/[escript]/trunk/doc/cookbook/cookbook_defs.tex
ViewVC logotype

Annotation of /trunk/doc/cookbook/cookbook_defs.tex

Parent Directory Parent Directory | Revision Log Revision Log


Revision 2606 - (hide annotations)
Thu Aug 13 04:32:23 2009 UTC (10 years, 1 month ago) by ahallam
Original Path: trunk/doc/cookbook/TEXT/cookbook_defs.tex
File MIME type: application/x-tex
File size: 14542 byte(s)
Updates to first chapter in cookbook -> approaching completion.
New figures added for model descriptions.
Scripts updated to use pylab/matplotlib and movie making scripts added for *.avi creation.
Still to finalise in chapter 1
- twodheatdiff model of intrusion
	-contouring

- heat refraction scripts and begin cookbook sections
	- pycad discussion
	- steady state pde discussion
	- quiver plot discussion
1 ahallam 2411
2     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3     %
4 jfenwick 2548 % Copyright (c) 2003-2009 by University of Queensland
5 ahallam 2411 % Earth Systems Science Computational Center (ESSCC)
6     % http://www.uq.edu.au/esscc
7     %
8     % Primary Business: Queensland, Australia
9     % Licensed under the Open Software License version 3.0
10     % http://www.opensource.org/licenses/osl-3.0.php
11     %
12     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
13    
14    
15     \usepackage{subfigure}
16     \usepackage{epsfig}
17     \usepackage{graphicx,color}
18     \usepackage{makeidx} % handle the index properly
19     \usepackage{xspace} % handle spaces after commands more nicely
20     % use the ams math stuff, as it makes the maths easier to code, and
21     % nicer output than the standard LaTeX stuff
22 gross 2477 \usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physici % see http://www.ams.org/tex/amslatex.html
23 ahallam 2411 \usepackage{alltt} % handy verbatim stuff
24 ahallam 2495 \usepackage{textcomp}
25 ahallam 2411
26     %Tony's Commands
27     \newcommand{\editor}[1] {\textit{EDITORIAL: {#1}}}
28     %\newcommand{\eqref}[1] {(\ref{#1})}
29     \newcommand{\esc}{\module{escript}\xspace}
30 ahallam 2426 \newcommand{\fileex}[1]{\module{\textbackslash examples\textbackslash {#1}}\xspace}
31 gross 2477 \newcommand{\TODO}[1]{\textbf{TODO}:\xspace\textit{#1} }
32     \newcommand{\ESCRIPT}{\textit{escript}\xspace}
33     \newcommand{\ESYS}{\textit{esys}\xspace}
34     \newcommand{\FINLEY}{\textit{finley}\xspace}
35 ahallam 2411
36 ahallam 2495 %referencing
37     \newcommand{\reffig}[1]{(Figure \ref{#1})}
38     \newcommand{\refeq}[1]{equation \ref{#1}}
39     \newcommand{\refEq}[1]{Equation \ref{#1}}
40    
41     %modules
42     \newcommand{\modesys}{\module{esys}\xspace}
43     \newcommand{\modescript}{\module{esys.escript}\xspace}
44     \newcommand{\modfinley}{\module{esys.finley}\xspace}
45     \newcommand{\modpycad}{\module{esys.pycad}\xspace}
46     \newcommand{\modvtk}{\module{vtk}\xspace}
47     \newcommand{\modnumpy}{\module{numpy}\xspace}
48     \newcommand{\modmpl}{\module{matplotlib}\xspace}
49 ahallam 2589 \newcommand{\pycad}{\module{esys.pycad}\xspace}
50     \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
51 ahallam 2606 \newcommand{\pylab}{\module{pylab}\xspace}
52     \newcommand{\mpl}{\module{matplotlib}\xspace}
53     \newcommand{\numpy}{\module{numpy}\xspace}
54 ahallam 2495
55 ahallam 2411 % % define some handy commands for escript stuff
56     % \newcommand{\LINUX}{{\it Linux}\xspace}
57     % \newcommand{\WINDOWS}{{\it MS Windows}\xspace}
58     % \newcommand{\PYTHON}{{\it python}\xspace}
59     % % \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
60     % \newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace}
61     % \newcommand{\escript}{\module{esys.escript}\xspace}
62     % \newcommand{\finley}{\module{esys.finley}\xspace}
63     % \newcommand{\esys}{\module{esys}\xspace}
64     % \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
65     % \newcommand{\pycad}{\module{esys.pycad}\xspace}
66     % \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
67     % \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
68     % \newcommand{\env}[1]{\textbf{\mbox{#1}}\index{Environment!#1}}
69     % % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\cite{MPI}\xspace}
70     % % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\cite{OPENMP}\xspace}
71     % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\xspace}
72     % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\xspace}
73     % \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
74     % \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
75     % \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
76     % \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
77     % \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
78     % \newcommand{\esysxml}{{\it esysxml}}
79     %
80     % \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
81     % \newcommand{\Poisson}{\class{Poisson}\xspace}
82     % \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
83     % \newcommand{\Lame}{\class{Lame}\xspace}
84     % \newcommand{\Data}{\class{Data}\xspace}
85     % \newcommand{\EmptyData}{empty \class{Data}\index{empty Data}\xspace}
86     % \newcommand{\Domain}{\class{Domain}\xspace}
87     % %\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
88     % \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
89     % \newcommand{\mayavi}{{\it mayavi}\index{visualization!mayavi}\index{mayavi}}
90     % \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
91     % \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
92     % \newcommand{\False}{\constant{False}\xspace}
93     % \newcommand{\True}{\constant{True}\xspace}
94     % \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
95     % \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
96     % \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
97     % \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
98     % \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
99     % \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
100     % \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
101     % \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
102     % \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
103     % \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}
104     % \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
105     % \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
106     %
107     % \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
108     % \newcommand{\Operator}{\class{Operator}\xspace}
109     % \newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace}
110     % \newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace}
111     % \newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace}
112     % \newcommand{\Function}{general \class{FunctionSpace}\xspace}
113     % \newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace}
114     % \newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace}
115     % \newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace}
116     % \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
117     % \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
118     % \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
119     % \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
120     % \newcommand{\Tensor}{{tensor \Data object}\xspace}
121     % \newcommand{\Vector}{{vector \Data object}\xspace}
122     % \newcommand{\Scalar}{{scalar \Data object}\xspace}
123     % \newcommand{\DataSample}{{data sample}\index{data sample}\xspace}
124     % \newcommand{\DataSamplePoints}{{data sample points}\index{data sample!points}\xspace}
125     % \newcommand{\numarray}{\module{numarray}\xspace}
126     % \newcommand{\numarrayNA}{\module{numarray}.\class{NumArray}\xspace}
127     % \newcommand{\Shape}{shape\xspace\index{shape}}
128     % \newcommand{\Rank}{rank\xspace\index{shape}}
129     % \newcommand{\ExampleDirectory}{example directory\xspace}
130     % \newcommand{\ReferenceGuide}{\url{http://shake200.esscc.uq.edu.au/esys/docs.html}\xspace}
131     % \newcommand{\Point}{\class{Point} \xspace}
132     % \newcommand{\PropertySet}{\class{PropertySet} \xspace}
133     % \newcommand{\Design}{\class{Design} \xspace}
134     % \newcommand{\TagMap}{\class{TagMap} \xspace}
135     % \newcommand{\ManifoldOneD}{\class{Manifold1D} \xspace}
136     % \newcommand{\ManifoldTwoD}{\class{Manifold2D} \xspace}
137     % \newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace}
138     %
139     % % default width for figures
140     % \newcommand{\figwidth}{100mm}
141     % % commands useful in cross-referencing
142     % \newcommand {\Ref}[1] {Reference~\cite{#1}}
143     % \newcommand {\Sec}[1] {Section~\ref{#1}}
144     % \newcommand {\App}[1] {Appendix~\ref{#1}}
145     % \newcommand {\Chap}[1] {Chapter~\ref{#1}}
146     % \newcommand {\etal} {\emph{~et~al.}}
147     % \newcommand {\fig}[1] {Figure~\ref{#1}}
148     % \newcommand {\eqn}[1] {Equation~(\ref{#1})}
149     % \newcommand {\tab}[1] {Table~\ref{#1}}
150     %
151     % % this stops one figure taking up a whole page and lets more text onto
152     % % the one page when a figure exists
153     % \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
154     %
155     % % improved version of caption handling
156     % \usepackage{ccaption}
157     % \captionnamefont{\scshape}
158     % \captionstyle{}
159     % \makeatletter
160     % \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
161     % \renewcommand{\@makecaption}[2]{%
162     % \vskip\abovecaptionskip
163     % \sbox\@tempboxa{#1: #2}%
164     % \ifdim \wd\@tempboxa >\hsize
165     % \def\baselinestretch{1}\@normalsize
166     % #1: #2\par
167     % \def\baselinestretch{1.5}\@normalsize
168     % \else
169     % \global \@minipagefalse
170     % \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
171     % \fi
172     % \vskip\belowcaptionskip}
173     % \makeatother
174     %
175     % % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
176     % %%% this code grabbed from the PyScript docs
177     % %%% pyscript.sourceforge.net
178 ahallam 2426
179     % --------------------------------------------------------------
180     % Code format within \Verb
181     % --------------------------------------------------------------
182    
183     % \definecolor{pycolor}{rgb}{0,0.4,0}
184    
185     %% \DefineVerbatimEnvironment{python}{Verbatim}
186     %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
187     %% formatcom=\color{pycolor}\small,fontshape=rm}
188    
189     %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
190    
191     % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
192    
193     %%% end of grabbed code
194    
195     % this is for when one uses pdflatex and therefore needs to load pdf
196     % figures into \includegraphics
197 ahallam 2411 % \ifpdf
198     % \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
199     % \pdfcompresslevel=9 % 0: no compression, 9: highest compression
200     % % or, set compress_level 9 in file pdftex.cfg
201     % \else
202     % \DeclareGraphicsExtensions{.eps}
203     % \fi
204     %
205     % % defines the colour for the background of code examples
206     % \definecolor{LightGrey}{gray}{0.9}
207     %
208     % % add the listings package to pretty print the code output
209     % \usepackage{listings}
210     %
211     %
212     % %Some colour definitions added to keep pdflatex happy
213     % %I make no claim that these values are particularly good
214     % \definecolor{Purple}{rgb}{0.7, 0, 0.6}
215     % \definecolor{Tan}{rgb}{0.5,0.5,0.5}
216     % \definecolor{BrickRed}{rgb}{0.7, 0.2, 0.2}
217     %
218     % % All the \color{x} used to be \color[named]{x}
219     % %end color defs
220     %
221     % \lstdefinestyle{myC++}{%
222     % %\lstset{%
223     % language=C++,
224     % showstringspaces=false,
225     % basicstyle=\small\ttfamily,
226     % commentstyle=\color{BrickRed}\ttfamily,
227     % keywordstyle=\color{Purple}\ttfamily,
228     % %identifierstyle=\color{Blue}\ttfamily,
229     % %functionstyle=\color{Blue}\ttfamily,
230     % %typestyle=\color{ForestGreen}\ttfamily,
231     % stringstyle=\color{Tan}\ttfamily,%
232     % morekeywords={,complex,}%
233     % frame=none,%
234     % backgroundcolor=\color{LightGrey}%
235     % }
236     %
237     % \lstdefinestyle{myMatlab}{%
238     % %\lstset{%
239     % language=Matlab,
240     % showstringspaces=false,
241     % basicstyle=\small\ttfamily,
242     % commentstyle=\color{BrickRed}\ttfamily,
243     % keywordstyle=\color{Purple}\ttfamily,
244     % %identifierstyle=\color{Blue}\ttfamily,
245     % %functionstyle=\color{Blue}\ttfamily,
246     % %typestyle=\color{ForestGreen}\ttfamily,
247     % stringstyle=\color{Tan}\ttfamily,%
248     % frame=none,%
249     % backgroundcolor=\color{LightGrey}%
250     % }
251     %
252     % \lstdefinestyle{myScilab}{%
253     % %\lstset{%
254     % language=Scilab,
255     % showstringspaces=false,
256     % basicstyle=\small\ttfamily,
257     % commentstyle=\color{BrickRed}\ttfamily,
258     % keywordstyle=\color{Purple}\ttfamily,
259     % %identifierstyle=\color{Blue}\ttfamily,
260     % %functionstyle=\color{Blue}\ttfamily,
261     % %typestyle=\color{ForestGreen}\ttfamily,
262     % stringstyle=\color{Tan}\ttfamily,%
263     % frame=none,%
264     % backgroundcolor=\color{LightGrey}%
265     % }
266     %
267     % \lstdefinestyle{myShell}{%
268     % %\lstset{%
269     % language=ksh,
270     % showstringspaces=false,
271     % basicstyle=\small\ttfamily,
272     % commentstyle=\color{Black}\ttfamily,
273     % keywordstyle=\color{Black}\ttfamily,
274     % %identifierstyle=\color{Blue}\ttfamily,
275     % %functionstyle=\color{Blue}\ttfamily,
276     % %typestyle=\color{ForestGreen}\ttfamily,
277     % stringstyle=\color{Black}\ttfamily,%
278     % frame=none,%
279     % backgroundcolor=\color{LightGrey}%
280     % }
281     %
282     % \lstdefinestyle{myPython}{%
283     % %\lstset{%
284     % language=python,
285     % showstringspaces=false,
286     % basicstyle=\small\ttfamily,
287     % commentstyle=\color{BrickRed}\ttfamily,
288     % keywordstyle=\color{Purple}\ttfamily,
289     % %identifierstyle=\color{Blue}\ttfamily,
290     % %functionstyle=\color{Blue}\ttfamily,
291     % %typestyle=\color{ForestGreen}\ttfamily,
292     % stringstyle=\color{Tan}\ttfamily,%
293     % frame=none,%
294     % %backgroundcolor=\color{LightGrey}%
295     % }
296     %
297     % \lstdefinestyle{myhtml}{%
298     % %\lstset{%
299     % language=xml,
300     % showstringspaces=false,
301     % basicstyle=\small\ttfamily,
302     % commentstyle=\color{BrickRed}\ttfamily,
303     % keywordstyle=\color{Purple}\ttfamily,
304     % %identifierstyle=\color{Blue}\ttfamily,
305     % %functionstyle=\color{Blue}\ttfamily,
306     % %typestyle=\color{ForestGreen}\ttfamily,
307     % stringstyle=\color{Tan}\ttfamily,
308     % morekeywords={,simulation,prop_dim,error_check,stochastic,%
309     % globals,field,dimensions,lattice,domains,samples,vector,%
310     % components,fourier_space,sequence,integrate,algorithm,%
311     % interval,k_operators,constant,operator_names,vectors,%
312     % output,filename,group,sampling,moments,benchmark,use_double,%
313     % use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
314     % default_value,argv,arg,iterations,cross_propagation,%
315     % use_mpi,paths,seed,noises,author,description,name,type,%
316     % }
317     % frame=none,%
318     % %framerule=2pt,%
319     % backgroundcolor=\color{LightGrey}%
320     % }
321     %
322     % % this implements producing nice code blocks
323     % % it also saves time, typing and
324     % % *should* reduce errors in the text by removing doubling up of code
325     % \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
326     %
327     % % this implements nicely formatted shell code
328     % \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
329     %
330     % % this implements nicely formatted Perl code
331     % \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
332     %
333     % % this implements nicely formatted Python code
334     % \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
335     %
336     % % this implements nicely formatted C++ code
337     % \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
338     %
339     % % this implements nicely formatted matlab code
340     % \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
341     %
342     % % this implements nicely formatted scilab code
343     % \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
344     %
345     % %Ensures that latex doesn't have an error if we don't specify the version
346     % \providecommand{\RepVersion}{Unknown\xspace}
347 ahallam 2426 % to set this value use:
348     % (pdf)latex '\newcommand{\RepVersion}{version\xspace}\input{guide.tex}'
349     % as your command-line

  ViewVC Help
Powered by ViewVC 1.1.26