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	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 2085e084281fe031a970af25d140832b27642e5c
	parent 460bcf1cd69bf981cffc443468bd21e168fbfadf
	Author: Anders Damsgaard <[email protected]>
	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(-)
	---
	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">checkerboardColo…
	+ </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…
	</dt>

	+
	+ <dt><a href="python_api.html#sphere.sim.interiaParameterPlanarShear">interia…
	+ </dt>
	+
	</dl></td>
	</tr></table>

	t@@ -355,6 +363,10 @@
	</dt>


	+ <dt><a href="python_api.html#sphere.sim.plotLoadCurve">plotLoadCurve() (sphe…
	+ </dt>
	+
	+
	<dt><a href="python_api.html#sphere.sim.plotPrescribedFluidPressures">plotPr…
	</dt>

	t@@ -453,6 +465,10 @@
	</dt>


	+ <dt><a href="python_api.html#sphere.sim.setFluidBottomNoFlowNoSlip">setFluid…
	+ </dt>
	+
	+
	<dt><a href="python_api.html#sphere.sim.setFluidPressureModulation">setFluid…
	</dt>

	t@@ -465,16 +481,20 @@
	</dt>


	- <dt><a href="python_api.html#sphere.sim.setGamma">setGamma() (sphere.sim met…
	+ <dt><a href="python_api.html#sphere.sim.setFluidTopNoFlowNoSlip">setFluidTop…
	</dt>


	- <dt><a href="python_api.html#sphere.sim.setMaxIterations">setMaxIterations()…
	+ <dt><a href="python_api.html#sphere.sim.setGamma">setGamma() (sphere.sim met…
	</dt>

	</dl></td>
	<td style="width: 33%" valign="top"><dl>

	+ <dt><a href="python_api.html#sphere.sim.setMaxIterations">setMaxIterations()…
	+ </dt>
	+
	+
	<dt><a href="python_api.html#sphere.sim.setTheta">setTheta() (sphere.sim met…
	</dt>

	t@@ -495,6 +515,10 @@
	</dt>


	+ <dt><a href="python_api.html#sphere.sim.shearStrainRate">shearStrainRate() (…
	+ </dt>
	+
	+
	<dt><a href="python_api.html#sphere.sim.shearVel">shearVel() (sphere.sim met…
	</dt>

	diff --git a/doc/html/objects.inv b/doc/html/objects.inv
	Binary files differ.
	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=…
	+<dd><p>Assign checkerboard color values to the particles in an orthogonal grid…
	+<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="…
	+<li><strong>nx</strong> (<em>int</em>) – Number of color values along th…
	+<li><strong>ny</strong> (<em>int</em>) – Number of color values along th…
	+<li><strong>nz</strong> (<em>int</em>) – Number of color values along th…
	+</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"…
	<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><…
	+<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="fie…
	+</tr>
	+<tr class="field-even field"><th class="field-name">Return type:</th><td class…
	+</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 …
	<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'</…
	+<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="…
	+</tr>
	+</tbody>
	+</table>
	+</dd></dl>
	+
	+<dl class="method">
	<dt id="sphere.sim.plotPrescribedFluidPressures">
	<tt class="descname">plotPrescribedFluidPressures</tt><big>(</big><em>graphics…
	<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>hideinputf…
	+<tt class="descname">run</tt><big>(</big><em>verbose=True</em>, <em>hideinputf…
	<dd><p>Start <tt class="docutils literal"><span class="pre">sphere</span></tt>…
	<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…
	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 e…
	+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">n…
	</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…
	<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" t…
	+</dd></dl>
	+
	+<dl class="method">
	+<dt id="sphere.sim.setFluidBottomNoFlowNoSlip">
	+<tt class="descname">setFluidBottomNoFlowNoSlip</tt><big>(</big><big>)</big><a…
	+<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" t…
	</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="h…
	<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" titl…
	+</dd></dl>
	+
	+<dl class="method">
	+<dt id="sphere.sim.setFluidTopNoFlowNoSlip">
	+<tt class="descname">setFluidTopNoFlowNoSlip</tt><big>(</big><big>)</big><a cl…
	+<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" titl…
	</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="hea…
	+<dd><p>Calculates the shear strain rate (dot(gamma)) value of the experiment.<…
	+<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="fie…
	+</tr>
	+<tr class="field-even field"><th class="field-name">Return type:</th><td class…
	+</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 i…
	session. The particles are visualized by selecting the imported data in
	the “Pipeline Browser”. Afterwards, click the “Glyph” …
	“Common” toolbar, or go to the “Filters” menu, and pre…
	-the “Common” list. Choose “Sphere” as the “Glyph…
	-1.0, choose “scalar” as the “Scale Mode”. Check the &#…
	-set the “Set Scale Factor” to 1.0. The field “Maximum Number…
	-may be increased if the number of particles exceed the default value.
	-Finally press “Apply”, and the particles will appear in the main w…
	+the “Common” list. Choose “Sphere” as the “Glyph…
	+as the “Scale Mode”. Check the “Edit” checkbox, and se…
	+Factor” to 1.0. The field “Maximum Number of Points” may be …
	+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”, &#82…
	resolution”) to increase the quality and the computational requirements
	of the rendering. All adjustments by default require the “Apply” b…
	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,""],con…
	-\ No newline at end of file
	+Search.setIndex({objects:{"":{sphere:[5,0,1,""]},sphere:{status:[5,1,1,""],con…
	+\ No newline at end of file
	diff --git a/doc/html/sphere_internals.html b/doc/html/sphere_internals.html
	t@@ -243,8 +243,8 @@ An important note is that the texttt{C} examples of the NV…
	<div><p></p>
	<p></p>
	<em>Public Functions</em><blockquote>
	-<div><p id=""><span id="project0classDEM_1a59ab83e9cbdb7bbeb3f43564fbb294b4"><…
	-<div class="line"> <strong>DEM</strong>(std::string inputbin, const int verbos…
	+<div><p id=""><span id="project0classDEM_1a991dd9d5ffe9935e1105d3c024a06a8c"><…
	+<div class="line"> <strong>DEM</strong>(std::string inputbin, const int verbos…
	</div>
	</p>
	<blockquote>
	diff --git a/doc/pdf/sphere.pdf b/doc/pdf/sphere.pdf
	Binary files differ.