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
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DIR LICENSE
---
DIR commit 45dae0d7df32bf24406dfc860e2c3f806f571413
DIR parent 06df2fb69034c673e2ff6c2fe0411f46ea597d9e
HTML Author: Anders Damsgaard <anders.damsgaard@geo.au.dk>
Date: Wed, 2 Apr 2014 09:18:38 +0200
updated documentation
Diffstat:
M doc/html/genindex.html | 2 +-
M doc/html/objects.inv | 10 ++++------
M doc/html/python_api.html | 85 +++++++++++++++++++------------
M doc/html/searchindex.js | 4 ++--
M doc/pdf/sphere.pdf | 0
5 files changed, 59 insertions(+), 42 deletions(-)
---
DIR diff --git a/doc/html/genindex.html b/doc/html/genindex.html
t@@ -498,7 +498,7 @@
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="python_api.html#sphere.visualize">visualize() (in module sphere)</a>
+ <dt><a href="python_api.html#sphere.sim.visualize">visualize() (sphere.sim method)</a>
</dt>
DIR diff --git a/doc/html/objects.inv b/doc/html/objects.inv
t@@ -2,8 +2,6 @@
# Project: sphere
# Version: 1.00
# The remainder of this file is compressed using zlib.
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-,2"5Rz}e<aFJ TB!|uyҸ" ŠK]
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-Lˎ
- IHX>$LGg _'% 2ީlC31\\_[Mz}Gōyv?\!]:kEzQ[G :w?F4%,
-\ No newline at end of file
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+-@V p)Ce^ q$8i2:G[X3J3!20IֽfVRx"$FڼVi:&M +2{rD(jXk}Aކ4)d휢ve%="7THs:TCk `텶CexMh
+ ݷ:ϕT3*K,JQRAZM>v8]% 3X{wՃMje?^^߂ԹyO3 9HwGoN \}~ TUJ 63m<s T9KJH*}n(RGe(rM6쬦}Uer}ਲ਼X|Viڵ+lW5-Q[ h}>@o.6Cy
+\ No newline at end of file
DIR diff --git a/doc/html/python_api.html b/doc/html/python_api.html
t@@ -339,7 +339,9 @@ parameters are the position (x) and the radius (radius).</p>
<li><strong>x</strong> (<em>numpy.array</em>) – A vector pointing to the particle center coordinate.</li>
<li><strong>radius</strong> (<em>float</em>) – The particle radius</li>
<li><strong>vel</strong> (<em>numpy.array</em>) – The particle linear velocity (default = [0,0,0])</li>
-<li><strong>fixvel</strong> (<em>float</em>) – Fix horizontal linear velocity (0: No, 1: Yes, default=0)</li>
+<li><strong>fixvel</strong> (<em>float</em>) – 0: Do not fix particle velocity (default), 1: Fix
+horizontal linear velocity, -1: Fix horizontal and vertical linear
+velocity</li>
<li><strong>angpos</strong> (<em>numpy.array</em>) – The particle angular position (default = [0,0,0])</li>
<li><strong>angvel</strong> (<em>numpy.array</em>) – The particle angular velocity (default = [0,0,0])</li>
<li><strong>torque</strong> (<em>numpy.array</em>) – The particle torque (default = [0,0,0])</li>
t@@ -372,8 +374,13 @@ allow for wall movement.</td>
<dl class="method">
<dt id="sphere.sim.adjustWall">
-<tt class="descname">adjustWall</tt><big>(</big><em>idx</em>, <em>adjust=1.1</em><big>)</big><a class="headerlink" href="#sphere.sim.adjustWall" title="Permalink to this definition">¶</a></dt>
-<dd><p>Adjust grid and dynamic wall to max. particle position</p>
+<tt class="descname">adjustWall</tt><big>(</big><em>idx</em>, <em>adjust=1.1</em>, <em>wall_mass_factor=1.0</em><big>)</big><a class="headerlink" href="#sphere.sim.adjustWall" title="Permalink to this definition">¶</a></dt>
+<dd><p>Adjust grid and dynamic wall to max. particle position. The wall
+thickness will by standard equal the maximum particle diameter. The
+density equals the particle density, and the wall size is equal to the
+width and depth of the simulation domain (<cite>self.L[0]</cite> and <cite>self.L[1]</cite>).
+The total wall mass can be linearly scaled by the <cite>wall_mass_factor</cite>
+parameter.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
t@@ -387,6 +394,7 @@ allow for wall movement.</td>
</tr>
</tbody>
</table>
+<p>:param</p>
</dd></dl>
<dl class="method">
t@@ -704,7 +712,7 @@ value is <tt class="docutils literal"><span class="pre">uni</span></tt>, which i
<dl class="method">
<dt id="sphere.sim.initFluid">
-<tt class="descname">initFluid</tt><big>(</big><em>mu=0.00089</em><big>)</big><a class="headerlink" href="#sphere.sim.initFluid" title="Permalink to this definition">¶</a></dt>
+<tt class="descname">initFluid</tt><big>(</big><em>mu=0.00089</em>, <em>rho=1000.0</em>, <em>p=1.0</em>, <em>hydrostatic=True</em><big>)</big><a class="headerlink" href="#sphere.sim.initFluid" title="Permalink to this definition">¶</a></dt>
<dd><p>Initialize the fluid arrays and the fluid viscosity. The default value
of <tt class="docutils literal"><span class="pre">mu</span></tt> equals the dynamic viscosity of water at 25 degrees Celcius.
The value for water at 0 degrees Celcius is 17.87e-4 kg/(m*s).</p>
t@@ -712,7 +720,18 @@ The value for water at 0 degrees Celcius is 17.87e-4 kg/(m*s).</p>
<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>mu</strong> (<em>float</em>) – The fluid dynamic viscosity [kg/(m*s)]</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mu</strong> (<em>float</em>) – The fluid dynamic viscosity [kg/(m*s)]</li>
+<li><strong>rho</strong> (<em>float</em>) – The fluid density [kg/(m^3)]</li>
+<li><strong>p</strong> – The hydraulic pressure to initialize the cells to. If the
+parameter <cite>hydrostatic</cite> is set to <cite>True</cite>, this value will apply to
+the fluid cells at the top</li>
+<li><strong>hydrostatic</strong> (<em>bool</em>) – Initialize the fluid pressures to the hydrostatic
+pressure distribution. A pressure gradient with depth is only
+created if a gravitational acceleration along <img class="math" src="_images/math/b13f21416d84e13708696f34dea81026cda583c9.png" alt="z"/> previously
+has been specified</li>
+</ul>
+</td>
</tr>
</tbody>
</table>
t@@ -725,14 +744,14 @@ The value for water at 0 degrees Celcius is 17.87e-4 kg/(m*s).</p>
The margin parameter adjusts the distance (in no. of max. radii)
from the particle boundaries.
<em>Important</em>: The particle radii have to be set beforehand if the cell
-width isn’t specified by <cite>dx</cite>.
-:param dx: The cell width in any direction. If the default value is used</p>
-<blockquote>
-<div>(-1), the cell width is calculated to fit the largest particle.</div></blockquote>
+width isn’t specified by <cite>dx</cite>.</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>dx</strong> (<em>float</em>) – The cell width in any direction. If the default value is used
+(-1), the cell width is calculated to fit the largest particle.</td>
+</tr>
</tbody>
</table>
</dd></dl>
t@@ -1580,6 +1599,30 @@ rendered beforehand using func:<cite>render()</cite>.</p>
</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
+of interest. The output will be saved in the current folder with a name
+combining the simulation id of the simulation, and the visualization
+method.</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>method</strong> (<em>str</em>) – The type of plot to render. Possible values are ‘energy’,
+‘walls’, ‘triaxial’ and ‘shear’</li>
+<li><strong>savefig</strong> (<em>bool</em>) – Save the image instead of showing it on screen</li>
+<li><strong>outformat</strong> – The output format of the plot data. This can be an
+image format, or in text (‘txt’).</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
<dt id="sphere.sim.voidRatio">
<tt class="descname">voidRatio</tt><big>(</big><big>)</big><a class="headerlink" href="#sphere.sim.voidRatio" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates the current void ratio</p>
t@@ -1881,30 +1924,6 @@ rendered beforehand using func:<cite>render()</cite>.</p>
</table>
</dd></dl>
-<dl class="function">
-<dt id="sphere.visualize">
-<tt class="descclassname">sphere.</tt><tt class="descname">visualize</tt><big>(</big><em>project</em>, <em>method='energy'</em>, <em>savefig=True</em>, <em>outformat='png'</em><big>)</big><a class="headerlink" href="#sphere.visualize" title="Permalink to this definition">¶</a></dt>
-<dd><p>Visualize output from the target project, where the temporal progress is of
-interest. The output will be saved in the current folder with a name
-combining the simulation id of the project, and the visualization method.</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>project</strong> (<em>str</em>) – The simulation id of the project to render</li>
-<li><strong>method</strong> (<em>str</em>) – The type of plot to render. Possible values are ‘energy’,
-‘walls’, ‘triaxial’ and ‘shear’</li>
-<li><strong>savefig</strong> (<em>bool</em>) – Save the image instead of showing it on screen</li>
-<li><strong>outformat</strong> – The output format of the plot data. This can be an image
-format, or in text (‘txt’).</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
</div>
</div>
DIR diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
t@@ -1 +1 @@
mx1.adamsgaard.dk:70 /src/sphere/commit/45dae0d7df32bf24406dfc860e2c3f806f571413.gph:197: line too long