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<a href="CFDEMcoupling_Manual.html" class="icon icon-home"> CFDEMcoupling
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<div class="version">
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v3.X
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<li><a class="reference internal" href="#">githubAccess_public</a><ul>
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<li><a class="reference internal" href="#description">Description</a></li>
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<a href="http://www.cfdem.com"> Website</a>
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<div class="section" id="githubaccess-public">
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<h1>githubAccess_public<a class="headerlink" href="#githubaccess-public" title="Permalink to this headline">¶</a></h1>
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<hr class="docutils" />
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>This routine describes how to pull repositories of the CFDEM(R)project from <a href="#id2"><span class="problematic" id="id4">`github.com <github_>`_</span></a><a href="#id2"><span class="problematic" id="id3"> <github_></span></a>.
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After setting some environment variables, LIGGGHTS(R) and CFDEM(R)coupling can be compiled.</p>
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<p><strong>Procedure:</strong></p>
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<p>Basically the following steps have to be performed:</p>
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<ul class="simple">
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<li><em>git clone</em> and setup OpenFOAM</li>
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<li><em>git clone</em> the desired repositories</li>
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<li>update your repositories by <em>git pull</em></li>
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<li>set environment variables</li>
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<li>compile LIGGGHTS(R) and CFDEM(R)coupling</li>
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<li>run your own cases</li>
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</ul>
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<p><strong>*git clone* and setup OpenFOAM:</strong></p>
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<p>Have a look at the latest compatible OpenFOAM(R)-version in the versionInfo.H file at <a href="#id7"><span class="problematic" id="id8">`github <compOF_>`_</span></a>.
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This file will later be downloaded as a part of the source-code.
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Look for the git commit hashtag in the following line:</p>
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<div class="highlight-python"><div class="highlight"><pre>word OFversion="&lt;OF-Release&gt;-commit-&lt;commitHashtag&gt;";
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>e.g. word OFversion="2.4.x-commit-3d8da0e960c717ff582f1517a27724144f086b83";
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</pre></div>
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</div>
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<p>However sometimes even newer versions are supported, please check the <a href="#id9"><span class="problematic" id="id10">`release notes <relNotes_>`_</span></a> and the “Advanced Settings”-section.</p>
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<p>Basically follow the OpenFOAM(R) git compilation <a href="#id11"><span class="problematic" id="id12">`instructions <downOF_>`_</span></a>, with a small number of exceptions:</p>
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<p>When you git clone the repository, replace the release-version with &lt;OF-Release&gt;.</p>
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<p>with git-protocol:</p>
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<div class="highlight-python"><div class="highlight"><pre>git clone git://github.com/OpenFOAM/OpenFOAM-&lt;OF-Release&gt;.git
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</pre></div>
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</div>
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<p>or with https:</p>
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<div class="highlight-python"><div class="highlight"><pre>git clone https://github.com/OpenFOAM/OpenFOAM-&lt;OF-Release&gt;.git
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</pre></div>
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</div>
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<p>Now change into the new directory and checkout the correct compatible version:</p>
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<div class="highlight-python"><div class="highlight"><pre>cd OpenFOAM-&lt;OF-Release&gt;
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git checkout &lt;commitHashtag&gt;
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</pre></div>
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</div>
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<p>The result will be a status report, that indicates a ‘detached head state’.
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Now continue with installing and compiling OpenFOAM(R).
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Make sure that OpenFOAM(R) works properly with a parallel Simulation!</p>
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<p>If you want to use an older OpenFOAM(R)-version, please have a look at the “Backwards Compatibility”-section.</p>
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<p><strong>*git clone* the desired repositories:</strong></p>
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<p>You may want to take a look around on CFDEMproject on github: github.com/CFDEMproject_gitCFDEM</p>
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<p>If not already done, open a terminal and create a directory for LIGGGHTS(R) in $HOME:</p>
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<div class="highlight-python"><div class="highlight"><pre>cd
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mkdir LIGGGHTS
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cd LIGGGHTS
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</pre></div>
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</div>
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<p>To clone the public LIGGGHTS repository, open a terminal and execute:
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with git-protocol:</p>
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<div class="highlight-python"><div class="highlight"><pre>git clone git://github.com/CFDEMproject/LIGGGHTS-PUBLIC.git LIGGGHTS-PUBLIC
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</pre></div>
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</div>
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<p>or with https:</p>
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<div class="highlight-python"><div class="highlight"><pre>git clone https://github.com/CFDEMproject/LIGGGHTS-PUBLIC.git LIGGGHTS-PUBLIC
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</pre></div>
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</div>
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<p>If not already done, open a terminal and create a directory for CFDEM(R)coupling in $HOME:</p>
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<div class="highlight-python"><div class="highlight"><pre>cd
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mkdir CFDEM
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cd CFDEM
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</pre></div>
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</div>
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<p>To clone the public CFDEM(R)coupling repository, open a terminal and execute:
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with git-protocol:</p>
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<div class="highlight-python"><div class="highlight"><pre>git clone git://github.com/CFDEMproject/CFDEMcoupling-PUBLIC.git CFDEMcoupling-PUBLIC-$WM_PROJECT_VERSION
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</pre></div>
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</div>
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<p>or with https:</p>
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<div class="highlight-python"><div class="highlight"><pre>git clone https://github.com/CFDEMcoupling-PUBLIC.git CFDEMcoupling-PUBLIC-$WM_PROJECT_VERSION
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>Additionally the lpp tool for converting LIGGGHTS dump-files into the paraview readable VTK-format might be of use:
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with git-protocol:
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git clone git://github.com:CFDEMproject/LPP.git $HOME/LIGGGHTS/mylpp
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>or with https:
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git clone https://github.com:CFDEMproject/LPP.git $HOME/LIGGGHTS/mylpp
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</pre></div>
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</div>
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<p>Please have a look at README and INSTALL.txt in the root directory of LPP for further information.</p>
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<p>Troubles? See Troubleshooting git section below.</p>
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<p><strong>Update your repositories by *git pull*:</strong></p>
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<p>To get the latest version, open a terminal, go to the location of your local installation and type:
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<em>Warning: git stash will remove your changes in $HOME/CFDEM/CFDEMcoupling-PUBLIC-$WM_PROJECT_VERSION !</em></p>
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<div class="highlight-python"><div class="highlight"><pre>cd $HOME/CFDEM/CFDEMcoupling-PUBLIC-$WM_PROJECT_VERSION
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git stash
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git pull
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</pre></div>
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</div>
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<p><strong>Set Environment Variables:</strong></p>
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<p>Now you need to set some environment variables in ~/.bashrc (if you use c-shell, manipulate ~/.cshrc accordingly). Open ~/.bashrc</p>
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<div class="highlight-python"><div class="highlight"><pre>gedit ~/.bashrc &
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</pre></div>
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</div>
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<p>add the lines (you find them also in CFDEMCoupling-$WM_PROJECT_VERSION/src/lagrangian/cfdemParticle/etc/bashrc and cshrc respectively):</p>
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<div class="highlight-python"><div class="highlight"><pre>#================================================#
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#- source cfdem env vars
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export CFDEM_VERSION=PUBLIC
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export CFDEM_PROJECT_DIR=$HOME/CFDEM/CFDEMcoupling-$CFDEM_VERSION-$WM_PROJECT_VERSION
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export CFDEM_SRC_DIR=$CFDEM_PROJECT_DIR/src
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export CFDEM_SOLVER_DIR=$CFDEM_PROJECT_DIR/applications/solvers
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export CFDEM_DOC_DIR=$CFDEM_PROJECT_DIR/doc
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export CFDEM_UT_DIR=$CFDEM_PROJECT_DIR/applications/utilities
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export CFDEM_TUT_DIR=$CFDEM_PROJECT_DIR/tutorials
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export CFDEM_PROJECT_USER_DIR=$HOME/CFDEM/$LOGNAME-$CFDEM_VERSION-$WM_PROJECT_VERSION
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export CFDEM_bashrc=$CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/bashrc
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export CFDEM_LIGGGHTS_SRC_DIR=$HOME/LIGGGHTS/LIGGGHTS-PUBLIC/src
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export CFDEM_LIGGGHTS_MAKEFILE_NAME=fedora_fpic
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export CFDEM_LPP_DIR=$HOME/LIGGGHTS/mylpp/src
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export CFDEM_PIZZA_DIR=$HOME/LIGGGHTS/PIZZA/gran_pizza_17Aug10/src
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. $CFDEM_bashrc
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#================================================#
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</pre></div>
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</div>
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<p>If you installed LIGGGHTS(R) or CFDEM(R)coupling in non-standard paths, please have a look at least at CFDEM_PROJECT_DIR and CFDEM_LIGGGHTS_SRC_DIR.
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The standard CFDEM_LIGGGHTS_MAKEFILE_NAME is fedora_fpic, which works on most systems. However please checkout LIGGGHTS-PUBLIC/src/MAKE for additional makefiles, wich are available. The most used ones are fedora_fpic and ubuntuVTK_fpic. Beware that the CFDEMcoupling needs a fpic compilation to use LIGGGHTS as a library. Please check the “Advanced Settings” for VTK information.</p>
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<p>Save the ~/.bashrc, open a new terminal and test the settings. The commands:</p>
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<div class="highlight-python"><div class="highlight"><pre>$CFDEM_PROJECT_DIR
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$CFDEM_SRC_DIR
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$CFDEM_LIGGGHTS_SRC_DIR
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</pre></div>
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</div>
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<p>should give ”...: is a directory” otherwise something went wrong and the environment variables in ~/.bashrc are not set correctly.</p>
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<p>To specify the paths of pizza, please check the settings in $CFDEM_SRC_DIR/lagrangian/cfdemParticle/etc/bashrc.</p>
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<p>If $CFDEM_SRC_DIR is set correctly, you can type</p>
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<div class="highlight-python"><div class="highlight"><pre><span class="n">cfdemSysTest</span>
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</pre></div>
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</div>
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<p>to get some information if the paths are set correctly.</p>
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<p><strong>Compile LIGGGHTS(R) and CFDEM(R)coupling:</strong></p>
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<p>If above settings were done correctly, you can compile LIGGGHTS(R) by typing:</p>
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<div class="highlight-python"><div class="highlight"><pre><span class="n">cfdemCompLIG</span>
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</pre></div>
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</div>
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<p>and you can then compile CFDEM(R)coupling by typing:</p>
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<div class="highlight-python"><div class="highlight"><pre><span class="n">cfdemCompCFDEM</span>
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</pre></div>
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</div>
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<p>or compile both at once with:</p>
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<div class="highlight-python"><div class="highlight"><pre><span class="n">cfdemCompCFDEMall</span>
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</pre></div>
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</div>
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<p>You can run the tutorial cases by executing .../etc/testTutorial.sh through the alias <em>cfdemTestTUT</em>.
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Alternatively you can run each tutorial using the <em>Allrun.sh</em> scripts in the tutorial directories.</p>
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<p>In case questions concerning the installation arise, please feel free to contact our forum at www.cfdem.com.</p>
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<p><strong>Run Your Own Cases:</strong></p>
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<p>If you want to run your own cases, please do so in $CFDEM_PROJECT_USER_DIR/run which is automatically being generated. E.g. copy one of the tutorial cases there, adapt it to your needs.
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Changes in $CFDEM_TUT_DIR will be lost after every <em>git stash</em>!</p>
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<p><strong>Additional Installations:</strong></p>
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<p>Optionally you can install lpp which will help you convert the DEM (dump) data to VTK format. For standard CFD-DEM runs this will not be necessary. To get the DEM postprocessing tool “lpp” you need python-numpy package installed:</p>
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<div class="highlight-python"><div class="highlight"><pre>sudo apt-get install python-numpy
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</pre></div>
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</div>
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<p>You can pull the latest version of lpp with:</p>
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<div class="highlight-python"><div class="highlight"><pre>cd $HOME/LIGGGHTS
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</pre></div>
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</div>
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<p>with git-protocol:
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git clone git://github.com/CFDEMproject/LPP.git
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with https:
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git clone https://github.com/CFDEMproject/LPP.git</p>
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<p><strong>Backwards Compatibility:</strong></p>
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<p>Basically CFDEM(R)coupling supports one OpenFOAM(R) version therefore all settings are prepared for that. Nevertheless we try to maintain backwards compatibility as long as it works with reasonable effort.</p>
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<p>The supported OpenFOAM(R) and LIGGGHTS(R) versions are stated in:
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src/lagrangian/cfdemParticle/cfdTools/versionInfo.H</p>
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<p>For using other versions you can manipulate:
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src/lagrangian/cfdemParticle/etc/OFversion/OFversion.H
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(still not all functionality might work then!)</p>
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<p><strong>Advanced Settings:</strong></p>
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<p>Here some advanced settings and hints for non-standard compilations are presented.
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As stated in the “Backwards Compatibility”-section, there are compiler flags for different OpenFOAM versions. Checkout src/lagrangian/cfdemParticle/etc/OFversion/OFversion.H for compatibility settings. Just comment the current “#define version2X” in the top-section and uncomment the one you want to compile it with.</p>
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<p>There are advanced compilation settings for library-paths, includes and libraries are within the additionalLibs file in src/lagrangian/cfdemParticle/etc/additionalLibs. There are predefined files for different OpenFOAM versions. To use a different version, add the following lines to your .bashrc (.cshrc) before the standard CFDEM variables:</p>
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<div class="highlight-python"><div class="highlight"><pre>export CFDEM_ADD_LIBS_DIR=FOLDER_OF_NEW_additionalLibs_FILE/
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>export CFDEM_ADD_LIBS_NAME=additionalLibs30x
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</pre></div>
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</div>
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<p>This is an example to use a predefined additionalLibs file for OpenFOAM-3.0.x.</p>
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<p>To enable direct VTK-dump (dump custom/vtk) support of LIGGGHTS and CFDEMcoupling, you have to install the VTK libraries. Either 5.8 or 6 are predefined for ubuntu.</p>
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<div class="highlight-python"><div class="highlight"><pre>sudo apt-get libvtk5.8 libvtk5-dev
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</pre></div>
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</div>
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<p>Change “export CFDEM_LIGGGHTS_MAKEFILE_NAME=fedora_fpic” in your .bashrc according to your preferred LIGGGHTS makefile.
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If you have a non-standard installation location you have to adapt the LIGGGHTS makefile accordingly.
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To enable this feature in a coupled run the additionalLibs file has to be modified.
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It basically needs to include the same libraries as the LIGGGHTS-Makefile.
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E.g. for Ubuntu-14.04 with vtk-5.8:</p>
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<div class="highlight-python"><div class="highlight"><pre><span class="n">CFDEM_ADD_LIB_PATHS</span> <span class="o">=</span> <span class="o">-</span><span class="n">L</span><span class="o">/</span><span class="n">usr</span><span class="o">/</span><span class="n">include</span><span class="o">/</span><span class="n">vtk</span><span class="o">-</span><span class="mf">5.8</span>
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre><span class="n">CFDEM_ADD_LIBS</span> <span class="o">=</span> <span class="o">-</span><span class="n">lvtkCommon</span> <span class="o">-</span><span class="n">lvtkFiltering</span> <span class="o">-</span><span class="n">lvtkIO</span>
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</pre></div>
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</div>
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<p><strong>Troubleshooting git:</strong></p>
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<ul class="simple">
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<li>Troubles with git clone?</li>
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</ul>
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<p><strong>a)</strong> The git protocol will not work if your computer is behind a firewall which blocks the relevant TCP port, you can use alternatively https instead of git (write command in one line):</p>
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<p>git clone <a class="reference external" href="https://github.com/CFDEMproject/CFDEMcoupling-PUBLIC.git">https://github.com/CFDEMproject/CFDEMcoupling-PUBLIC.git</a> CFDEMcoupling-PUBLIC-$WM_PROJECT_VERSION</p>
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<p><strong>b)</strong> If you face the error: “error: SSL certificate problem, verify that the CA cert is OK. Details: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed while accessing https://github.com/...”,</p>
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<p>please use: env GIT_SSL_NO_VERIFY=true git clone <a class="reference external" href="https://github">https://github</a>...</p>
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<p>(see <a class="reference external" href="http://stackoverflow.com/questions/3777075/https-github-access">http://stackoverflow.com/questions/3777075/https-github-access</a>)</p>
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<p><strong>c)</strong> If you face the error: “Agent admitted failure to sign using the key. Permission denied (publickey).”, after ssh -T <a class="reference external" href="mailto:git%40github.com">git<span>@</span>github<span>.</span>com</a></p>
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<p>please type: “ssh-add”</p>
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<p>(see: <a class="reference external" href="https://help.github.com/articles/error-agent-admitted-failure-to-sign">https://help.github.com/articles/error-agent-admitted-failure-to-sign</a>)</p>
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</div>
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</div>
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</div>
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</div>
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<footer>
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<hr/>
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<div role="contentinfo">
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<p>
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