tsmall fixes - 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 5dbc0a8544a6dfa40505639271fb7ca1a1834be5
DIR parent 63cf7ba3c83aac1a3f2b7836262fbc7b9052b84f
HTML Author: Anders Damsgaard <adc@geo.au.dk>
Date: Sun, 17 Mar 2013 21:22:39 +0100
small fixes
Diffstat:
M INSTALL.sh | 2 +-
M doc/html/_sources/introduction.txt | 16 ++++++++++------
M doc/html/genindex.html | 4 ++++
M doc/html/introduction.html | 30 ++++++++++++++++++++++--------
M doc/html/objects.inv | 0
M doc/html/python_api.html | 10 ++++++++--
M doc/html/searchindex.js | 4 ++--
M doc/pdf/sphere.pdf | 0
M doc/sphinx/conf.py | 8 ++++----
M doc/sphinx/introduction.rst | 16 ++++++++++------
D python/bondtest.py | 44 -------------------------------
M python/shear-test.py | 12 ++++++------
M src/sphere.cpp | 13 ++++++++-----
D tests/tests.py | 114 -------------------------------
14 files changed, 75 insertions(+), 198 deletions(-)
---
DIR diff --git a/INSTALL.sh b/INSTALL.sh
t@@ -1,2 +1,2 @@
-export NVSDKCOMPUTE_ROOT=/home/adc/NVIDIA_GPU_Computing_SDK
+export NVSDKCOMPUTE_ROOT=/home/adc/NVIDIA_CUDA-5.0_Samples
cmake . && make
DIR diff --git a/doc/html/_sources/introduction.txt b/doc/html/_sources/introduction.txt
t@@ -14,6 +14,7 @@ Requirements
The build requirements are:
* A Nvidia CUDA-supported version of Linux or Mac OS X (see the `CUDA toolkit release notes <http://docs.nvidia.com/cuda/cuda-toolkit-release-notes/index.html>`_ for more information)
* `GNU Make <https://www.gnu.org/software/make/>`_
+ * `CMake <http://www.cmake.org>`_
* The `GNU Compiler Collection <http://gcc.gnu.org/>`_ (GCC)
* The `Nvidia CUDA toolkit and SDK <https://developer.nvidia.com/cuda-downloads>`_
t@@ -42,18 +43,21 @@ Optional tools, required for building the documentation:
Building *sphere*
-----------------
-All instructions required for building *sphere* are provided in a number of ``Makefiles``. To generate the main *sphere* command-line executable, go to the source code directory, and invoke GNU Make::
+All instructions required for building *sphere* are provided in a number of ``Makefiles``. To generate the main *sphere* command-line executable, go to the root directory, and invoke CMake and GNU Make::
- $ cd src
- $ make
+ $ cmake . && make
-If successfull, the GNU Makefile will create the required data folders, object files, as well as the *sphere* executable in the root folder. The executable will be named after the host architecture, e.g. ``sphere_darwin_i386`` on a 32-bit OS X system, or ``sphere_linux_x86_64`` on a 64-bit linux system. Issue the following command to check the executable::
+If successfull, the Makefiles will create the required data folders, object files, as well as the *sphere* executable in the root folder. Issue the following commands to check the executable::
- $ ./sphere_* --version
+ $ ./sphere --version
The output should look similar to this:
-.. program-output:: ../../sphere_linux_X86_64 --version
+.. program-output:: ../../sphere --version
+
+The build can be verified by running a number of automated tests::
+
+ $ make test
The documentation can be read in the `reStructuredText <http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html>`_-format in the ``doc/sphinx/`` folder, or build into e.g. HTML or PDF format with the following commands::
DIR diff --git a/doc/html/genindex.html b/doc/html/genindex.html
t@@ -100,6 +100,10 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
+ <dt><a href="python_api.html#sphere.cleanup">cleanup() (in module sphere)</a>
+ </dt>
+
+
<dt><a href="python_api.html#sphere.Spherebin.consolidate">consolidate() (sphere.Spherebin method)</a>
</dt>
DIR diff --git a/doc/html/introduction.html b/doc/html/introduction.html
t@@ -72,6 +72,7 @@ The ultimate aim of the <em>sphere</em> software is to simulate soft-bedded subg
<dd><ul class="first last simple">
<li>A Nvidia CUDA-supported version of Linux or Mac OS X (see the <a class="reference external" href="http://docs.nvidia.com/cuda/cuda-toolkit-release-notes/index.html">CUDA toolkit release notes</a> for more information)</li>
<li><a class="reference external" href="https://www.gnu.org/software/make/">GNU Make</a></li>
+<li><a class="reference external" href="http://www.cmake.org">CMake</a></li>
<li>The <a class="reference external" href="http://gcc.gnu.org/">GNU Compiler Collection</a> (GCC)</li>
<li>The <a class="reference external" href="https://developer.nvidia.com/cuda-downloads">Nvidia CUDA toolkit and SDK</a></li>
</ul>
t@@ -107,17 +108,30 @@ The ultimate aim of the <em>sphere</em> software is to simulate soft-bedded subg
</div>
<div class="section" id="building-sphere">
<h2>Building <em>sphere</em><a class="headerlink" href="#building-sphere" title="Permalink to this headline">¶</a></h2>
-<p>All instructions required for building <em>sphere</em> are provided in a number of <tt class="docutils literal"><span class="pre">Makefiles</span></tt>. To generate the main <em>sphere</em> command-line executable, go to the source code directory, and invoke GNU Make:</p>
-<div class="highlight-python"><pre>$ cd src
-$ make</pre>
+<p>All instructions required for building <em>sphere</em> are provided in a number of <tt class="docutils literal"><span class="pre">Makefiles</span></tt>. To generate the main <em>sphere</em> command-line executable, go to the root directory, and invoke CMake and GNU Make:</p>
+<div class="highlight-python"><pre>$ cmake . && make</pre>
</div>
-<p>If successfull, the GNU Makefile will create the required data folders, object files, as well as the <em>sphere</em> executable in the root folder. The executable will be named after the host architecture, e.g. <tt class="docutils literal"><span class="pre">sphere_darwin_i386</span></tt> on a 32-bit OS X system, or <tt class="docutils literal"><span class="pre">sphere_linux_x86_64</span></tt> on a 64-bit linux system. Issue the following command to check the executable:</p>
-<div class="highlight-python"><pre>$ ./sphere_* --version</pre>
+<p>If successfull, the Makefiles will create the required data folders, object files, as well as the <em>sphere</em> executable in the root folder. Issue the following commands to check the executable:</p>
+<div class="highlight-python"><pre>$ ./sphere --version</pre>
</div>
<p>The output should look similar to this:</p>
-<div class="system-message">
-<p class="system-message-title">System Message: ERROR/3 (<tt class="docutils">/home/adc/code/sphere/doc/sphinx/introduction.rst</tt>, line 56)</p>
-Command u’../../sphere_linux_X86_64 –version’ failed: [Errno 2] No such file or directory</div>
+<div class="highlight-text"><div class="highlight"><pre>.-------------------------------------.
+| _ Compiled for 3D |
+| | | |
+| ___ _ __ | |__ ___ _ __ ___ |
+| / __| '_ \| '_ \ / _ \ '__/ _ \ |
+| \__ \ |_) | | | | __/ | | __/ |
+| |___/ .__/|_| |_|\___|_| \___| |
+| | | |
+| |_| Version: 0.35 |
+`-------------------------------------´
+ A discrete element method particle dynamics simulator.
+ Written by Anders Damsgaard Christensen, license GPLv3+.
+</pre></div>
+</div>
+<p>The build can be verified by running a number of automated tests:</p>
+<div class="highlight-python"><pre>$ make test</pre>
+</div>
<p>The documentation can be read in the <a class="reference external" href="http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html">reStructuredText</a>-format in the <tt class="docutils literal"><span class="pre">doc/sphinx/</span></tt> folder, or build into e.g. HTML or PDF format with the following commands:</p>
<div class="highlight-python"><pre>$ cd doc/sphinx
$ make html
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@@ -179,7 +179,7 @@ Returns porosity values and depth</p>
<dl class="method">
<dt id="sphere.Spherebin.run">
-<tt class="descname">run</tt><big>(</big><em>verbose=True</em>, <em>hideinputfile=False</em>, <em>dry=False</em><big>)</big><a class="headerlink" href="#sphere.Spherebin.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><big>)</big><a class="headerlink" href="#sphere.Spherebin.run" title="Permalink to this definition">¶</a></dt>
<dd><p>Execute sphere with target project</p>
</dd></dl>
t@@ -206,7 +206,7 @@ initial height per second.</p>
<dl class="method">
<dt id="sphere.Spherebin.thinsection_x1x3">
-<tt class="descname">thinsection_x1x3</tt><big>(</big><em>x2='center'</em>, <em>graphicsformat='png'</em>, <em>cbmax=None</em>, <em>arrowscale=0.01</em>, <em>slipscale=1.0</em>, <em>verbose=False</em><big>)</big><a class="headerlink" href="#sphere.Spherebin.thinsection_x1x3" title="Permalink to this definition">¶</a></dt>
+<tt class="descname">thinsection_x1x3</tt><big>(</big><em>x2='center'</em>, <em>graphicsformat='png'</em>, <em>cbmax=None</em>, <em>arrowscale=0.01</em>, <em>velarrowscale=1.0</em>, <em>slipscale=1.0</em>, <em>verbose=False</em><big>)</big><a class="headerlink" href="#sphere.Spherebin.thinsection_x1x3" title="Permalink to this definition">¶</a></dt>
<dd><p>Produce a 2D image of particles on a x1,x3 plane, intersecting the second axis at x2.
Output is saved as ‘<sid>-ts-x1x3.txt’ in the current folder.</p>
<p>An upper limit to the pressure color bar range can be set by the cbmax parameter.</p>
t@@ -258,6 +258,12 @@ velocity in m/s, default value is -0.001 m/s (i.e. downwards).</p>
</dd></dl>
<dl class="function">
+<dt id="sphere.cleanup">
+<tt class="descclassname">sphere.</tt><tt class="descname">cleanup</tt><big>(</big><em>spherebin</em><big>)</big><a class="headerlink" href="#sphere.cleanup" title="Permalink to this definition">¶</a></dt>
+<dd><p>Remove input/output files and images from simulation</p>
+</dd></dl>
+
+<dl class="function">
<dt id="sphere.convert">
<tt class="descclassname">sphere.</tt><tt class="descname">convert</tt><big>(</big><em>graphicsformat='png'</em>, <em>folder='../img_out'</em><big>)</big><a class="headerlink" href="#sphere.convert" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts all PPM images in img_out to graphicsformat, using ImageMagick</p>
DIR diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
t@@ -1 +1 @@
mx1.adamsgaard.dk:70 /src/sphere/commit/5dbc0a8544a6dfa40505639271fb7ca1a1834be5.gph:171: line too long