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Commit d09fb5ac authored by Alessandro Bolis's avatar Alessandro Bolis
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Removed obsolete files from the docs/ folder to speed up check-out. 

The files are stored on the web page server.


git-svn-id: https://gforge.sci.utah.edu/svn/nektar/trunk@4069 305cdda6-5ce1-45b3-a98d-dfc68c8b3305
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<p><a href="downloads.html" id="menu_Downloads">Downloads</a></p>
<p><a href="compile.html" id="menu_Compile">Compilation Instructions</a></p>
<p><a href="usage.html" id="menu_Usage">Example Usage</a></p>
<p><a href="educational_material.html" id="menu_EducationalMaterial">Educational
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<p><a href="acknowledgments.html" id="menu_Acknowledgments">Acknowledgments</a></p>
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<h1>Acknowledgments</h1>
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<hr/>
<!-- InstanceBeginEditable name="BodyText" --><p>Air Force Office of Scientific Research (USA)</p>
<p>Army Research Office (USA)</p>
<p>British Heart Foundation (UK)</p>
<p>Engineering and Physical Sciences Research Council (UK)</p>
<p>National Science Foundation (USA)</p>
<p>National Institutes of Health (USA)</p>
<p>Royal Academy of Engineering (UK)</p>
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<title>Nektar++ - Compilation Instructions</title>
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<body class="twoColHybLt">
<div id="container">
<div id="sidebar1">
<h3 style="text-align: center;"><a href="index.html" id="menu_Nektar"><img src="images/nektar.png" alt="Nektar++" width="155" height="38" /></a></h3>
<p><a href="downloads.html" id="menu_Downloads">Downloads</a></p>
<p><a href="compile.html" id="menu_Compile">Compilation Instructions</a>
<br/>
&nbsp;&nbsp;&nbsp;<a href="compile_linux.html" id="menu_CompileLinux">Linux</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_windows.html" id="menu_CompileWindows">Windows</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_osx.html" id="menu_CompileOSX">Mac OS X</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_unit_tests.html" id="menu_CompileUnitTests">Unit Tests</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_regression_tests.html" id="menu_CompileRegressionTests">Regression Tests</a><br/>
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<p><a href="acknowledgments.html" id="menu_Acknowledgments">Acknowledgments</a></p>
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Nektar++ is designed to be supported across a range of platforms and
architectures using the CMake build system. In addition to the Nektar++
code package, a number of third party applications and libraries may be
necessary to perform the build process. Instructions on configuring and
compiling the Nektar++ libraries on various platforms are given below.
<p><a href="compile_linux.html">Linux</a> (using GCC 4.1+)</p>
<p><a href="compile_windows.html">Windows</a> (using Visual Studio 2008)</p>
<p><a href="compile_osx.html">Mac OS X</a> (using GCC or Xcode)</p>
<br>
<h2>Validating the build</h2>
To ensure the validity and resilience of the code, two test mechansims are
provided to allow the user to quickly establish the correctness of their
build. The <em>Unit Tests</em> test basic low-level operations, while the
<em>Regression Tests</em> check the accuracy of the spectral/hp element
formulation ranging from standard region projections up to full
incompressible Navier-Stokes solutions.
<p><a href="compile_unit_tests.html">Running the Unit Tests</a></p>
<p><a href="compile_regression_tests.html">Running the Regression Tests</a></p>
<br>
<h2>Documentation</h2>
The primary source of documentation for the Nektar++ library is generated
using <a href="www.doxygen.org">Doxygen</a>. This includes both high-level
operational details as well as low-level code functionality documentation.
Due to its size, it is not distributed in a pre-compiled state and so
instructions are provided on how the user may generate this documentation
after downloading the code package.
<p><a href="compile_documentation.html">Generate <em> doxygen </em> documentation</a></p>
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<div id="sidebar1">
<h3 style="text-align: center;">
<a href="index.html" id="menu_Nektar">
<img src="images/nektar.png" alt="Nektar++" width="155" height="38" />
</a>
</h3>
<p><a href="downloads.html" id="menu_Downloads">Downloads</a></p>
<p><a href="compile.html" id="menu_Compile">Compilation Instructions</a>
<br/>
&nbsp;&nbsp;&nbsp;<a href="compile_linux.html" id="menu_CompileLinux">Linux</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_windows.html" id="menu_CompileWindows">Windows</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_osx.html" id="menu_CompileOSX">Mac OS X</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_unit_tests.html" id="menu_CompileUnitTests">Unit Tests</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_regression_tests.html" id="menu_CompileRegressionTests">Regression Tests</a><br/>
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<p><a href="educational_material.html" id="menu_EducationalMaterial">Educational
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<p><a href="code/index.html" id="menu_Library">Documentation</a></p>
<p><a href="team.html" id="menu_Team">Team Members</a></p>
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<p><a href="acknowledgments.html" id="menu_Acknowledgments">Acknowledgments</a></p>
<p><a href="mailto:nektar-inquiry@sci.utah.edu" id="menu_Contact">Contact</a></p>
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<h1>Generate Doxygen Documentation</h1>
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<hr/>
<p>
Nektar++ uses the documentation system <em> Doxygen </em> for generating documentation. The Doxygen HTML files are not included in the tarball because the size prohibits it. To generate the full documentation, follow the steps below:
<ol>
<li>Required packages</li>
<ul>
<li><strong>Doxygen</strong><br />
If you do not have Doxygen installed, you may obtain it from <a href="http://www.stack.nl/~dimitri/doxygen/">http://www.stack.nl/~dimitri/doxygen/</a>. The web site also offers a manual for installation on both Windows and Unix.</li>
<li><strong>Graphviz Dot<br />
</strong>The <em>dot</em> program in the Graphviz package is also recommended. Having <em>dot</em> allows for the creation of graph diagrams at the top of the HTML pages. You may obtain it from <a href="http://www.graphviz.org/Download..php">http://www.graphviz.org/Download..php</a>. Once installed, make sure the Graphviz's bin directory is in your path, so Doxygen can see the programs.</li>
<li><strong>LaTeX<br />
</strong><em>LaTeX</em> is also a recommended program that may be installed with your Unix distribution's package manager. The LaTeX web site is at <a href="http://www.latex-project.org/">http://www.latex-project.org/</a>. A common Windows TeX package is called MiKTeX and can be downloaded from <a href="http://miktex.org/">http://miktex.org/</a>. After installation, make sure it is in your path so Doxygen can use it. Doxygen uses LaTeX to generate PNG images for the website.</li>
</ul>
</li>
<li>Doxygen instructions<br />
<ul>
<li>Windows
<ul>
<li>From the icon group that the Doxygen installation created, run the <em>Doxywizard</em> program.</li>
<li>Press the &quot;Load&quot; button and choose the <em>Nektar++/docs/html/doxygen/doxygen</em> file.</li>
<li>Press the &quot;Start&quot; button and wait until the HTML generation completes.</li>
</ul>
</li>
<li>Unix
<ul>
<li>Navigate to the <em>Nektar++/docs/html/doxygen/</em> from the terminal.</li>
<li>Execute the command
<div class="code"><pre>doxygen ./doxygen</pre></div> to start documentation generation, and wait until it completes.</li>
</ul>
</li>
</ul>
</li>
<li>Open <em>Nektar++/docs/html/code/index.html</em> with your web browser to view the full Nektar++ doxygen documentation.</li>
</ol>
<b>The Doxyen documenation has been generated with <em>Doxygen 1.7.1<em> which is the recommended version.<b>
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<div id="sidebar1">
<h3 style="text-align: center;"><a href="index.html" id="menu_Nektar"><img src="images/nektar.png" alt="Nektar++" width="155" height="38" /></a></h3>
<p><a href="downloads.html" id="menu_Downloads">Downloads</a></p>
<p><a href="compile.html" id="menu_Compile">Compilation Instructions</a>
<br/>
&nbsp;&nbsp;&nbsp;<a href="compile_linux.html" id="menu_CompileLinux">Linux</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_windows.html" id="menu_CompileWindows">Windows</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_osx.html" id="menu_CompileOSX">Mac OS X</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_unit_tests.html" id="menu_CompileUnitTests">Unit Tests</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_regression_tests.html" id="menu_CompileRegressionTests">Regression Tests</a><br/>
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<p><a href="educational_material.html" id="menu_EducationalMaterial">Educational
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<p><a href="acknowledgments.html" id="menu_Acknowledgments">Acknowledgments</a></p>
<p><a href="mailto:nektar-inquiry@sci.utah.edu" id="menu_Contact">Contact</a></p>
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<p>The current distribution of the code has been set up with a series
of regression tests based around the <a href="usage.html">demos</a> and <a href="usage.html">solvers</a> in the library. The source wrapper source code for these tests can be found under:
<ul>
<li><em>Nektar++/regressionTests/</em></li>
<li><em>Nektar++/library/Demos/</em></li>
</ul>
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<p>
The compilation instructions for the regression tests can be found at
the end of the <a href="compile.html"> compile instructions</a> for
your machine. Once Nektar++ and the regression tests have been
compiled you can execute the regression tests in the following way:
<ol>
<li>Change directory to the Demo of solver that you wish to run regression tests on for example <em>Nektar++/regressionTest/builds/Demos/StdRegions</em></li>
<li>Execute the regression test, for example <em>./StdRegionsDemosTest</em></li>
and you should see a series of test being run with output similar to:
<p>
<div class="code"><pre>
..........
..........
PASSED: StdProject3D (Hex Ortho Basis, P=4, Q=7)
PASSED: StdProject3D (Hex Modified Basis P=6, Q=7)
PASSED: StdProject3D (Hex Lagrange Basis P=6, Q=7)
PASSED: StdProject3D (Hex Legendre Basis P=6, Q=7)
PASSED: StdProject3D (Hex Chebyshev Basis P=6, Q=7)
PASSED: StdProject_Diff3D (Tet Ortho Basis, P=4, Q=7)
PASSED: StdProject_Diff3D (Tet Modified Basis P=6, Q=7)
PASSED: StdProject_Diff3D (Hex Ortho Basis, P=4, Q=7)
PASSED: StdProject_Diff3D (Hex Modified Basis P=6, Q=7)
PASSED: StdProject_Diff3D (Hex Lagrange Basis P=6, Q=7)
PASSED: StdProject_Diff3D (Hex Legendre Basis P=6, Q=7)
PASSED: StdProject_Diff3D (Hex Cheby. Basis P=6, Q=7)
</pre></div>
<p>
<li>The same can be done for the solver you wish to run regression tests on for example <em>Nektar++/regressionTest/builds/Solvers/ADRSolver</em></li>
<li>Execute the regression test, for example <em>./ADRSolverTest</em></li>
and you should see a series of test being run with output similar to:
<p>
<div class="code"><pre>
..........
..........
PASSED: ADRSolver (2D unsteady DG advection, order 1, P=12)
PASSED: ADRSolver (2D unsteady DG advection, order 2, P=12)
PASSED: ADRSolver (2D unsteady DG advection, order 4, P=14)
PASSED: ADRSolver (2D unsteady DG implicit diffusion, order 3, P=6)
PASSED: ADRSolver (2D unsteady DG implicit diffusion, order 3, P=12)
PASSED: ADRSolver (2D unsteady DG explicit diffusion, order 4, P=3)
PASSED: ADRSolver (2D unsteady DG explicit diffusion, order 4, P=8)
PASSED: ADRSolver (2D unsteady advection-diffusion, IMEXOrder1, P=9, dt=0.001)
PASSED: ADRSolver (2D unsteady advection-diffusion, IMEXOrder1, P=9, dt=0.0001)
PASSED: ADRSolver (2D unsteady advection-diffusion, IMEXOrder2, P=9, dt=0.001)
PASSED: ADRSolver (2D unsteady advection-diffusion, IMEXOrder2, P=9, dt=0.0001)
</pre></div>
<p>
</ol>
</ul>
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</div>
</div>
</body>
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<link rel="shortcut icon" href="images/favicon.ico" >
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<title>Nektar++ - Windows Compile Instructions</title>
<!-- InstanceEndEditable -->
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<!-- InstanceParam name="CompileMenu" type="boolean" value="true" -->
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<body class="twoColHybLt">
<div id="container">
<div id="sidebar1">
<h3 style="text-align: center;"><a href="index.html" id="menu_Nektar"><img src="images/nektar.png" alt="Nektar++" width="155" height="38" /></a></h3>
<p><a href="downloads.html" id="menu_Downloads">Downloads</a></p>
<p><a href="compile.html" id="menu_Compile">Compilation Instructions</a>
<br/>
&nbsp;&nbsp;&nbsp;<a href="compile_linux.html" id="menu_CompileLinux">Linux</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_windows.html" id="menu_CompileWindows">Windows</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_osx.html" id="menu_CompileOSX">Mac OS X</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_unit_tests.html" id="menu_CompileUnitTests">Unit Tests</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_regression_tests.html" id="menu_CompileRegressionTests">Regression Tests</a><br/>
&nbsp;&nbsp;&nbsp;<a href="compile_documentation.html" id="menu_CompileDocumentation">Documentation</a><br/>
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<p><a href="educational_material.html" id="menu_EducationalMaterial">Educational
Material</a></p>
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<p><a href="acknowledgments.html" id="menu_Acknowledgments">Acknowledgments</a></p>
<p><a href="mailto:nektar-inquiry@sci.utah.edu" id="menu_Contact">Contact</a></p>
</div>
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<!-- InstanceBeginEditable name="Title" -->
<h1>Running the Unit Tests</h1>
<hr>
Nektar++ comes with several unit test modules that can be used to verify that it has
been compiled correctly on your architecture. To build the unit tests, enable the
NEKTAR_BUILD_UNIT_TESTS options in cmake.
<p>
After building Nektar++, you will find
several executables in the bin directory that has the string "UnitTest" in their name.
To run the test, simply execute the desired executable from the command line. If
everything has compiled correctly, you will see the following output:
<p>
<div class="code"><pre>
Running n test cases ...
*** No errors detected
</pre></div>
<p>
<p>
<p>
<b>Note</b>
<p>
In Mac OS X systems some errors messages could appear, an example is:
<p>
<div class="code"><pre>
UnitTests-g(13232) malloc: *** error for object 0x3000100600f10: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
</pre></div>
<p>
As long as they are after the <em>"*** No errors detected"<em>
message, the libraries have been built correctly.
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<div id="container">
<div id="sidebar1">
<h3 style="text-align: center;"><a href="index.html" id="menu_Nektar"><img src="images/nektar.png" alt="Nektar++" width="155" height="38" /></a></h3>
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<p>
<a href="compile.html" id="menu_Compile">Compile Instructions</a>
</p>
<p>
<a href="library.html" id="menu_Library">Library Overview</a>
</p>
<p><a href="team.html" id="menu_Team">Team Members</a></p>
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<p><a href="post-processing.html" id="menu_PostProcessing">Post-processing</a></p>
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<p><a href="http://www.nektar.info/2nd_edition/" target="_blank" id="menu_Book2ndEd">Spectral/hp element methods for CFD</a> (Karniadakis and Sherwin)</p>
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<p><br class="clearfloat" /></p>
</div>
</div>
</body>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN" "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
<html xmlns="http://www.w3.org/1999/xhtml"><!-- InstanceBegin template="/Templates/Main.dwt" codeOutsideHTMLIsLocked="false" -->
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link rel="shortcut icon" href="images/favicon.ico" >
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<title>Nektar++ - Downloads</title>
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<link rel="stylesheet" href="style.css">
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<style type="text/css">
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font-weight: bold;
}
-->
</style>
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<style type="text/css">
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</head>
<body class="twoColHybLt">
<div id="container">
<div id="sidebar1">
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