/[escript]/trunk/doc/user/guide_defs.tex
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trunk/esys2/doc/user/guide_defs.tex revision 100 by jgs, Wed Dec 15 03:48:48 2004 UTC trunk/doc/user/guide_defs.tex revision 1078 by jongui, Thu Apr 5 06:18:47 2007 UTC
# Line 1  Line 1 
1  % $Id$  % $Id$
2    %
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    
10    
11  \usepackage{epsfig}  \usepackage{epsfig}
12  \usepackage{graphicx,color}  \usepackage{graphicx,color}
# Line 12  Line 20 
20    
21    
22  % define some handy commands for escript stuff  % define some handy commands for escript stuff
23  \newcommand{\ESyS}{\module{ESyS}\xspace}  \newcommand{\LINUX}{{\it Linux}\xspace}
24  \newcommand{\escript}{\module{escript}\xspace}  \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
25  \newcommand{\finley}{\module{finley}\xspace}  \newcommand{\escript}{\module{esys.escript}\xspace}
26  \newcommand{\linearPDE}{\class{linearPDE}\xspace}  \newcommand{\finley}{\module{esys.finley}\xspace}
27    \newcommand{\esys}{\module{esys}\xspace}
28    \newcommand{\bruce}{\module{esys.bruce}\xspace}
29    \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
30    \newcommand{\pycad}{\module{esys.pycad}\xspace}
31    \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
32    \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
33    
34    
35    \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
36    \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
37    \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
38    \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
39    \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
40    
41    \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
42    \newcommand{\Poisson}{\class{Poisson}\xspace}
43    \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
44    \newcommand{\Lame}{\class{Lame}\xspace}
45  \newcommand{\Data}{\class{Data}\xspace}  \newcommand{\Data}{\class{Data}\xspace}
46    \newcommand{\EmptyData}{empty \class{Data} \index{empty Data}\xspace}
47    \newcommand{\Domain}{\class{Domain}\xspace}
48    %\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
49    \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
50    \newcommand{\mayavi}{{\it mayavi} \index{visualization!mayavi}\index{mayavi}}
51    \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
52    \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
53    \newcommand{\False}{\constant{False}\xspace}
54    \newcommand{\True}{\constant{True}\xspace}
55    \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    
68    \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    \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
78    \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
79    \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
80    \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
81    \newcommand{\Tensor}{{tensor \Data object}\xspace}
82    \newcommand{\Vector}{{vector \Data object}\xspace}
83    \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    \newcommand{\Rank}{rank\xspace\index{shape}}
89    \newcommand{\ExampleDirectory}{example directory\xspace}
90    \newcommand{\ReferenceGuide}{\url{http://www.iservo.edu.au/esys/epydoc/index.html} \xspace}
91    \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    
99    % handy commands for pyvisi
100    \newcommand{\VTK}{{\it VTK} \xspace}
101    \newcommand{\VTKUrl}{\url{http://www.vtk.org/}\xspace}
102    \newcommand{\Scene}{\class{Scene}\xspace}
103    \newcommand{\Camera}{\class{Camera}\xspace}
104    \newcommand{\Light}{\class{Light}\xspace}
105    \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    \newcommand{\Map}{\class{Map}\xspace}
113    \newcommand{\MapOnPlaneCut}{\class{MapOnPlaneCut}\xspace}
114    \newcommand{\MapOnPlaneClip}{\class{MapOnPlaneClip}\xspace}
115    \newcommand{\MapOnScalarClip}{\class{MapOnScalarClip}\xspace}
116    \newcommand{\GlyphThreeD}{\class{Glyph3D}\xspace}
117    \newcommand{\MaskPoints}{\class{MaskPoints}\xspace}
118    \newcommand{\Velocity}{\class{Velocity}\xspace}
119    \newcommand{\VelocityOnPlaneCut}{\class{VelocityOnPlaneCut}\xspace}
120    \newcommand{\VelocityOnPlaneClip}{\class{VelocityOnPlaneClip}\xspace}
121    \newcommand{\Sphere}{\class{Sphere}\xspace}
122    \newcommand{\TensorGlyph}{\class{TensorGlyph}\xspace}
123    \newcommand{\Ellipsoid}{\class{Ellipsoid}\xspace}
124    \newcommand{\EllipsoidOnPlaneCut}{\class{EllipsoidOnPlaneCut}\xspace}
125    \newcommand{\EllipsoidOnPlaneClip}{\class{EllipsoidOnPlaneClip}\xspace}
126    \newcommand{\ContourModule}{\class{ContourModule}\xspace}
127    \newcommand{\Contour}{\class{Contour}\xspace}
128    \newcommand{\ContourOnPlaneCut}{\class{ContourOnPlaneCut}\xspace}
129    \newcommand{\ContourOnPlaneClip}{\class{ContourOnPlaneClip}\xspace}
130    \newcommand{\PointSource}{\class{PointSource}\xspace}
131    \newcommand{\StreamLineModule}{\class{StreamLineModule}\xspace}
132    \newcommand{\Tube}{\class{Tube}\xspace}
133    \newcommand{\StreamLine}{\class{StreamLine}\xspace}
134    \newcommand{\Warp}{\class{Warp}\xspace}
135    \newcommand{\Carpet}{\class{Carpet}\xspace}
136    \newcommand{\PlaneSource}{\class{PlaneSource}\xspace}
137    \newcommand{\Image}{\class{Image}\xspace}
138    \newcommand{\Position}{\class{Position}\xspace}
139    
140  % default width for figures  % default width for figures
141  \newcommand{\figwidth}{100mm}  \newcommand{\figwidth}{100mm}
   
142  % commands useful in cross-referencing  % commands useful in cross-referencing
143  \newcommand {\Ref}[1] {Reference~\cite{#1}}  \newcommand {\Ref}[1] {Reference~\cite{#1}}
144  \newcommand {\Sec}[1] {Section~\ref{#1}}  \newcommand {\Sec}[1] {Section~\ref{#1}}
# Line 31  Line 149 
149  \newcommand {\eqn}[1] {Equation~(\ref{#1})}  \newcommand {\eqn}[1] {Equation~(\ref{#1})}
150  \newcommand {\tab}[1] {Table~\ref{#1}}  \newcommand {\tab}[1] {Table~\ref{#1}}
151    
152    % this stops one figure taking up a whole page and lets more text onto
153    % the one page when a figure exists
154    \renewcommand{\floatpagefraction}{0.8} %   Default = 0.5
155    
156  % improved version of caption handling  % improved version of caption handling
157  \usepackage{ccaption}  \usepackage{ccaption}
158  \captionnamefont{\scshape}  \captionnamefont{\scshape}
# Line 51  Line 173 
173  \vskip\belowcaptionskip}  \vskip\belowcaptionskip}
174  \makeatother  \makeatother
175    
176  \usepackage{fancyvrb}  % fancy verbatim stuff.  Needed so code below goes  % \usepackage{fancyvrb}  % fancy verbatim stuff.  Needed so code below goes
177  %%% this code grabbed from the PyScript docs  %%% this code grabbed from the PyScript docs
178  %%% pyscript.sourceforge.net  %%% pyscript.sourceforge.net
179    
# Line 59  Line 181 
181  % Code format within \Verb  % Code format within \Verb
182  % --------------------------------------------------------------  % --------------------------------------------------------------
183    
184  \definecolor{pycolor}{rgb}{0,0.4,0}  % \definecolor{pycolor}{rgb}{0,0.4,0}
185    
186  \DefineVerbatimEnvironment{python}{Verbatim}  %% \DefineVerbatimEnvironment{python}{Verbatim}
187  {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},  %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
188  formatcom=\color{pycolor}\small,fontshape=rm}  %% formatcom=\color{pycolor}\small,fontshape=rm}
189    
190  %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}  %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
191    
192  \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}  % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
193    
194  %%% end of grabbed code  %%% end of grabbed code
195    
# Line 80  formatcom=\color{pycolor}\small,fontshap Line 202  formatcom=\color{pycolor}\small,fontshap
202  \else  \else
203      \DeclareGraphicsExtensions{.eps}      \DeclareGraphicsExtensions{.eps}
204  \fi  \fi
205    
206    % defines the colour for the background of code examples
207    \definecolor{LightGrey}{gray}{0.9}
208    
209    % add the listings package to pretty print the code output
210    \usepackage{listings}
211    
212    \lstdefinestyle{myC++}{%
213    %\lstset{%
214    language=C++,
215    showstringspaces=false,
216    basicstyle=\small\ttfamily,
217    commentstyle=\color[named]{BrickRed}\ttfamily,
218    keywordstyle=\color[named]{Purple}\ttfamily,
219    %identifierstyle=\color[named]{Blue}\ttfamily,
220    %functionstyle=\color[named]{Blue}\ttfamily,
221    %typestyle=\color[named]{ForestGreen}\ttfamily,
222    stringstyle=\color[named]{Tan}\ttfamily,%
223    morekeywords={,complex,}%
224    frame=none,%
225    backgroundcolor=\color{LightGrey}%
226    }
227    
228    \lstdefinestyle{myMatlab}{%
229    %\lstset{%
230    language=Matlab,
231    showstringspaces=false,
232    basicstyle=\small\ttfamily,
233    commentstyle=\color[named]{BrickRed}\ttfamily,
234    keywordstyle=\color[named]{Purple}\ttfamily,
235    %identifierstyle=\color[named]{Blue}\ttfamily,
236    %functionstyle=\color[named]{Blue}\ttfamily,
237    %typestyle=\color[named]{ForestGreen}\ttfamily,
238    stringstyle=\color[named]{Tan}\ttfamily,%
239    frame=none,%
240    backgroundcolor=\color{LightGrey}%
241    }
242    
243    \lstdefinestyle{myScilab}{%
244    %\lstset{%
245    language=Scilab,
246    showstringspaces=false,
247    basicstyle=\small\ttfamily,
248    commentstyle=\color[named]{BrickRed}\ttfamily,
249    keywordstyle=\color[named]{Purple}\ttfamily,
250    %identifierstyle=\color[named]{Blue}\ttfamily,
251    %functionstyle=\color[named]{Blue}\ttfamily,
252    %typestyle=\color[named]{ForestGreen}\ttfamily,
253    stringstyle=\color[named]{Tan}\ttfamily,%
254    frame=none,%
255    backgroundcolor=\color{LightGrey}%
256    }
257    
258    \lstdefinestyle{myShell}{%
259    %\lstset{%
260    language=ksh,
261    showstringspaces=false,
262    basicstyle=\small\ttfamily,
263    commentstyle=\color[named]{Black}\ttfamily,
264    keywordstyle=\color[named]{Black}\ttfamily,
265    %identifierstyle=\color[named]{Blue}\ttfamily,
266    %functionstyle=\color[named]{Blue}\ttfamily,
267    %typestyle=\color[named]{ForestGreen}\ttfamily,
268    stringstyle=\color[named]{Black}\ttfamily,%
269    frame=none,%
270    backgroundcolor=\color{LightGrey}%
271    }
272    
273    \lstdefinestyle{myPython}{%
274    %\lstset{%
275    language=python,
276    showstringspaces=false,
277    basicstyle=\small\ttfamily,
278    commentstyle=\color[named]{BrickRed}\ttfamily,
279    keywordstyle=\color[named]{Purple}\ttfamily,
280    %identifierstyle=\color[named]{Blue}\ttfamily,
281    %functionstyle=\color[named]{Blue}\ttfamily,
282    %typestyle=\color[named]{ForestGreen}\ttfamily,
283    stringstyle=\color[named]{Tan}\ttfamily,%
284    frame=none,%
285    %backgroundcolor=\color{LightGrey}%
286    }
287    
288    \lstdefinestyle{myhtml}{%
289    %\lstset{%
290    language=xml,
291    showstringspaces=false,
292    basicstyle=\small\ttfamily,
293    commentstyle=\color[named]{BrickRed}\ttfamily,
294    keywordstyle=\color[named]{Purple}\ttfamily,
295    %identifierstyle=\color[named]{Blue}\ttfamily,
296    %functionstyle=\color[named]{Blue}\ttfamily,
297    %typestyle=\color[named]{ForestGreen}\ttfamily,
298    stringstyle=\color[named]{Tan}\ttfamily,
299    morekeywords={,simulation,prop_dim,error_check,stochastic,%
300      globals,field,dimensions,lattice,domains,samples,vector,%
301      components,fourier_space,sequence,integrate,algorithm,%
302      interval,k_operators,constant,operator_names,vectors,%
303      output,filename,group,sampling,moments,benchmark,use_double,%
304      use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
305      default_value,argv,arg,iterations,cross_propagation,%
306      use_mpi,paths,seed,noises,author,description,name,type,%
307    }
308    frame=none,%
309    %framerule=2pt,%
310    backgroundcolor=\color{LightGrey}%
311    }
312    
313    % this implements producing nice code blocks
314    % it also saves time, typing and
315    % *should* reduce errors in the text by removing doubling up of code
316    \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
317    
318    % this implements nicely formatted shell code
319    \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
320    
321    % this implements nicely formatted Perl code
322    \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
323    
324    % this implements nicely formatted Python code
325    \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
326    
327    % this implements nicely formatted C++ code
328    \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
329    
330    % this implements nicely formatted matlab code
331    \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
332    
333    % this implements nicely formatted scilab code
334    \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
335    

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