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Revision 2411 - (show annotations)
Fri May 8 03:13:15 2009 UTC (10 years, 3 months ago) by ahallam
Original Path: trunk/doc/cookbook/TEXT/cookbook_defs.tex
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Week 6 I think?? Started work on 2d wave solution, want to change from verlet according to lutz. Have semi finished heat diffusion but is ready for review and further modification in the future. Added new sections to first chapter, may or may not be needed but added as a reminder anyway.
1
2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3 %
4 % Copyright (c) 2003-2008 by University of Queensland
5 % 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 \usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physicists
23 % see http://www.ams.org/tex/amslatex.html
24 \usepackage{alltt} % handy verbatim stuff
25
26
27 %Tony's Commands
28 \newcommand{\editor}[1] {\textit{EDITORIAL: {#1}}}
29 %\newcommand{\eqref}[1] {(\ref{#1})}
30 \newcommand{\esc}{\module{escript}\xspace}
31
32 % % define some handy commands for escript stuff
33 % \newcommand{\LINUX}{{\it Linux}\xspace}
34 % \newcommand{\WINDOWS}{{\it MS Windows}\xspace}
35 % \newcommand{\PYTHON}{{\it python}\xspace}
36 % % \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
37 % \newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace}
38 % \newcommand{\escript}{\module{esys.escript}\xspace}
39 % \newcommand{\finley}{\module{esys.finley}\xspace}
40 % \newcommand{\esys}{\module{esys}\xspace}
41 % \newcommand{\pyvisi}{\module{esys.pyvisi}\xspace}
42 % \newcommand{\pycad}{\module{esys.pycad}\xspace}
43 % \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
44 % \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
45 % \newcommand{\env}[1]{\textbf{\mbox{#1}}\index{Environment!#1}}
46 % % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\cite{MPI}\xspace}
47 % % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\cite{OPENMP}\xspace}
48 % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\xspace}
49 % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\xspace}
50 % \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
51 % \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
52 % \newcommand{\timeseries}{\module{esys.timeseries}\xspace}
53 % \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
54 % \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
55 % \newcommand{\esysxml}{{\it esysxml}}
56 %
57 % \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}
58 % \newcommand{\Poisson}{\class{Poisson}\xspace}
59 % \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
60 % \newcommand{\Lame}{\class{Lame}\xspace}
61 % \newcommand{\Data}{\class{Data}\xspace}
62 % \newcommand{\EmptyData}{empty \class{Data}\index{empty Data}\xspace}
63 % \newcommand{\Domain}{\class{Domain}\xspace}
64 % %\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace}
65 % \newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}}
66 % \newcommand{\mayavi}{{\it mayavi}\index{visualization!mayavi}\index{mayavi}}
67 % \newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace}
68 % \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
69 % \newcommand{\False}{\constant{False}\xspace}
70 % \newcommand{\True}{\constant{True}\xspace}
71 % \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
72 % \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
73 % \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
74 % \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
75 % \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
76 % \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
77 % \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
78 % \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
79 % \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
80 % \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}
81 % \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
82 % \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
83 %
84 % \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
85 % \newcommand{\Operator}{\class{Operator}\xspace}
86 % \newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace}
87 % \newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace}
88 % \newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace}
89 % \newcommand{\Function}{general \class{FunctionSpace}\xspace}
90 % \newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace}
91 % \newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace}
92 % \newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace}
93 % \newcommand{\RankOne}{{rank-1 \Data object}\xspace}
94 % \newcommand{\RankTwo}{{rank-2 \Data object}\xspace}
95 % \newcommand{\RankThree}{{rank-3 \Data object}\xspace}
96 % \newcommand{\RankFour}{{rank-4 \Data object}\xspace}
97 % \newcommand{\Tensor}{{tensor \Data object}\xspace}
98 % \newcommand{\Vector}{{vector \Data object}\xspace}
99 % \newcommand{\Scalar}{{scalar \Data object}\xspace}
100 % \newcommand{\DataSample}{{data sample}\index{data sample}\xspace}
101 % \newcommand{\DataSamplePoints}{{data sample points}\index{data sample!points}\xspace}
102 % \newcommand{\numarray}{\module{numarray}\xspace}
103 % \newcommand{\numarrayNA}{\module{numarray}.\class{NumArray}\xspace}
104 % \newcommand{\Shape}{shape\xspace\index{shape}}
105 % \newcommand{\Rank}{rank\xspace\index{shape}}
106 % \newcommand{\ExampleDirectory}{example directory\xspace}
107 % \newcommand{\ReferenceGuide}{\url{http://shake200.esscc.uq.edu.au/esys/docs.html}\xspace}
108 % \newcommand{\Point}{\class{Point} \xspace}
109 % \newcommand{\PropertySet}{\class{PropertySet} \xspace}
110 % \newcommand{\Design}{\class{Design} \xspace}
111 % \newcommand{\TagMap}{\class{TagMap} \xspace}
112 % \newcommand{\ManifoldOneD}{\class{Manifold1D} \xspace}
113 % \newcommand{\ManifoldTwoD}{\class{Manifold2D} \xspace}
114 % \newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace}
115 %
116 % % default width for figures
117 % \newcommand{\figwidth}{100mm}
118 % % commands useful in cross-referencing
119 % \newcommand {\Ref}[1] {Reference~\cite{#1}}
120 % \newcommand {\Sec}[1] {Section~\ref{#1}}
121 % \newcommand {\App}[1] {Appendix~\ref{#1}}
122 % \newcommand {\Chap}[1] {Chapter~\ref{#1}}
123 % \newcommand {\etal} {\emph{~et~al.}}
124 % \newcommand {\fig}[1] {Figure~\ref{#1}}
125 % \newcommand {\eqn}[1] {Equation~(\ref{#1})}
126 % \newcommand {\tab}[1] {Table~\ref{#1}}
127 %
128 % % this stops one figure taking up a whole page and lets more text onto
129 % % the one page when a figure exists
130 % \renewcommand{\floatpagefraction}{0.8} % Default = 0.5
131 %
132 % % improved version of caption handling
133 % \usepackage{ccaption}
134 % \captionnamefont{\scshape}
135 % \captionstyle{}
136 % \makeatletter
137 % \renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:}
138 % \renewcommand{\@makecaption}[2]{%
139 % \vskip\abovecaptionskip
140 % \sbox\@tempboxa{#1: #2}%
141 % \ifdim \wd\@tempboxa >\hsize
142 % \def\baselinestretch{1}\@normalsize
143 % #1: #2\par
144 % \def\baselinestretch{1.5}\@normalsize
145 % \else
146 % \global \@minipagefalse
147 % \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
148 % \fi
149 % \vskip\belowcaptionskip}
150 % \makeatother
151 %
152 % % \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes
153 % %%% this code grabbed from the PyScript docs
154 % %%% pyscript.sourceforge.net
155 %
156 % % --------------------------------------------------------------
157 % % Code format within \Verb
158 % % --------------------------------------------------------------
159 %
160 % % \definecolor{pycolor}{rgb}{0,0.4,0}
161 %
162 % %% \DefineVerbatimEnvironment{python}{Verbatim}
163 % %% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor},
164 % %% formatcom=\color{pycolor}\small,fontshape=rm}
165 %
166 % %\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|}
167 %
168 % % \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm}
169 %
170 % %%% end of grabbed code
171 %
172 % % this is for when one uses pdflatex and therefore needs to load pdf
173 % % figures into \includegraphics
174 % \ifpdf
175 % \DeclareGraphicsExtensions{.pdf} % this command defined in graphicx
176 % \pdfcompresslevel=9 % 0: no compression, 9: highest compression
177 % % or, set compress_level 9 in file pdftex.cfg
178 % \else
179 % \DeclareGraphicsExtensions{.eps}
180 % \fi
181 %
182 % % defines the colour for the background of code examples
183 % \definecolor{LightGrey}{gray}{0.9}
184 %
185 % % add the listings package to pretty print the code output
186 % \usepackage{listings}
187 %
188 %
189 % %Some colour definitions added to keep pdflatex happy
190 % %I make no claim that these values are particularly good
191 % \definecolor{Purple}{rgb}{0.7, 0, 0.6}
192 % \definecolor{Tan}{rgb}{0.5,0.5,0.5}
193 % \definecolor{BrickRed}{rgb}{0.7, 0.2, 0.2}
194 %
195 % % All the \color{x} used to be \color[named]{x}
196 % %end color defs
197 %
198 % \lstdefinestyle{myC++}{%
199 % %\lstset{%
200 % language=C++,
201 % showstringspaces=false,
202 % basicstyle=\small\ttfamily,
203 % commentstyle=\color{BrickRed}\ttfamily,
204 % keywordstyle=\color{Purple}\ttfamily,
205 % %identifierstyle=\color{Blue}\ttfamily,
206 % %functionstyle=\color{Blue}\ttfamily,
207 % %typestyle=\color{ForestGreen}\ttfamily,
208 % stringstyle=\color{Tan}\ttfamily,%
209 % morekeywords={,complex,}%
210 % frame=none,%
211 % backgroundcolor=\color{LightGrey}%
212 % }
213 %
214 % \lstdefinestyle{myMatlab}{%
215 % %\lstset{%
216 % language=Matlab,
217 % showstringspaces=false,
218 % basicstyle=\small\ttfamily,
219 % commentstyle=\color{BrickRed}\ttfamily,
220 % keywordstyle=\color{Purple}\ttfamily,
221 % %identifierstyle=\color{Blue}\ttfamily,
222 % %functionstyle=\color{Blue}\ttfamily,
223 % %typestyle=\color{ForestGreen}\ttfamily,
224 % stringstyle=\color{Tan}\ttfamily,%
225 % frame=none,%
226 % backgroundcolor=\color{LightGrey}%
227 % }
228 %
229 % \lstdefinestyle{myScilab}{%
230 % %\lstset{%
231 % language=Scilab,
232 % showstringspaces=false,
233 % basicstyle=\small\ttfamily,
234 % commentstyle=\color{BrickRed}\ttfamily,
235 % keywordstyle=\color{Purple}\ttfamily,
236 % %identifierstyle=\color{Blue}\ttfamily,
237 % %functionstyle=\color{Blue}\ttfamily,
238 % %typestyle=\color{ForestGreen}\ttfamily,
239 % stringstyle=\color{Tan}\ttfamily,%
240 % frame=none,%
241 % backgroundcolor=\color{LightGrey}%
242 % }
243 %
244 % \lstdefinestyle{myShell}{%
245 % %\lstset{%
246 % language=ksh,
247 % showstringspaces=false,
248 % basicstyle=\small\ttfamily,
249 % commentstyle=\color{Black}\ttfamily,
250 % keywordstyle=\color{Black}\ttfamily,
251 % %identifierstyle=\color{Blue}\ttfamily,
252 % %functionstyle=\color{Blue}\ttfamily,
253 % %typestyle=\color{ForestGreen}\ttfamily,
254 % stringstyle=\color{Black}\ttfamily,%
255 % frame=none,%
256 % backgroundcolor=\color{LightGrey}%
257 % }
258 %
259 % \lstdefinestyle{myPython}{%
260 % %\lstset{%
261 % language=python,
262 % showstringspaces=false,
263 % basicstyle=\small\ttfamily,
264 % commentstyle=\color{BrickRed}\ttfamily,
265 % keywordstyle=\color{Purple}\ttfamily,
266 % %identifierstyle=\color{Blue}\ttfamily,
267 % %functionstyle=\color{Blue}\ttfamily,
268 % %typestyle=\color{ForestGreen}\ttfamily,
269 % stringstyle=\color{Tan}\ttfamily,%
270 % frame=none,%
271 % %backgroundcolor=\color{LightGrey}%
272 % }
273 %
274 % \lstdefinestyle{myhtml}{%
275 % %\lstset{%
276 % language=xml,
277 % showstringspaces=false,
278 % basicstyle=\small\ttfamily,
279 % commentstyle=\color{BrickRed}\ttfamily,
280 % keywordstyle=\color{Purple}\ttfamily,
281 % %identifierstyle=\color{Blue}\ttfamily,
282 % %functionstyle=\color{Blue}\ttfamily,
283 % %typestyle=\color{ForestGreen}\ttfamily,
284 % stringstyle=\color{Tan}\ttfamily,
285 % morekeywords={,simulation,prop_dim,error_check,stochastic,%
286 % globals,field,dimensions,lattice,domains,samples,vector,%
287 % components,fourier_space,sequence,integrate,algorithm,%
288 % interval,k_operators,constant,operator_names,vectors,%
289 % output,filename,group,sampling,moments,benchmark,use_double,%
290 % use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,%
291 % default_value,argv,arg,iterations,cross_propagation,%
292 % use_mpi,paths,seed,noises,author,description,name,type,%
293 % }
294 % frame=none,%
295 % %framerule=2pt,%
296 % backgroundcolor=\color{LightGrey}%
297 % }
298 %
299 % % this implements producing nice code blocks
300 % % it also saves time, typing and
301 % % *should* reduce errors in the text by removing doubling up of code
302 % \lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{}
303 %
304 % % this implements nicely formatted shell code
305 % \lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{}
306 %
307 % % this implements nicely formatted Perl code
308 % \lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{}
309 %
310 % % this implements nicely formatted Python code
311 % \lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{}
312 %
313 % % this implements nicely formatted C++ code
314 % \lstnewenvironment{CCode}{\lstset{style=myC++}}{}
315 %
316 % % this implements nicely formatted matlab code
317 % \lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{}
318 %
319 % % this implements nicely formatted scilab code
320 % \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
321 %
322 % %Ensures that latex doesn't have an error if we don't specify the version
323 % \providecommand{\RepVersion}{Unknown\xspace}
324 % % to set this value use:
325 % % (pdf)latex '\newcommand{\RepVersion}{version\xspace}\input{guide.tex}'
326 % % as your command-line

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