/[escript]/branches/stage3.1/doc/user/guide_defs.tex
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Revision 983 - (hide annotations)
Tue Feb 20 02:49:08 2007 UTC (12 years, 8 months ago) by gross
Original Path: trunk/doc/user/guide_defs.tex
File MIME type: application/x-tex
File size: 12752 byte(s)
full Data object dump and load now available. Tests added.
1 jgs 82 % $Id$
2 gross 625 %
3     % Copyright © 2006 by ACcESS MNRF
4     % \url{http://www.access.edu.au
5     % Primary Business: Queensland, Australia.
6     % Licensed under the Open Software License version 3.0
7     % http://www.opensource.org/licenses/osl-3.0.php
8     %
9 jgs 82
10 gross 625
11 jgs 82 \usepackage{epsfig}
12     \usepackage{graphicx,color}
13     \usepackage{makeidx} % handle the index properly
14     \usepackage{xspace} % handle spaces after commands more nicely
15     % use the ams math stuff, as it makes the maths easier to code, and
16     % nicer output than the standard LaTeX stuff
17     \usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physicists
18     % see http://www.ams.org/tex/amslatex.html
19     \usepackage{alltt} % handy verbatim stuff
20    
21    
22     % define some handy commands for escript stuff
23 gross 565 \newcommand{\LINUX}{{\it Linux}\xspace}
24 gross 983 \newcommand{\netCDF}{{\it netCDF}\xspace}
25 jgs 107 \newcommand{\escript}{\module{esys.escript}\xspace}
26     \newcommand{\finley}{\module{esys.finley}\xspace}
27 gross 606 \newcommand{\bruce}{\module{esys.bruce}\xspace}
28 gross 565 \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
29    
30     \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
31 jgs 102 \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
32 jgs 121 \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
33     \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
34     \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
35 gross 565
36 jgs 102 \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
37     \newcommand{\Poisson}{\class{Poisson}\xspace}
38 gross 568 \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
39 gross 653 \newcommand{\Lame}{\class{Lame}\xspace}
40 jgs 82 \newcommand{\Data}{\class{Data}\xspace}
41 jgs 102 \newcommand{\EmptyData}{empty \class{Data} \index{empty Data}\xspace}
42     \newcommand{\Domain}{\class{Domain}\xspace}
43 jongui 879 \newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
44 gross 606 \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
45 gross 565 \newcommand{\mayavi}{{\it mayavi} \index{visualization!mayavi}\index{mayavi}}
46 gross 599 \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
47 jgs 102 \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
48     \newcommand{\False}{\constant{False}\xspace}
49     \newcommand{\True}{\constant{True}\xspace}
50 gross 653 \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
51     \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
52     \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
53     \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
54     \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
55     \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
56     \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
57     \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
58     \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
59     \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}
60     \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
61     \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
62 jgs 82
63 jgs 102 \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
64     \newcommand{\Operator}{\class{Operator}\xspace}
65     \newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace}
66     \newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace}
67     \newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace}
68     \newcommand{\Function}{general \class{FunctionSpace}\xspace}
69     \newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace}
70     \newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace}
71     \newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace}
72 gross 565 \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
73 jgs 102 \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
74     \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
75     \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
76 gross 660 \newcommand{\Tensor}{{tensor \Data object}\xspace}
77     \newcommand{\Vector}{{vector \Data object}\xspace}
78 jgs 102 \newcommand{\Scalar}{{scalar \Data object}\xspace}
79     \newcommand{\DataSample}{{data sample} \index{data sample}\xspace}
80     \newcommand{\DataSamplePoints}{{data sample points} \index{data sample!points}\xspace}
81     \newcommand{\numarray}{\module{numarray}\xspace}
82     \newcommand{\Shape}{shape\xspace\index{shape}}
83 gross 565 \newcommand{\Rank}{rank\xspace\index{shape}}
84 jgs 102 \newcommand{\ExampleDirectory}{example directory\xspace}
85 gross 593 \newcommand{\ReferenceGuide}{\url{http://www.iservo.edu.au/esys/epydoc/index.html}}
86 jgs 102
87    
88 jongui 879 % handy commands for pyvisi
89     \newcommand{\Scene}{\class{Scene}\xspace}
90 jongui 886 \newcommand{\Image}{\class{Image}\xspace}
91     \newcommand{\Text}{\class{Text}\xspace}
92 jongui 879 \newcommand{\DataCollector}{\class{DataCollector}\xspace}
93     \newcommand{\Camera}{\class{Camera}\xspace}
94 jongui 886 \newcommand{\Light}{\class{Light}\xspace}
95 jongui 879 \newcommand{\Map}{\class{Map}\xspace}
96     \newcommand{\MapOnPlane}{\class{MapOnPlane}\xspace}
97     \newcommand{\MapOnClip}{\class{MapOnClip}\xspace}
98 jongui 886 \newcommand{\MapOnScalarClip}{\class{MapOnScalarClip}\xspace}
99     \newcommand{\Arrows}{\class{Arrows}\xspace}
100     \newcommand{\ArrowsOnPlane}{\class{ArrowsOnPlane}\xspace}
101     \newcommand{\ArrowsOnClip}{\class{ArrowsOnClip}\xspace}
102     \newcommand{\IsoSurface}{\class{IsoSurface}\xspace}
103     \newcommand{\IsoSurfaceOnPlane}{\class{IsoSurfaceOnPlane}\xspace}
104     \newcommand{\IsoSurfaceOnClip}{\class{IsoSurfaceOnClip}\xspace}
105 jongui 879 \newcommand{\Contour}{\class{Contour}\xspace}
106     \newcommand{\ContourOnPlane}{\class{ContourOnPlane}\xspace}
107     \newcommand{\ContourOnClip}{\class{ContourOnClip}\xspace}
108     \newcommand{\TensorC}{\class{Tensor}\xspace}
109     \newcommand{\TensorOnPlane}{\class{TensorOnPlane}\xspace}
110     \newcommand{\TensorOnClip}{\class{TensorOnClip}\xspace}
111 jongui 886 \newcommand{\StreamLines}{\class{StreamLines}\xspace}
112 jongui 879 \newcommand{\Carpet}{\class{Carpet}\xspace}
113     \newcommand{\Position}{\class{Position}\xspace}
114     \newcommand{\Transform}{\class{Transform}\xspace}
115     \newcommand{\Style}{\class{Style}\xspace}
116     \newcommand{\BlueToRed}{\class{BlueToRed}\xspace}
117     \newcommand{\RedToBlue}{\class{RedToBlue}\xspace}
118 jongui 886 \newcommand{\Plane}{\class{Plane}\xspace}
119 jgs 102
120 gross 593
121 jgs 82 % default width for figures
122     \newcommand{\figwidth}{100mm}
123     % commands useful in cross-referencing
124     \newcommand {\Ref}[1] {Reference~\cite{#1}}
125     \newcommand {\Sec}[1] {Section~\ref{#1}}
126     \newcommand {\App}[1] {Appendix~\ref{#1}}
127     \newcommand {\Chap}[1] {Chapter~\ref{#1}}
128     \newcommand {\etal} {\emph{~et~al.}}
129     \newcommand {\fig}[1] {Figure~\ref{#1}}
130     \newcommand {\eqn}[1] {Equation~(\ref{#1})}
131     \newcommand {\tab}[1] {Table~\ref{#1}}
132    
133 jgs 102 % this stops one figure taking up a whole page and lets more text onto
134     % the one page when a figure exists
135     \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
136    
137 jgs 82 % improved version of caption handling
138     \usepackage{ccaption}
139     \captionnamefont{\scshape}
140     \captionstyle{}
141     \makeatletter
142     \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
143     \renewcommand{\@makecaption}[2]{%
144     \vskip\abovecaptionskip
145     \sbox\@tempboxa{#1: #2}%
146     \ifdim \wd\@tempboxa >\hsize
147     \def\baselinestretch{1}\@normalsize
148     #1: #2\par
149     \def\baselinestretch{1.5}\@normalsize
150     \else
151     \global \@minipagefalse
152     \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
153     \fi
154     \vskip\belowcaptionskip}
155     \makeatother
156    
157 gross 572 % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
158 jgs 82 %%% this code grabbed from the PyScript docs
159     %%% pyscript.sourceforge.net
160    
161     % --------------------------------------------------------------
162     % Code format within \Verb
163     % --------------------------------------------------------------
164    
165 gross 572 % \definecolor{pycolor}{rgb}{0,0.4,0}
166 jgs 82
167 jgs 102 %% \DefineVerbatimEnvironment{python}{Verbatim}
168     %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
169     %% formatcom=\color{pycolor}\small,fontshape=rm}
170 jgs 82
171     %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
172    
173 gross 572 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
174 jgs 82
175     %%% end of grabbed code
176    
177     % this is for when one uses pdflatex and therefore needs to load pdf
178     % figures into \includegraphics
179     \ifpdf
180     \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
181     \pdfcompresslevel=9 % 0: no compression, 9: highest compression
182     % or, set compress_level 9 in file pdftex.cfg
183     \else
184     \DeclareGraphicsExtensions{.eps}
185     \fi
186 jgs 102
187     % defines the colour for the background of code examples
188     \definecolor{LightGrey}{gray}{0.9}
189    
190     % add the listings package to pretty print the code output
191     \usepackage{listings}
192    
193     \lstdefinestyle{myC++}{%
194     %\lstset{%
195     language=C++,
196     showstringspaces=false,
197     basicstyle=\small\ttfamily,
198     commentstyle=\color[named]{BrickRed}\ttfamily,
199     keywordstyle=\color[named]{Purple}\ttfamily,
200     %identifierstyle=\color[named]{Blue}\ttfamily,
201     %functionstyle=\color[named]{Blue}\ttfamily,
202     %typestyle=\color[named]{ForestGreen}\ttfamily,
203     stringstyle=\color[named]{Tan}\ttfamily,%
204     morekeywords={,complex,}%
205     frame=none,%
206     backgroundcolor=\color{LightGrey}%
207     }
208    
209     \lstdefinestyle{myMatlab}{%
210     %\lstset{%
211     language=Matlab,
212     showstringspaces=false,
213     basicstyle=\small\ttfamily,
214     commentstyle=\color[named]{BrickRed}\ttfamily,
215     keywordstyle=\color[named]{Purple}\ttfamily,
216     %identifierstyle=\color[named]{Blue}\ttfamily,
217     %functionstyle=\color[named]{Blue}\ttfamily,
218     %typestyle=\color[named]{ForestGreen}\ttfamily,
219     stringstyle=\color[named]{Tan}\ttfamily,%
220     frame=none,%
221     backgroundcolor=\color{LightGrey}%
222     }
223    
224     \lstdefinestyle{myScilab}{%
225     %\lstset{%
226     language=Scilab,
227     showstringspaces=false,
228     basicstyle=\small\ttfamily,
229     commentstyle=\color[named]{BrickRed}\ttfamily,
230     keywordstyle=\color[named]{Purple}\ttfamily,
231     %identifierstyle=\color[named]{Blue}\ttfamily,
232     %functionstyle=\color[named]{Blue}\ttfamily,
233     %typestyle=\color[named]{ForestGreen}\ttfamily,
234     stringstyle=\color[named]{Tan}\ttfamily,%
235     frame=none,%
236     backgroundcolor=\color{LightGrey}%
237     }
238    
239     \lstdefinestyle{myShell}{%
240     %\lstset{%
241     language=ksh,
242     showstringspaces=false,
243     basicstyle=\small\ttfamily,
244     commentstyle=\color[named]{Black}\ttfamily,
245     keywordstyle=\color[named]{Black}\ttfamily,
246     %identifierstyle=\color[named]{Blue}\ttfamily,
247     %functionstyle=\color[named]{Blue}\ttfamily,
248     %typestyle=\color[named]{ForestGreen}\ttfamily,
249     stringstyle=\color[named]{Black}\ttfamily,%
250     frame=none,%
251     backgroundcolor=\color{LightGrey}%
252     }
253    
254     \lstdefinestyle{myPython}{%
255     %\lstset{%
256     language=python,
257     showstringspaces=false,
258     basicstyle=\small\ttfamily,
259     commentstyle=\color[named]{BrickRed}\ttfamily,
260     keywordstyle=\color[named]{Purple}\ttfamily,
261     %identifierstyle=\color[named]{Blue}\ttfamily,
262     %functionstyle=\color[named]{Blue}\ttfamily,
263     %typestyle=\color[named]{ForestGreen}\ttfamily,
264     stringstyle=\color[named]{Tan}\ttfamily,%
265     frame=none,%
266     %backgroundcolor=\color{LightGrey}%
267     }
268    
269     \lstdefinestyle{myhtml}{%
270     %\lstset{%
271     language=xml,
272     showstringspaces=false,
273     basicstyle=\small\ttfamily,
274     commentstyle=\color[named]{BrickRed}\ttfamily,
275     keywordstyle=\color[named]{Purple}\ttfamily,
276     %identifierstyle=\color[named]{Blue}\ttfamily,
277     %functionstyle=\color[named]{Blue}\ttfamily,
278     %typestyle=\color[named]{ForestGreen}\ttfamily,
279     stringstyle=\color[named]{Tan}\ttfamily,
280     morekeywords={,simulation,prop_dim,error_check,stochastic,%
281     globals,field,dimensions,lattice,domains,samples,vector,%
282     components,fourier_space,sequence,integrate,algorithm,%
283     interval,k_operators,constant,operator_names,vectors,%
284     output,filename,group,sampling,moments,benchmark,use_double,%
285     use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
286     default_value,argv,arg,iterations,cross_propagation,%
287     use_mpi,paths,seed,noises,author,description,name,type,%
288     }
289     frame=none,%
290     %framerule=2pt,%
291     backgroundcolor=\color{LightGrey}%
292     }
293    
294     % this implements producing nice code blocks
295     % it also saves time, typing and
296     % *should* reduce errors in the text by removing doubling up of code
297     \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
298    
299     % this implements nicely formatted shell code
300     \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
301    
302     % this implements nicely formatted Perl code
303     \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
304    
305     % this implements nicely formatted Python code
306     \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
307    
308     % this implements nicely formatted C++ code
309     \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
310    
311     % this implements nicely formatted matlab code
312     \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
313    
314     % this implements nicely formatted scilab code
315     \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
316    

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