trebuilt documentation - sphere - GPU-based 3D discrete element method algorithm with optional fluid coupling
HTML git clone git://src.adamsgaard.dk/sphere
DIR Log
DIR Files
DIR Refs
DIR LICENSE
---
DIR commit 85cb16e537cf83c60149c96f1b0f4a565382ef1c
DIR parent f9bbc90bd68dfd3516e9e50bb9fd7333caf5f85c
HTML 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 @@
mx1.adamsgaard.dk:70 /src/sphere/commit/85cb16e537cf83c60149c96f1b0f4a565382ef1c.gph:665: line too long