tupdated documentation - sphere - GPU-based 3D discrete element method algorithm with optional fluid coupling
 (HTM) git clone git://src.adamsgaard.dk/sphere
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       ---
 (DIR) commit 2085e084281fe031a970af25d140832b27642e5c
 (DIR) parent 460bcf1cd69bf981cffc443468bd21e168fbfadf
 (HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
       Date:   Mon,  1 Sep 2014 14:45:11 +0200
       
       updated documentation
       
       Diffstat:
         M doc/html/genindex.html              |      28 ++++++++++++++++++++++++++--
         M doc/html/objects.inv                |       0 
         M doc/html/python_api.html            |     113 ++++++++++++++++++++++++++++---
         M doc/html/searchindex.js             |       4 ++--
         M doc/html/sphere_internals.html      |       4 ++--
         M doc/pdf/sphere.pdf                  |       0 
       
       6 files changed, 135 insertions(+), 14 deletions(-)
       ---
 (DIR) diff --git a/doc/html/genindex.html b/doc/html/genindex.html
       t@@ -123,6 +123,10 @@
        <table style="width: 100%" class="indextable genindextable"><tr>
          <td style="width: 33%" valign="top"><dl>
              
       +  <dt><a href="python_api.html#sphere.sim.checkerboardColors">checkerboardColors() (sphere.sim method)</a>
       +  </dt>
       +
       +      
          <dt><a href="python_api.html#sphere.cleanup">cleanup() (in module sphere)</a>
          </dt>
        
       t@@ -264,6 +268,10 @@
          <dt><a href="python_api.html#sphere.sim.initTemporal">initTemporal() (sphere.sim method)</a>
          </dt>
        
       +      
       +  <dt><a href="python_api.html#sphere.sim.interiaParameterPlanarShear">interiaParameterPlanarShear() (sphere.sim method)</a>
       +  </dt>
       +
          </dl></td>
        </tr></table>
        
       t@@ -355,6 +363,10 @@
          </dt>
        
              
       +  <dt><a href="python_api.html#sphere.sim.plotLoadCurve">plotLoadCurve() (sphere.sim method)</a>
       +  </dt>
       +
       +      
          <dt><a href="python_api.html#sphere.sim.plotPrescribedFluidPressures">plotPrescribedFluidPressures() (sphere.sim method)</a>
          </dt>
        
       t@@ -453,6 +465,10 @@
          </dt>
        
              
       +  <dt><a href="python_api.html#sphere.sim.setFluidBottomNoFlowNoSlip">setFluidBottomNoFlowNoSlip() (sphere.sim method)</a>
       +  </dt>
       +
       +      
          <dt><a href="python_api.html#sphere.sim.setFluidPressureModulation">setFluidPressureModulation() (sphere.sim method)</a>
          </dt>
        
       t@@ -465,16 +481,20 @@
          </dt>
        
              
       -  <dt><a href="python_api.html#sphere.sim.setGamma">setGamma() (sphere.sim method)</a>
       +  <dt><a href="python_api.html#sphere.sim.setFluidTopNoFlowNoSlip">setFluidTopNoFlowNoSlip() (sphere.sim method)</a>
          </dt>
        
              
       -  <dt><a href="python_api.html#sphere.sim.setMaxIterations">setMaxIterations() (sphere.sim method)</a>
       +  <dt><a href="python_api.html#sphere.sim.setGamma">setGamma() (sphere.sim method)</a>
          </dt>
        
          </dl></td>
          <td style="width: 33%" valign="top"><dl>
              
       +  <dt><a href="python_api.html#sphere.sim.setMaxIterations">setMaxIterations() (sphere.sim method)</a>
       +  </dt>
       +
       +      
          <dt><a href="python_api.html#sphere.sim.setTheta">setTheta() (sphere.sim method)</a>
          </dt>
        
       t@@ -495,6 +515,10 @@
          </dt>
        
              
       +  <dt><a href="python_api.html#sphere.sim.shearStrainRate">shearStrainRate() (sphere.sim method)</a>
       +  </dt>
       +
       +      
          <dt><a href="python_api.html#sphere.sim.shearVel">shearVel() (sphere.sim method)</a>
          </dt>
        
 (DIR) diff --git a/doc/html/objects.inv b/doc/html/objects.inv
       Binary files differ.
 (DIR) diff --git a/doc/html/python_api.html b/doc/html/python_api.html
       t@@ -448,6 +448,25 @@ The plot is saved in the current folder as
        </dd></dl>
        
        <dl class="method">
       +<dt id="sphere.sim.checkerboardColors">
       +<tt class="descname">checkerboardColors</tt><big>(</big><em>nx=6</em>, <em>ny=6</em>, <em>nz=6</em><big>)</big><a class="headerlink" href="#sphere.sim.checkerboardColors" title="Permalink to this definition">¶</a></dt>
       +<dd><p>Assign checkerboard color values to the particles in an orthogonal grid.</p>
       +<table class="docutils field-list" frame="void" rules="none">
       +<col class="field-name" />
       +<col class="field-body" />
       +<tbody valign="top">
       +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
       +<li><strong>nx</strong> (<em>int</em>) &#8211; Number of color values along the x axis</li>
       +<li><strong>ny</strong> (<em>int</em>) &#8211; Number of color values along the y ayis</li>
       +<li><strong>nz</strong> (<em>int</em>) &#8211; Number of color values along the z azis</li>
       +</ul>
       +</td>
       +</tr>
       +</tbody>
       +</table>
       +</dd></dl>
       +
       +<dl class="method">
        <dt id="sphere.sim.cleanup">
        <tt class="descname">cleanup</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.cleanup" title="Permalink to this definition">¶</a></dt>
        <dd><p>Removes the input/output files and images belonging to the object
       t@@ -902,6 +921,24 @@ included.</p>
        </dd></dl>
        
        <dl class="method">
       +<dt id="sphere.sim.interiaParameterPlanarShear">
       +<tt class="descname">interiaParameterPlanarShear</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.interiaParameterPlanarShear" title="Permalink to this definition">¶</a></dt>
       +<dd><p>Returns the value of the inertia parameter $I$ during planar shear
       +proposed by GDR-MiDi 2004.</p>
       +<table class="docutils field-list" frame="void" rules="none">
       +<col class="field-name" />
       +<col class="field-body" />
       +<tbody valign="top">
       +<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The value of $I$</td>
       +</tr>
       +<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">float</td>
       +</tr>
       +</tbody>
       +</table>
       +<p>:see also:<cite>func:shearStrainRate()</cite>,`func:shearVel()`</p>
       +</dd></dl>
       +
       +<dl class="method">
        <dt id="sphere.sim.kineticEnergy">
        <tt class="descname">kineticEnergy</tt><big>(</big><em>idx</em><big>)</big><a class="headerlink" href="#sphere.sim.kineticEnergy" title="Permalink to this definition">¶</a></dt>
        <dd><p>Returns the (linear) kinetic energy for a particle.</p>
       t@@ -1139,6 +1176,26 @@ this value is -1, the center z position is used.</li>
        </dd></dl>
        
        <dl class="method">
       +<dt id="sphere.sim.plotLoadCurve">
       +<tt class="descname">plotLoadCurve</tt><big>(</big><em>graphics_format='png'</em><big>)</big><a class="headerlink" href="#sphere.sim.plotLoadCurve" title="Permalink to this definition">¶</a></dt>
       +<dd><p>Plot the load curve (log time vs. upper wall movement).  The plot is
       +saved in the current folder with the file name
       +&#8216;&lt;simulation id&gt;-loadcurve.&lt;graphics_format&gt;&#8217;.
       +The consolidation coefficient calculations are done on the base of
       +Bowles 1992, p. 129&#8211;139, using the &#8220;Casagrande&#8221; method.
       +It is assumed that the consolidation has stopped at the end of the
       +simulation (i.e. flat curve).</p>
       +<table class="docutils field-list" frame="void" rules="none">
       +<col class="field-name" />
       +<col class="field-body" />
       +<tbody valign="top">
       +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>graphics_format</strong> (<em>str</em>) &#8211; Save the plot in this format</td>
       +</tr>
       +</tbody>
       +</table>
       +</dd></dl>
       +
       +<dl class="method">
        <dt id="sphere.sim.plotPrescribedFluidPressures">
        <tt class="descname">plotPrescribedFluidPressures</tt><big>(</big><em>graphics_format='png'</em><big>)</big><a class="headerlink" href="#sphere.sim.plotPrescribedFluidPressures" title="Permalink to this definition">¶</a></dt>
        <dd><p>Plot the prescribed fluid pressures through time that may be
       t@@ -1365,7 +1422,7 @@ tracer to this image format using Imagemagick</li>
        
        <dl class="method">
        <dt id="sphere.sim.run">
       -<tt class="descname">run</tt><big>(</big><em>verbose=True</em>, <em>hideinputfile=False</em>, <em>dry=False</em>, <em>valgrind=False</em>, <em>cudamemcheck=False</em><big>)</big><a class="headerlink" href="#sphere.sim.run" title="Permalink to this definition">¶</a></dt>
       +<tt class="descname">run</tt><big>(</big><em>verbose=True</em>, <em>hideinputfile=False</em>, <em>dry=False</em>, <em>valgrind=False</em>, <em>cudamemcheck=False</em>, <em>device=-1</em><big>)</big><a class="headerlink" href="#sphere.sim.run" title="Permalink to this definition">¶</a></dt>
        <dd><p>Start <tt class="docutils literal"><span class="pre">sphere</span></tt> calculations on the <tt class="docutils literal"><span class="pre">sim</span></tt> object</p>
        <table class="docutils field-list" frame="void" rules="none">
        <col class="field-name" />
       t@@ -1382,6 +1439,9 @@ computational time.</li>
        <li><strong>cudamemcheck</strong> (<em>bool</em>) &#8211; Run the program with <tt class="docutils literal"><span class="pre">cudamemcheck</span></tt> in order to
        check for device memory leaks and errors. This causes a significant
        increase in computational time.</li>
       +<li><strong>device</strong> (<em>int</em>) &#8211; Specify the GPU device to execute the program on.
       +If not specified, sphere will use the device with the most CUDA cores.
       +To see a list of devices, run <tt class="docutils literal"><span class="pre">nvidia-smi</span></tt> in the system shell.</li>
        </ul>
        </td>
        </tr>
       t@@ -1472,7 +1532,16 @@ value (Dirichlet) boundary condition.</p>
        <dt id="sphere.sim.setFluidBottomNoFlow">
        <tt class="descname">setFluidBottomNoFlow</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.setFluidBottomNoFlow" title="Permalink to this definition">¶</a></dt>
        <dd><p>Set the lower boundary of the fluid domain to follow the no-flow
       -(Neumann) boundary condition.</p>
       +(Neumann) boundary condition with free slip parallel to the boundary.</p>
       +<p>The default behavior for the boundary is fixed value (Dirichlet), see
       +<a class="reference internal" href="#sphere.sim.setFluidBottomFixedPressure" title="sphere.sim.setFluidBottomFixedPressure"><tt class="xref py py-func docutils literal"><span class="pre">setFluidBottomFixedPressure()</span></tt></a>.</p>
       +</dd></dl>
       +
       +<dl class="method">
       +<dt id="sphere.sim.setFluidBottomNoFlowNoSlip">
       +<tt class="descname">setFluidBottomNoFlowNoSlip</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.setFluidBottomNoFlowNoSlip" title="Permalink to this definition">¶</a></dt>
       +<dd><p>Set the lower boundary of the fluid domain to follow the no-flow
       +(Neumann) boundary condition with no slip parallel to the boundary.</p>
        <p>The default behavior for the boundary is fixed value (Dirichlet), see
        <a class="reference internal" href="#sphere.sim.setFluidBottomFixedPressure" title="sphere.sim.setFluidBottomFixedPressure"><tt class="xref py py-func docutils literal"><span class="pre">setFluidBottomFixedPressure()</span></tt></a>.</p>
        </dd></dl>
       t@@ -1511,7 +1580,16 @@ value (Dirichlet) boundary condition.</p>
        <dt id="sphere.sim.setFluidTopNoFlow">
        <tt class="descname">setFluidTopNoFlow</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.setFluidTopNoFlow" title="Permalink to this definition">¶</a></dt>
        <dd><p>Set the upper boundary of the fluid domain to follow the no-flow
       -(Neumann) boundary condition.</p>
       +(Neumann) boundary condition with free slip parallel to the boundary.</p>
       +<p>The default behavior for the boundary is fixed value (Dirichlet), see
       +<a class="reference internal" href="#sphere.sim.setFluidTopFixedPressure" title="sphere.sim.setFluidTopFixedPressure"><tt class="xref py py-func docutils literal"><span class="pre">setFluidTopFixedPressure()</span></tt></a>.</p>
       +</dd></dl>
       +
       +<dl class="method">
       +<dt id="sphere.sim.setFluidTopNoFlowNoSlip">
       +<tt class="descname">setFluidTopNoFlowNoSlip</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.setFluidTopNoFlowNoSlip" title="Permalink to this definition">¶</a></dt>
       +<dd><p>Set the upper boundary of the fluid domain to follow the no-flow
       +(Neumann) boundary condition with no slip parallel to the boundary.</p>
        <p>The default behavior for the boundary is fixed value (Dirichlet), see
        <a class="reference internal" href="#sphere.sim.setFluidTopFixedPressure" title="sphere.sim.setFluidTopFixedPressure"><tt class="xref py py-func docutils literal"><span class="pre">setFluidTopFixedPressure()</span></tt></a>.</p>
        </dd></dl>
       t@@ -1638,6 +1716,24 @@ displacement of the upper, fixed particles.</p>
        </tr>
        </tbody>
        </table>
       +<p>:see also:<cite>func:shearStrainRate()</cite>,`func:shearVel()`</p>
       +</dd></dl>
       +
       +<dl class="method">
       +<dt id="sphere.sim.shearStrainRate">
       +<tt class="descname">shearStrainRate</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.shearStrainRate" title="Permalink to this definition">¶</a></dt>
       +<dd><p>Calculates the shear strain rate (dot(gamma)) value of the experiment.</p>
       +<table class="docutils field-list" frame="void" rules="none">
       +<col class="field-name" />
       +<col class="field-body" />
       +<tbody valign="top">
       +<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The value of $I$</td>
       +</tr>
       +<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">float</td>
       +</tr>
       +</tbody>
       +</table>
       +<p>:see also:<cite>func:shearStrain()</cite>,`func:shearVel()`</p>
        </dd></dl>
        
        <dl class="method">
       t@@ -1656,6 +1752,7 @@ upper particles.</p>
        </tr>
        </tbody>
        </table>
       +<p>:see also:<cite>func:shearStrainRate()</cite>,`func:shearStrain()`</p>
        </dd></dl>
        
        <dl class="method">
       t@@ -2058,11 +2155,11 @@ The vtu files can be used to visualize the particles in ParaView.</p>
        session. The particles are visualized by selecting the imported data in
        the &#8220;Pipeline Browser&#8221;. Afterwards, click the &#8220;Glyph&#8221; button in the
        &#8220;Common&#8221; toolbar, or go to the &#8220;Filters&#8221; menu, and press &#8220;Glyph&#8221; from
       -the &#8220;Common&#8221; list. Choose &#8220;Sphere&#8221; as the &#8220;Glyph Type&#8221;, set &#8220;Radius&#8221; to
       -1.0, choose &#8220;scalar&#8221; as the &#8220;Scale Mode&#8221;. Check the &#8220;Edit&#8221; checkbox, and
       -set the &#8220;Set Scale Factor&#8221; to 1.0. The field &#8220;Maximum Number of Points&#8221;
       -may be increased if the number of particles exceed the default value.
       -Finally press &#8220;Apply&#8221;, and the particles will appear in the main window.</p>
       +the &#8220;Common&#8221; list. Choose &#8220;Sphere&#8221; as the &#8220;Glyph Type&#8221;, choose &#8220;scalar&#8221;
       +as the &#8220;Scale Mode&#8221;. Check the &#8220;Edit&#8221; checkbox, and set the &#8220;Set Scale
       +Factor&#8221; to 1.0. The field &#8220;Maximum Number of Points&#8221; may be increased if
       +the number of particles exceed the default value. Finally press &#8220;Apply&#8221;,
       +and the particles will appear in the main window.</p>
        <p>The sphere resolution may be adjusted (&#8220;Theta resolution&#8221;, &#8220;Phi
        resolution&#8221;) to increase the quality and the computational requirements
        of the rendering. All adjustments by default require the &#8220;Apply&#8221; button
 (DIR) diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
       t@@ -1 +1 @@
       -Search.setIndex({objects:{"":{sphere:[5,0,1,""]},sphere:{status:[5,1,1,""],convert:[5,1,1,""],run:[5,1,1,""],render:[5,1,1,""],thinsectionVideo:[5,1,1,""],torqueScriptParallel3:[5,1,1,""],V_sphere:[5,1,1,""],cleanup:[5,1,1,""],video:[5,1,1,""],sim:[5,3,1,""]},"sphere.sim":{setFluidTopFixedPressure:[5,2,1,""],totalFrictionalEnergy:[5,2,1,""],setTheta:[5,2,1,""],setTolerance:[5,2,1,""],generateBimodalRadii:[5,2,1,""],defaultParams:[5,2,1,""],initRandomGridPos:[5,2,1,""],porosity:[5,2,1,""],writebin:[5,2,1,""],momentum:[5,2,1,""],thinsection_x1x3:[5,2,1,""],largestMass:[5,2,1,""],readbin:[5,2,1,""],writeFluidVTK:[5,2,1,""],kineticEnergy:[5,2,1,""],defineWorldBoundaries:[5,2,1,""],uniaxialStrainRate:[5,2,1,""],readlast:[5,2,1,""],bond:[5,2,1,""],consolidate:[5,2,1,""],setDampingNormal:[5,2,1,""],energy:[5,2,1,""],disableFluidPressureModulation:[5,2,1,""],video:[5,2,1,""],initRandomPos:[5,2,1,""],writeVTKall:[5,2,1,""],frictionalEnergy:[5,2,1,""],smallestMass:[5,2,1,""],zeroKinematics:[5,2,1,""],visualize:[5,2,1,""],randomBondPairs:[5,2,1,""],setBeta:[5,2,1,""],setDEMstepsPerCFDstep:[5,2,1,""],run:[5,2,1,""],deleteParticle:[5,2,1,""],setGamma:[5,2,1,""],plotFluidVelocitiesZ:[5,2,1,""],plotFluidVelocitiesY:[5,2,1,""],forcechainsRose:[5,2,1,""],adjustUpperWall:[5,2,1,""],setFluidTopNoFlow:[5,2,1,""],viscousEnergy:[5,2,1,""],readsecond:[5,2,1,""],plotPrescribedFluidPressures:[5,2,1,""],forcechains:[5,2,1,""],render:[5,2,1,""],triaxial:[5,2,1,""],rotationalEnergy:[5,2,1,""],initGrid:[5,2,1,""],readfirst:[5,2,1,""],periodicBoundariesX:[5,2,1,""],sheardisp:[5,2,1,""],totalRotationalEnergy:[5,2,1,""],adjustWall:[5,2,1,""],setFluidPressureModulation:[5,2,1,""],initFluid:[5,2,1,""],volume:[5,2,1,""],normalBoundariesXY:[5,2,1,""],bulkPorosity:[5,2,1,""],setFluidBottomNoFlow:[5,2,1,""],createBondPair:[5,2,1,""],torqueScript:[5,2,1,""],generateRadii:[5,2,1,""],periodicBoundariesXY:[5,2,1,""],shearStrain:[5,2,1,""],deleteAllParticles:[5,2,1,""],shear:[5,2,1,""],initTemporal:[5,2,1,""],setMaxIterations:[5,2,1,""],initGridAndWorldsize:[5,2,1,""],totalMomentum:[5,2,1,""],shearVel:[5,2,1,""],porosities:[5,2,1,""],readstep:[5,2,1,""],acceleration:[5,2,1,""],plotFluidDiffAdvPresZ:[5,2,1,""],writeVTK:[5,2,1,""],bondsRose:[5,2,1,""],cleanup:[5,2,1,""],addParticle:[5,2,1,""],setFluidBottomFixedPressure:[5,2,1,""],currentNormalStress:[5,2,1,""],plotConvergence:[5,2,1,""],status:[5,2,1,""],voidRatio:[5,2,1,""],momentOfInertia:[5,2,1,""],totalViscousEnergy:[5,2,1,""],setDampingTangential:[5,2,1,""],totalKineticEnergy:[5,2,1,""],initGridPos:[5,2,1,""],plotFluidPressuresY:[5,2,1,""],plotFluidPressuresZ:[5,2,1,""],mass:[5,2,1,""],contactModel:[5,2,1,""]}},terms:{prefix:3,whose:[],s_law:[],"const":3,under:[1,0,5],everi:2,"void":[3,5],readbin:[3,5],mp4:5,vector:[3,2,4,5],bulkporos:5,p_f:5,seper:3,direct:[4,5],second:[3,2,4,5],even:[3,4],supervis:0,hide:5,neg:[2,4,5],lundbek:0,"new":[2,4,5],symmetr:2,topolog:3,behavior:[1,4,5],here:2,path:[1,5],interpret:1,dry:[3,5],initgridandworlds:5,precis:[3,5],linearli:[2,5],releas:1,instabl:5,total:[3,2,4,5],univ:[],unit:1,plot:5,describ:[2,4],initfluid:5,call:[3,5],recommend:5,type:[1,3,4,5],relax:5,successful:1,relat:3,warn:5,exce:[2,5],loss:[4,5],must:5,setup:[1,5],work:[1,0,5],setfluidtopnoflow:5,coalesc:3,root:[1,3,5],unnam:5,kinet:[4,5],give:3,img_width:3,indic:0,want:2,readstep:5,keep:[1,2],unsign:3,setdemstepspercfdstep:5,end:[3,2,5],mu_w:5,travel:3,mu_r:5,how:[3,5],env:5,place:[1,3,5],mu_d:5,updat:[1,0,2,3],after:[1,3,2,5],befor:[3,5],wrong:[],mesh:5,law:[3,2,4],parallel:[1,2,5],averag:[2,5],third:[0,2,5],maintain:1,environ:1,incorpor:2,enter:2,exclus:5,order:[1,3,2,4,5],oper:[1,0,2,3],over:4,visc_n_rat:5,pascal:5,flexibl:[1,2],totalviscousenergi:5,img:[],fix:5,welcome_:[],fig:3,hidden:[],shear:[2,5],them:5,anim:5,thei:[3,2],choic:[],include_cod:[],arrow:5,each:[3,2,4,5],angvel:[3,5],side:[2,5],mean:[1,2,5],pdflatex:1,logn:5,euler_method:[],network:4,gradient:[2,5],content:0,rewrit:2,gov:[],linear:[2,4,5],slipscal:5,situat:2,free:[1,2],standard:5,configuraion:3,angl:5,filter:5,isn:[2,5],rang:[2,5],render:[1,3,5],restrict:1,hook:[],instruct:1,thick:5,sort_by_kei:3,advect:[2,5],top:[2,5],evolut:[3,5],addparticl:5,tool:1,bondsros:5,max_val:5,somewhat:[4,5],conserv:[2,5],target:[3,5],provid:1,zero:[3,2,4,5],project:[0,2,5],matter:4,rad:5,setfluidpressuremodul:5,xdisp:[3,5],ram:3,rai:[1,5],raw:4,seed:4,increment:4,ldot:3,latter:4,blue:5,though:[3,4],object:[1,5],regular:5,phase:[2,5],prematur:5,don:3,doc:1,flow:[1,0,2,5],vector_norm:[],sum:[2,4,5],dot:4,radix:3,opposit:2,random:[3,5],radiu:[2,4,5],radii:5,pkg:1,involv:3,consolid:5,layout:3,menu:5,explain:[3,0],configur:[1,3,5],settheta:5,folder:[1,3,5],loopstart:3,stop:5,fluid:[0,2,4,5],net:3,bar:5,cuda_sdk_root_dir:1,"public":[1,3],mu_:5,datatyp:3,result:[1,3,2,4,5],elasto:5,deleteallparticl:5,fail:[],best:[1,5],tensor:2,wikipedia:5,figur:3,simplest:4,angpo:[3,5],approach:2,attribut:2,extend:[],cfdem:[],toler:[2,5],subfold:3,howev:[3,4],kineticene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 (DIR) diff --git a/doc/html/sphere_internals.html b/doc/html/sphere_internals.html
       t@@ -243,8 +243,8 @@ An important note is that the texttt{C} examples of the NVIDIA CUDA SDK should b
        <div><p></p>
        <p></p>
        <em>Public Functions</em><blockquote>
       -<div><p id=""><span id="project0classDEM_1a59ab83e9cbdb7bbeb3f43564fbb294b4"></span><div class="line-block">
       -<div class="line"> <strong>DEM</strong>(std::string inputbin, const int verbosity = 1, const int checkVals = 1, const int dry = 0, const int initCuda = 1, const int transferConstMem = 1, const int darcyflow = 0)</div>
       +<div><p id=""><span id="project0classDEM_1a991dd9d5ffe9935e1105d3c024a06a8c"></span><div class="line-block">
       +<div class="line"> <strong>DEM</strong>(std::string inputbin, const int verbosity = 1, const int checkVals = 1, const int dry = 0, const int initCuda = 1, const int transferConstMem = 1, const int fluidFlow = 0, const int exclusive = 0)</div>
        </div>
        </p>
        <blockquote>
 (DIR) diff --git a/doc/pdf/sphere.pdf b/doc/pdf/sphere.pdf
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