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	tsmall fixes - sphere - GPU-based 3D discrete element method algorithm with opt…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 5dbc0a8544a6dfa40505639271fb7ca1a1834be5
	parent 63cf7ba3c83aac1a3f2b7836262fbc7b9052b84f
	Author: Anders Damsgaard <[email protected]>
	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(-)
	---
	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
	diff --git a/doc/html/_sources/introduction.txt b/doc/html/_sources/introductio…
	t@@ -14,6 +14,7 @@ Requirements
	The build requirements are:
	* A Nvidia CUDA-supported version of Linux or Mac OS X (see the `CUDA toolki…
	* `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-downlo…

	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 ``…
	+All instructions required for building sphere are provided in a number of ``…

	- $ cd src
	- $ make
	+ $ cmake . && make

	-If successfull, the GNU Makefile will create the required data folders, object…
	+If successfull, the Makefiles will create the required data folders, object fi…

	- $ ./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.source…

	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() (sp…
	</dt>

	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 simul…
	<dd><ul class="first last simple">
	<li>A Nvidia CUDA-supported version of Linux or Mac OS X (see the <a class="re…
	<li><a class="reference external" href="https://www.gnu.org/software/make/">GN…
	+<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 …
	<li>The <a class="reference external" href="https://developer.nvidia.com/cuda-…
	</ul>
	t@@ -107,17 +108,30 @@ The ultimate aim of the <em>sphere</em> software is to s…
	</div>
	<div class="section" id="building-sphere">
	<h2>Building <em>sphere</em><a class="headerlink" href="#building-sphere" titl…
	-<p>All instructions required for building <em>sphere</em> are provided in a nu…
	-<div class="highlight-python"><pre>$ cd src
	-$ make</pre>
	+<p>All instructions required for building <em>sphere</em> are provided in a nu…
	+<div class="highlight-python"><pre>$ cmake . && make</pre>
	</div>
	-<p>If successfull, the GNU Makefile will create the required data folders, obj…
	-<div class="highlight-python"><pre>$ ./sphere_* --version</pre>
	+<p>If successfull, the Makefiles will create the required data folders, object…
	+<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">…
	-Command u’../../sphere_linux_X86_64 –version’ failed: [Errno…
	+<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="ht…
	<div class="highlight-python"><pre>$ cd doc/sphinx
	$ make html
	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@@ -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>hideinputf…
	+<tt class="descname">run</tt><big>(</big><em>verbose=True</em>, <em>hideinputf…
	<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>, <e…
	+<tt class="descname">thinsection_x1x3</tt><big>(</big><em>x2='center'</em>, <e…
	<dd><p>Produce a 2D image of particles on a x1,x3 plane, intersecting the seco…
	Output is saved as ‘<sid>-ts-x1x3.txt’ in the current folder…
	<p>An upper limit to the pressure color bar range can be set by the cbmax para…
	t@@ -258,6 +258,12 @@ velocity in m/s, default value is -0.001 m/s (i.e. downwa…
	</dd></dl>

	<dl class="function">
	+<dt id="sphere.cleanup">
	+<tt class="descclassname">sphere.</tt><tt class="descname">cleanup</tt><big>(<…
	+<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>(<…
	<dd><p>Converts all PPM images in img_out to graphicsformat, using ImageMagick…
	diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
	t@@ -1 +1 @@
	-Search.setIndex({objects:{"":{sphere:[4,0,1,""]},sphere:{status:[4,2,1,""],con…
	-\ No newline at end of file
	+Search.setIndex({objects:{"":{sphere:[4,0,1,""]},sphere:{status:[4,2,1,""],con…
	+\ No newline at end of file
	diff --git a/doc/pdf/sphere.pdf b/doc/pdf/sphere.pdf
	Binary files differ.
	diff --git a/doc/sphinx/conf.py b/doc/sphinx/conf.py
	t@@ -50,7 +50,7 @@ master_doc = 'index'

	# General information about the project.
	project = u'sphere'
	-copyright = u'2012, Anders Damsgaard Christensen'
	+copyright = u'2012, Anders Damsgaard'

	# The version info for the project you're documenting, acts as replacement for
	# \|version\| and \|release\|, also used in various other places throughout the
	t@@ -193,7 +193,7 @@ latex_elements = {
	# (source start file, target name, title, author, documentclass [howto/manual]…
	latex_documents = [
	('index', 'sphere.tex', u'sphere Documentation',
	- u'Anders Damsgaard Christensen', 'manual'),
	+ u'Anders Damsgaard', 'manual'),
	]

	# The name of an image file (relative to this directory) to place at the top of
	t@@ -223,7 +223,7 @@ latex_documents = [
	# (source start file, name, description, authors, manual section).
	man_pages = [
	('index', 'sphere', u'sphere Documentation',
	- [u'Anders Damsgaard Christensen'], 1)
	+ [u'Anders Damsgaard'], 1)
	]

	# If true, show URL addresses after external links.
	t@@ -237,7 +237,7 @@ man_pages = [
	# dir menu entry, description, category)
	texinfo_documents = [
	('index', 'sphere', u'sphere Documentation',
	- u'Anders Damsgaard Christensen', 'sphere', 'One line description of project…
	+ u'Anders Damsgaard', 'sphere', 'One line description of project.',
	'Miscellaneous'),
	]

	diff --git a/doc/sphinx/introduction.rst b/doc/sphinx/introduction.rst
	t@@ -14,6 +14,7 @@ Requirements
	The build requirements are:
	* A Nvidia CUDA-supported version of Linux or Mac OS X (see the `CUDA toolki…
	* `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-downlo…

	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 ``…
	+All instructions required for building sphere are provided in a number of ``…

	- $ cd src
	- $ make
	+ $ cmake . && make

	-If successfull, the GNU Makefile will create the required data folders, object…
	+If successfull, the Makefiles will create the required data folders, object fi…

	- $ ./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.source…

	diff --git a/python/bondtest.py b/python/bondtest.py
	t@@ -1,44 +0,0 @@
	-#!/usr/bin/env python
	-
	-from sphere import *
	-
	-sb = Spherebin(np=2, sid='bondtest')
	-
	-cleanup(sb)
	-
	-sb.x[0,:] = numpy.array((2,2,2))
	-sb.x[1,:] = numpy.array((3.5,2,2))
	-sb.radius = numpy.ones(sb.np)*0.5
	-
	-#sb.vel[1,2] = 1
	-sb.angvel[1,1] = 0.01
	-
	-
	-sb.initGridAndWorldsize(margin = 10, periodic = 1, contactmodel = 2, g = numpy…
	-
	-sb.bond(0, 1)
	-
	-sb.defaultParams()
	-#sb.gamma_n[0] = 10000
	-#sb.initTemporal(total=4.0)
	-sb.initTemporal(total=0.01, file_dt=2e-4)
	-
	-sb.writebin()
	-
	-sb.run(dry=True)
	-sb.run()
	-
	-sb.render(verbose=False)
	-
	-visualize(sb.sid, "energy")
	-
	-sb.readlast()
	-print(sb.bonds_delta_n)
	-print(sb.bonds_delta_t)
	-print(sb.bonds_omega_n)
	-print(sb.bonds_omega_t)
	-print()
	-print(sb.force)
	-print(sb.torque)
	-print(sb.vel)
	-print(sb.angvel)
	diff --git a/python/shear-test.py b/python/shear-test.py
	t@@ -5,13 +5,13 @@ from sphere import *

	### EXPERIMENT SETUP ###
	initialization = True
	-consolidation = True
	-shearing = True
	-rendering = True
	-plots = True
	+consolidation = False
	+shearing = False
	+rendering = False
	+plots = False

	# Number of particles
	-np = 2e3
	+np = 1e4

	# Common simulation id
	sim_id = "shear-test"
	t@@ -35,7 +35,7 @@ init.defaultParams(gamma_n = 0.0, mu_s = 0.4, mu_d = 0.4)
	init.initRandomGridPos(gridnum = numpy.array([12, 12, 1000]), periodic = 1, co…

	# Set duration of simulation
	-init.initTemporal(total = 5.0)
	+init.initTemporal(total = 0.2)

	if (initialization == True):
	# Write input file for sphere
	diff --git a/src/sphere.cpp b/src/sphere.cpp
	t@@ -621,15 +621,18 @@ void DEM::forcechains(const std::string format, const in…
	<< "# the forcechain utility in sphere. For more information,\n"
	<< "# see https://github.com/anders-dc/sphere\n"
	<< "set size ratio -1\n";
	- if (format == "png")
	- cout << "set term pngcairo size 50 cm,40 cm\n";
	- else if (format == "epslatex") {
	+ if (format == "png") {
	+ cout << "set term pngcairo size 30 cm,20 cm\n";
	+ cout << "set out '" << s << "-fc.png'\n";
	+ } else if (format == "epslatex") {
	cout << "set term epslatex size 8.6 cm, 5.6 cm\n";
	- cout << "set out 'plots/" << s << "-fc.tex'\n";
	+ //cout << "set out 'plots/" << s << "-fc.tex'\n";
	+ cout << "set out '" << s << "-fc.tex'\n";
	} else if (format == "epslatex-color") {
	//cout << "set term epslatex color size 12 cm, 8.6 cm\n";
	- cout << "set term epsla color size 8.6 cm, 5.6 cm\n";
	+ cout << "set term epslatex color size 8.6 cm, 5.6 cm\n";
	cout << "set out 'plots/" << s << "-fc.tex'\n";
	+ //cout << "set out '" << s << "-fc.tex'\n";
	}
	cout << "set xlabel '\\sffamily $x_1$, [m]'\n";
	if (threedim == 1) {
	diff --git a/tests/tests.py b/tests/tests.py
	t@@ -1,114 +0,0 @@
	-#!/usr/bin/env python
	-from sphere import *
	-import subprocess
	-
	-def passed():
	- return "\tPassed"
	-
	-def failed():
	- return "\tFailed"
	-
	-def compare(first, second, string):
	- if (first == second):
	- print(string + passed())
	- else:
	- print(string + failed())
	-
	-def compareFloats(first, second, string, criterion=1e-5):
	- if abs(first-second) < criterion:
	- print(string + passed())
	- else :
	- print(string + failed())
	-
	-def cleanup(spherebin):
	- 'Remove temporary files'
	- subprocess.call("rm -f ../input/" + spherebin.sid + ".bin", shell=True)
	- subprocess.call("rm -f ../output/" + spherebin.sid + ".*.bin", shell=True)
	- print("")
	-
	-
	-#### Input/output tests ####
	-print("### Input/output tests ###")
	-
	-# Generate data in python
	-orig = Spherebin(np = 100, nw = 1, sid = "test-initgrid")
	-orig.generateRadii(histogram = False)
	-orig.defaultParams()
	-orig.initRandomGridPos(g = numpy.zeros(orig.nd))
	-orig.initTemporal(current = 0.0, total = 0.0)
	-orig.time_total = 2.0*orig.time_dt;
	-orig.time_file_dt = orig.time_dt;
	-orig.writebin(verbose=False)
	-
	-# Test Python IO routines
	-py = Spherebin()
	-py.readbin("../input/" + orig.sid + ".bin", verbose=False)
	-compare(orig, py, "Python IO:")
	-
	-# Test C++ IO routines
	-orig.run(verbose=False, hideinputfile=True)
	-#orig.run()
	-cpp = Spherebin()
	-cpp.readbin("../output/" + orig.sid + ".output00000.bin", verbose=False)
	-compare(orig, cpp, "C++ IO: ")
	-
	-# Test CUDA IO routines
	-cuda = Spherebin()
	-cuda.readbin("../output/" + orig.sid + ".output00001.bin", verbose=False)
	-cuda.time_current = orig.time_current
	-cuda.time_step_count = orig.time_step_count
	-compare(orig, cuda, "CUDA IO: ")
	-
	-# Remove temporary files
	-cleanup(orig)
	-
	-
	-#### Porosity tests ####
	-print("### porosity tests ###")
	-
	-def testPorosities(spherebin):
	-
	- # Number of vertical slices
	- slicevals = [1, 2, 4]
	- i = 1 # iterator var
	- for slices in slicevals:
	-
	- # Find correct value of bulk porosity
	- n_bulk = spherebin.bulkPorosity()
	- #print("Bulk: " + str(n_bulk))
	-
	- porosity = spherebin.porosity(slices = slices)[0]
	- #print("Avg: " + str(numpy.average(porosity)))
	- #print(porosity)
	-
	- # Check if average of porosity function values matches the bulk porosi…
	- compareFloats(n_bulk, numpy.average(porosity), \
	- spherebin.sid + ": Porosity average to bulk porosity ("\
	- + str(i) + "/" + str(len(slicevals)) + "):")
	- i += 1
	-
	-# Test data from previous test
	-testPorosities(orig)
	-
	-# Simple cubic packing of uniform spheres
	-# The theoretical porosity is (4/3pir^3)/(2r)^3 = 0.476
	-sidelen = 10
	-cubic = Spherebin(np = sidelen**3, sid='cubic')
	-radius = 1.0
	-cubic.generateRadii(psd='uni', radius_mean=radius, radius_variance=0.0, histog…
	-for ix in range(sidelen):
	- for iy in range(sidelen):
	- for iz in range(sidelen):
	- i = ix + sidelen * (iy + sidelen * iz) # linear index
	- cubic.x[i,0] = ixradius2.0 + radius
	- cubic.x[i,1] = iyradius2.0 + radius
	- cubic.x[i,2] = izradius2.0 + radius
	-cubic.L[:] = 2.0 * radius * sidelen
	-
	-cubic.initTemporal(0.2)
	-cubic.initGrid()
	-
	-testPorosities(cubic)
	-
	-cleanup(cubic)
	-