trebuilt documentation - sphere - GPU-based 3D discrete element method algorithm with optional fluid coupling
(HTM) git clone git://src.adamsgaard.dk/sphere
(DIR) Log
(DIR) Files
(DIR) Refs
(DIR) LICENSE
---
(DIR) commit 85cb16e537cf83c60149c96f1b0f4a565382ef1c
(DIR) parent f9bbc90bd68dfd3516e9e50bb9fd7333caf5f85c
(HTM) Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
Date: Fri, 20 Jun 2014 22:48:44 +0200
rebuilt documentation
Diffstat:
M doc/html/genindex.html | 105 ++++++++++++++++++++++++++++---
M doc/html/objects.inv | 0
M doc/html/python_api.html | 314 ++++++++++++++++++++++++++++---
M doc/html/searchindex.js | 4 ++--
M doc/pdf/sphere.pdf | 0
5 files changed, 391 insertions(+), 32 deletions(-)
---
(DIR) diff --git a/doc/html/genindex.html b/doc/html/genindex.html
t@@ -61,6 +61,9 @@
| <a href="#F"><strong>F</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#I"><strong>I</strong></a>
+ | <a href="#K"><strong>K</strong></a>
+ | <a href="#L"><strong>L</strong></a>
+ | <a href="#M"><strong>M</strong></a>
| <a href="#N"><strong>N</strong></a>
| <a href="#P"><strong>P</strong></a>
| <a href="#R"><strong>R</strong></a>
t@@ -165,10 +168,14 @@
<dt><a href="python_api.html#sphere.sim.defineWorldBoundaries">defineWorldBoundaries() (sphere.sim method)</a>
</dt>
+
+ <dt><a href="python_api.html#sphere.sim.deleteAllParticles">deleteAllParticles() (sphere.sim method)</a>
+ </dt>
+
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="python_api.html#sphere.sim.deleteAllParticles">deleteAllParticles() (sphere.sim method)</a>
+ <dt><a href="python_api.html#sphere.sim.deleteParticle">deleteParticle() (sphere.sim method)</a>
</dt>
t@@ -195,10 +202,14 @@
<dt><a href="python_api.html#sphere.sim.forcechains">forcechains() (sphere.sim method)</a>
</dt>
+
+ <dt><a href="python_api.html#sphere.sim.forcechainsRose">forcechainsRose() (sphere.sim method)</a>
+ </dt>
+
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="python_api.html#sphere.sim.forcechainsRose">forcechainsRose() (sphere.sim method)</a>
+ <dt><a href="python_api.html#sphere.sim.frictionalEnergy">frictionalEnergy() (sphere.sim method)</a>
</dt>
</dl></td>
t@@ -256,6 +267,46 @@
</dl></td>
</tr></table>
+<h2 id="K">K</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="python_api.html#sphere.sim.kineticEnergy">kineticEnergy() (sphere.sim method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="python_api.html#sphere.sim.largestMass">largestMass() (sphere.sim method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="M">M</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="python_api.html#sphere.sim.mass">mass() (sphere.sim method)</a>
+ </dt>
+
+
+ <dt><a href="python_api.html#sphere.sim.momentOfInertia">momentOfInertia() (sphere.sim method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="python_api.html#sphere.sim.momentum">momentum() (sphere.sim method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
t@@ -337,12 +388,12 @@
<dt><a href="python_api.html#sphere.sim.readlast">readlast() (sphere.sim method)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="python_api.html#sphere.sim.readsecond">readsecond() (sphere.sim method)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="python_api.html#sphere.sim.readstep">readstep() (sphere.sim method)</a>
</dt>
t@@ -358,6 +409,10 @@
</dl></dd>
+ <dt><a href="python_api.html#sphere.sim.rotationalEnergy">rotationalEnergy() (sphere.sim method)</a>
+ </dt>
+
+
<dt><a href="python_api.html#sphere.run">run() (in module sphere)</a>
</dt>
t@@ -378,6 +433,14 @@
</dt>
+ <dt><a href="python_api.html#sphere.sim.setDampingNormal">setDampingNormal() (sphere.sim method)</a>
+ </dt>
+
+
+ <dt><a href="python_api.html#sphere.sim.setDampingTangential">setDampingTangential() (sphere.sim method)</a>
+ </dt>
+
+
<dt><a href="python_api.html#sphere.sim.setDEMstepsPerCFDstep">setDEMstepsPerCFDstep() (sphere.sim method)</a>
</dt>
t@@ -440,6 +503,10 @@
</dt>
+ <dt><a href="python_api.html#sphere.sim.smallestMass">smallestMass() (sphere.sim method)</a>
+ </dt>
+
+
<dt><a href="python_api.html#module-sphere">sphere (module)</a>
</dt>
t@@ -471,10 +538,18 @@
<dt><a href="python_api.html#sphere.sim.torqueScript">torqueScript() (sphere.sim method)</a>
</dt>
+
+ <dt><a href="python_api.html#sphere.torqueScriptParallel3">torqueScriptParallel3() (in module sphere)</a>
+ </dt>
+
+
+ <dt><a href="python_api.html#sphere.sim.totalFrictionalEnergy">totalFrictionalEnergy() (sphere.sim method)</a>
+ </dt>
+
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="python_api.html#sphere.torqueScriptParallel3">torqueScriptParallel3() (in module sphere)</a>
+ <dt><a href="python_api.html#sphere.sim.totalKineticEnergy">totalKineticEnergy() (sphere.sim method)</a>
</dt>
t@@ -482,6 +557,14 @@
</dt>
+ <dt><a href="python_api.html#sphere.sim.totalRotationalEnergy">totalRotationalEnergy() (sphere.sim method)</a>
+ </dt>
+
+
+ <dt><a href="python_api.html#sphere.sim.totalViscousEnergy">totalViscousEnergy() (sphere.sim method)</a>
+ </dt>
+
+
<dt><a href="python_api.html#sphere.sim.triaxial">triaxial() (sphere.sim method)</a>
</dt>
t@@ -506,10 +589,6 @@
</dt>
- <dt><a href="python_api.html#sphere.vector_norm">vector_norm() (in module sphere)</a>
- </dt>
-
-
<dt><a href="python_api.html#sphere.video">video() (in module sphere)</a>
</dt>
t@@ -519,6 +598,10 @@
</dt>
</dl></dd>
+
+ <dt><a href="python_api.html#sphere.sim.viscousEnergy">viscousEnergy() (sphere.sim method)</a>
+ </dt>
+
</dl></td>
<td style="width: 33%" valign="top"><dl>
t@@ -529,6 +612,10 @@
<dt><a href="python_api.html#sphere.sim.voidRatio">voidRatio() (sphere.sim method)</a>
</dt>
+
+ <dt><a href="python_api.html#sphere.sim.volume">volume() (sphere.sim method)</a>
+ </dt>
+
</dl></td>
</tr></table>
(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@@ -328,7 +328,7 @@ are returned.</p>
<dl class="method">
<dt id="sphere.sim.addParticle">
-<tt class="descname">addParticle</tt><big>(</big><em>x</em>, <em>radius</em>, <em>xysum=array([ 0.</em>, <em>0.])</em>, <em>vel=array([ 0.</em>, <em>0.</em>, <em>0.])</em>, <em>fixvel=array([ 0.])</em>, <em>force=array([ 0.</em>, <em>0.</em>, <em>0.])</em>, <em>angpos=array([ 0.</em>, <em>0.</em>, <em>0.])</em>, <em>angvel=array([ 0.</em>, <em>0.</em>, <em>0.])</em>, <em>torque=array([ 0.</em>, <em>0.</em>, <em>0.])</em>, <em>es_dot=array([ 0.])</em>, <em>es=array([ 0.])</em>, <em>ev_dot=array([ 0.])</em>, <em>ev=array([ 0.])</em>, <em>p=array([ 0.])</em><big>)</big><a class="headerlink" href="#sphere.sim.addParticle" title="Permalink to this definition">¶</a></dt>
+<tt class="descname">addParticle</tt><big>(</big><em>x</em>, <em>radius</em>, <em>xysum=array([ 0.</em>, <em>0.])</em>, <em>vel=array([ 0.</em>, <em>0.</em>, <em>0.])</em>, <em>fixvel=array([ 0.])</em>, <em>force=array([ 0.</em>, <em>0.</em>, <em>0.])</em>, <em>angpos=array([ 0.</em>, <em>0.</em>, <em>0.])</em>, <em>angvel=array([ 0.</em>, <em>0.</em>, <em>0.])</em>, <em>torque=array([ 0.</em>, <em>0.</em>, <em>0.])</em>, <em>es_dot=array([ 0.])</em>, <em>es=array([ 0.])</em>, <em>ev_dot=array([ 0.])</em>, <em>ev=array([ 0.])</em>, <em>p=array([ 0.])</em>, <em>color=0</em><big>)</big><a class="headerlink" href="#sphere.sim.addParticle" title="Permalink to this definition">¶</a></dt>
<dd><p>Add a single particle to the simulation object. The only required
parameters are the position (x) and the radius (radius).</p>
<table class="docutils field-list" frame="void" rules="none">
t@@ -587,6 +587,20 @@ won’t work. Default = [0.0, 0.0, 0.0].</li>
</dd></dl>
<dl class="method">
+<dt id="sphere.sim.deleteParticle">
+<tt class="descname">deleteParticle</tt><big>(</big><em>i</em><big>)</big><a class="headerlink" href="#sphere.sim.deleteParticle" title="Permalink to this definition">¶</a></dt>
+<dd><p>Delete particle with index <tt class="docutils literal"><span class="pre">i</span></tt>.</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>i</strong> (<em>int</em>) – Particle index to delete</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.disableFluidPressureModulation">
<tt class="descname">disableFluidPressureModulation</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.disableFluidPressureModulation" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the parameters for the sine wave modulating the fluid pressures
t@@ -665,6 +679,24 @@ contact force magnitude, in ]0;1[</li>
</dd></dl>
<dl class="method">
+<dt id="sphere.sim.frictionalEnergy">
+<tt class="descname">frictionalEnergy</tt><big>(</big><em>idx</em><big>)</big><a class="headerlink" href="#sphere.sim.frictionalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the frictional dissipated energy for a particle.</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>idx</strong> (<em>int</em>) – Particle index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The frictional energy lost of the particle [J]</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.generateBimodalRadii">
<tt class="descname">generateBimodalRadii</tt><big>(</big><em>r_small=0.005</em>, <em>r_large=0.05</em>, <em>ratio=0.2</em>, <em>verbose=True</em><big>)</big><a class="headerlink" href="#sphere.sim.generateBimodalRadii" title="Permalink to this definition">¶</a></dt>
<dd><p>Draw random radii from two distinct sizes.</p>
t@@ -841,7 +873,7 @@ make space for their radii within the bounding box.</p>
<dl class="method">
<dt id="sphere.sim.initTemporal">
-<tt class="descname">initTemporal</tt><big>(</big><em>total</em>, <em>current=0.0</em>, <em>file_dt=0.05</em>, <em>step_count=0</em>, <em>dt=-1</em><big>)</big><a class="headerlink" href="#sphere.sim.initTemporal" title="Permalink to this definition">¶</a></dt>
+<tt class="descname">initTemporal</tt><big>(</big><em>total</em>, <em>current=0.0</em>, <em>file_dt=0.05</em>, <em>step_count=0</em>, <em>dt=-1</em>, <em>epsilon=0.01</em><big>)</big><a class="headerlink" href="#sphere.sim.initTemporal" title="Permalink to this definition">¶</a></dt>
<dd><p>Set temporal parameters for the simulation. <em>Important</em>: Particle radii,
physical parameters, and the optional fluid grid need to be set prior to
these if the computational time step (dt) isn’t set explicitly. If the
t@@ -858,6 +890,7 @@ included.</p>
<li><strong>current</strong> – The current time [s] (default = 0.0 s)</li>
<li><strong>file_dt</strong> – The interval between output files [s] (default = 0.05 s)</li>
<li><strong>dt</strong> – The computational time step length [s]</li>
+<li><strong>epsilon</strong> (<em>float</em>) – Time step multiplier (default = 0.01)</li>
</ul>
</td>
</tr>
t@@ -869,6 +902,96 @@ included.</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>
+<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>idx</strong> (<em>int</em>) – Particle index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The kinetic energy of the particle [J]</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sphere.sim.largestMass">
+<tt class="descname">largestMass</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.largestMass" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the mass of the heaviest particle.</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>idx</strong> (<em>int</em>) – Particle index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The mass of the particle [kg]</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sphere.sim.mass">
+<tt class="descname">mass</tt><big>(</big><em>idx</em><big>)</big><a class="headerlink" href="#sphere.sim.mass" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the mass of a particle.</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>idx</strong> (<em>int</em>) – Particle index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The mass of the particle [kg]</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sphere.sim.momentOfInertia">
+<tt class="descname">momentOfInertia</tt><big>(</big><em>idx</em><big>)</big><a class="headerlink" href="#sphere.sim.momentOfInertia" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the moment of inertia of a particle.</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>idx</strong> (<em>int</em>) – Particle index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The moment of inertia [kg*m^2]</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sphere.sim.momentum">
+<tt class="descname">momentum</tt><big>(</big><em>idx</em><big>)</big><a class="headerlink" href="#sphere.sim.momentum" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the momentum (m*v) of a particle.</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>idx</strong> (<em>int</em>) – The particle index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The particle momentum [N*s]</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">numpy.array</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.normalBoundariesXY">
<tt class="descname">normalBoundariesXY</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.normalBoundariesXY" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the x and y boundary conditions to be static walls.</p>
t@@ -1223,6 +1346,24 @@ tracer to this image format using Imagemagick</li>
</dd></dl>
<dl class="method">
+<dt id="sphere.sim.rotationalEnergy">
+<tt class="descname">rotationalEnergy</tt><big>(</big><em>idx</em><big>)</big><a class="headerlink" href="#sphere.sim.rotationalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the rotational energy for a particle.</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>idx</strong> (<em>int</em>) – Particle index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The rotational kinetic energy of the particle [J]</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<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>
<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>
t@@ -1285,6 +1426,40 @@ number of DEM time steps to be performed per CFD time step.</p>
</dd></dl>
<dl class="method">
+<dt id="sphere.sim.setDampingNormal">
+<tt class="descname">setDampingNormal</tt><big>(</big><em>gamma</em><big>)</big><a class="headerlink" href="#sphere.sim.setDampingNormal" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the dampening coefficient (gamma) in the normal direction of the
+particle-particle contact model. The function will print the fraction
+between the chosen damping and the critical damping value.</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>gamma</strong> (<em>float</em>) – The viscous damping constant [N/(m/s)]</td>
+</tr>
+</tbody>
+</table>
+<p>:see also:<cite>func:setDampingTangential(gamma)</cite></p>
+</dd></dl>
+
+<dl class="method">
+<dt id="sphere.sim.setDampingTangential">
+<tt class="descname">setDampingTangential</tt><big>(</big><em>gamma</em><big>)</big><a class="headerlink" href="#sphere.sim.setDampingTangential" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the dampening coefficient (gamma) in the tangential direction of the
+particle-particle contact model. The function will print the fraction
+between the chosen damping and the critical damping value.</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>gamma</strong> (<em>float</em>) – The viscous damping constant [N/(m/s)]</td>
+</tr>
+</tbody>
+</table>
+<p>:see also:<cite>func:setDampingNormal(gamma)</cite></p>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.setFluidBottomFixedPressure">
<tt class="descname">setFluidBottomFixedPressure</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.setFluidBottomFixedPressure" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the lower boundary of the fluid domain to follow the fixed pressure
t@@ -1349,7 +1524,7 @@ values. The epsilon (pressure) values are smoothed by including the
average epsilon value of the six closest (face) neighbor cells. This
parameter should be in the range [0.0;1.0[. The higher the value, the
more averaging is introduced. A value of 0.0 disables all averaging.</p>
-<p>The default and recommended value is 0.5.</p>
+<p>The default and recommended value is 0.0.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
t@@ -1500,6 +1675,24 @@ file name ‘<simulation id>-sheardisp.<graphics_format>’.
</dd></dl>
<dl class="method">
+<dt id="sphere.sim.smallestMass">
+<tt class="descname">smallestMass</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.smallestMass" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the mass of the leightest particle.</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>idx</strong> (<em>int</em>) – Particle index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The mass of the particle [kg]</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.status">
<tt class="descname">status</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.status" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the current simulation status by using the simulation id
t@@ -1586,6 +1779,36 @@ folder</li>
</dd></dl>
<dl class="method">
+<dt id="sphere.sim.totalFrictionalEnergy">
+<tt class="descname">totalFrictionalEnergy</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.totalFrictionalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the total frictional dissipated energy for all particles.</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 total frictional energy lost of all particles [J]</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sphere.sim.totalKineticEnergy">
+<tt class="descname">totalKineticEnergy</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.totalKineticEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the total linear kinetic energy for all particles.</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 kinetic energy of all particles [J]</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.totalMomentum">
<tt class="descname">totalMomentum</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.totalMomentum" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the sum of particle momentums.</p>
t@@ -1595,6 +1818,36 @@ folder</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The sum of particle momentums (m*v) [N*s]</td>
</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">numpy.array</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sphere.sim.totalRotationalEnergy">
+<tt class="descname">totalRotationalEnergy</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.totalRotationalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the total rotational kinetic energy for all particles.</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 rotational energy of all particles [J]</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="sphere.sim.totalViscousEnergy">
+<tt class="descname">totalViscousEnergy</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.totalViscousEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the total viscous dissipated energy for all particles.</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 normal viscous energy lost by all particles [J]</td>
+</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">float</td>
</tr>
</tbody>
t@@ -1664,6 +1917,24 @@ rendered beforehand using func:<cite>render()</cite>.</p>
</dd></dl>
<dl class="method">
+<dt id="sphere.sim.viscousEnergy">
+<tt class="descname">viscousEnergy</tt><big>(</big><em>idx</em><big>)</big><a class="headerlink" href="#sphere.sim.viscousEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the viscous dissipated energy for a particle.</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>idx</strong> (<em>int</em>) – Particle index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The energy lost by the particle by viscous dissipation [J]</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.visualize">
<tt class="descname">visualize</tt><big>(</big><em>method='energy'</em>, <em>savefig=True</em>, <em>outformat='png'</em><big>)</big><a class="headerlink" href="#sphere.sim.visualize" title="Permalink to this definition">¶</a></dt>
<dd><p>Visualize output from the simulation, where the temporal progress is
t@@ -1704,6 +1975,24 @@ image format, or in text (‘txt’).</li>
</dd></dl>
<dl class="method">
+<dt id="sphere.sim.volume">
+<tt class="descname">volume</tt><big>(</big><em>idx</em><big>)</big><a class="headerlink" href="#sphere.sim.volume" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the volume of a particle.</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>idx</strong> (<em>int</em>) – Particle index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The volume of the particle [m^3]</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.writeFluidVTK">
<tt class="descname">writeFluidVTK</tt><big>(</big><em>folder='../output/'</em>, <em>cell_centered=True</em>, <em>verbose=True</em><big>)</big><a class="headerlink" href="#sphere.sim.writeFluidVTK" title="Permalink to this definition">¶</a></dt>
<dd><p>Writes a VTK file for the fluid grid to the <tt class="docutils literal"><span class="pre">../output/</span></tt> folder by
t@@ -1798,7 +2087,7 @@ visualization through time by using the ParaView controls.</p>
<dl class="method">
<dt id="sphere.sim.writeVTKall">
-<tt class="descname">writeVTKall</tt><big>(</big><em>verbose=True</em><big>)</big><a class="headerlink" href="#sphere.sim.writeVTKall" title="Permalink to this definition">¶</a></dt>
+<tt class="descname">writeVTKall</tt><big>(</big><em>cell_centered=True</em>, <em>verbose=True</em><big>)</big><a class="headerlink" href="#sphere.sim.writeVTKall" title="Permalink to this definition">¶</a></dt>
<dd><p>Writes a VTK file for each simulation output file with particle
information and the fluid grid to the <tt class="docutils literal"><span class="pre">../output/</span></tt> folder by default.
The file name will be in the format <tt class="docutils literal"><span class="pre"><self.sid>.vtu</span></tt> and
t@@ -1960,23 +2249,6 @@ in any order.</li>
</dd></dl>
<dl class="function">
-<dt id="sphere.vector_norm">
-<tt class="descclassname">sphere.</tt><tt class="descname">vector_norm</tt><big>(</big><em>ndvector</em><big>)</big><a class="headerlink" href="#sphere.vector_norm" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns a 1D vector of normalized values. The input array should have
-one row per particle, and three rows; one per Euclidean axis.</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">A value of the velocity magnutude per particle</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">numpy.array</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
<dt id="sphere.video">
<tt class="descclassname">sphere.</tt><tt class="descname">video</tt><big>(</big><em>project</em>, <em>out_folder='./'</em>, <em>video_format='mp4'</em>, <em>graphics_folder='../img_out/'</em>, <em>graphics_format='png'</em>, <em>fps=25</em>, <em>qscale=1</em>, <em>bitrate=1800</em>, <em>verbose=False</em><big>)</big><a class="headerlink" href="#sphere.video" title="Permalink to this definition">¶</a></dt>
<dd><p>Uses ffmpeg to combine images to animation. All images should be
(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,""],vector_norm:[5,1,1,""],cleanup:[5,1,1,""],video:[5,1,1,""],sim:[5,3,1,""]},"sphere.sim":{consolidate:[5,2,1,""],forcechains:[5,2,1,""],initGridAndWorldsize:[5,2,1,""],initRandomPos:[5,2,1,""],render:[5,2,1,""],readsecond:[5,2,1,""],energy:[5,2,1,""],setFluidTopFixedPressure:[5,2,1,""],disableFluidPressureModulation:[5,2,1,""],plotPrescribedFluidPressures:[5,2,1,""],totalMomentum:[5,2,1,""],plotFluidPressuresY:[5,2,1,""],shearVel:[5,2,1,""],porosities:[5,2,1,""],initGrid:[5,2,1,""],readfirst:[5,2,1,""],writeVTKall:[5,2,1,""],setTolerance:[5,2,1,""],readstep:[5,2,1,""],initRandomGridPos:[5,2,1,""],acceleration:[5,2,1,""],defaultParams:[5,2,1,""],zeroKinematics:[5,2,1,""],visualize:[5,2,1,""],readbin:[5,2,1,""],randomBondPairs:[5,2,1,""],setFluidTopNoFlow:[5,2,1,""],periodicBoundariesX:[5,2,1,""],sheardisp:[5,2,1,""],writeVTK:[5,2,1,""],writebin:[5,2,1,""],setBeta:[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,""],periodicBoundariesXY:[5,2,1,""],porosity:[5,2,1,""],setDEMstepsPerCFDstep:[5,2,1,""],status:[5,2,1,""],generateBimodalRadii:[5,2,1,""],thinsection_x1x3:[5,2,1,""],run:[5,2,1,""],setFluidPressureModulation:[5,2,1,""],voidRatio:[5,2,1,""],plotFluidDiffAdvPresZ:[5,2,1,""],initFluid:[5,2,1,""],setGamma:[5,2,1,""],plotFluidVelocitiesZ:[5,2,1,""],writeFluidVTK:[5,2,1,""],plotFluidVelocitiesY:[5,2,1,""],normalBoundariesXY:[5,2,1,""],defineWorldBoundaries:[5,2,1,""],forcechainsRose:[5,2,1,""],bulkPorosity:[5,2,1,""],setFluidBottomNoFlow:[5,2,1,""],createBondPair:[5,2,1,""],setTheta:[5,2,1,""],torqueScript:[5,2,1,""],adjustUpperWall:[5,2,1,""],generateRadii:[5,2,1,""],uniaxialStrainRate:[5,2,1,""],adjustWall:[5,2,1,""],initGridPos:[5,2,1,""],shearStrain:[5,2,1,""],deleteAllParticles:[5,2,1,""],plotFluidPressuresZ:[5,2,1,""],readlast:[5,2,1,""],shear:[5,2,1,""],video:[5,2,1,""],triaxial:[5,2,1,""],bond:[5,2,1,""],initTemporal:[5,2,1,""],setMaxIterations:[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],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:5,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],against:5,uni:5,browser:5,com:[1,3,5],pre:[3,5],height:5,guid:[3,0],assum:[2,5],gamma_n:5,numpi:[1,5],three:[1,3,2,4,5],been:[4,5],spherebin:5,interest:[0,5],gamma_t:5,gamma_r:5,suppress:3,search:[3,0,4],emploi:3,ident:2,cudamemcheck:5,plotconverg:5,gnu:[1,3],properti:[1,2,5],setfluidtopfixedpressur:5,aim:[1,0],euclidean:5,calcul:[3,2,4,5],seven:2,conv:5,tabl:0,toolkit:1,shami:2,sever:[3,5],perform:[1,3,5],make:[1,3,5],transpar:5,complex:[],split:[0,2],dimensionless:2,complet:5,hang:5,hand:[3,2,4],kin:5,"0e3f":3,thu:3,contact:[3,0,2,4,5],thi:[0,1,2,3,4,5],left:5,identifi:[3,4,5],savefig:5,newton:[3,2,4],yet:4,previous:[2,5],expos:1,character:[2,4],save:5,applic:[3,5],dissip:4,mennu:5,background:[3,2],maxval:3,specif:[1,3],initcuda:3,www:[],right:[2,5],old:[2,5],deal:2,interv:[3,5],maxim:[2,5],intern:[1,3],maxit:5,raytrac:[3,5],txt:[1,5],bottom:2,ev_dot:5,adjustwal:5,condit:[1,0,2,5],core:[],bold:4,torquescriptparallel3:5,post:[4,5],zerokinemat:5,simul:[0,1,2,3,4,5],coars:5,produc:5,step_count:5,"float":[3,5],bound:5,ppm:5,readfirst:5,wrap:3,often:3,git:1,wai:[1,3,5],gridnum:5,support:1,avail:1,width:[2,5],fraction:2,analysi:[1,5],medium:2,form:[3,2,4],forc:[3,2,4,5],epsilon:5,setbeta:5,berg:4,"true":5,again:1,bugfix:1,maximum:5,dens:3,inaccur:4,fermi:1,fundament:4,plotfluiddiffadvpresz:5,featur:4,"abstract":[],diagnost:[3,5],exist:3,ship:1,check:[1,3,5],when:[4,5],test:1,roll:5,node:[2,5],intend:5,intent:3,consid:[2,5],stoke:[0,2],spherealgo:3,longer:4,bullet:[],chrono:[],geometr:4,time:[1,3,2,4,5],backward:2,mathrm:3,concept:2,sandia:[],global:3,plotprescribedfluidpressur:5,signific:5,z_slice:3,computation:4,rot:5,row:5,depend:[1,3,2],graph:3,vec:[],text:5,vel:[3,5],sourc:[1,3],string:3,solver:[2,5],iter:[2,5],mu_wn:5,item:3,sine:5,targetbin:5,calcparticlecellid:3,upper:5,slower:5,trend:5,sign:2,corner:5,appear:5,uniform:5,current:[3,2,5],boost:3,deriv:[0,2,4],gener:[1,4,5],coeffici:[2,4,5],water:5,explicitli:5,address:5,along:[4,5],sphere_:3,toolbar:5,box:5,shift:5,avconv:1,queue:5,poisson:[2,5],modul:[1,0,5],gamma_dot:5,volumetr:[2,5],instal:[1,0],memorytyp:3,memori:[3,5],univers:0,live:1,criteria:[2,5],scope:3,reorder:3,writevtkal:5,finit:2,damsgaard:[1,0,4],visual:[1,3,5],appendix:3,rigid:[],templat:[],graphic:1,can:[1,3,2,4,5],capillarycohes:5,transferconstmem:3,purpos:[1,5],obj1:5,stream:3,predict:[2,5],reynold:2,critic:[],unfortun:1,alwai:3,differenti:2,write:[3,5],criterion:4,minpo:3,map:[],contact_mechan:[],arrowscal:5,max:5,clone:1,mac:1,devsmod:5,date:1,data:[1,3,5],stress:[2,5],liquid:4,repuls:[],explicit:2,inform:[1,3,5],setgamma:5,combin:5,block:3,superscript:[],findoverlap:3,dynam:[0,1,2,3,4,5],entiti:4,vti:5,vtk:[1,5],platform:1,window:5,vtu:5,mail:5,main:[1,3,5],non:[1,3,4,5],initi:[1,3,5],half:2,now:[3,4],introduct:[1,0,4],term:2,workload:3,plung:5,realist:[4,5],separ:4,initgridpo:5,compil:[1,3],domain:5,replac:1,individu:[3,2],continu:[3,2],significantli:5,createbondpair:5,shown:5,space:[2,5],lagrangian:2,profil:3,correct:[2,4],theori:0,org:[],"___":1,torqu:[3,4,5],prescrib:[2,5],frequenc:5,graphics_fold:5,pageref:3,synchron:3,motion:[3,4],initrandompo:5,neglect:2,first:[2,5],origin:[2,4,5],arrai:[3,5],open:[3,5],angular:5,size:5,given:2,z_adjust:5,conservation_of_energi:[],circl:5,copi:1,specifi:[1,5],video_format:5,subsequ:[1,5],than:[2,5],png:5,wide:4,posit:[2,4,5],wvel:5,seri:3,cell_cent:5,ani:5,slam:5,slab:5,engin:[],hydrostat:5,bulletphys:[],note:[1,3,2,4,5],ideal:5,take:[1,2],begin:[3,5],sure:[1,5],trace:5,normal:[3,2,4,5],beta:5,uniaxialstrainr:5,pair:[2,4,5],later:2,lower_cutoff:[3,5],typeset:1,runtim:1,readjust:5,axi:5,cmakelist:1,viscou:[2,4,5],viscos:[2,4,5],show:[3,5],friction:[4,5],dphi:5,help:[1,3],onli:[2,4,5],slow:3,ratio:[2,5],written:[1,3,5],analyz:5,"440e":5,offici:0,get:[1,3],kinemat:5,cannot:[1,3,2],settoler:5,theta:5,geo:[0,5],requir:[1,0,5,3],v_f:5,yield:3,across:2,where:[1,3,2,4,5],wiki:[],kernel:3,infinit:5,writensarrai:3,label:3,between:[2,5],"import":[3,2,5],disablefluidpressuremodul:5,assumpt:2,screen:5,fit:5,reorderarrai:3,quiet:3,nearbi:2,mani:[],laplac:2,acceler:[2,4,5],color:[3,5],pot:5,period:[2,5],ultim:1,breath:1,checkval:3,thousand:[],resolut:5,ndvector:5,former:4,"case":[1,3,2],invok:[1,3,5],margin:5,stdout:3,soil:4,equal:[3,2,5],strain:[2,5],img_height:3,egholm:0,subglaci:1,develop:[1,0],author:0,alphabet:5,same:5,binari:[1,3,5],html:1,lammp:[],document:[1,0,5,3],closest:5,kelvin:4,driver:1,driven:4,capabl:1,foat:5,improv:3,extern:5,model:[3,0,2,4,5],dimension:[1,3,2,4],execut:[1,3,5],excel:1,touch:[],speed:3,rose:5,except:3,param:5,blog:4,rescal:5,momentum:[2,5],real:4,read:[1,3,5],psd:5,grid:[3,2,4,5],voigt:4,world:5,findcuda:1,cdot:3,either:[3,2,4,5],initgrid:5,output:[1,3,5],downward:5,inter:[4,5],manag:5,fulfil:5,qfermi:5,hydraul:5,slice:5,cudapath:5,definit:3,evolv:[],exit:[3,2,5],readlast:5,refer:3,inspect:1,starttim:3,fulli:2,src:[1,3],central:2,greatli:3,gplv3:1,degre:[3,5],cuda:[1,3,2,5],neighbor:[3,2,5],act:5,industri:4,bond:5,routin:1,effici:4,paraview:5,your:1,log:5,area:[],aren:2,start:[1,3,5],interfac:[4,5],low:5,gravit:[2,5],generateradii:5,newtonian:2,regard:4,diffus:5,satur:2,faster:5,notat:4,coulomb:4,possibl:[3,5],"default":[3,4,5],k_r:5,k_t:5,k_n:5,taylor:3,creat:[1,5],checkvalu:3,limach:2,"27s_laws_of_mot":[],rearrang:4,denot:[2,4,5],collid:5,googl:3,orient:[4,5],field:5,defaultparam:5,cleanup:5,collis:[3,5],spatial:[3,2,5],magnutud:5,you:1,architectur:[1,3],sequenc:3,symbol:[1,4],xysum:5,directori:[1,5],descript:3,lmgc:[],mass:[3,2,4,5],potenti:5,cpp:3,delta_n_ij:3,cpu:[3,2],disp:5,represent:5,all:[0,1,2,3,4,5],scalar:[3,2,5],disc:[],abil:2,cundal:4,follow:[1,3,2,4,5],disk:5,chain:5,opensourcedem:[],totalmomentum:5,program:[3,5],introduc:[2,5],sound:3,fals:5,capillari:5,verb:3,mechan:4,veri:4,list:[1,3,5],inittempor:[3,5],sand:4,adjust:[2,5],small:[3,4,5],dimens:5,shearrat:5,tex:1,rate:[2,5],pressur:[2,5],pass:[3,4],excit:[],section:[3,2,4,5],abl:5,delet:5,version:[1,3,2,5],intersect:[2,5],method:[0,1,2,3,4,5],movement:[3,5],hasn:4,full:[1,3,5],hash:3,visc_n:5,variat:2,modifi:[1,2],valu:[1,3,2,4,5],gidaspow:2,prior:5,amount:5,magnitud:[2,5],diamet:[2,5],via:3,depart:0,filenam:[3,5],select:5,qscale:5,distinct:5,liber:3,two:[2,4,5],formul:[2,4],more:[1,3,4,5],desir:[4,5],setmaxiter:5,dictat:5,none:5,cluster:5,outlin:2,x1x3:5,histori:3,periodicboundariesx:5,remain:2,paragraph:3,dem:[1,3,4,5],gpu_gener:1,thinsectionvideo:5,loopend:3,sphere:[0,1,2,3,4,5],attain:2,hookean:4,divid:5,rather:3,anoth:5,divis:4,simpl:5,regener:5,gase:4,thrustfootnot:3,plane:[4,5],chronoengin:[],varianc:5,stabil:[3,5],lmgc90:[],github:1,img_out:5,caus:5,spheric:2,nvidia:[1,3],checkbox:5,rotat:[3,4,5],soon:1,through:[1,3,2,4,5],nobord:5,paramet:[3,2,4,5],geoscienc:0,segfault:5,jacobi:[2,5],"return":[3,5],food:4,complain:1,piotrowski:0,found:[1,3,2,4,5],rheologi:2,procedur:[1,0,2],energi:[4,5],todo:3,event:3,molecular_dynam:[],print:3,subsubsect:3,occurr:4,dvipng:1,focallength:3,reason:[2,5],base:[3,2,5],visco:[4,5],put:[2,5],maxpo:3,thread:3,launch:3,veloc:[2,4,5],aarhu:0,interact:[0,1,2,3,4,5],dont:3,exchang:2,number:[1,3,2,5],randombondpair:5,done:3,differ:[3,2,5],script:5,sheardisp:5,least:5,gpu:[1,3,2,5],molecular:4,idelsohn:2,store:[3,2,4,5],printnsarrai:3,option:[1,3,2,5],relationship:[3,2],part:[0,2],consult:3,std:3,scheme:4,contrari:4,ffmpeg:[1,5],fold:5,remov:5,horizont:[2,5],reus:5,str:5,arrang:1,randomli:5,comput:[1,3,2,4,5],exert:5,p_mod_a:5,beforehand:5,p_mod_f:5,built:[1,5],voidratio:5,also:[3,4,5],build:[1,0],upper_cutoff:3,pipelin:5,ergun:2,distribut:[1,5],interpol:5,reach:[3,4],mixtur:2,most:[3,5],plan:1,rho:5,adjustupperwal:5,abnorm:5,reportvalu:3,session:5,find:[2,5],access:3,solut:[0,2,5],factor:5,writebin:[3,5],unus:3,programoutput:1,v_sphere:5,p_mod_phi:5,continuum:2,graphics_format:5,common:[1,3,2,4,5],origo:5,deviator:2,arr:3,set:[1,3,2,4,5],decompos:[2,4],see:[1,3,4,5],float4:3,close:[],analog:5,float3:3,someth:[],won:5,experi:[3,4,5],altern:[1,5],imagemagick:[1,5],numer:[1,0,2,4,3],induc:2,isol:2,matplotlib:1,solv:2,popul:5,both:[3,4,5],last:5,alon:[3,2],tempor:[3,0,4,5],pdf:[1,5],point:[3,2,4,5],schedul:5,residu:[2,5],suppli:3,cudamemset:3,becom:2,damp:4,devic:[1,3,5],due:[1,2,4,5],empti:3,modern:[],imag:5,coordin:5,understand:[1,4],func:5,tangenti:[4,5],look:1,solid:[2,4,5],durat:4,"while":[1,3,2,5],abov:[1,2,4,5],error:[3,5],loos:5,loop:[3,5],pack:[],subsect:3,rightarrow:[],out_fold:5,belong:5,fixvel:5,shorter:5,latexpdf:1,higher:5,shearstrain:5,temporari:5,user:1,typic:[1,5],recent:5,lower:[3,5],task:[],darcyflow:3,"87e":5,velarrowscal:5,shape:2,contactmodel:5,langtangen:[2,5],"0e9":3,restructuredtext:1,theoret:[3,2],input:[1,3,5],desc:3,triaxial:5,euler:[2,4],cuh:3,bin:[3,5],format:[1,3,5],big:5,delta_n:[],characterist:3,zslice:5,semi:2,resolv:[3,4],collect:1,popular:[],encount:3,neumann:[2,5],simplifi:2,spring:4,some:[1,4,5],back:5,emph:3,strongest:5,sampl:[1,0,5],scale:[2,5],per:[3,5],mathemat:4,larg:5,shearvel:5,previou:[3,2],run:[1,3,5],perpendicular:2,step:[3,2,4,5],ndem:5,idx:5,reappear:2,materi:[1,2,4,5],incompress:2,readsecond:5,gamma:5,cutoff:[3,5],file1:3,within:[2,5],diff_adv:5,ensur:3,dev_:3,span:5,errno:[],question:[],fast:[3,2],custom:2,adjac:5,includ:[1,3,2,4,5],contactsearch:3,bondpot:5,translat:5,newer:1,delta:3,line:1,sdk:3,info:[],zhu:2,consist:4,normalboundariesxi:5,assemblag:1,"0xffffffff":3,highlight:4,similar:1,constant:[3,2],doesn:5,repres:2,"char":3,threedim:3,helper_math:1,cmake:1,gnuplot:5,draw:5,normal_stress:5,drag:2,amplitud:5,dram:3,setfluidbottomnoflow:5,algorithm:[3,5],depth:5,epslatex:5,celciu:5,code:[1,3,2,5],partial:2,edg:5,scratch:5,radius_mean:5,plotfluidvelocitiesi:5,send:5,granular:[1,3,2,4],plotfluidvelocitiesz:5,aris:[],gravel:4,sent:5,datafil:3,thinsection_x1x3:5,wave:[3,5],volum:[2,5],relev:0,walltim:5,stiff:[3,5],button:5,montp2:[],smaller:5,natur:4,cfd:5,gamma_wt:5,gamma_wn:5,video:5,click:5,append:3,compat:3,index:[0,4,5],compar:5,resembl:4,cell:[3,2,5],experiment:2,len:2,bodi:[2,4],lower_limit:5,setfluidbottomfixedpressur:5,vertic:5,sinc:[3,2],convert:[3,5],larger:[2,5],converg:5,cbmax:5,chang:[1,3,2,5],apx:3,torquescript:5,outformat:5,appli:[3,2,5],approxim:[2,5],apt:1,api:[1,0,5,3],from:[1,3,2,4,5],commun:2,doubl:3,isotrop:2,implic:5,few:[],asteroid:4,usr:5,chip:3,sort:[3,5],discrete_element_method:[],zhegal:2,use_workdir:5,annot:5,thin:5,control:[1,3,5],process:[1,0,5,3],sudo:1,high:[],slip:[2,5],writefluidvtk:5,generatebimodalradii:5,gcc:[1,3],palett:5,six:[2,5],subdirectori:1,instead:[1,3,5],sim:[3,5],frac:[],surfac:5,esysparticl:5,physic:[1,3,5],alloc:[3,5],essenti:1,bind:1,counter:3,correspond:[2,5],element:[1,0,4],issu:1,allow:[2,5],move:5,sourcecodevari:3,libav:1,r_larg:5,restrain:5,therefor:4,greater:[1,2],python:[1,0,5,3],sid:5,yade:[],dat:[3,5],mention:[1,2],front:5,subsubsec:3,spheredir:5,edit:5,kpa:5,mode:[3,5],tracer:[1,5],chorin:[2,5],"static":[4,5],subsec:3,fluctuat:5,variabl:[1,3],matrix:5,hideinputfil:5,texliv:1,suitabl:5,rel:[3,2,4,5],inaccess:3,ref:3,red:5,forcechainsros:5,simulation_id:3,christensen:1,thrust:3,afterward:5,dirichlet:[2,5],could:2,timer:3,david:0,length:[3,4,5],enforc:2,navier:[0,2],geometri:[],retain:1,softwar:[1,0,3],qualiti:5,scene:1,mai:5,transfertoconstantmemori:3,"1e4":5,stencil:2,strict:1,unknown:2,licens:1,system:[1,3,2,5],messag:[3,5],initrandomgridpo:5,termin:3,"final":5,defineworldboundari:5,shell:[1,3],methodolog:2,exactli:[],bitrat:5,bed:1,charact:5,writeppm:3,kepler:1,have:[1,3,4,5],cohes:5,need:[2,5],diverg:2,discret:[1,0,2,4],which:[1,3,2,5],graviti:[],singl:[3,5],radius_vari:5,unless:3,"class":[3,5],homogen:4,placement:3,strack:4,url:3,face:[2,5],determin:[2,4,5],constrain:[2,5],email_alert:5,mainloop:3,verbos:[3,5],empir:2,trivial:2,locat:[1,3],launchpad:[],should:[1,3,5],jan:0,smallest:[3,5],local:1,meant:1,obj3:5,obj2:5,contribut:[3,2,5],pull:1,writevtk:5,autom:[1,3],increas:5,enabl:[1,5],denmark:0,inputbin:3,file_dt:5,grai:5,integr:[3,0,2,4],contain:[2,5],currentnormalstress:5,sediment:5,view:5,legaci:5,frame:5,elast:[3,4,5],powder:4,sphinxcontrib:1,particl:[0,1,2,3,4,5],statu:[3,5],wall_mass_factor:5,correctli:1,boundari:[0,2,5],state:4,progress:[0,5],email:5,verifi:1,kei:3,job:5,entir:[4,5],addit:[1,2],doxygen:1,valgrind:5,etc:[1,3],equat:[3,0,2,4,5],wall:[3,5],walk:1,ipython:1,es_dot:5,respect:1,mailto:0,quit:3,cauchi:2,compon:[1,3,2,4,5],treat:[],r_small:5,bulk:[2,5],present:2,align:[],defin:[3,2,4,5],file:[1,3,5],texttt:3,archiv:1,welcom:0,parti:0,handl:[1,3],largest:5,inc:1,phi:5,workdir:5,http:[3,0],cubic:[2,4,5],expans:[3,5],periodicboundariesxi:5,eulerian:2,expand:[3,2],off:3,center:[2,5],well:[1,2,5],exampl:[1,3,5],command:1,choos:5,usual:[],plotfluidpressuresi:5,distanc:[2,5],less:2,marginpar:3,obtain:[1,0,2,5],plotfluidpressuresz:5,simultan:[],makefil:[1,3],wen:2,add:[1,5],adc:[0,5],densiti:[2,5],press:5,name:5,insert:3,resid:3,like:5,lost:[4,5],poros:[3,0,2,5],necessari:3,porou:2,output0:3,soft:1,page:[3,0,5],integratewal:3,liggght:[],linux:1,self:5,smoothli:5,home:5,librari:5,glyph:5,nvcc:[1,3],summat:3,leak:5,avoid:[4,5],overlap:[4,5],estim:[0,2,5],leav:2,esi:[],usag:[3,0,5],host:[3,5],file_io:3,about:[1,3,5],actual:5,freedom:3,ander:[1,0],devc_:3,discard:3,disabl:5,own:[],automat:3,shear_strain_r:5,laplacian:2,forcechain:[3,5],val:3,transfer:3,"function":[1,3,2,5],histogram:5,wise:5,displac:[4,5],smooth:5,displai:[4,5],troubl:1,below:[3,5],limit:[2,4,5],otherwis:[4,5],problem:3,evalu:2,"int":[3,5],dure:[2,5],implement:[0,2,4],pip:1,inf:5,probabl:5,detail:[3,4],other:[1,2,4,5],bool:5,futur:2,repeat:2,prealloc:5,zhou:2,gpumain:3,debian:1,stai:5,ghost:2,sphinx:1,scientif:[]},objtypes:{"0":"py:module","1":"py:function","2":"py:method","3":"py:class"},titles:["The sphere documentation","Introduction","Fluid simulation and particle-fluid interaction","sphere internals","Discrete element method","Python API"],objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","method","Python method"],"3":["py","class","Python class"]},filenames:["index","introduction","cfd","sphere_internals","dem","python_api"]})
-\ No newline at end of file
+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],scalar:[3,2,5],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],net:3,topolog:3,abov:[1,2,4,5],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],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,david:0,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],name:5,addparticl:5,tool:1,lower:[3,5],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:[],section:[3,2,4,5],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],symmetr:2,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],kineticenergi:5,against:5,uni:5,seri:3,com:[1,3,5],cell_cent:5,height:5,guid:[3,0],assum:[2,5],gamma_n:5,numpi:[1,5],three:[1,3,2,4,5],been:[4,5],spherebin:5,interest:[0,5],gamma_t:5,gamma_r:5,suppress:3,gidaspow:2,emploi:3,ident:2,cudamemcheck:5,plotconverg:5,gnu:[1,3],properti:[1,2,5],setfluidtopfixedpressur:5,aim:[1,0],euclidean:[],calcul:[3,2,4,5],seven:2,conv:5,tabl:0,toolkit:1,shami:2,sever:[3,5],perform:[1,3,5],make:[1,3,5],transpar:5,complex:[],split:[0,2],dimensionless:2,complet:5,hang:5,hand:[3,2,4],kin:5,"0e3f":3,thu:3,contact:[3,0,2,4,5],thi:[0,1,2,3,4,5],left:5,identifi:[3,4,5],savefig:5,newton:[3,2,4],yet:4,previous:[2,5],expos:1,character:[2,4],save:5,applic:[3,5],dissip:[4,5],mennu:5,background:[3,2],maxval:3,specif:[1,3],initcuda:3,www:[],right:[2,5],old:[2,5],deal:2,interv:[3,5],maxim:[2,5],intern:[1,3],maxit:5,raytrac:[3,5],txt:[1,5],bottom:2,normal:[3,2,4,5],z_slice:3,condit:[1,0,2,5],core:[],bold:4,torquescriptparallel3:5,post:[4,5],zerokinemat:5,unfortun:1,coars:5,produc:5,step_count:5,"float":[3,5],bound:5,ppm:5,readfirst:5,wrap:3,neumann:[2,5],git:1,wai:[1,3,5],gridnum:5,frictionalenergi:5,support:1,avail:1,width:[2,5],fraction:[2,5],analysi:[1,5],medium:2,form:[3,2,4],forc:[3,2,4,5],epsilon:5,setbeta:5,berg:4,"true":5,again:1,bugfix:1,maximum:5,url:3,inaccur:4,fermi:1,fundament:4,plotfluiddiffadvpresz:5,featur:4,"abstract":[],diagnost:[3,5],exist:3,ship:1,check:[1,3,5],excel:1,test:1,totalkineticenergi:5,roll:5,node:[2,5],intend:5,intent:3,consid:[2,5],stoke:[0,2],spherealgo:3,faster:5,coulomb:4,chrono:[],geometr:4,xysum:5,backward:2,mathrm:3,concept:2,sandia:[],global:3,plotprescribedfluidpressur:5,signific:5,adjustwal:5,computation:4,rot:5,row:[],depend:[1,3,2],graph:3,vec:[],text:5,vel:[3,5],sourc:[1,3],string:3,solver:[2,5],iter:[2,5],mu_wn:5,item:3,sine:5,targetbin:5,calcparticlecellid:3,upper:5,slower:5,trend:5,sign:2,corner:5,appear:5,uniform:5,current:[3,2,5],boost:3,deriv:[0,2,4],gener:[1,4,5],coeffici:[2,4,5],water:5,explicitli:5,address:5,along:[4,5],sphere_:3,toolbar:5,box:5,shift:5,avconv:1,queue:5,poisson:[2,5],modul:[1,0,5],gamma_dot:5,volumetr:[2,5],instal:[1,0],memorytyp:3,memori:[3,5],univers:0,live:1,bondpot:5,scope:3,reorder:3,writevtkal:5,finit:2,damsgaard:[1,0,4],visual:[1,3,5],appendix:3,rigid:[],templat:[],setdampingnorm:5,graphic:1,can:[1,3,2,4,5],capillarycohes:5,transferconstmem:3,purpos:[1,5],obj1:5,stream:3,predict:[2,5],reynold:2,critic:5,simul:[0,1,2,3,4,5],alwai:3,differenti:2,write:[3,5],criterion:4,minpo:3,map:[],contact_mechan:[],arrowscal:5,max:5,clone:1,mac:1,devsmod:5,date:1,data:[1,3,5],stress:[2,5],liquid:4,repuls:[],explicit:2,inform:[1,3,5],setgamma:5,combin:5,block:3,superscript:[],findoverlap:3,dynam:[0,1,2,3,4,5],entiti:4,vti:5,vtk:[1,5],platform:1,window:5,vtu:5,mail:5,main:[1,3,5],non:[1,3,4,5],initi:[1,3,5],half:2,now:[3,4],introduct:[1,0,4],term:2,workload:3,plung:5,realist:[4,5],separ:4,initgridpo:5,compil:[1,3],domain:5,replac:1,individu:[3,2],continu:[3,2],significantli:5,createbondpair:5,shown:5,space:[2,5],lagrangian:2,profil:3,correct:[2,4],theori:0,org:[],"___":1,torqu:[3,4,5],prescrib:[2,5],frequenc:5,graphics_fold:5,pageref:3,synchron:3,motion:[3,4],initrandompo:5,neglect:2,first:[2,5],origin:[2,4,5],arrai:[3,5],open:[3,5],angular:5,size:5,given:2,z_adjust:5,conservation_of_energi:[],circl:5,viscousenergi:5,copi:1,specifi:[1,5],rotationalenergi:5,video_format:5,than:[2,5],png:5,wide:4,posit:[2,4,5],wvel:5,browser:5,pre:[3,5],ani:5,slam:5,slab:5,engin:[],hydrostat:5,bulletphys:[],note:[1,3,2,4,5],ideal:5,take:[1,2],begin:[3,5],sure:[1,5],trace:5,ev_dot:5,multipli:5,beta:5,uniaxialstrainr:5,pair:[2,4,5],later:2,lower_cutoff:[3,5],typeset:1,runtim:1,readjust:5,axi:5,cmakelist:1,totalfrictionalenergi:5,viscou:[2,4,5],viscos:[2,4,5],show:[3,5],friction:[4,5],dphi:5,rotat:[3,4,5],onli:[2,4,5],slow:3,ratio:[2,5],written:[1,3,5],analyz:5,"440e":5,offici:0,get:[1,3],kinemat:5,cannot:[1,3,2],settoler:5,theta:5,geo:[0,5],requir:[1,0,5,3],v_f:5,yield:3,across:2,where:[1,3,2,4,5],wiki:[],kernel:3,momentofinertia:5,infinit:5,writensarrai:3,label:3,between:[2,5],"import":[3,2,5],disablefluidpressuremodul:5,assumpt:2,screen:5,fit:5,reorderarrai:3,quiet:3,nearbi:2,leightest:5,mani:[],acceler:[2,4,5],color:[3,5],pot:5,period:[2,5],ultim:1,breath:1,checkval:3,thousand:[],resolut:5,ndvector:[],former:4,"case":[1,3,2],invok:[1,3,5],margin:5,stdout:3,soil:4,equal:[3,2,5],cluster:5,img_height:3,egholm:0,subglaci:1,develop:[1,0],author:0,alphabet:5,same:5,binari:[1,3,5],html:1,lammp:[],document:[1,0,5,3],closest:5,kelvin:4,driver:1,driven:4,capabl:1,foat:5,improv:3,extern:5,model:[3,0,2,4,5],dimension:[1,3,2,4],execut:[1,3,5],when:[4,5],touch:[],speed:3,rose:5,except:3,param:5,blog:4,rescal:5,momentum:[2,5],real:4,read:[1,3,5],psd:5,grid:[3,2,4,5],voigt:4,world:5,findcuda:1,cdot:3,either:[3,2,4,5],initgrid:5,output:[1,3,5],downward:5,inter:[4,5],manag:5,fulfil:5,qfermi:5,hydraul:5,slice:5,cudapath:5,definit:3,evolv:[],exit:[3,2,5],readlast:5,refer:3,inspect:1,starttim:3,found:[1,3,2,4,5],src:[1,3],central:2,greatli:3,gplv3:1,degre:[3,5],cuda:[1,3,2,5],neighbor:[3,2,5],act:5,industri:4,bond:5,routin:1,effici:4,paraview:5,hideinputfil:5,log:5,area:[],aren:2,start:[1,3,5],interfac:[4,5],low:5,gravit:[2,5],generateradii:5,newtonian:2,regard:4,diffus:5,satur:2,longer:4,pull:1,bullet:[],inputbin:3,"default":[3,4,5],k_r:5,k_t:5,k_n:5,taylor:3,creat:[1,5],checkvalu:3,setdampingtangenti:5,file:[1,3,5],rearrang:4,denot:[2,4,5],collid:5,googl:3,orient:[4,5],field:5,defaultparam:5,cleanup:5,collis:[3,5],spatial:[3,2,5],magnutud:[],you:1,architectur:[1,3],sequenc:3,symbol:[1,4],time:[1,3,2,4,5],directori:[1,5],descript:3,lmgc:[],mass:[3,2,4,5],potenti:5,cpp:3,delta_n_ij:3,cpu:[3,2],disp:5,represent:5,all:[0,1,2,3,4,5],mp4:5,disc:[],abil:2,cundal:4,follow:[1,3,2,4,5],disk:5,chain:5,opensourcedem:[],totalmomentum:5,program:[3,5],introduc:[2,5],sound:3,fals:5,capillari:5,verb:3,mechan:4,veri:4,dampen:5,list:[1,3,5],inittempor:[3,5],sand:4,adjust:[2,5],small:[3,4,5],dimens:5,shearrat:5,tex:1,rate:[2,5],pressur:[2,5],pass:[3,4],excit:[],sum:[2,4,5],abl:5,delet:5,version:[1,3,2,5],intersect:[2,5],method:[0,1,2,3,4,5],movement:[3,5],hasn:4,full:[1,3,5],hash:3,visc_n:5,variat:2,modifi:[1,2],valu:[1,3,2,4,5],search:[3,0,4],prior:5,amount:5,magnitud:[2,5],diamet:[2,5],via:3,depart:0,filenam:[3,5],select:5,qscale:5,distinct:5,liber:3,two:[2,4,5],formul:[2,4],more:[1,3,4,5],desir:[4,5],setmaxiter:5,dictat:5,none:5,strain:[2,5],outlin:2,x1x3:5,histori:3,periodicboundariesx:5,remain:2,paragraph:3,dem:[1,3,4,5],gpu_gener:1,thinsectionvideo:5,loopend:3,sphere:[0,1,2,3,4,5],attain:2,hookean:4,divid:5,rather:3,anoth:5,divis:4,simpl:5,regener:5,gase:4,thrustfootnot:3,plane:[4,5],chronoengin:[],varianc:5,stabil:[3,5],lmgc90:[],github:1,img_out:5,caus:5,spheric:2,nvidia:[1,3],checkbox:5,help:[1,3],soon:1,through:[1,3,2,4,5],nobord:5,paramet:[3,2,4,5],geoscienc:0,segfault:5,jacobi:[2,5],"return":[3,5],food:4,complain:1,piotrowski:0,fulli:2,rheologi:2,procedur:[1,0,2],energi:[4,5],todo:3,event:3,molecular_dynam:[],print:[3,5],subsubsect:3,occurr:4,dvipng:1,focallength:3,reason:[2,5],base:[3,2,5],visco:[4,5],put:[2,5],maxpo:3,thread:3,launch:3,veloc:[2,4,5],aarhu:0,interact:[0,1,2,3,4,5],dont:3,exchang:2,number:[1,3,2,5],randombondpair:5,done:3,differ:[3,2,5],script:5,sheardisp:5,least:5,gpu:[1,3,2,5],molecular:4,idelsohn:2,store:[3,2,4,5],gamma_wt:5,option:[1,3,2,5],relationship:[3,2],part:[0,2],consult:3,std:3,scheme:4,contrari:4,ffmpeg:[1,5],gamma_wn:5,deviator:2,horizont:[2,5],reus:5,str:5,arrang:1,randomli:5,comput:[1,3,2,4,5],exert:5,p_mod_a:5,heaviest:5,beforehand:5,p_mod_f:5,deleteparticl:5,built:[1,5],voidratio:5,also:[3,4,5],build:[1,0],upper_cutoff:3,pipelin:5,ergun:2,distribut:[1,5],interpol:5,reach:[3,4],mixtur:2,most:[3,5],plan:1,rho:5,adjustupperwal:5,abnorm:5,reportvalu:3,session:5,find:[2,5],cell:[3,2,5],solut:[0,2,5],factor:5,writebin:[3,5],unus:3,palett:5,v_sphere:5,p_mod_phi:5,continuum:2,graphics_format:5,common:[1,3,2,4,5],origo:5,remov:5,arr:3,transfertoconstantmemori:3,decompos:[2,4],see:[1,3,4,5],float4:3,close:[],analog:5,float3:3,someth:[],won:5,experi:[3,4,5],altern:[1,5],imagemagick:[1,5],numer:[1,0,2,4,3],induc:2,isol:2,len:2,solv:2,inertia:5,popul:5,both:[3,4,5],last:5,alon:[3,2],tempor:[3,0,4,5],pdf:[1,5],point:[3,2,4,5],schedul:5,residu:[2,5],suppli:3,cudamemset:3,becom:2,damp:[4,5],devic:[1,3,5],due:[1,2,4,5],empti:3,modern:[],imag:5,coordin:5,understand:[1,4],func:5,tangenti:[4,5],look:1,solid:[2,4,5],durat:4,"while":[1,3,2,5],behavior:[1,4,5],error:[3,5],loos:5,loop:[3,5],pack:[],subsect:3,rightarrow:[],out_fold:5,belong:5,fixvel:5,shorter:5,latexpdf:1,higher:5,shearstrain:5,moment:5,temporari:5,user:1,chang:[1,3,2,5],recent:5,bondsros:5,task:[],darcyflow:3,"87e":5,velarrowscal:5,shape:2,contactmodel:5,langtangen:[2,5],"0e9":3,restructuredtext:1,theoret:[3,2],input:[1,3,5],subsequ:[1,5],triaxial:5,euler:[2,4],cuh:3,bin:[3,5],format:[1,3,5],big:5,insert:3,delta_n:[],characterist:3,zslice:5,semi:2,resolv:[3,4],collect:1,popular:[],encount:3,often:3,simplifi:2,spring:4,some:[1,4,5],back:5,emph:3,strongest:5,sampl:[1,0,5],scale:[2,5],per:[3,5],mathemat:4,larg:5,necessari:3,previou:[3,2],run:[1,3,5],perpendicular:2,step:[3,2,4,5],ndem:5,idx:5,reappear:2,materi:[1,2,4,5],incompress:2,readsecond:5,gamma:5,cutoff:[3,5],file1:3,within:[2,5],diff_adv:5,ensur:3,dev_:3,span:5,errno:[],question:[],fast:[3,2],custom:2,adjac:5,includ:[1,3,2,4,5],contactsearch:3,criteria:[2,5],translat:5,newer:1,delta:3,line:1,sdk:3,info:[],zhu:2,consist:4,normalboundariesxi:5,assemblag:1,"0xffffffff":3,highlight:4,similar:1,constant:[3,2,5],doesn:5,repres:2,"char":3,threedim:3,helper_math:1,cmake:1,gnuplot:5,draw:5,normal_stress:5,drag:2,amplitud:5,dram:3,setfluidbottomnoflow:5,algorithm:[3,5],depth:5,epslatex:5,celciu:5,code:[1,3,2,5],partial:2,edg:5,scratch:5,radius_mean:5,plotfluidvelocitiesi:5,send:5,granular:[1,3,2,4],plotfluidvelocitiesz:5,aris:[],gravel:4,sent:5,datafil:3,thinsection_x1x3:5,wave:[3,5],volum:[2,5],relev:0,walltim:5,stiff:[3,5],button:5,montp2:[],smaller:5,natur:4,cfd:5,printnsarrai:3,fold:5,video:5,click:5,append:3,compat:3,index:[0,4,5],compar:5,resembl:4,access:3,experiment:2,matplotlib:1,bodi:[2,4],lower_limit:5,setfluidbottomfixedpressur:5,vertic:5,sinc:[3,2],convert:[3,5],larger:[2,5],converg:5,cbmax:5,typic:[1,5],apx:3,torquescript:5,outformat:5,appli:[3,2,5],approxim:[2,5],apt:1,api:[1,0,5,3],from:[1,3,2,4,5],commun:2,doubl:3,isotrop:2,implic:5,few:[],asteroid:4,usr:5,chip:3,sort:[3,5],discrete_element_method:[],zhegal:2,use_workdir:5,annot:5,thin:5,control:[1,3,5],process:[1,0,5,3],sudo:1,high:[],slip:[2,5],writefluidvtk:5,generatebimodalradii:5,gcc:[1,3],programoutput:1,six:[2,5],subdirectori:1,instead:[1,3,5],sim:[3,5],frac:[],surfac:5,esysparticl:5,physic:[1,3,5],alloc:[3,5],essenti:1,bind:1,counter:3,correspond:[2,5],element:[1,0,4],issu:1,allow:[2,5],move:5,sourcecodevari:3,libav:1,r_larg:5,chosen:5,restrain:5,therefor:4,greater:[1,2],python:[1,0,5,3],sid:5,yade:[],dat:[3,5],mention:[1,2],front:5,subsubsec:3,spheredir:5,edit:5,kpa:5,mode:[3,5],tracer:[1,5],chorin:[2,5],"static":[4,5],subsec:3,fluctuat:5,variabl:[1,3],matrix:5,your:1,texliv:1,suitabl:5,rel:[3,2,4,5],inaccess:3,ref:3,red:5,forcechainsros:5,simulation_id:3,christensen:1,thrust:3,afterward:5,dirichlet:[2,5],could:2,timer:3,keep:[1,2],length:[3,4,5],enforc:2,navier:[0,2],geometri:[],retain:1,softwar:[1,0,3],qualiti:5,scene:1,mai:5,set:[1,3,2,4,5],"1e4":5,stencil:2,strict:1,unknown:2,licens:1,system:[1,3,2,5],messag:[3,5],initrandomgridpo:5,termin:3,"final":5,defineworldboundari:5,shell:[1,3],methodolog:2,exactli:[],bitrat:5,bed:1,charact:5,writeppm:3,kepler:1,have:[1,3,4,5],cohes:5,need:[2,5],diverg:2,discret:[1,0,2,4],which:[1,3,2,5],graviti:[],singl:[3,5],radius_vari:5,unless:3,"class":[3,5],homogen:4,placement:3,strack:4,dens:3,face:[2,5],determin:[2,4,5],constrain:[2,5],email_alert:5,mainloop:3,verbos:[3,5],empir:2,trivial:2,locat:[1,3],launchpad:[],should:[1,3,5],jan:0,smallest:[3,5],local:1,meant:1,obj3:5,obj2:5,contribut:[3,2,5],notat:4,writevtk:5,autom:[1,3],increas:5,enabl:[1,5],denmark:0,possibl:[3,5],file_dt:5,grai:5,integr:[3,0,2,4],contain:[2,5],currentnormalstress:5,sediment:5,view:5,legaci:5,frame:5,elast:[3,4,5],powder:4,sphinxcontrib:1,particl:[0,1,2,3,4,5],statu:[3,5],wall_mass_factor:5,correctli:1,boundari:[0,2,5],state:4,progress:[0,5],email:5,verifi:1,kei:3,job:5,entir:[4,5],addit:[1,2],doxygen:1,largestmass:5,valgrind:5,etc:[1,3],equat:[3,0,2,4,5],wall:[3,5],walk:1,ipython:1,es_dot:5,respect:1,mailto:0,quit:3,cauchi:2,compon:[1,3,2,4,5],treat:[],r_small:5,bulk:[2,5],present:2,totalrotationalenergi:5,align:[],defin:[3,2,4,5],limach:2,"27s_laws_of_mot":[],texttt:3,archiv:1,welcom:0,parti:0,handl:[1,3],largest:5,probabl:5,phi:5,workdir:5,http:[3,0],cubic:[2,4,5],expans:[3,5],periodicboundariesxi:5,eulerian:2,expand:[3,2],smallestmass:5,off:3,center:[2,5],well:[1,2,5],exampl:[1,3,5],command:1,choos:5,usual:[],plotfluidpressuresi:5,distanc:[2,5],less:2,marginpar:3,obtain:[1,0,2,5],plotfluidpressuresz:5,simultan:[],makefil:[1,3],wen:2,add:[1,5],other:[1,2,4,5],adc:[0,5],densiti:[2,5],press:5,desc:3,loss:[4,5],resid:3,like:5,lost:[4,5],poros:[3,0,2,5],shearvel:5,porou:2,output0:3,soft:1,page:[3,0,5],integratewal:3,liggght:[],linux:1,self:5,smoothli:5,home:5,librari:5,glyph:5,nvcc:[1,3],summat:3,leak:5,avoid:[4,5],overlap:[4,5],estim:[0,2,5],leav:2,esi:[],usag:[3,0,5],host:[3,5],file_io:3,about:[1,3,5],actual:5,freedom:3,ander:[1,0],devc_:3,discard:3,disabl:5,own:[],automat:3,shear_strain_r:5,laplacian:2,forcechain:[3,5],val:3,transfer:3,"function":[1,3,2,5],histogram:5,wise:5,displac:[4,5],smooth:5,displai:[4,5],troubl:1,below:[3,5],limit:[2,4,5],otherwis:[4,5],problem:3,evalu:2,"int":[3,5],dure:[2,5],implement:[0,2,4],pip:1,inf:5,inc:1,detail:[3,4],laplac:2,bool:5,futur:2,repeat:2,prealloc:5,zhou:2,gpumain:3,debian:1,stai:5,ghost:2,sphinx:1,scientif:[]},objtypes:{"0":"py:module","1":"py:function","2":"py:method","3":"py:class"},titles:["The sphere documentation","Introduction","Fluid simulation and particle-fluid interaction","sphere internals","Discrete element method","Python API"],objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","method","Python method"],"3":["py","class","Python class"]},filenames:["index","introduction","cfd","sphere_internals","dem","python_api"]})
+\ No newline at end of file
(DIR) diff --git a/doc/pdf/sphere.pdf b/doc/pdf/sphere.pdf
Binary files differ.