampling,moments,benchmark,use_double,%
339     use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
340     default_value,argv,arg,iterations,cross_propagation,%
341     use_mpi,paths,seed,noises,author,description,name,type,%
342     }
343     frame=none,%
344     %framerule=2pt,%
345     backgroundcolor=\color{LightGrey}%
346     }
347    
348     % this implements producing nice code blocks
349     % it also saves time, typing and
350     % *should* reduce errors in the text by removing doubling up of code
351     \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
352    
353     % this implements nicely formatted shell code
354     \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
355    
356     % this implements nicely formatted Perl code
357     \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
358    
359     % this implements nicely formatted Python code
360     \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
361    
362     % this implements nicely formatted C++ code
363     \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
364    
365     % this implements nicely formatted matlab code
366     \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
367    
368     % this implements nicely formatted scilab code
369     \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
370    
371 jfenwick 2338 %Ensures that latex doesn't have an error if we don't specify the version
372     \providecommand{\RepVersion}{Unknown\xspace}
373     % to set this value use:
374     % (pdf)latex '\newcommand{\RepVersion}{version\xspace}\input{guide.tex}'
375 gross 2372 % as your command-line

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