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Revision 1811 - (hide annotations)
Thu Sep 25 23:11:13 2008 UTC (11 years ago) by ksteube
Original Path: trunk/doc/user/guide_defs.tex
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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 jgs 82 \usepackage{epsfig}
16     \usepackage{graphicx,color}
17     \usepackage{makeidx} % handle the index properly
18     \usepackage{xspace} % handle spaces after commands more nicely
19     % use the ams math stuff, as it makes the maths easier to code, and
20     % nicer output than the standard LaTeX stuff
21     \usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physicists
22     % see http://www.ams.org/tex/amslatex.html
23     \usepackage{alltt} % handy verbatim stuff
24    
25    
26     % define some handy commands for escript stuff
27 gross 565 \newcommand{\LINUX}{{\it Linux}\xspace}
28 gross 993 \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
29 jgs 107 \newcommand{\escript}{\module{esys.escript}\xspace}
30     \newcommand{\finley}{\module{esys.finley}\xspace}
31 gross 999 \newcommand{\esys}{\module{esys}\xspace}
32 gross 606 \newcommand{\bruce}{\module{esys.bruce}\xspace}
33 gross 565 \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
34 gross 993 \newcommand{\pycad}{\module{esys.pycad}\xspace}
35 gross 999 \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
36     \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
37 gross 565
38 gross 999
39 gross 565 \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
40 jgs 102 \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
41 jgs 121 \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
42     \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
43     \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
44 gross 565
45 jgs 102 \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
46     \newcommand{\Poisson}{\class{Poisson}\xspace}
47 gross 568 \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
48 gross 653 \newcommand{\Lame}{\class{Lame}\xspace}
49 jgs 82 \newcommand{\Data}{\class{Data}\xspace}
50 jgs 102 \newcommand{\EmptyData}{empty \class{Data} \index{empty Data}\xspace}
51     \newcommand{\Domain}{\class{Domain}\xspace}
52 jongui 1002 %\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
53 gross 606 \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
54 gross 565 \newcommand{\mayavi}{{\it mayavi} \index{visualization!mayavi}\index{mayavi}}
55 gross 599 \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
56 jgs 102 \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
57     \newcommand{\False}{\constant{False}\xspace}
58     \newcommand{\True}{\constant{True}\xspace}
59 gross 653 \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
60     \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
61     \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
62     \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
63     \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
64     \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
65     \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
66     \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
67     \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
68     \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}
69     \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
70     \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
71 jgs 82
72 jgs 102 \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
73     \newcommand{\Operator}{\class{Operator}\xspace}
74     \newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace}
75     \newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace}
76     \newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace}
77     \newcommand{\Function}{general \class{FunctionSpace}\xspace}
78     \newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace}
79     \newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace}
80     \newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace}
81 gross 565 \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
82 jgs 102 \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
83     \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
84     \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
85 gross 660 \newcommand{\Tensor}{{tensor \Data object}\xspace}
86     \newcommand{\Vector}{{vector \Data object}\xspace}
87 jgs 102 \newcommand{\Scalar}{{scalar \Data object}\xspace}
88     \newcommand{\DataSample}{{data sample} \index{data sample}\xspace}
89     \newcommand{\DataSamplePoints}{{data sample points} \index{data sample!points}\xspace}
90     \newcommand{\numarray}{\module{numarray}\xspace}
91     \newcommand{\Shape}{shape\xspace\index{shape}}
92 gross 565 \newcommand{\Rank}{rank\xspace\index{shape}}
93 jgs 102 \newcommand{\ExampleDirectory}{example directory\xspace}
94 jongui 1002 \newcommand{\ReferenceGuide}{\url{http://www.iservo.edu.au/esys/epydoc/index.html} \xspace}
95 gross 999 \newcommand{\Point}{\class{Point} \xspace}
96     \newcommand{\PropertySet}{\class{PropertySet} \xspace}
97     \newcommand{\Design}{\class{Design} \xspace}
98     \newcommand{\TagMap}{\class{TagMap} \xspace}
99     \newcommand{\ManifoldOneD}{\class{Manifold1D} \xspace}
100     \newcommand{\ManifoldTwoD}{\class{Manifold2D} \xspace}
101     \newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace}
102 jgs 102
103 jongui 879 % handy commands for pyvisi
104 jongui 1002 \newcommand{\VTK}{{\it VTK} \xspace}
105     \newcommand{\VTKUrl}{\url{http://www.vtk.org/}\xspace}
106 jongui 879 \newcommand{\Scene}{\class{Scene}\xspace}
107     \newcommand{\Camera}{\class{Camera}\xspace}
108 jongui 886 \newcommand{\Light}{\class{Light}\xspace}
109 jongui 1035 \newcommand{\DataCollector}{\class{DataCollector}\xspace}
110     \newcommand{\ImageReader}{\class{ImageReader}\xspace}
111     \newcommand{\TextTwoD}{\class{Text2D}\xspace}
112     \newcommand{\ActorTwoD}{\class{Actor2D}\xspace}
113     \newcommand{\ActorThreeD}{\class{Actor3D}\xspace}
114     \newcommand{\Transform}{\class{Transform}\xspace}
115     \newcommand{\Clipper}{\class{Clipper}\xspace}
116 jongui 879 \newcommand{\Map}{\class{Map}\xspace}
117 jongui 1035 \newcommand{\MapOnPlaneCut}{\class{MapOnPlaneCut}\xspace}
118     \newcommand{\MapOnPlaneClip}{\class{MapOnPlaneClip}\xspace}
119 jongui 886 \newcommand{\MapOnScalarClip}{\class{MapOnScalarClip}\xspace}
120 jongui 1211 \newcommand{\MapOnScalarClipWithRotation}{\class{MapOnScalarClipWithRotation}\xspace}
121 jongui 1035 \newcommand{\GlyphThreeD}{\class{Glyph3D}\xspace}
122 jongui 1078 \newcommand{\MaskPoints}{\class{MaskPoints}\xspace}
123 jongui 1035 \newcommand{\Velocity}{\class{Velocity}\xspace}
124     \newcommand{\VelocityOnPlaneCut}{\class{VelocityOnPlaneCut}\xspace}
125     \newcommand{\VelocityOnPlaneClip}{\class{VelocityOnPlaneClip}\xspace}
126     \newcommand{\Sphere}{\class{Sphere}\xspace}
127     \newcommand{\TensorGlyph}{\class{TensorGlyph}\xspace}
128     \newcommand{\Ellipsoid}{\class{Ellipsoid}\xspace}
129     \newcommand{\EllipsoidOnPlaneCut}{\class{EllipsoidOnPlaneCut}\xspace}
130     \newcommand{\EllipsoidOnPlaneClip}{\class{EllipsoidOnPlaneClip}\xspace}
131     \newcommand{\ContourModule}{\class{ContourModule}\xspace}
132 jongui 879 \newcommand{\Contour}{\class{Contour}\xspace}
133 jongui 1035 \newcommand{\ContourOnPlaneCut}{\class{ContourOnPlaneCut}\xspace}
134     \newcommand{\ContourOnPlaneClip}{\class{ContourOnPlaneClip}\xspace}
135     \newcommand{\PointSource}{\class{PointSource}\xspace}
136     \newcommand{\StreamLineModule}{\class{StreamLineModule}\xspace}
137     \newcommand{\Tube}{\class{Tube}\xspace}
138     \newcommand{\StreamLine}{\class{StreamLine}\xspace}
139     \newcommand{\Warp}{\class{Warp}\xspace}
140 jongui 879 \newcommand{\Carpet}{\class{Carpet}\xspace}
141 jongui 1035 \newcommand{\PlaneSource}{\class{PlaneSource}\xspace}
142     \newcommand{\Image}{\class{Image}\xspace}
143 jongui 1112 \newcommand{\Logo}{\class{Logo}\xspace}
144     \newcommand{\ImageReslice}{\class{ImageReslice}\xspace}
145 jongui 879 \newcommand{\Position}{\class{Position}\xspace}
146 jongui 1194 \newcommand{\DataSetMapper}{\class{DataSetMapper}\xspace}
147     \newcommand{\Legend}{\class{Legend}\xspace}
148     \newcommand{\ScalarBar}{\class{ScalarBar}\xspace}
149     \newcommand{\Movie}{\class{Movie}\xspace}
150 jongui 1205 \newcommand{\CubeSource}{\class{CubeSource}\xspace}
151     \newcommand{\Rectangle}{\class{Rectangle}\xspace}
152     \newcommand{\LocalPosition}{\class{LocalPosition}\xspace}
153     \newcommand{\GlobalPosition}{\class{GlobalPosition}\xspace}
154 jongui 1211 \newcommand{\Rotation}{\class{Rotation}\xspace}
155 jongui 1081 \newcommand{\thumbnailwidth}{50mm}
156 jgs 102
157 jgs 82 % default width for figures
158     \newcommand{\figwidth}{100mm}
159     % commands useful in cross-referencing
160     \newcommand {\Ref}[1] {Reference~\cite{#1}}
161     \newcommand {\Sec}[1] {Section~\ref{#1}}
162     \newcommand {\App}[1] {Appendix~\ref{#1}}
163     \newcommand {\Chap}[1] {Chapter~\ref{#1}}
164     \newcommand {\etal} {\emph{~et~al.}}
165     \newcommand {\fig}[1] {Figure~\ref{#1}}
166     \newcommand {\eqn}[1] {Equation~(\ref{#1})}
167     \newcommand {\tab}[1] {Table~\ref{#1}}
168    
169 jgs 102 % this stops one figure taking up a whole page and lets more text onto
170     % the one page when a figure exists
171     \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
172    
173 jgs 82 % improved version of caption handling
174     \usepackage{ccaption}
175     \captionnamefont{\scshape}
176     \captionstyle{}
177     \makeatletter
178     \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
179     \renewcommand{\@makecaption}[2]{%
180     \vskip\abovecaptionskip
181     \sbox\@tempboxa{#1: #2}%
182     \ifdim \wd\@tempboxa >\hsize
183     \def\baselinestretch{1}\@normalsize
184     #1: #2\par
185     \def\baselinestretch{1.5}\@normalsize
186     \else
187     \global \@minipagefalse
188     \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
189     \fi
190     \vskip\belowcaptionskip}
191     \makeatother
192    
193 gross 572 % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
194 jgs 82 %%% this code grabbed from the PyScript docs
195     %%% pyscript.sourceforge.net
196    
197     % --------------------------------------------------------------
198     % Code format within \Verb
199     % --------------------------------------------------------------
200    
201 gross 572 % \definecolor{pycolor}{rgb}{0,0.4,0}
202 jgs 82
203 jgs 102 %% \DefineVerbatimEnvironment{python}{Verbatim}
204     %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
205     %% formatcom=\color{pycolor}\small,fontshape=rm}
206 jgs 82
207     %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
208    
209 gross 572 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
210 jgs 82
211     %%% end of grabbed code
212    
213     % this is for when one uses pdflatex and therefore needs to load pdf
214     % figures into \includegraphics
215     \ifpdf
216     \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
217     \pdfcompresslevel=9 % 0: no compression, 9: highest compression
218     % or, set compress_level 9 in file pdftex.cfg
219     \else
220     \DeclareGraphicsExtensions{.eps}
221     \fi
222 jgs 102
223     % defines the colour for the background of code examples
224     \definecolor{LightGrey}{gray}{0.9}
225    
226     % add the listings package to pretty print the code output
227     \usepackage{listings}
228    
229     \lstdefinestyle{myC++}{%
230     %\lstset{%
231     language=C++,
232     showstringspaces=false,
233     basicstyle=\small\ttfamily,
234     commentstyle=\color[named]{BrickRed}\ttfamily,
235     keywordstyle=\color[named]{Purple}\ttfamily,
236     %identifierstyle=\color[named]{Blue}\ttfamily,
237     %functionstyle=\color[named]{Blue}\ttfamily,
238     %typestyle=\color[named]{ForestGreen}\ttfamily,
239     stringstyle=\color[named]{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[named]{BrickRed}\ttfamily,
251     keywordstyle=\color[named]{Purple}\ttfamily,
252     %identifierstyle=\color[named]{Blue}\ttfamily,
253     %functionstyle=\color[named]{Blue}\ttfamily,
254     %typestyle=\color[named]{ForestGreen}\ttfamily,
255     stringstyle=\color[named]{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[named]{BrickRed}\ttfamily,
266     keywordstyle=\color[named]{Purple}\ttfamily,
267     %identifierstyle=\color[named]{Blue}\ttfamily,
268     %functionstyle=\color[named]{Blue}\ttfamily,
269     %typestyle=\color[named]{ForestGreen}\ttfamily,
270     stringstyle=\color[named]{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[named]{Black}\ttfamily,
281     keywordstyle=\color[named]{Black}\ttfamily,
282     %identifierstyle=\color[named]{Blue}\ttfamily,
283     %functionstyle=\color[named]{Blue}\ttfamily,
284     %typestyle=\color[named]{ForestGreen}\ttfamily,
285     stringstyle=\color[named]{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[named]{BrickRed}\ttfamily,
296     keywordstyle=\color[named]{Purple}\ttfamily,
297     %identifierstyle=\color[named]{Blue}\ttfamily,
298     %functionstyle=\color[named]{Blue}\ttfamily,
299     %typestyle=\color[named]{ForestGreen}\ttfamily,
300     stringstyle=\color[named]{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[named]{BrickRed}\ttfamily,
311     keywordstyle=\color[named]{Purple}\ttfamily,
312     %identifierstyle=\color[named]{Blue}\ttfamily,
313     %functionstyle=\color[named]{Blue}\ttfamily,
314     %typestyle=\color[named]{ForestGreen}\ttfamily,
315     stringstyle=\color[named]{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    

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