Commit 2a79a5a6 authored by Ann Almgren's avatar Ann Almgren
Browse files

update and remove unused files

parent 217bb70a

docs/webroot/gallery.html

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<html lang="en">

  <head>

    <meta charset="UTF-8">

    <title>AMReX: Gallery</title>

    <title>MFiX-Exa: Gallery</title>

    <link rel="icon" href="web_icon.ico" type="image/x-icon">

    <meta http-equiv="content-type" content="text/html; charset=utf-8" />

    <meta name="description" content="" />
@@ -25,31 +25,11 @@ 
  </head>

  <body>



    <!-- Header -->

    <header id="header">

      <h1><a href="index.html">AMReX</a></h1>

      <nav id="nav">

	<ul>

	  <li><a href="overview.html">Overview</a></li>

	  <li><a href="science.html">Science</a></li>

	  <li><a href="gallery.html">Gallery</a></li>

	  <li><a href="help.html" class="button special">Get Help</a></li>

	</ul>

      </nav>

    </header>



    <!-- Main -->

    <section id="main" class="wrapper">

      

      <div class="container">



	<header class="major">

          <p>

            If you would like to contribute to our gallery, 

            <a href="mailto:AJNonaka@lbl.gov?subject=AMReX Gallery">please contact us</a>.

          </p>

	</header>



        <header class="major">

          <h2>Microstructure Evolution Using Solid Mechanics</h2>

          <p>Simulation of microstructure evolution in a polycrystalline solid using Alamo</p>

docs/webroot/help.html

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<!DOCTYPE html>

<!--

	Transit by TEMPLATED

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	Released for free under the Creative Commons Attribution 3.0 license (templated.co/license)

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<html lang="en">

  <head>

    <meta charset="UTF-8">

    <title>MFiX-Exa: Getting Help</title>

    <link rel="icon" href="web_icon.png" type="image/x-icon">

    <meta http-equiv="content-type" content="text/html; charset=utf-8" />

    <meta name="description" content="" />

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      <link rel="stylesheet" href="css/style.css" />

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  </head>

  <body>



    <!-- Header -->

    <header id="header">

      <h1><a href="index.html">MFiX-Exa</a></h1>

      <nav id="nav">

	<ul>

	  <li><a href="overview.html">Overview</a></li>

	  <li><a href="science.html">Science</a></li>

	  <li><a href="gallery.html">Gallery</a></li>

	  <li><a href="help.html" class="button special">Get Help</a></li>

	</ul>

      </nav>

    </header>



    <!-- Footer -->

    <footer id="footer">

      <div class="container">

	<section class="links">

	  <div class="row">

	    <section class="4u 12u$(small)">

	      <ul class="unstyled">

		<li><h3>Getting Help</h3></li>

		<li>To obtain help, simply post an issue in the 

                  <a href="https://github.com/AMReX-Codes/MFIX-Exa">MFIX-Exa GitHub webpage</a></li>

	      </ul>

	    </section>

	    

	    <section class="4u 12u$(small)">

	      <ul class="unstyled">

		<li><h3>MFIX-Exa documentation</h3></li>

		<li>The <a href="https://amrex-codes.github.io/MFIX-Exa/docs_html">

                    MFIX-Exa Documentation</a> contains a 

                    <em>Getting Started</em> guide and details on the code.</li>

	      </ul>

	    </section>



	  </div>

	</section>



    <!-- Footer -->

    <footer id="footer">

      <div class="container">

	<section class="ack">

	  MFIX-Exa is developed at 

          <a href="https://www.netl.doe.gov/"> NETL </a>, and

          <a href="http://www.lbl.gov/"> LBNL </a>,

          <a href="http://www.colorado.edu/"> CU Boulder </a>

          as part of the MFIX-Exa Project in DOE's Exascale Computing Project.

	</section>

	<div class="row">

	  <div class="8u 12u$(medium)">

	    <ul class="copyright">

	      <li>&copy; MFIX-Exa development team. All rights reserved.</li>

	      <li>Design: <a href="http://templated.co">TEMPLATED</a></li>

	    </ul>

	  </div>

	</div>

      </div>

    </footer>



  </body>

</html>

docs/webroot/overview.html

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<!DOCTYPE html>

<!--

	Transit by TEMPLATED

	templated.co @templatedco

	Released for free under the Creative Commons Attribution 3.0 license (templated.co/license)

-->

<html lang="en">

  <head>

    <meta charset="UTF-8">

    <title>AMReX: Overview</title>

    <link rel="icon" href="web_icon.ico" type="image/x-icon">

    <meta http-equiv="content-type" content="text/html; charset=utf-8" />

    <meta name="description" content="" />

    <meta name="keywords" content="" />

    <!--[if lte IE 8]><script src="js/html5shiv.js"></script><![endif]-->

    <script src="js/jquery.min.js"></script>

    <script src="js/skel.min.js"></script>

    <script src="js/skel-layers.min.js"></script>

    <script src="js/init.js"></script>

    <noscript>

      <link rel="stylesheet" href="css/skel.css" />

      <link rel="stylesheet" href="css/style.css" />

      <link rel="stylesheet" href="css/style-xlarge.css" />

    </noscript>

  </head>

  <body>



    <!-- Header -->

    <header id="header">

      <h1><a href="index.html">AMReX</a></h1>

      <nav id="nav">

	<ul>

	  <li><a href="overview.html">Overview</a></li>

	  <li><a href="science.html">Science</a></li>

	  <li><a href="gallery.html">Gallery</a></li>

	  <li><a href="help.html" class="button special">Get Help</a></li>

	</ul>

      </nav>

    </header>



    <!-- Main -->

    <section id="main" class="wrapper">



      <div class="container">



	<div class="row">

	  <div id="sidebar" class="4u 12u$(small)">

	    <section>

	      <ul class="unstyled">



		<li><center><h3>AMReX at a Glance</h3></center>

		AMReX is a publicly available software framework 

                designed for building massively parallel block-

                structured adaptive mesh refinement (AMR) applications.</li>



                <li><center><h3>Features</h3></center>

                       <ul>

                         <li style="margin-bottom: -15px; margin-left:20px; LINE-HEIGHT:25px">

                           C++ and Fortran interfaces</li>

                         <li style="margin-bottom: -15px; margin-left:20px; LINE-HEIGHT:25px">

                           Support for cell-centered, 

                           face-centered, edge-centered, and nodal data</li>

                         <li style="margin-bottom: -15px; margin-left:20px; LINE-HEIGHT:25px">

                           Support for hyperbolic, parabolic, 

                           and elliptic solves on hierarchical adaptive grid structure</li>

                         <li style="margin-bottom: -15px; margin-left:20px; LINE-HEIGHT:25px">

                           Optional subcycling in time for time-dependent PDEs</li>

                         <li style="margin-bottom: -15px; margin-left:20px; LINE-HEIGHT:25px">

                           Support for particles</li>

                         <li style="margin-bottom: -15px; margin-left:20px; LINE-HEIGHT:25px">

                           Embedded boundary description of irregular geometry</li>

                         <li style="margin-bottom: -15px; margin-left:20px; LINE-HEIGHT:25px">

                           Parallelization via flat MPI, OpenMP, hybrid MPI/OpenMP, or MPI/MPI</li>

                         <li style="margin-bottom: -15px; margin-left:20px; LINE-HEIGHT:25px">

                           Parallel I/O</li>

                         <li style="margin-bottom: -15px; margin-left:20px; LINE-HEIGHT:25px">

                           Plotfile format supported by Amrvis, VisIt, ParaView, and yt</li>

                         <li style="margin-bottom: -15px; margin-left:20px; LINE-HEIGHT:25px">

                           Built-in profiling tools</li>

                       </ul>

                </li>



                <li><center><h3>Open Development Model</h3></center>

                  All of AMReX's development is done

                  in the github repository under the development branch;

                  anyone can see the latest updates.  Changes are merged into

                  the master branch at the beginning of each month.</li>



                <li><center><h3>Contribute to AMReX</h3></center>

                  We encourage users contribute to the AMReX source code.

                  To contribute, issue a pull request against the

                  <b>development</b> branch

                  (<a href="https://help.github.com/articles/creating-a-pull-request/">details</a>).

                  Any level of changes are welcomed:

                  documentation, bug fixes, new test problems,

                  new solvers, ...</li>



                <li><center><h3>Getting Help</h3></center>

                  To obtain help, simply post an issue on the 

                  <a href="https://github.com/AMReX-Codes/amrex">AMReX GitHub webpage</a>

                </li>

              </ul>

            </section>

          </div>



          <div class="8u$ 12u$(small) important(small)">



            <div class="10u$ 12u$(small) important(small)">

              

              <header class="major">

                <h3>Why Block-Structured AMR?</h3>

              </header>



              Block-structured AMR provides a way to exploit varying resolution requirements

              in space and time by focusing computational resources in spatiotemporal

              regions of interest.  Note that there is no parent-child relationship between

              coarser grids and finer grids as the grid structure dynamically evolves 

              over time.<p><p>



                <center>

                  <img src="images/KH.gif" style="width: 512px; height: 256px" alt="" ><p>

                </center>

                

                Depicted above is a Kelvin-Helmholtz instability using 3 total levels of 

                refinement generated

                by the publicly available <b>IAMR</b> code 

                (available <a href="https://github.com/AMReX-Codes/IAMR">HERE</a>)

                for solving the variable-density incompressible Navier-Stokes equations.

                <p><p>

                

              <header class="major">

                <h3>Particles</h3>

              </header>



              AMReX provides data structures and iterators for performing 

              data-parallel particle simulations. Our approach is particularly 

              suited to particles that interact with data defined on a 

              (possibly adaptive) block-structured hierarchy of meshes. Example 

              applications include Particle-in-Cell (PIC) simulations, Lagrangian 

              tracers, or particles that exert drag forces onto a fluid, such as 

              in multi-phase flow calculations.<p><p>



                <center>

                  <img src="images/particles.gif" style="width: 347px; height: 456px" alt="" ><p>

                </center>

                

                Depicted above is granular material color coded according

                to their speed, falling into a bucket.  This simulation was performed

                with the <b>MFiX-Exa</b> code developed by NETL, LBNL, and University 

                of Colorado.<p><p>

                

              <header class="major">

                <h3>Embedded Boundaries</h3>

              </header>



              For computations with complex geometries, AMReX provides data structures 

              and algorithms to employ an embedded boundary (EB) approach to PDE 

              discretizations. In this approach, the underlying computational mesh 

              is uniform and block-structured, but the boundary of the irregular-shaped 

              computational domain conceptually cuts through this mesh.<p><p>



                <center>

                  <img src="images/EmbeddedBoundaries.png" style="width: 347px; height: 456px" alt="" ><p>

                </center>

                

                Depicted above is a compressible high speed swirling jet conducted 

                using the <b>PeleC</b> simulation code created by NREL & LBNL with 

                the support of the Exascale Computing Project.  Isosurface shows 

                velocity magnitude.<p><p>

             

              <header class="major">

                <h3>Profiling Tools</h3>

              </header>



              AMReX-based application codes can be instrumented using AMReX-specific performance profiling tools that take into account the hierarchical nature of the mesh in most AMReX-based applications. These codes can be instrumented for varying levels of profiling detail.<p><p>



                <center>

                  <img src="images/Profiling.png" style="width: 728px; height: 358px" alt="" ><p>

                </center>

                

                Depicted above is a sample output of the <b>ProfParser</b> tool, a 

                command line application that can create performance summaries, 

                plotfiles showing point to point communication and timelines, 

                HTML call trees, communication call statistics, function timing 

                graphs, and other data products.  Read more in the 

                <a href="https://amrex-codes.github.io/amrex/docs_html">Documentation.</a><p><p>



            </div>



          </div>



        </div>



    </section>

    <!-- End Main -->



    <!-- Footer -->

    <footer id="footer">

      <div class="container">

	<section class="ack">

	  AMReX is developed at 

          <a href="http://www.lbl.gov/"> LBNL </a>,

          <a href="https://www.nrel.gov/"> NREL </a>, and

          <a href="http://www.anl.gov/"> ANL </a>

          as part of the Block-Structured AMR Co-Design Center in DOE's 

          Exascale Computing Project.

	</section>

	<div class="row">

	  <div class="8u 12u$(medium)">

	    <ul class="copyright">

	      <li>&copy; AMReX development team. All rights reserved.</li>

	      <li>Design: <a href="http://templated.co">TEMPLATED</a></li>

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