/[escript]/branches/stage3.1/doc/user/guide_defs.tex
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Revision 886 - (hide annotations)
Thu Nov 2 01:34:58 2006 UTC (12 years, 11 months ago) by jongui
Original Path: trunk/doc/user/guide_defs.tex
File MIME type: application/x-tex
File size: 12710 byte(s)
- Fixed a couple of minor bugs but the bug relating to the plane normal still exists.
- Updated the documentation.

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

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