/[escript]/trunk/doc/user/guide_defs.tex
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Revision 1211 - (hide annotations)
Wed Jul 4 05:16:46 2007 UTC (12 years, 5 months ago) by jongui
File MIME type: application/x-tex
File size: 14562 byte(s)
- Fixed some minor bugs.
- Added a new feature called 'MapOnScalarClipWithRotation' that clips a two-dimensional data with a scalar value and subsequently rotating it to create a three-dimensional effect.
- Corresponding examples, test cases and documentation of the new module have also been 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 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     \newcommand{\Camera}{\class{Camera}\xspace}
104 jongui 886 \newcommand{\Light}{\class{Light}\xspace}
105 jongui 1035 \newcommand{\DataCollector}{\class{DataCollector}\xspace}
106     \newcommand{\ImageReader}{\class{ImageReader}\xspace}
107     \newcommand{\TextTwoD}{\class{Text2D}\xspace}
108     \newcommand{\ActorTwoD}{\class{Actor2D}\xspace}
109     \newcommand{\ActorThreeD}{\class{Actor3D}\xspace}
110     \newcommand{\Transform}{\class{Transform}\xspace}
111     \newcommand{\Clipper}{\class{Clipper}\xspace}
112 jongui 879 \newcommand{\Map}{\class{Map}\xspace}
113 jongui 1035 \newcommand{\MapOnPlaneCut}{\class{MapOnPlaneCut}\xspace}
114     \newcommand{\MapOnPlaneClip}{\class{MapOnPlaneClip}\xspace}
115 jongui 886 \newcommand{\MapOnScalarClip}{\class{MapOnScalarClip}\xspace}
116 jongui 1211 \newcommand{\MapOnScalarClipWithRotation}{\class{MapOnScalarClipWithRotation}\xspace}
117 jongui 1035 \newcommand{\GlyphThreeD}{\class{Glyph3D}\xspace}
118 jongui 1078 \newcommand{\MaskPoints}{\class{MaskPoints}\xspace}
119 jongui 1035 \newcommand{\Velocity}{\class{Velocity}\xspace}
120     \newcommand{\VelocityOnPlaneCut}{\class{VelocityOnPlaneCut}\xspace}
121     \newcommand{\VelocityOnPlaneClip}{\class{VelocityOnPlaneClip}\xspace}
122     \newcommand{\Sphere}{\class{Sphere}\xspace}
123     \newcommand{\TensorGlyph}{\class{TensorGlyph}\xspace}
124     \newcommand{\Ellipsoid}{\class{Ellipsoid}\xspace}
125     \newcommand{\EllipsoidOnPlaneCut}{\class{EllipsoidOnPlaneCut}\xspace}
126     \newcommand{\EllipsoidOnPlaneClip}{\class{EllipsoidOnPlaneClip}\xspace}
127     \newcommand{\ContourModule}{\class{ContourModule}\xspace}
128 jongui 879 \newcommand{\Contour}{\class{Contour}\xspace}
129 jongui 1035 \newcommand{\ContourOnPlaneCut}{\class{ContourOnPlaneCut}\xspace}
130     \newcommand{\ContourOnPlaneClip}{\class{ContourOnPlaneClip}\xspace}
131     \newcommand{\PointSource}{\class{PointSource}\xspace}
132     \newcommand{\StreamLineModule}{\class{StreamLineModule}\xspace}
133     \newcommand{\Tube}{\class{Tube}\xspace}
134     \newcommand{\StreamLine}{\class{StreamLine}\xspace}
135     \newcommand{\Warp}{\class{Warp}\xspace}
136 jongui 879 \newcommand{\Carpet}{\class{Carpet}\xspace}
137 jongui 1035 \newcommand{\PlaneSource}{\class{PlaneSource}\xspace}
138     \newcommand{\Image}{\class{Image}\xspace}
139 jongui 1112 \newcommand{\Logo}{\class{Logo}\xspace}
140     \newcommand{\ImageReslice}{\class{ImageReslice}\xspace}
141 jongui 879 \newcommand{\Position}{\class{Position}\xspace}
142 jongui 1194 \newcommand{\DataSetMapper}{\class{DataSetMapper}\xspace}
143     \newcommand{\Legend}{\class{Legend}\xspace}
144     \newcommand{\ScalarBar}{\class{ScalarBar}\xspace}
145     \newcommand{\Movie}{\class{Movie}\xspace}
146 jongui 1205 \newcommand{\CubeSource}{\class{CubeSource}\xspace}
147     \newcommand{\Rectangle}{\class{Rectangle}\xspace}
148     \newcommand{\LocalPosition}{\class{LocalPosition}\xspace}
149     \newcommand{\GlobalPosition}{\class{GlobalPosition}\xspace}
150 jongui 1211 \newcommand{\Rotation}{\class{Rotation}\xspace}
151 jongui 1081 \newcommand{\thumbnailwidth}{50mm}
152 jgs 102
153 jgs 82 % default width for figures
154     \newcommand{\figwidth}{100mm}
155     % commands useful in cross-referencing
156     \newcommand {\Ref}[1] {Reference~\cite{#1}}
157     \newcommand {\Sec}[1] {Section~\ref{#1}}
158     \newcommand {\App}[1] {Appendix~\ref{#1}}
159     \newcommand {\Chap}[1] {Chapter~\ref{#1}}
160     \newcommand {\etal} {\emph{~et~al.}}
161     \newcommand {\fig}[1] {Figure~\ref{#1}}
162     \newcommand {\eqn}[1] {Equation~(\ref{#1})}
163     \newcommand {\tab}[1] {Table~\ref{#1}}
164    
165 jgs 102 % this stops one figure taking up a whole page and lets more text onto
166     % the one page when a figure exists
167     \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
168    
169 jgs 82 % improved version of caption handling
170     \usepackage{ccaption}
171     \captionnamefont{\scshape}
172     \captionstyle{}
173     \makeatletter
174     \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
175     \renewcommand{\@makecaption}[2]{%
176     \vskip\abovecaptionskip
177     \sbox\@tempboxa{#1: #2}%
178     \ifdim \wd\@tempboxa >\hsize
179     \def\baselinestretch{1}\@normalsize
180     #1: #2\par
181     \def\baselinestretch{1.5}\@normalsize
182     \else
183     \global \@minipagefalse
184     \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
185     \fi
186     \vskip\belowcaptionskip}
187     \makeatother
188    
189 gross 572 % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
190 jgs 82 %%% this code grabbed from the PyScript docs
191     %%% pyscript.sourceforge.net
192    
193     % --------------------------------------------------------------
194     % Code format within \Verb
195     % --------------------------------------------------------------
196    
197 gross 572 % \definecolor{pycolor}{rgb}{0,0.4,0}
198 jgs 82
199 jgs 102 %% \DefineVerbatimEnvironment{python}{Verbatim}
200     %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
201     %% formatcom=\color{pycolor}\small,fontshape=rm}
202 jgs 82
203     %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
204    
205 gross 572 % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
206 jgs 82
207     %%% end of grabbed code
208    
209     % this is for when one uses pdflatex and therefore needs to load pdf
210     % figures into \includegraphics
211     \ifpdf
212     \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
213     \pdfcompresslevel=9 % 0: no compression, 9: highest compression
214     % or, set compress_level 9 in file pdftex.cfg
215     \else
216     \DeclareGraphicsExtensions{.eps}
217     \fi
218 jgs 102
219     % defines the colour for the background of code examples
220     \definecolor{LightGrey}{gray}{0.9}
221    
222     % add the listings package to pretty print the code output
223     \usepackage{listings}
224    
225     \lstdefinestyle{myC++}{%
226     %\lstset{%
227     language=C++,
228     showstringspaces=false,
229     basicstyle=\small\ttfamily,
230     commentstyle=\color[named]{BrickRed}\ttfamily,
231     keywordstyle=\color[named]{Purple}\ttfamily,
232     %identifierstyle=\color[named]{Blue}\ttfamily,
233     %functionstyle=\color[named]{Blue}\ttfamily,
234     %typestyle=\color[named]{ForestGreen}\ttfamily,
235     stringstyle=\color[named]{Tan}\ttfamily,%
236     morekeywords={,complex,}%
237     frame=none,%
238     backgroundcolor=\color{LightGrey}%
239     }
240    
241     \lstdefinestyle{myMatlab}{%
242     %\lstset{%
243     language=Matlab,
244     showstringspaces=false,
245     basicstyle=\small\ttfamily,
246     commentstyle=\color[named]{BrickRed}\ttfamily,
247     keywordstyle=\color[named]{Purple}\ttfamily,
248     %identifierstyle=\color[named]{Blue}\ttfamily,
249     %functionstyle=\color[named]{Blue}\ttfamily,
250     %typestyle=\color[named]{ForestGreen}\ttfamily,
251     stringstyle=\color[named]{Tan}\ttfamily,%
252     frame=none,%
253     backgroundcolor=\color{LightGrey}%
254     }
255    
256     \lstdefinestyle{myScilab}{%
257     %\lstset{%
258     language=Scilab,
259     showstringspaces=false,
260     basicstyle=\small\ttfamily,
261     commentstyle=\color[named]{BrickRed}\ttfamily,
262     keywordstyle=\color[named]{Purple}\ttfamily,
263     %identifierstyle=\color[named]{Blue}\ttfamily,
264     %functionstyle=\color[named]{Blue}\ttfamily,
265     %typestyle=\color[named]{ForestGreen}\ttfamily,
266     stringstyle=\color[named]{Tan}\ttfamily,%
267     frame=none,%
268     backgroundcolor=\color{LightGrey}%
269     }
270    
271     \lstdefinestyle{myShell}{%
272     %\lstset{%
273     language=ksh,
274     showstringspaces=false,
275     basicstyle=\small\ttfamily,
276     commentstyle=\color[named]{Black}\ttfamily,
277     keywordstyle=\color[named]{Black}\ttfamily,
278     %identifierstyle=\color[named]{Blue}\ttfamily,
279     %functionstyle=\color[named]{Blue}\ttfamily,
280     %typestyle=\color[named]{ForestGreen}\ttfamily,
281     stringstyle=\color[named]{Black}\ttfamily,%
282     frame=none,%
283     backgroundcolor=\color{LightGrey}%
284     }
285    
286     \lstdefinestyle{myPython}{%
287     %\lstset{%
288     language=python,
289     showstringspaces=false,
290     basicstyle=\small\ttfamily,
291     commentstyle=\color[named]{BrickRed}\ttfamily,
292     keywordstyle=\color[named]{Purple}\ttfamily,
293     %identifierstyle=\color[named]{Blue}\ttfamily,
294     %functionstyle=\color[named]{Blue}\ttfamily,
295     %typestyle=\color[named]{ForestGreen}\ttfamily,
296     stringstyle=\color[named]{Tan}\ttfamily,%
297     frame=none,%
298     %backgroundcolor=\color{LightGrey}%
299     }
300    
301     \lstdefinestyle{myhtml}{%
302     %\lstset{%
303     language=xml,
304     showstringspaces=false,
305     basicstyle=\small\ttfamily,
306     commentstyle=\color[named]{BrickRed}\ttfamily,
307     keywordstyle=\color[named]{Purple}\ttfamily,
308     %identifierstyle=\color[named]{Blue}\ttfamily,
309     %functionstyle=\color[named]{Blue}\ttfamily,
310     %typestyle=\color[named]{ForestGreen}\ttfamily,
311     stringstyle=\color[named]{Tan}\ttfamily,
312     morekeywords={,simulation,prop_dim,error_check,stochastic,%
313     globals,field,dimensions,lattice,domains,samples,vector,%
314     components,fourier_space,sequence,integrate,algorithm,%
315     interval,k_operators,constant,operator_names,vectors,%
316     output,filename,group,sampling,moments,benchmark,use_double,%
317     use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
318     default_value,argv,arg,iterations,cross_propagation,%
319     use_mpi,paths,seed,noises,author,description,name,type,%
320     }
321     frame=none,%
322     %framerule=2pt,%
323     backgroundcolor=\color{LightGrey}%
324     }
325    
326     % this implements producing nice code blocks
327     % it also saves time, typing and
328     % *should* reduce errors in the text by removing doubling up of code
329     \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
330    
331     % this implements nicely formatted shell code
332     \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
333    
334     % this implements nicely formatted Perl code
335     \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
336    
337     % this implements nicely formatted Python code
338     \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
339    
340     % this implements nicely formatted C++ code
341     \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
342    
343     % this implements nicely formatted matlab code
344     \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
345    
346     % this implements nicely formatted scilab code
347     \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
348    

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