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revision 2128 by lgraham, Thu Dec 4 03:48:22 2008 UTC revision 2573 by gross, Mon Aug 3 04:30:09 2009 UTC
# Line 1  Line 1 
1    
2  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3  %  %
4  % Copyright (c) 2003-2008 by University of Queensland  % Copyright (c) 2003-2009 by University of Queensland
5  % Earth Systems Science Computational Center (ESSCC)  % Earth Systems Science Computational Center (ESSCC)
6  % http://www.uq.edu.au/esscc  % http://www.uq.edu.au/esscc
7  %  %
# Line 19  Line 19 
19  \usepackage{xspace}   % handle spaces after commands more nicely  \usepackage{xspace}   % handle spaces after commands more nicely
20  % use the ams math stuff, as it makes the maths easier to code, and  % use the ams math stuff, as it makes the maths easier to code, and
21  % nicer output than the standard LaTeX stuff  % nicer output than the standard LaTeX stuff
22  \usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physicists  \usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physici
23                            % see http://www.ams.org/tex/amslatex.html                        % see http://www.ams.org/tex/amslatex.html
24  \usepackage{alltt}   % handy verbatim stuff  \usepackage{alltt}   % handy verbatim stuff
25    
26    
27  % define some handy commands for escript stuff  % define some handy commands for escript stuff
28  \newcommand{\LINUX}{{\it Linux}\xspace}  \newcommand{\LINUX}{{\it Linux}\xspace}
29  \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}  \newcommand{\WINDOWS}{{\it MS Windows}\xspace}
30    \newcommand{\PYTHON}{{\it python}\xspace}
31    % \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace}
32    \newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace}
33  \newcommand{\escript}{\module{esys.escript}\xspace}  \newcommand{\escript}{\module{esys.escript}\xspace}
34  \newcommand{\finley}{\module{esys.finley}\xspace}  \newcommand{\finley}{\module{esys.finley}\xspace}
35  \newcommand{\esys}{\module{esys}\xspace}  \newcommand{\esys}{\module{esys}\xspace}
# Line 34  Line 37 
37  \newcommand{\pycad}{\module{esys.pycad}\xspace}  \newcommand{\pycad}{\module{esys.pycad}\xspace}
38  \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}  \newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace}
39  \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}  \newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace}
40    \newcommand{\env}[1]{\textbf{\mbox{#1}}\index{Environment!#1}}
41    % \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\cite{MPI}\xspace}
42    % \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\cite{OPENMP}\xspace}
43    \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\xspace}
44    \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\xspace}
45  \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}  \newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace}
46  \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}  \newcommand{\LinearPDE}{\class{LinearPDE}\xspace}
 \newcommand{\timeseries}{\module{esys.timeseries}\xspace}  
47  \newcommand{\modelframe}{\module{esys.modelframe}\xspace}  \newcommand{\modelframe}{\module{esys.modelframe}\xspace}
48  \newcommand{\pdetools}{\module{esys.pdetools}\xspace}  \newcommand{\pdetools}{\module{esys.pdetools}\xspace}
49    \newcommand{\esysxml}{{\it esysxml}}
50    
51  \newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace}  \newcommand{\SolverOptions}{\class{SolverOptions}\xspace}
52  \newcommand{\Poisson}{\class{Poisson}\xspace}  \newcommand{\Poisson}{\class{Poisson}\xspace}
53  \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}  \newcommand{\Helmholtz}{\class{Helmholtz}\xspace}
54  \newcommand{\Lame}{\class{Lame}\xspace}  \newcommand{\Lame}{\class{Lame}\xspace}
# Line 56  Line 62 
62  \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}  \newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}}
63  \newcommand{\False}{\constant{False}\xspace}  \newcommand{\False}{\constant{False}\xspace}
64  \newcommand{\True}{\constant{True}\xspace}  \newcommand{\True}{\constant{True}\xspace}
65  \newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}}  \newcommand{\PCG}{\member{SolverOptions.PCG}\xspace\index{linear solver!PCG}\index{PCG}}
66  \newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}  \newcommand{\BiCGStab}{\member{SolverOptions.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}}
67  \newcommand{\Direct}{\constant{LinearPDE.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}  \newcommand{\Direct}{\member{SolverOptions.DIRECT}\xspace\index{linear solver!Direct}\index{Direct solver}}
68  \newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}  \newcommand{\GMRES}{\member{SolverOptions.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}}
69  \newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}  \newcommand{\PRESTWENTY}{\member{SolverOptions.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}}
70  \newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}  \newcommand{\JACOBI}{\member{SolverOptions.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}}
71  \newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}  \newcommand{\ILU}{\member{SolverOptions.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}}
72  \newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}  \newcommand{\ILUT}{\member{SolverOptions.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}}
73  \newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}  \newcommand{\RILU}{\member{SolverOptions.RILU}\xspace\index{preconditioner!RILU}\index{RILU}}
74  \newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace}  \newcommand{\LUMPING}{\member{SolverOptions.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}}
75  \newcommand{\MINIMUMFILLIN}{\constant{LinearPDE.MINIMUM\hackscore FILL\hackscore IN}\xspace\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}  \newcommand{\NOREORDERING}{\member{SolverOptions.NO\hackscore REORDERING}\xspace}
76  \newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}  \newcommand{\MINIMUMFILLIN}{\member{SolverOptions.MINIMUM\hackscore FILL\hackscore IN}\xspace
77    \index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}}
78    \newcommand{\NESTEDDESCTION}{\member{SolverOptions.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}}
79    \newcommand{\AMG}{\member{SolverOptions.AMG}\xspace\index{linear solver!AMG}\index{algebraic Multi-grid}\index{AMG}}
80    \newcommand{\GAUSSSEIDEL}{\member{SolverOptions.GAUSS\hackscore SEIDEL}\xspace\index{linear solver!Gauss-Seidel}\index{preconditioner!Gauss-Seidel}\index{Gauss-Seidel Scheme}}
81    \newcommand{\MKL}{\texttt{MKL}\xspace\index{packages!MKL}\index{MKL}}
82    \newcommand{\UMFPACK}{\texttt{UMFPACK}\xspace\index{packages!UMFPACK}\index{UMFPACK}}
83    \newcommand{\PASO}{\texttt{PASO}\xspace\index{packages!PASO}\index{PASO}}
84    
85  \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}  \newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace}
86  \newcommand{\Operator}{\class{Operator}\xspace}  \newcommand{\Operator}{\class{Operator}\xspace}
# Line 87  Line 100 
100  \newcommand{\Scalar}{{scalar \Data object}\xspace}  \newcommand{\Scalar}{{scalar \Data object}\xspace}
101  \newcommand{\DataSample}{{data sample}\index{data sample}\xspace}  \newcommand{\DataSample}{{data sample}\index{data sample}\xspace}
102  \newcommand{\DataSamplePoints}{{data sample points}\index{data sample!points}\xspace}  \newcommand{\DataSamplePoints}{{data sample points}\index{data sample!points}\xspace}
103  \newcommand{\numarray}{\module{numarray}\xspace}  \newcommand{\numpy}{\module{numpy}\xspace}
104  \newcommand{\numarrayNA}{\module{numarray}.\class{NumArray}\xspace}  \newcommand{\numpyNDA}{\module{numpy.\class{ndarray}\xspace}}
105    
106  \newcommand{\Shape}{shape\xspace\index{shape}}  \newcommand{\Shape}{shape\xspace\index{shape}}
107  \newcommand{\Rank}{rank\xspace\index{shape}}  \newcommand{\Rank}{rank\xspace\index{shape}}
108  \newcommand{\ExampleDirectory}{example directory\xspace}  \newcommand{\ExampleDirectory}{example directory\xspace}
109  \newcommand{\ReferenceGuide}{\url{http://shake200.esscc.uq.edu.au/esys/esys13/release/epydoc/index.html}\xspace}  \newcommand{\ReferenceGuide}{\url{http://esys.esscc.uq.edu.au/docs.html}\xspace}
110  \newcommand{\Point}{\class{Point} \xspace}  \newcommand{\Point}{\class{Point} \xspace}
111  \newcommand{\PropertySet}{\class{PropertySet} \xspace}  \newcommand{\PropertySet}{\class{PropertySet} \xspace}
112  \newcommand{\Design}{\class{Design} \xspace}  \newcommand{\Design}{\class{Design} \xspace}
# Line 227  Line 241 
241  % add the listings package to pretty print the code output  % add the listings package to pretty print the code output
242  \usepackage{listings}  \usepackage{listings}
243    
244    
245    %Some colour definitions added to keep pdflatex happy
246    %I make no claim that these values are particularly good
247    \definecolor{Purple}{rgb}{0.7, 0, 0.6}
248    \definecolor{Tan}{rgb}{0.5,0.5,0.5}
249    \definecolor{BrickRed}{rgb}{0.7, 0.2, 0.2}
250    \definecolor{Black}{rgb}{0, 0, 0}
251    
252    % All the \color{x} used to be \color[named]{x}
253    %end color defs
254    
255  \lstdefinestyle{myC++}{%  \lstdefinestyle{myC++}{%
256  %\lstset{%  %\lstset{%
257  language=C++,  language=C++,
258  showstringspaces=false,  showstringspaces=false,
259  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,
260  commentstyle=\color[named]{BrickRed}\ttfamily,  commentstyle=\color{BrickRed}\ttfamily,
261  keywordstyle=\color[named]{Purple}\ttfamily,  keywordstyle=\color{Purple}\ttfamily,
262  %identifierstyle=\color[named]{Blue}\ttfamily,  %identifierstyle=\color{Blue}\ttfamily,
263  %functionstyle=\color[named]{Blue}\ttfamily,  %functionstyle=\color{Blue}\ttfamily,
264  %typestyle=\color[named]{ForestGreen}\ttfamily,  %typestyle=\color{ForestGreen}\ttfamily,
265  stringstyle=\color[named]{Tan}\ttfamily,%  stringstyle=\color{Tan}\ttfamily,%
266  morekeywords={,complex,}%  morekeywords={,complex,}%
267  frame=none,%  frame=none,%
268  backgroundcolor=\color{LightGrey}%  backgroundcolor=\color{LightGrey}%
# Line 248  backgroundcolor=\color{LightGrey}% Line 273  backgroundcolor=\color{LightGrey}%
273  language=Matlab,  language=Matlab,
274  showstringspaces=false,  showstringspaces=false,
275  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,
276  commentstyle=\color[named]{BrickRed}\ttfamily,  commentstyle=\color{BrickRed}\ttfamily,
277  keywordstyle=\color[named]{Purple}\ttfamily,  keywordstyle=\color{Purple}\ttfamily,
278  %identifierstyle=\color[named]{Blue}\ttfamily,  %identifierstyle=\color{Blue}\ttfamily,
279  %functionstyle=\color[named]{Blue}\ttfamily,  %functionstyle=\color{Blue}\ttfamily,
280  %typestyle=\color[named]{ForestGreen}\ttfamily,  %typestyle=\color{ForestGreen}\ttfamily,
281  stringstyle=\color[named]{Tan}\ttfamily,%  stringstyle=\color{Tan}\ttfamily,%
282  frame=none,%  frame=none,%
283  backgroundcolor=\color{LightGrey}%  backgroundcolor=\color{LightGrey}%
284  }  }
# Line 263  backgroundcolor=\color{LightGrey}% Line 288  backgroundcolor=\color{LightGrey}%
288  language=Scilab,  language=Scilab,
289  showstringspaces=false,  showstringspaces=false,
290  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,
291  commentstyle=\color[named]{BrickRed}\ttfamily,  commentstyle=\color{BrickRed}\ttfamily,
292  keywordstyle=\color[named]{Purple}\ttfamily,  keywordstyle=\color{Purple}\ttfamily,
293  %identifierstyle=\color[named]{Blue}\ttfamily,  %identifierstyle=\color{Blue}\ttfamily,
294  %functionstyle=\color[named]{Blue}\ttfamily,  %functionstyle=\color{Blue}\ttfamily,
295  %typestyle=\color[named]{ForestGreen}\ttfamily,  %typestyle=\color{ForestGreen}\ttfamily,
296  stringstyle=\color[named]{Tan}\ttfamily,%  stringstyle=\color{Tan}\ttfamily,%
297  frame=none,%  frame=none,%
298  backgroundcolor=\color{LightGrey}%  backgroundcolor=\color{LightGrey}%
299  }  }
# Line 278  backgroundcolor=\color{LightGrey}% Line 303  backgroundcolor=\color{LightGrey}%
303  language=ksh,  language=ksh,
304  showstringspaces=false,  showstringspaces=false,
305  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,
306  commentstyle=\color[named]{Black}\ttfamily,  commentstyle=\color{Black}\ttfamily,
307  keywordstyle=\color[named]{Black}\ttfamily,  keywordstyle=\color{Black}\ttfamily,
308  %identifierstyle=\color[named]{Blue}\ttfamily,  %identifierstyle=\color{Blue}\ttfamily,
309  %functionstyle=\color[named]{Blue}\ttfamily,  %functionstyle=\color{Blue}\ttfamily,
310  %typestyle=\color[named]{ForestGreen}\ttfamily,  %typestyle=\color{ForestGreen}\ttfamily,
311  stringstyle=\color[named]{Black}\ttfamily,%  stringstyle=\color{Black}\ttfamily,%
312  frame=none,%  frame=none,%
313  backgroundcolor=\color{LightGrey}%  backgroundcolor=\color{LightGrey}%
314  }  }
# Line 293  backgroundcolor=\color{LightGrey}% Line 318  backgroundcolor=\color{LightGrey}%
318  language=python,  language=python,
319  showstringspaces=false,  showstringspaces=false,
320  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,
321  commentstyle=\color[named]{BrickRed}\ttfamily,  commentstyle=\color{BrickRed}\ttfamily,
322  keywordstyle=\color[named]{Purple}\ttfamily,  keywordstyle=\color{Purple}\ttfamily,
323  %identifierstyle=\color[named]{Blue}\ttfamily,  %identifierstyle=\color{Blue}\ttfamily,
324  %functionstyle=\color[named]{Blue}\ttfamily,  %functionstyle=\color{Blue}\ttfamily,
325  %typestyle=\color[named]{ForestGreen}\ttfamily,  %typestyle=\color{ForestGreen}\ttfamily,
326  stringstyle=\color[named]{Tan}\ttfamily,%  stringstyle=\color{Tan}\ttfamily,%
327  frame=none,%  frame=none,%
328  %backgroundcolor=\color{LightGrey}%  %backgroundcolor=\color{LightGrey}%
329  }  }
# Line 308  frame=none,% Line 333  frame=none,%
333  language=xml,  language=xml,
334  showstringspaces=false,  showstringspaces=false,
335  basicstyle=\small\ttfamily,  basicstyle=\small\ttfamily,
336  commentstyle=\color[named]{BrickRed}\ttfamily,  commentstyle=\color{BrickRed}\ttfamily,
337  keywordstyle=\color[named]{Purple}\ttfamily,  keywordstyle=\color{Purple}\ttfamily,
338  %identifierstyle=\color[named]{Blue}\ttfamily,  %identifierstyle=\color{Blue}\ttfamily,
339  %functionstyle=\color[named]{Blue}\ttfamily,  %functionstyle=\color{Blue}\ttfamily,
340  %typestyle=\color[named]{ForestGreen}\ttfamily,  %typestyle=\color{ForestGreen}\ttfamily,
341  stringstyle=\color[named]{Tan}\ttfamily,  stringstyle=\color{Tan}\ttfamily,
342  morekeywords={,simulation,prop_dim,error_check,stochastic,%  morekeywords={,simulation,prop_dim,error_check,stochastic,%
343    globals,field,dimensions,lattice,domains,samples,vector,%    globals,field,dimensions,lattice,domains,samples,vector,%
344    components,fourier_space,sequence,integrate,algorithm,%    components,fourier_space,sequence,integrate,algorithm,%
# Line 351  backgroundcolor=\color{LightGrey}% Line 376  backgroundcolor=\color{LightGrey}%
376  % this implements nicely formatted scilab code  % this implements nicely formatted scilab code
377  \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}  \lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{}
378    
379    %Ensures that latex doesn't have an error if we don't specify the version
380    \providecommand{\RepVersion}{Unknown\xspace}
381    % to set this value use:
382    % (pdf)latex '\newcommand{\RepVersion}{version\xspace}\input{guide.tex}'
383    % as your command-line

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