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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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% |
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% Copyright (c) 2003-2008 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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% |
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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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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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\usepackage{subfigure} |
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\usepackage{epsfig} |
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\usepackage{graphicx,color} |
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\usepackage{makeidx} % handle the index properly |
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\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 |
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% nicer output than the standard LaTeX stuff |
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\usepackage{amsmath,amsfonts,amssymb} % this is handy for mathematicians and physicists |
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% see http://www.ams.org/tex/amslatex.html |
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\usepackage{alltt} % handy verbatim stuff |
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|
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|
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% define some handy commands for escript stuff |
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\newcommand{\LINUX}{{\it Linux}\xspace} |
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\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} |
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\newcommand{\finley}{\module{esys.finley}\xspace} |
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\newcommand{\esys}{\module{esys}\xspace} |
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\newcommand{\pyvisi}{\module{esys.pyvisi}\xspace} |
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\newcommand{\pycad}{\module{esys.pycad}\xspace} |
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\newcommand{\gmsh}{\module{esys.pycad.gmsh}\xspace} |
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\newcommand{\gmshextern}{{\it Gmsh}\cite{GMSH}\index{Gmsh} \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} |
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\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} |
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\newcommand{\pdetools}{\module{esys.pdetools}\xspace} |
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\newcommand{\esysxml}{{\it esysxml}} |
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|
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\newcommand{\AdvectivePDE}{\class{AdvectivePDE}\xspace} |
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\newcommand{\Poisson}{\class{Poisson}\xspace} |
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\newcommand{\Helmholtz}{\class{Helmholtz}\xspace} |
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\newcommand{\Lame}{\class{Lame}\xspace} |
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\newcommand{\Data}{\class{Data}\xspace} |
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\newcommand{\EmptyData}{empty \class{Data}\index{empty Data}\xspace} |
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\newcommand{\Domain}{\class{Domain}\xspace} |
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%\newcommand{\VTK}{{\it vtk} \cite{VTK}\index{visualization!vtk} \xspace} |
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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}} |
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\newcommand{\False}{\constant{False}\xspace} |
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\newcommand{\True}{\constant{True}\xspace} |
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\newcommand{\PCG}{\constant{LinearPDE.PCG}\xspace\index{linear solver!PCG}\index{PCG}} |
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\newcommand{\BiCGStab}{\constant{LinearPDE.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}} |
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\newcommand{\GMRES}{\constant{LinearPDE.GMRES}\xspace\index{linear solver!GMRES}\index{GMRES}} |
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\newcommand{\PRESTWENTY}{\constant{LinearPDE.PRES20}\xspace\index{linear solver!PRES20}\index{PRES20}} |
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\newcommand{\JACOBI}{\constant{LinearPDE.JACOBI}\xspace\index{preconditioner!Jacobi}\index{Jacobi}} |
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\newcommand{\ILU}{\constant{LinearPDE.ILU0}\xspace\index{preconditioner!ILU0}\index{ILU0}} |
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\newcommand{\ILUT}{\constant{LinearPDE.ILUT}\xspace\index{preconditioner!ILUT}\index{ILUT}} |
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\newcommand{\LUMPING}{\constant{LinearPDE.LUMPING}\xspace\index{linear solver!lumping}\index{lumping}} |
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\newcommand{\NOREORDERING}{\constant{LinearPDE.NO\hackscore REORDERING}\xspace} |
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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}} |
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\newcommand{\NESTEDDESCTION}{\constant{LinearPDE.NESTED\hackscore DISSECTION}\xspace\index{linear solver!nested dissection ordering}\index{nested dissection}} |
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|
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\newcommand{\FunctionSpace}{\class{FunctionSpace}\xspace} |
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\newcommand{\Operator}{\class{Operator}\xspace} |
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\newcommand{\SolutionFS}{solution \class{FunctionSpace}\index{solution}\xspace} |
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\newcommand{\ReducedSolutionFS}{reduced solution \class{FunctionSpace}\index{solution!reduced}\xspace} |
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\newcommand{\FunctionOnBoundary}{boundary \class{FunctionSpace}\xspace} |
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\newcommand{\Function}{general \class{FunctionSpace}\xspace} |
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\newcommand{\FunctionOnContactZero}{contact \class{FunctionSpace} on side 0\xspace} |
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\newcommand{\FunctionOnContactOne}{contact \class{FunctionSpace} on side 1\xspace} |
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\newcommand{\ContinuousFunction}{continuous \class{FunctionSpace}\xspace} |
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\newcommand{\RankOne}{{rank-1 \Data object}\xspace} |
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\newcommand{\RankTwo}{{rank-2 \Data object}\xspace} |
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\newcommand{\RankThree}{{rank-3 \Data object}\xspace} |
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\newcommand{\RankFour}{{rank-4 \Data object}\xspace} |
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\newcommand{\Tensor}{{tensor \Data object}\xspace} |
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\newcommand{\Vector}{{vector \Data object}\xspace} |
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\newcommand{\Scalar}{{scalar \Data object}\xspace} |
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\newcommand{\DataSample}{{data sample}\index{data sample}\xspace} |
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\newcommand{\DataSamplePoints}{{data sample points}\index{data sample!points}\xspace} |
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\newcommand{\numarray}{\module{numarray}\xspace} |
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\newcommand{\numarrayNA}{\module{numarray}.\class{NumArray}\xspace} |
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\newcommand{\Shape}{shape\xspace\index{shape}} |
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\newcommand{\Rank}{rank\xspace\index{shape}} |
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\newcommand{\ExampleDirectory}{example directory\xspace} |
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\newcommand{\ReferenceGuide}{\url{http://shake200.esscc.uq.edu.au/esys/esys13/release/epydoc/index.html}\xspace} |
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\newcommand{\Point}{\class{Point} \xspace} |
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\newcommand{\PropertySet}{\class{PropertySet} \xspace} |
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\newcommand{\Design}{\class{Design} \xspace} |
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\newcommand{\TagMap}{\class{TagMap} \xspace} |
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\newcommand{\ManifoldOneD}{\class{Manifold1D} \xspace} |
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\newcommand{\ManifoldTwoD}{\class{Manifold2D} \xspace} |
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\newcommand{\ManifoldThreeD}{\class{Manifold3D} \xspace} |
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|
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% handy commands for pyvisi |
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\newcommand{\VTK}{{\it VTK} \xspace} |
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\newcommand{\VTKUrl}{\url{http://www.vtk.org/}\xspace} |
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\newcommand{\Scene}{\class{Scene}\xspace} |
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\newcommand{\Camera}{\class{Camera}\xspace} |
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\newcommand{\Light}{\class{Light}\xspace} |
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\newcommand{\DataCollector}{\class{DataCollector}\xspace} |
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\newcommand{\ImageReader}{\class{ImageReader}\xspace} |
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\newcommand{\TextTwoD}{\class{Text2D}\xspace} |
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\newcommand{\ActorTwoD}{\class{Actor2D}\xspace} |
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\newcommand{\ActorThreeD}{\class{Actor3D}\xspace} |
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\newcommand{\Transform}{\class{Transform}\xspace} |
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\newcommand{\Clipper}{\class{Clipper}\xspace} |
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\newcommand{\Map}{\class{Map}\xspace} |
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\newcommand{\MapOnPlaneCut}{\class{MapOnPlaneCut}\xspace} |
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\newcommand{\MapOnPlaneClip}{\class{MapOnPlaneClip}\xspace} |
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\newcommand{\MapOnScalarClip}{\class{MapOnScalarClip}\xspace} |
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\newcommand{\MapOnScalarClipWithRotation}{\class{MapOnScalarClipWithRotation}\xspace} |
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\newcommand{\GlyphThreeD}{\class{Glyph3D}\xspace} |
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\newcommand{\MaskPoints}{\class{MaskPoints}\xspace} |
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\newcommand{\Velocity}{\class{Velocity}\xspace} |
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\newcommand{\VelocityOnPlaneCut}{\class{VelocityOnPlaneCut}\xspace} |
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\newcommand{\VelocityOnPlaneClip}{\class{VelocityOnPlaneClip}\xspace} |
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\newcommand{\Sphere}{\class{Sphere}\xspace} |
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\newcommand{\TensorGlyph}{\class{TensorGlyph}\xspace} |
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\newcommand{\Ellipsoid}{\class{Ellipsoid}\xspace} |
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\newcommand{\EllipsoidOnPlaneCut}{\class{EllipsoidOnPlaneCut}\xspace} |
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\newcommand{\EllipsoidOnPlaneClip}{\class{EllipsoidOnPlaneClip}\xspace} |
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\newcommand{\ContourModule}{\class{ContourModule}\xspace} |
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\newcommand{\Contour}{\class{Contour}\xspace} |
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\newcommand{\ContourOnPlaneCut}{\class{ContourOnPlaneCut}\xspace} |
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\newcommand{\ContourOnPlaneClip}{\class{ContourOnPlaneClip}\xspace} |
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\newcommand{\PointSource}{\class{PointSource}\xspace} |
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\newcommand{\StreamLineModule}{\class{StreamLineModule}\xspace} |
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\newcommand{\Tube}{\class{Tube}\xspace} |
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\newcommand{\StreamLine}{\class{StreamLine}\xspace} |
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\newcommand{\Warp}{\class{Warp}\xspace} |
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\newcommand{\Carpet}{\class{Carpet}\xspace} |
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\newcommand{\PlaneSource}{\class{PlaneSource}\xspace} |
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\newcommand{\Image}{\class{Image}\xspace} |
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\newcommand{\Logo}{\class{Logo}\xspace} |
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\newcommand{\ImageReslice}{\class{ImageReslice}\xspace} |
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\newcommand{\Position}{\class{Position}\xspace} |
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\newcommand{\DataSetMapper}{\class{DataSetMapper}\xspace} |
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\newcommand{\Legend}{\class{Legend}\xspace} |
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\newcommand{\ScalarBar}{\class{ScalarBar}\xspace} |
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\newcommand{\Movie}{\class{Movie}\xspace} |
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\newcommand{\CubeSource}{\class{CubeSource}\xspace} |
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\newcommand{\Rectangle}{\class{Rectangle}\xspace} |
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\newcommand{\LocalPosition}{\class{LocalPosition}\xspace} |
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\newcommand{\GlobalPosition}{\class{GlobalPosition}\xspace} |
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\newcommand{\Rotation}{\class{Rotation}\xspace} |
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\newcommand{\thumbnailwidth}{50mm} |
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% default width for figures |
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\newcommand{\figwidth}{100mm} |
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% commands useful in cross-referencing |
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\newcommand {\Ref}[1] {Reference~\cite{#1}} |
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\newcommand {\Sec}[1] {Section~\ref{#1}} |
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\newcommand {\App}[1] {Appendix~\ref{#1}} |
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\newcommand {\Chap}[1] {Chapter~\ref{#1}} |
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\newcommand {\etal} {\emph{~et~al.}} |
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\newcommand {\fig}[1] {Figure~\ref{#1}} |
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\newcommand {\eqn}[1] {Equation~(\ref{#1})} |
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\newcommand {\tab}[1] {Table~\ref{#1}} |
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% this stops one figure taking up a whole page and lets more text onto |
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% the one page when a figure exists |
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\renewcommand{\floatpagefraction}{0.8} % Default = 0.5 |
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|
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% improved version of caption handling |
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\usepackage{ccaption} |
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\captionnamefont{\scshape} |
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\captionstyle{} |
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\makeatletter |
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\renewcommand{\fnum@figure}[1]{\quad\small\textsc{\figurename~\thefigure}:} |
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\renewcommand{\@makecaption}[2]{% |
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\vskip\abovecaptionskip |
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\sbox\@tempboxa{#1: #2}% |
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\ifdim \wd\@tempboxa >\hsize |
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\def\baselinestretch{1}\@normalsize |
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#1: #2\par |
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\def\baselinestretch{1.5}\@normalsize |
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\else |
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\global \@minipagefalse |
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\hb@xt@\hsize{\hfil\box\@tempboxa\hfil}% |
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\fi |
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\vskip\belowcaptionskip} |
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\makeatother |
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% \usepackage{fancyvrb} % fancy verbatim stuff. Needed so code below goes |
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%%% this code grabbed from the PyScript docs |
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%%% pyscript.sourceforge.net |
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|
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% -------------------------------------------------------------- |
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% Code format within \Verb |
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% -------------------------------------------------------------- |
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% \definecolor{pycolor}{rgb}{0,0.4,0} |
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%% \DefineVerbatimEnvironment{python}{Verbatim} |
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%% {frame=leftline,framerule=.5mm,rulecolor=\color{pycolor}, |
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%% formatcom=\color{pycolor}\small,fontshape=rm} |
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%\DefineShortVerb[formatcom=\color{dgreen}\small,fontshape=sl]{\|} |
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% \RecustomVerbatimCommand{\Verb}{Verb}{formatcom=\color{pycolor}\small,fontshape=rm} |
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|
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%%% end of grabbed code |
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|
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% this is for when one uses pdflatex and therefore needs to load pdf |
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% figures into \includegraphics |
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\ifpdf |
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\DeclareGraphicsExtensions{.pdf} % this command defined in graphicx |
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\pdfcompresslevel=9 % 0: no compression, 9: highest compression |
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% or, set compress_level 9 in file pdftex.cfg |
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\else |
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\DeclareGraphicsExtensions{.eps} |
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\fi |
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|
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% defines the colour for the background of code examples |
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\definecolor{LightGrey}{gray}{0.9} |
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|
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% add the listings package to pretty print the code output |
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\usepackage{listings} |
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|
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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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|
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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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|
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\lstdefinestyle{myC++}{% |
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%\lstset{% |
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language=C++, |
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showstringspaces=false, |
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basicstyle=\small\ttfamily, |
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commentstyle=\color{BrickRed}\ttfamily, |
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keywordstyle=\color{Purple}\ttfamily, |
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%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color{Tan}\ttfamily,% |
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morekeywords={,complex,}% |
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frame=none,% |
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backgroundcolor=\color{LightGrey}% |
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} |
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|
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\lstdefinestyle{myMatlab}{% |
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%\lstset{% |
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language=Matlab, |
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showstringspaces=false, |
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basicstyle=\small\ttfamily, |
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commentstyle=\color{BrickRed}\ttfamily, |
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keywordstyle=\color{Purple}\ttfamily, |
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%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color{Tan}\ttfamily,% |
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frame=none,% |
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backgroundcolor=\color{LightGrey}% |
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} |
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|
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\lstdefinestyle{myScilab}{% |
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%\lstset{% |
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language=Scilab, |
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showstringspaces=false, |
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basicstyle=\small\ttfamily, |
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commentstyle=\color{BrickRed}\ttfamily, |
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keywordstyle=\color{Purple}\ttfamily, |
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%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color{Tan}\ttfamily,% |
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frame=none,% |
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backgroundcolor=\color{LightGrey}% |
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} |
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|
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\lstdefinestyle{myShell}{% |
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%\lstset{% |
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language=ksh, |
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showstringspaces=false, |
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basicstyle=\small\ttfamily, |
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commentstyle=\color{Black}\ttfamily, |
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keywordstyle=\color{Black}\ttfamily, |
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%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color{Black}\ttfamily,% |
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frame=none,% |
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backgroundcolor=\color{LightGrey}% |
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} |
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|
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\lstdefinestyle{myPython}{% |
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%\lstset{% |
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language=python, |
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showstringspaces=false, |
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basicstyle=\small\ttfamily, |
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commentstyle=\color{BrickRed}\ttfamily, |
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keywordstyle=\color{Purple}\ttfamily, |
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%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color{Tan}\ttfamily,% |
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frame=none,% |
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%backgroundcolor=\color{LightGrey}% |
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} |
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|
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\lstdefinestyle{myhtml}{% |
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%\lstset{% |
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language=xml, |
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showstringspaces=false, |
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basicstyle=\small\ttfamily, |
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commentstyle=\color{BrickRed}\ttfamily, |
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keywordstyle=\color{Purple}\ttfamily, |
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%identifierstyle=\color{Blue}\ttfamily, |
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%functionstyle=\color{Blue}\ttfamily, |
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%typestyle=\color{ForestGreen}\ttfamily, |
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stringstyle=\color{Tan}\ttfamily, |
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morekeywords={,simulation,prop_dim,error_check,stochastic,% |
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globals,field,dimensions,lattice,domains,samples,vector,% |
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components,fourier_space,sequence,integrate,algorithm,% |
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interval,k_operators,constant,operator_names,vectors,% |
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output,filename,group,sampling,moments,benchmark,use_double,% |
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use_wisdom,use_prefs,binary_output,cycles,filter,post_propagation,% |
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default_value,argv,arg,iterations,cross_propagation,% |
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use_mpi,paths,seed,noises,author,description,name,type,% |
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} |
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frame=none,% |
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%framerule=2pt,% |
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backgroundcolor=\color{LightGrey}% |
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} |
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|
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% this implements producing nice code blocks |
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% it also saves time, typing and |
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% *should* reduce errors in the text by removing doubling up of code |
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\lstnewenvironment{xmdsCode}[1][]{\lstset{style=myhtml}\lstset{#1}}{} |
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|
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% this implements nicely formatted shell code |
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\lstnewenvironment{shellCode}[1][]{\lstset{style=myShell}\lstset{#1}}{} |
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|
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% this implements nicely formatted Perl code |
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\lstnewenvironment{perlCode}[1][]{\lstset{style=myPerl}\lstset{#1}}{} |
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|
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% this implements nicely formatted Python code |
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\lstnewenvironment{python}[1][]{\lstset{style=myPython}\lstset{#1}}{} |
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|
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% this implements nicely formatted C++ code |
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\lstnewenvironment{CCode}{\lstset{style=myC++}}{} |
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|
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% this implements nicely formatted matlab code |
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\lstnewenvironment{matlabCode}{\lstset{style=myMatlab}}{} |
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|
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% this implements nicely formatted scilab code |
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\lstnewenvironment{scilabCode}{\lstset{style=myScilab}}{} |
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|
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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 |
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