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Revision 1002 - (hide annotations)
Wed Feb 28 06:51:33 2007 UTC (12 years, 7 months ago) by jongui
Original Path: trunk/doc/user/guide_defs.tex
File MIME type: application/x-tex
File size: 13445 byte(s)
Included some try/except statements for error checking and some documentation. Also fixed a bug in DataCollector.
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 993 \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
25 jgs 107 \newcommand{\escript}{\module{esys.escript}\xspace}
26     \newcommand{\finley}{\module{esys.finley}\xspace}
27 gross 999 \newcommand{\esys}{\module{esys}\xspace}
28 gross 606 \newcommand{\bruce}{\module{esys.bruce}\xspace}
29 gross 565 \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
30 gross 993 \newcommand{\pycad}{\module{esys.pycad}\xspace}
31 gross 999 \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
32     \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
33 gross 565
34 gross 999
35 gross 565 \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
36 jgs 102 \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
37 jgs 121 \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
38     \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
39     \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
40 gross 565
41 jgs 102 \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
42     \newcommand{\Poisson}{\class{Poisson}\xspace}
43 gross 568 \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
44 gross 653 \newcommand{\Lame}{\class{Lame}\xspace}
45 jgs 82 \newcommand{\Data}{\class{Data}\xspace}
46 jgs 102 \newcommand{\EmptyData}{empty \class{Data} \index{empty Data}\xspace}
47     \newcommand{\Domain}{\class{Domain}\xspace}
48 jongui 1002 %\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
49 gross 606 \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
50 gross 565 \newcommand{\mayavi}{{\it mayavi} \index{visualization!mayavi}\index{mayavi}}
51 gross 599 \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
52 jgs 102 \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
53     \newcommand{\False}{\constant{False}\xspace}
54     \newcommand{\True}{\constant{True}\xspace}
55 gross 653 \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
56     \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
57     \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
58     \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
59     \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
60     \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
61     \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
62     \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
63     \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
64     \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}
65     \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
66     \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
67 jgs 82
68 jgs 102 \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
69     \newcommand{\Operator}{\class{Operator}\xspace}
70     \newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace}
71     \newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace}
72     \newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace}
73     \newcommand{\Function}{general \class{FunctionSpace}\xspace}
74     \newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace}
75     \newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace}
76     \newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace}
77 gross 565 \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
78 jgs 102 \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
79     \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
80     \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
81 gross 660 \newcommand{\Tensor}{{tensor \Data object}\xspace}
82     \newcommand{\Vector}{{vector \Data object}\xspace}
83 jgs 102 \newcommand{\Scalar}{{scalar \Data object}\xspace}
84     \newcommand{\DataSample}{{data sample} \index{data sample}\xspace}
85     \newcommand{\DataSamplePoints}{{data sample points} \index{data sample!points}\xspace}
86     \newcommand{\numarray}{\module{numarray}\xspace}
87     \newcommand{\Shape}{shape\xspace\index{shape}}
88 gross 565 \newcommand{\Rank}{rank\xspace\index{shape}}
89 jgs 102 \newcommand{\ExampleDirectory}{example directory\xspace}
90 jongui 1002 \newcommand{\ReferenceGuide}{\url{http://www.iservo.edu.au/esys/epydoc/index.html} \xspace}
91 gross 999 \newcommand{\Point}{\class{Point} \xspace}
92     \newcommand{\PropertySet}{\class{PropertySet} \xspace}
93     \newcommand{\Design}{\class{Design} \xspace}
94     \newcommand{\TagMap}{\class{TagMap} \xspace}
95     \newcommand{\ManifoldOneD}{\class{Manifold1D} \xspace}
96     \newcommand{\ManifoldTwoD}{\class{Manifold2D} \xspace}
97     \newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace}
98 jgs 102
99 jongui 879 % handy commands for pyvisi
100 jongui 1002 \newcommand{\VTK}{{\it VTK} \xspace}
101     \newcommand{\VTKUrl}{\url{http://www.vtk.org/}\xspace}
102 jongui 879 \newcommand{\Scene}{\class{Scene}\xspace}
103 jongui 886 \newcommand{\Image}{\class{Image}\xspace}
104     \newcommand{\Text}{\class{Text}\xspace}
105 jongui 879 \newcommand{\DataCollector}{\class{DataCollector}\xspace}
106     \newcommand{\Camera}{\class{Camera}\xspace}
107 jongui 886 \newcommand{\Light}{\class{Light}\xspace}
108 jongui 879 \newcommand{\Map}{\class{Map}\xspace}
109     \newcommand{\MapOnPlane}{\class{MapOnPlane}\xspace}
110     \newcommand{\MapOnClip}{\class{MapOnClip}\xspace}
111 jongui 886 \newcommand{\MapOnScalarClip}{\class{MapOnScalarClip}\xspace}
112     \newcommand{\Arrows}{\class{Arrows}\xspace}
113     \newcommand{\ArrowsOnPlane}{\class{ArrowsOnPlane}\xspace}
114     \newcommand{\ArrowsOnClip}{\class{ArrowsOnClip}\xspace}
115     \newcommand{\IsoSurface}{\class{IsoSurface}\xspace}
116     \newcommand{\IsoSurfaceOnPlane}{\class{IsoSurfaceOnPlane}\xspace}
117     \newcommand{\IsoSurfaceOnClip}{\class{IsoSurfaceOnClip}\xspace}
118 jongui 879 \newcommand{\Contour}{\class{Contour}\xspace}
119     \newcommand{\ContourOnPlane}{\class{ContourOnPlane}\xspace}
120     \newcommand{\ContourOnClip}{\class{ContourOnClip}\xspace}
121     \newcommand{\TensorC}{\class{Tensor}\xspace}
122     \newcommand{\TensorOnPlane}{\class{TensorOnPlane}\xspace}
123     \newcommand{\TensorOnClip}{\class{TensorOnClip}\xspace}
124 jongui 886 \newcommand{\StreamLines}{\class{StreamLines}\xspace}
125 jongui 879 \newcommand{\Carpet}{\class{Carpet}\xspace}
126     \newcommand{\Position}{\class{Position}\xspace}
127     \newcommand{\Transform}{\class{Transform}\xspace}
128     \newcommand{\Style}{\class{Style}\xspace}
129     \newcommand{\BlueToRed}{\class{BlueToRed}\xspace}
130     \newcommand{\RedToBlue}{\class{RedToBlue}\xspace}
131 jongui 886 \newcommand{\Plane}{\class{Plane}\xspace}
132 jgs 102
133 gross 593
134 jgs 82 % default width for figures
135     \newcommand{\figwidth}{100mm}
136     % commands useful in cross-referencing
137     \newcommand {\Ref}[1] {Reference~\cite{#1}}
138     \newcommand {\Sec}[1] {Section~\ref{#1}}
139     \newcommand {\App}[1] {Appendix~\ref{#1}}
140     \newcommand {\Chap}[1] {Chapter~\ref{#1}}
141     \newcommand {\etal} {\emph{~et~al.}}
142     \newcommand {\fig}[1] {Figure~\ref{#1}}
143     \newcommand {\eqn}[1] {Equation~(\ref{#1})}
144     \newcommand {\tab}[1] {Table~\ref{#1}}
145    
146 jgs 102 % this stops one figure taking up a whole page and lets more text onto
147     % the one page when a figure exists
148     \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
149    
150 jgs 82 % improved version of caption handling
151     \usepackage{ccaption}
152     \captionnamefont{\scshape}
153     \captionstyle{}
154     \makeatletter
155     \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
156     \renewcommand{\@makecaption}[2]{%
157     \vskip\abovecaptionskip
158     \sbox\@tempboxa{#1: #2}%
159     \ifdim \wd\@tempboxa >\hsize
160     \def\baselinestretch{1}\@normalsize
161     #1: #2\par
162     \def\baselinestretch{1.5}\@normalsize
163     \else
164     \global \@minipagefalse
165     \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
166     \fi
167     \vskip\belowcaptionskip}
168     \makeatother
169    
170 gross 572 % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
171 jgs 82 %%% this code grabbed from the PyScript docs
172     %%% pyscript.sourceforge.net
173    
174     % --------------------------------------------------------------
175     % Code format within \Verb
176     % --------------------------------------------------------------
177    
178 gross 572 % \definecolor{pycolor}{rgb}{0,0.4,0}
179 jgs 82
180 jgs 102 %% \DefineVerbatimEnvironment{python}{Verbatim}
181     %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
182     %% formatcom=\color{pycolor}\small,fontshape=rm}
183 jgs 82
184     %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
185    
186 gross 572 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
187 jgs 82
188     %%% end of grabbed code
189    
190     % this is for when one uses pdflatex and therefore needs to load pdf
191     % figures into \includegraphics
192     \ifpdf
193     \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
194     \pdfcompresslevel=9 % 0: no compression, 9: highest compression
195     % or, set compress_level 9 in file pdftex.cfg
196     \else
197     \DeclareGraphicsExtensions{.eps}
198     \fi
199 jgs 102
200     % defines the colour for the background of code examples
201     \definecolor{LightGrey}{gray}{0.9}
202    
203     % add the listings package to pretty print the code output
204     \usepackage{listings}
205    
206     \lstdefinestyle{myC++}{%
207     %\lstset{%
208     language=C++,
209     showstringspaces=false,
210     basicstyle=\small\ttfamily,
211     commentstyle=\color[named]{BrickRed}\ttfamily,
212     keywordstyle=\color[named]{Purple}\ttfamily,
213     %identifierstyle=\color[named]{Blue}\ttfamily,
214     %functionstyle=\color[named]{Blue}\ttfamily,
215     %typestyle=\color[named]{ForestGreen}\ttfamily,
216     stringstyle=\color[named]{Tan}\ttfamily,%
217     morekeywords={,complex,}%
218     frame=none,%
219     backgroundcolor=\color{LightGrey}%
220     }
221    
222     \lstdefinestyle{myMatlab}{%
223     %\lstset{%
224     language=Matlab,
225     showstringspaces=false,
226     basicstyle=\small\ttfamily,
227     commentstyle=\color[named]{BrickRed}\ttfamily,
228     keywordstyle=\color[named]{Purple}\ttfamily,
229     %identifierstyle=\color[named]{Blue}\ttfamily,
230     %functionstyle=\color[named]{Blue}\ttfamily,
231     %typestyle=\color[named]{ForestGreen}\ttfamily,
232     stringstyle=\color[named]{Tan}\ttfamily,%
233     frame=none,%
234     backgroundcolor=\color{LightGrey}%
235     }
236    
237     \lstdefinestyle{myScilab}{%
238     %\lstset{%
239     language=Scilab,
240     showstringspaces=false,
241     basicstyle=\small\ttfamily,
242     commentstyle=\color[named]{BrickRed}\ttfamily,
243     keywordstyle=\color[named]{Purple}\ttfamily,
244     %identifierstyle=\color[named]{Blue}\ttfamily,
245     %functionstyle=\color[named]{Blue}\ttfamily,
246     %typestyle=\color[named]{ForestGreen}\ttfamily,
247     stringstyle=\color[named]{Tan}\ttfamily,%
248     frame=none,%
249     backgroundcolor=\color{LightGrey}%
250     }
251    
252     \lstdefinestyle{myShell}{%
253     %\lstset{%
254     language=ksh,
255     showstringspaces=false,
256     basicstyle=\small\ttfamily,
257     commentstyle=\color[named]{Black}\ttfamily,
258     keywordstyle=\color[named]{Black}\ttfamily,
259     %identifierstyle=\color[named]{Blue}\ttfamily,
260     %functionstyle=\color[named]{Blue}\ttfamily,
261     %typestyle=\color[named]{ForestGreen}\ttfamily,
262     stringstyle=\color[named]{Black}\ttfamily,%
263     frame=none,%
264     backgroundcolor=\color{LightGrey}%
265     }
266    
267     \lstdefinestyle{myPython}{%
268     %\lstset{%
269     language=python,
270     showstringspaces=false,
271     basicstyle=\small\ttfamily,
272     commentstyle=\color[named]{BrickRed}\ttfamily,
273     keywordstyle=\color[named]{Purple}\ttfamily,
274     %identifierstyle=\color[named]{Blue}\ttfamily,
275     %functionstyle=\color[named]{Blue}\ttfamily,
276     %typestyle=\color[named]{ForestGreen}\ttfamily,
277     stringstyle=\color[named]{Tan}\ttfamily,%
278     frame=none,%
279     %backgroundcolor=\color{LightGrey}%
280     }
281    
282     \lstdefinestyle{myhtml}{%
283     %\lstset{%
284     language=xml,
285     showstringspaces=false,
286     basicstyle=\small\ttfamily,
287     commentstyle=\color[named]{BrickRed}\ttfamily,
288     keywordstyle=\color[named]{Purple}\ttfamily,
289     %identifierstyle=\color[named]{Blue}\ttfamily,
290     %functionstyle=\color[named]{Blue}\ttfamily,
291     %typestyle=\color[named]{ForestGreen}\ttfamily,
292     stringstyle=\color[named]{Tan}\ttfamily,
293     morekeywords={,simulation,prop_dim,error_check,stochastic,%
294     globals,field,dimensions,lattice,domains,samples,vector,%
295     components,fourier_space,sequence,integrate,algorithm,%
296     interval,k_operators,constant,operator_names,vectors,%
297     output,filename,group,sampling,moments,benchmark,use_double,%
298     use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
299     default_value,argv,arg,iterations,cross_propagation,%
300     use_mpi,paths,seed,noises,author,description,name,type,%
301     }
302     frame=none,%
303     %framerule=2pt,%
304     backgroundcolor=\color{LightGrey}%
305     }
306    
307     % this implements producing nice code blocks
308     % it also saves time, typing and
309     % *should* reduce errors in the text by removing doubling up of code
310     \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
311    
312     % this implements nicely formatted shell code
313     \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
314    
315     % this implements nicely formatted Perl code
316     \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
317    
318     % this implements nicely formatted Python code
319     \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
320    
321     % this implements nicely formatted C++ code
322     \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
323    
324     % this implements nicely formatted matlab code
325     \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
326    
327     % this implements nicely formatted scilab code
328     \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
329    

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