tupdated 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 2085e084281fe031a970af25d140832b27642e5c
DIR parent 460bcf1cd69bf981cffc443468bd21e168fbfadf
HTML Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
Date: Mon, 1 Sep 2014 14:45:11 +0200
updated documentation
Diffstat:
M doc/html/genindex.html | 28 ++++++++++++++++++++++++++--
M doc/html/objects.inv | 0
M doc/html/python_api.html | 113 ++++++++++++++++++++++++++++---
M doc/html/searchindex.js | 4 ++--
M doc/html/sphere_internals.html | 4 ++--
M doc/pdf/sphere.pdf | 0
6 files changed, 135 insertions(+), 14 deletions(-)
---
DIR diff --git a/doc/html/genindex.html b/doc/html/genindex.html
t@@ -123,6 +123,10 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
+ <dt><a href="python_api.html#sphere.sim.checkerboardColors">checkerboardColors() (sphere.sim method)</a>
+ </dt>
+
+
<dt><a href="python_api.html#sphere.cleanup">cleanup() (in module sphere)</a>
</dt>
t@@ -264,6 +268,10 @@
<dt><a href="python_api.html#sphere.sim.initTemporal">initTemporal() (sphere.sim method)</a>
</dt>
+
+ <dt><a href="python_api.html#sphere.sim.interiaParameterPlanarShear">interiaParameterPlanarShear() (sphere.sim method)</a>
+ </dt>
+
</dl></td>
</tr></table>
t@@ -355,6 +363,10 @@
</dt>
+ <dt><a href="python_api.html#sphere.sim.plotLoadCurve">plotLoadCurve() (sphere.sim method)</a>
+ </dt>
+
+
<dt><a href="python_api.html#sphere.sim.plotPrescribedFluidPressures">plotPrescribedFluidPressures() (sphere.sim method)</a>
</dt>
t@@ -453,6 +465,10 @@
</dt>
+ <dt><a href="python_api.html#sphere.sim.setFluidBottomNoFlowNoSlip">setFluidBottomNoFlowNoSlip() (sphere.sim method)</a>
+ </dt>
+
+
<dt><a href="python_api.html#sphere.sim.setFluidPressureModulation">setFluidPressureModulation() (sphere.sim method)</a>
</dt>
t@@ -465,16 +481,20 @@
</dt>
- <dt><a href="python_api.html#sphere.sim.setGamma">setGamma() (sphere.sim method)</a>
+ <dt><a href="python_api.html#sphere.sim.setFluidTopNoFlowNoSlip">setFluidTopNoFlowNoSlip() (sphere.sim method)</a>
</dt>
- <dt><a href="python_api.html#sphere.sim.setMaxIterations">setMaxIterations() (sphere.sim method)</a>
+ <dt><a href="python_api.html#sphere.sim.setGamma">setGamma() (sphere.sim method)</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
+ <dt><a href="python_api.html#sphere.sim.setMaxIterations">setMaxIterations() (sphere.sim method)</a>
+ </dt>
+
+
<dt><a href="python_api.html#sphere.sim.setTheta">setTheta() (sphere.sim method)</a>
</dt>
t@@ -495,6 +515,10 @@
</dt>
+ <dt><a href="python_api.html#sphere.sim.shearStrainRate">shearStrainRate() (sphere.sim method)</a>
+ </dt>
+
+
<dt><a href="python_api.html#sphere.sim.shearVel">shearVel() (sphere.sim method)</a>
</dt>
DIR diff --git a/doc/html/objects.inv b/doc/html/objects.inv
Binary files differ.
DIR diff --git a/doc/html/python_api.html b/doc/html/python_api.html
t@@ -448,6 +448,25 @@ The plot is saved in the current folder as
</dd></dl>
<dl class="method">
+<dt id="sphere.sim.checkerboardColors">
+<tt class="descname">checkerboardColors</tt><big>(</big><em>nx=6</em>, <em>ny=6</em>, <em>nz=6</em><big>)</big><a class="headerlink" href="#sphere.sim.checkerboardColors" title="Permalink to this definition">¶</a></dt>
+<dd><p>Assign checkerboard color values to the particles in an orthogonal grid.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>nx</strong> (<em>int</em>) – Number of color values along the x axis</li>
+<li><strong>ny</strong> (<em>int</em>) – Number of color values along the y ayis</li>
+<li><strong>nz</strong> (<em>int</em>) – Number of color values along the z azis</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.cleanup">
<tt class="descname">cleanup</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.cleanup" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes the input/output files and images belonging to the object
t@@ -902,6 +921,24 @@ included.</p>
</dd></dl>
<dl class="method">
+<dt id="sphere.sim.interiaParameterPlanarShear">
+<tt class="descname">interiaParameterPlanarShear</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.interiaParameterPlanarShear" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the value of the inertia parameter $I$ during planar shear
+proposed by GDR-MiDi 2004.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The value of $I$</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+<p>:see also:<cite>func:shearStrainRate()</cite>,`func:shearVel()`</p>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.kineticEnergy">
<tt class="descname">kineticEnergy</tt><big>(</big><em>idx</em><big>)</big><a class="headerlink" href="#sphere.sim.kineticEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the (linear) kinetic energy for a particle.</p>
t@@ -1139,6 +1176,26 @@ this value is -1, the center z position is used.</li>
</dd></dl>
<dl class="method">
+<dt id="sphere.sim.plotLoadCurve">
+<tt class="descname">plotLoadCurve</tt><big>(</big><em>graphics_format='png'</em><big>)</big><a class="headerlink" href="#sphere.sim.plotLoadCurve" title="Permalink to this definition">¶</a></dt>
+<dd><p>Plot the load curve (log time vs. upper wall movement). The plot is
+saved in the current folder with the file name
+‘<simulation id>-loadcurve.<graphics_format>’.
+The consolidation coefficient calculations are done on the base of
+Bowles 1992, p. 129–139, using the “Casagrande” method.
+It is assumed that the consolidation has stopped at the end of the
+simulation (i.e. flat curve).</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>graphics_format</strong> (<em>str</em>) – Save the plot in this format</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.plotPrescribedFluidPressures">
<tt class="descname">plotPrescribedFluidPressures</tt><big>(</big><em>graphics_format='png'</em><big>)</big><a class="headerlink" href="#sphere.sim.plotPrescribedFluidPressures" title="Permalink to this definition">¶</a></dt>
<dd><p>Plot the prescribed fluid pressures through time that may be
t@@ -1365,7 +1422,7 @@ tracer to this image format using Imagemagick</li>
<dl class="method">
<dt id="sphere.sim.run">
-<tt class="descname">run</tt><big>(</big><em>verbose=True</em>, <em>hideinputfile=False</em>, <em>dry=False</em>, <em>valgrind=False</em>, <em>cudamemcheck=False</em><big>)</big><a class="headerlink" href="#sphere.sim.run" title="Permalink to this definition">¶</a></dt>
+<tt class="descname">run</tt><big>(</big><em>verbose=True</em>, <em>hideinputfile=False</em>, <em>dry=False</em>, <em>valgrind=False</em>, <em>cudamemcheck=False</em>, <em>device=-1</em><big>)</big><a class="headerlink" href="#sphere.sim.run" title="Permalink to this definition">¶</a></dt>
<dd><p>Start <tt class="docutils literal"><span class="pre">sphere</span></tt> calculations on the <tt class="docutils literal"><span class="pre">sim</span></tt> object</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
t@@ -1382,6 +1439,9 @@ computational time.</li>
<li><strong>cudamemcheck</strong> (<em>bool</em>) – Run the program with <tt class="docutils literal"><span class="pre">cudamemcheck</span></tt> in order to
check for device memory leaks and errors. This causes a significant
increase in computational time.</li>
+<li><strong>device</strong> (<em>int</em>) – Specify the GPU device to execute the program on.
+If not specified, sphere will use the device with the most CUDA cores.
+To see a list of devices, run <tt class="docutils literal"><span class="pre">nvidia-smi</span></tt> in the system shell.</li>
</ul>
</td>
</tr>
t@@ -1472,7 +1532,16 @@ value (Dirichlet) boundary condition.</p>
<dt id="sphere.sim.setFluidBottomNoFlow">
<tt class="descname">setFluidBottomNoFlow</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.setFluidBottomNoFlow" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the lower boundary of the fluid domain to follow the no-flow
-(Neumann) boundary condition.</p>
+(Neumann) boundary condition with free slip parallel to the boundary.</p>
+<p>The default behavior for the boundary is fixed value (Dirichlet), see
+<a class="reference internal" href="#sphere.sim.setFluidBottomFixedPressure" title="sphere.sim.setFluidBottomFixedPressure"><tt class="xref py py-func docutils literal"><span class="pre">setFluidBottomFixedPressure()</span></tt></a>.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="sphere.sim.setFluidBottomNoFlowNoSlip">
+<tt class="descname">setFluidBottomNoFlowNoSlip</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.setFluidBottomNoFlowNoSlip" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the lower boundary of the fluid domain to follow the no-flow
+(Neumann) boundary condition with no slip parallel to the boundary.</p>
<p>The default behavior for the boundary is fixed value (Dirichlet), see
<a class="reference internal" href="#sphere.sim.setFluidBottomFixedPressure" title="sphere.sim.setFluidBottomFixedPressure"><tt class="xref py py-func docutils literal"><span class="pre">setFluidBottomFixedPressure()</span></tt></a>.</p>
</dd></dl>
t@@ -1511,7 +1580,16 @@ value (Dirichlet) boundary condition.</p>
<dt id="sphere.sim.setFluidTopNoFlow">
<tt class="descname">setFluidTopNoFlow</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.setFluidTopNoFlow" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the upper boundary of the fluid domain to follow the no-flow
-(Neumann) boundary condition.</p>
+(Neumann) boundary condition with free slip parallel to the boundary.</p>
+<p>The default behavior for the boundary is fixed value (Dirichlet), see
+<a class="reference internal" href="#sphere.sim.setFluidTopFixedPressure" title="sphere.sim.setFluidTopFixedPressure"><tt class="xref py py-func docutils literal"><span class="pre">setFluidTopFixedPressure()</span></tt></a>.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="sphere.sim.setFluidTopNoFlowNoSlip">
+<tt class="descname">setFluidTopNoFlowNoSlip</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.setFluidTopNoFlowNoSlip" title="Permalink to this definition">¶</a></dt>
+<dd><p>Set the upper boundary of the fluid domain to follow the no-flow
+(Neumann) boundary condition with no slip parallel to the boundary.</p>
<p>The default behavior for the boundary is fixed value (Dirichlet), see
<a class="reference internal" href="#sphere.sim.setFluidTopFixedPressure" title="sphere.sim.setFluidTopFixedPressure"><tt class="xref py py-func docutils literal"><span class="pre">setFluidTopFixedPressure()</span></tt></a>.</p>
</dd></dl>
t@@ -1638,6 +1716,24 @@ displacement of the upper, fixed particles.</p>
</tr>
</tbody>
</table>
+<p>:see also:<cite>func:shearStrainRate()</cite>,`func:shearVel()`</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="sphere.sim.shearStrainRate">
+<tt class="descname">shearStrainRate</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.shearStrainRate" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculates the shear strain rate (dot(gamma)) value of the experiment.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The value of $I$</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">float</td>
+</tr>
+</tbody>
+</table>
+<p>:see also:<cite>func:shearStrain()</cite>,`func:shearVel()`</p>
</dd></dl>
<dl class="method">
t@@ -1656,6 +1752,7 @@ upper particles.</p>
</tr>
</tbody>
</table>
+<p>:see also:<cite>func:shearStrainRate()</cite>,`func:shearStrain()`</p>
</dd></dl>
<dl class="method">
t@@ -2058,11 +2155,11 @@ The vtu files can be used to visualize the particles in ParaView.</p>
session. The particles are visualized by selecting the imported data in
the “Pipeline Browser”. Afterwards, click the “Glyph” button in the
“Common” toolbar, or go to the “Filters” menu, and press “Glyph” from
-the “Common” list. Choose “Sphere” as the “Glyph Type”, set “Radius” to
-1.0, choose “scalar” as the “Scale Mode”. Check the “Edit” checkbox, and
-set the “Set Scale Factor” to 1.0. The field “Maximum Number of Points”
-may be increased if the number of particles exceed the default value.
-Finally press “Apply”, and the particles will appear in the main window.</p>
+the “Common” list. Choose “Sphere” as the “Glyph Type”, choose “scalar”
+as the “Scale Mode”. Check the “Edit” checkbox, and set the “Set Scale
+Factor” to 1.0. The field “Maximum Number of Points” may be increased if
+the number of particles exceed the default value. Finally press “Apply”,
+and the particles will appear in the main window.</p>
<p>The sphere resolution may be adjusted (“Theta resolution”, “Phi
resolution”) to increase the quality and the computational requirements
of the rendering. All adjustments by default require the “Apply” button
DIR diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
t@@ -1 +1 @@
mx1.adamsgaard.dk:70 /src/sphere/commit/2085e084281fe031a970af25d140832b27642e5c.gph:292: line too long