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% $Id$ |
% Copyright (c) 2003-2009 by University of Queensland |
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% Earth Systems Science Computational Center (ESSCC) |
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% http://www.uq.edu.au/esscc |
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% Copyright 2003-2007 by ACceSS MNRF |
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% Copyright 2007 by University of Queensland |
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% http://esscc.uq.edu.au |
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% Primary Business: Queensland, Australia |
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% Licensed under the Open Software License version 3.0 |
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% http://www.opensource.org/licenses/osl-3.0.php |
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
% Primary Business: Queensland, Australia |
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% Licensed under the Open Software License version 3.0 |
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% http://www.opensource.org/licenses/osl-3.0.php |
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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\usepackage{subfigure} |
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\usepackage{epsfig} |
\usepackage{epsfig} |
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\usepackage{graphicx,color} |
\usepackage{graphicx,color} |
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\usepackage{makeidx} % handle the index properly |
\usepackage{makeidx} % handle the index properly |
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\usepackage{xspace} % handle spaces after commands more nicely |
\usepackage{xspace} % handle spaces after commands more nicely |
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% 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 |
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% nicer output than the standard LaTeX stuff |
% nicer output than the standard LaTeX stuff |
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\usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physicists |
\usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physici |
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% see http://www.ams.org/tex/amslatex.html |
% see http://www.ams.org/tex/amslatex.html |
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\usepackage{alltt} % handy verbatim stuff |
\usepackage{alltt} % handy verbatim stuff |
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% define some handy commands for escript stuff |
% define some handy commands for escript stuff |
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\newcommand{\LINUX}{{\it Linux}\xspace} |
\newcommand{\LINUX}{{\it Linux}\xspace} |
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\newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace} |
\newcommand{\WINDOWS}{{\it MS Windows}\xspace} |
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\newcommand{\PYTHON}{{\it python}\xspace} |
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% \newcommand{\netCDF}{{\it netCDF}\cite{NETCDF}\index{netCDF} \xspace} |
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\newcommand{\netCDF}{{\it netCDF}\index{netCDF}\xspace} |
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\newcommand{\escript}{\module{esys.escript}\xspace} |
\newcommand{\escript}{\module{esys.escript}\xspace} |
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\newcommand{\finley}{\module{esys.finley}\xspace} |
\newcommand{\finley}{\module{esys.finley}\xspace} |
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\newcommand{\esys}{\module{esys}\xspace} |
\newcommand{\esys}{\module{esys}\xspace} |
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\newcommand{\bruce}{\module{esys.bruce}\xspace} |
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\newcommand{\pyvisi}{\module{esys.pyvisi}\xspace} |
\newcommand{\pyvisi}{\module{esys.pyvisi}\xspace} |
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\newcommand{\pycad}{\module{esys.pycad}\xspace} |
\newcommand{\pycad}{\module{esys.pycad}\xspace} |
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\newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace} |
\newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace} |
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\newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace} |
\newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \xspace} |
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\newcommand{\SCIPY}{{\it SciPy}\cite{SCIPY}\index{SciPy} \xspace} |
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\newcommand{\env}[1]{\textbf{\mbox{#1}}\index{Environment!#1}} |
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% \newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\cite{MPI}\xspace} |
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% \newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\cite{OPENMP}\xspace} |
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\newcommand{\MPI}{{\it MPI}\xspace\index{Message Passing Interface!MPI}\xspace} |
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\newcommand{\OPENMP}{{\it OpenMP}\xspace\index{OpenMP!threading}\xspace} |
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\newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace} |
\newcommand{\linearPDEs}{\module{esys.escript.linearPDEs}\xspace} |
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\newcommand{\LinearPDE}{\class{LinearPDE}\xspace} |
\newcommand{\LinearPDE}{\class{LinearPDE}\xspace} |
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\newcommand{\timeseries}{\module{esys.timeseries}\xspace} |
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\newcommand{\modelframe}{\module{esys.modelframe}\xspace} |
\newcommand{\modelframe}{\module{esys.modelframe}\xspace} |
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\newcommand{\pdetools}{\module{esys.pdetools}\xspace} |
\newcommand{\pdetools}{\module{esys.escript.pdetools}\xspace} |
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\newcommand{\esysxml}{{\it esysxml}} |
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\newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace} |
\newcommand{\SolverOptions}{\class{SolverOptions}\xspace} |
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\newcommand{\Poisson}{\class{Poisson}\xspace} |
\newcommand{\Poisson}{\class{Poisson}\xspace} |
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\newcommand{\Helmholtz}{\class{Helmholtz}\xspace} |
\newcommand{\Helmholtz}{\class{Helmholtz}\xspace} |
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\newcommand{\Lame}{\class{Lame}\xspace} |
\newcommand{\Lame}{\class{Lame}\xspace} |
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\newcommand{\Data}{\class{Data}\xspace} |
\newcommand{\Data}{\class{Data}\xspace} |
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\newcommand{\EmptyData}{empty \class{Data} \index{empty Data}\xspace} |
\newcommand{\EmptyData}{empty \class{Data}\index{empty Data}\xspace} |
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\newcommand{\Domain}{\class{Domain}\xspace} |
\newcommand{\Domain}{\class{Domain}\xspace} |
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%\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace} |
\newcommand{\gnuplot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}} |
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\newcommand{\GnuPlot}{{\it gnuplot} \cite{GNUPLOT}\index{visualization!gnuplot}\index{gnuplot}} |
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\newcommand{\mayavi}{{\it mayavi} \index{visualization!mayavi}\index{mayavi}} |
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\newcommand{\OpenDX}{{\it OpenDX} \cite{OPENDX}\xspace} |
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\newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}} |
\newcommand{\finleyelement}[1]{{\it #1}\index{finley!#1}} |
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\newcommand{\False}{\constant{False}\xspace} |
\newcommand{\False}{\constant{False}\xspace} |
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\newcommand{\True}{\constant{True}\xspace} |
\newcommand{\True}{\constant{True}\xspace} |
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\newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}} |
\newcommand{\PCG}{\member{SolverOptions.PCG}\xspace\index{linear solver!PCG}\index{PCG}} |
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\newcommand{\BiCGStab}{\constant{LinearPDE.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}} |
\newcommand{\BiCGStab}{\member{SolverOptions.BICGSTAB}\xspace\index{linear solver!BiCGStab}\index{BiCGStab}} |
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\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}} |
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\newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}} |
\newcommand{\GMRES}{\member{SolverOptions.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}} |
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\newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}} |
\newcommand{\PRESTWENTY}{\member{SolverOptions.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}} |
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\newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}} |
\newcommand{\JACOBI}{\member{SolverOptions.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}} |
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\newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}} |
\newcommand{\ILU}{\member{SolverOptions.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}} |
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\newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}} |
\newcommand{\ILUT}{\member{SolverOptions.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}} |
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\newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}} |
\newcommand{\RILU}{\member{SolverOptions.RILU}\xspace\index{preconditioner!RILU}\index{RILU}} |
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\newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace} |
\newcommand{\LUMPING}{\member{SolverOptions.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}} |
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\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} |
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\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 |
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\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering}} |
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\newcommand{\NESTEDDESCTION}{\member{SolverOptions.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}} |
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\newcommand{\AMG}{\member{SolverOptions.AMG}\xspace\index{linear solver!AMG}\index{algebraic Multi-grid}\index{AMG}} |
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\newcommand{\GAUSSSEIDEL}{\member{SolverOptions.GAUSS\hackscore SEIDEL}\xspace\index{linear solver!Gauss-Seidel}\index{preconditioner!Gauss-Seidel}\index{Gauss-Seidel Scheme}} |
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\newcommand{\MKL}{\texttt{MKL}\xspace\index{packages!MKL}\index{MKL}} |
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\newcommand{\UMFPACK}{\texttt{UMFPACK}\xspace\index{packages!UMFPACK}\index{UMFPACK}} |
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\newcommand{\PASO}{\texttt{PASO}\xspace\index{packages!PASO}\index{PASO}} |
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\newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace} |
\newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace} |
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\newcommand{\Operator}{\class{Operator}\xspace} |
\newcommand{\Operator}{\class{Operator}\xspace} |
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\newcommand{\Tensor}{{tensor \Data object}\xspace} |
\newcommand{\Tensor}{{tensor \Data object}\xspace} |
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\newcommand{\Vector}{{vector \Data object}\xspace} |
\newcommand{\Vector}{{vector \Data object}\xspace} |
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\newcommand{\Scalar}{{scalar \Data object}\xspace} |
\newcommand{\Scalar}{{scalar \Data object}\xspace} |
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\newcommand{\DataSample}{{data sample} \index{data sample}\xspace} |
\newcommand{\DataSample}{{data sample}\index{data sample}\xspace} |
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\newcommand{\DataSamplePoints}{{data sample points} \index{data sample!points}\xspace} |
\newcommand{\DataSamplePoints}{{data sample points}\index{data sample!points}\xspace} |
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\newcommand{\numarray}{\module{numarray}\xspace} |
\newcommand{\numpy}{\module{numpy}\xspace} |
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\newcommand{\numpyNDA}{\module{numpy.\class{ndarray}\xspace}} |
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\newcommand{\Shape}{shape\xspace\index{shape}} |
\newcommand{\Shape}{shape\xspace\index{shape}} |
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\newcommand{\Rank}{rank\xspace\index{shape}} |
\newcommand{\Rank}{rank\xspace\index{shape}} |
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\newcommand{\ExampleDirectory}{example directory\xspace} |
\newcommand{\ExampleDirectory}{example directory\xspace} |
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\newcommand{\ReferenceGuide}{\url{http://www.iservo.edu.au/esys/epydoc/index.html} \xspace} |
\newcommand{\ReferenceGuide}{\url{http://esys.esscc.uq.edu.au/docs.html}\xspace} |
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\newcommand{\Point}{\class{Point} \xspace} |
\newcommand{\Point}{\class{Point} \xspace} |
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\newcommand{\PropertySet}{\class{PropertySet} \xspace} |
\newcommand{\PropertySet}{\class{PropertySet} \xspace} |
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\newcommand{\Design}{\class{Design} \xspace} |
\newcommand{\Design}{\class{Design} \xspace} |
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\newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace} |
\newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace} |
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% handy commands for pyvisi |
% handy commands for pyvisi |
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\newcommand{\VTK}{{\it VTK} \xspace} |
\newcommand{\VTK}{{\it VTK}\index{visualization!VTK}\index{VTK}\xspace} |
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\newcommand{\VTKUrl}{\url{http://www.vtk.org/}\xspace} |
\newcommand{\MATPLOTLIB}{\module{matplotlib}\index{visualization!matplotlib}\index{matplotlib}\xspace} |
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\newcommand{\VTKUrl}{\url{http://www.vtk.org/}\index{visualization!VTK}\index{VTK}\xspace} |
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\newcommand{\VisIt}{{\it VisIt}\index{visualization!VisIt}\index{VisIt}\xspace} |
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\newcommand{\mayavi}{{\it mayavi}\index{visualization!mayavi}\index{mayavi}\xspace} |
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\newcommand{\OpenDX}{{\it OpenDX} \index{visualization!OpenDX}\index{OpenDX}\cite{OPENDX}\xspace} |
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\newcommand{\Scene}{\class{Scene}\xspace} |
\newcommand{\Scene}{\class{Scene}\xspace} |
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\newcommand{\Camera}{\class{Camera}\xspace} |
\newcommand{\Camera}{\class{Camera}\xspace} |
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\newcommand{\Light}{\class{Light}\xspace} |
\newcommand{\Light}{\class{Light}\xspace} |
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% add the listings package to pretty print the code output |
% add the listings package to pretty print the code output |
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\usepackage{listings} |
\usepackage{listings} |
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%Some colour definitions added to keep pdflatex happy |
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%I make no claim that these values are particularly good |
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\definecolor{Purple}{rgb}{0.7, 0, 0.6} |
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\definecolor{Tan}{rgb}{0.5,0.5,0.5} |
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\definecolor{BrickRed}{rgb}{0.7, 0.2, 0.2} |
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\definecolor{Black}{rgb}{0, 0, 0} |
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% All the \color{x} used to be \color[named]{x} |
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%end color defs |
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\lstdefinestyle{myC++}{% |
\lstdefinestyle{myC++}{% |
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%\lstset{% |
%\lstset{% |
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language=C++, |
language=C++, |
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showstringspaces=false, |
showstringspaces=false, |
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basicstyle=\small\ttfamily, |
basicstyle=\small\ttfamily, |
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commentstyle=\color[named]{BrickRed}\ttfamily, |
commentstyle=\color{BrickRed}\ttfamily, |
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keywordstyle=\color[named]{Purple}\ttfamily, |
keywordstyle=\color{Purple}\ttfamily, |
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%identifierstyle=\color[named]{Blue}\ttfamily, |
%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color[named]{Blue}\ttfamily, |
%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color[named]{ForestGreen}\ttfamily, |
%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color[named]{Tan}\ttfamily,% |
stringstyle=\color{Tan}\ttfamily,% |
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morekeywords={,complex,}% |
morekeywords={,complex,}% |
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frame=none,% |
frame=none,% |
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backgroundcolor=\color{LightGrey}% |
backgroundcolor=\color{LightGrey}% |
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language=Matlab, |
language=Matlab, |
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showstringspaces=false, |
showstringspaces=false, |
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basicstyle=\small\ttfamily, |
basicstyle=\small\ttfamily, |
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commentstyle=\color[named]{BrickRed}\ttfamily, |
commentstyle=\color{BrickRed}\ttfamily, |
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keywordstyle=\color[named]{Purple}\ttfamily, |
keywordstyle=\color{Purple}\ttfamily, |
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%identifierstyle=\color[named]{Blue}\ttfamily, |
%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color[named]{Blue}\ttfamily, |
%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color[named]{ForestGreen}\ttfamily, |
%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color[named]{Tan}\ttfamily,% |
stringstyle=\color{Tan}\ttfamily,% |
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frame=none,% |
frame=none,% |
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backgroundcolor=\color{LightGrey}% |
backgroundcolor=\color{LightGrey}% |
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} |
} |
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language=Scilab, |
language=Scilab, |
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showstringspaces=false, |
showstringspaces=false, |
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basicstyle=\small\ttfamily, |
basicstyle=\small\ttfamily, |
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commentstyle=\color[named]{BrickRed}\ttfamily, |
commentstyle=\color{BrickRed}\ttfamily, |
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keywordstyle=\color[named]{Purple}\ttfamily, |
keywordstyle=\color{Purple}\ttfamily, |
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%identifierstyle=\color[named]{Blue}\ttfamily, |
%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color[named]{Blue}\ttfamily, |
%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color[named]{ForestGreen}\ttfamily, |
%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color[named]{Tan}\ttfamily,% |
stringstyle=\color{Tan}\ttfamily,% |
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frame=none,% |
frame=none,% |
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backgroundcolor=\color{LightGrey}% |
backgroundcolor=\color{LightGrey}% |
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} |
} |
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language=ksh, |
language=ksh, |
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showstringspaces=false, |
showstringspaces=false, |
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basicstyle=\small\ttfamily, |
basicstyle=\small\ttfamily, |
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commentstyle=\color[named]{Black}\ttfamily, |
commentstyle=\color{Black}\ttfamily, |
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keywordstyle=\color[named]{Black}\ttfamily, |
keywordstyle=\color{Black}\ttfamily, |
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%identifierstyle=\color[named]{Blue}\ttfamily, |
%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color[named]{Blue}\ttfamily, |
%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color[named]{ForestGreen}\ttfamily, |
%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color[named]{Black}\ttfamily,% |
stringstyle=\color{Black}\ttfamily,% |
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frame=none,% |
frame=none,% |
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backgroundcolor=\color{LightGrey}% |
backgroundcolor=\color{LightGrey}% |
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} |
} |
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language=python, |
language=python, |
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showstringspaces=false, |
showstringspaces=false, |
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basicstyle=\small\ttfamily, |
basicstyle=\small\ttfamily, |
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commentstyle=\color[named]{BrickRed}\ttfamily, |
commentstyle=\color{BrickRed}\ttfamily, |
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keywordstyle=\color[named]{Purple}\ttfamily, |
keywordstyle=\color{Purple}\ttfamily, |
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%identifierstyle=\color[named]{Blue}\ttfamily, |
%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color[named]{Blue}\ttfamily, |
%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color[named]{ForestGreen}\ttfamily, |
%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color[named]{Tan}\ttfamily,% |
stringstyle=\color{Tan}\ttfamily,% |
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frame=none,% |
frame=none,% |
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%backgroundcolor=\color{LightGrey}% |
%backgroundcolor=\color{LightGrey}% |
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} |
} |
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language=xml, |
language=xml, |
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showstringspaces=false, |
showstringspaces=false, |
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basicstyle=\small\ttfamily, |
basicstyle=\small\ttfamily, |
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commentstyle=\color[named]{BrickRed}\ttfamily, |
commentstyle=\color{BrickRed}\ttfamily, |
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keywordstyle=\color[named]{Purple}\ttfamily, |
keywordstyle=\color{Purple}\ttfamily, |
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%identifierstyle=\color[named]{Blue}\ttfamily, |
%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color[named]{Blue}\ttfamily, |
%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color[named]{ForestGreen}\ttfamily, |
%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color[named]{Tan}\ttfamily, |
stringstyle=\color{Tan}\ttfamily, |
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morekeywords={,simulation,prop_dim,error_check,stochastic,% |
morekeywords={,simulation,prop_dim,error_check,stochastic,% |
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globals,field,dimensions,lattice,domains,samples,vector,% |
globals,field,dimensions,lattice,domains,samples,vector,% |
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components,fourier_space,sequence,integrate,algorithm,% |
components,fourier_space,sequence,integrate,algorithm,% |
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% this implements nicely formatted scilab code |
% this implements nicely formatted scilab code |
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\lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{} |
\lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{} |
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%Ensures that latex doesn't have an error if we don't specify the version |
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\providecommand{\RepVersion}{Unknown\xspace} |
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% to set this value use: |
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% (pdf)latex '\newcommand{\RepVersion}{version\xspace}\input{guide.tex}' |
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% as your command-line |