tupdated documentation - sphere - GPU-based 3D discrete element method algorithm with optional fluid coupling
(HTM) git clone git://src.adamsgaard.dk/sphere
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---
(DIR) commit 45dae0d7df32bf24406dfc860e2c3f806f571413
(DIR) parent 06df2fb69034c673e2ff6c2fe0411f46ea597d9e
(HTM) 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]
-ҩ@VMA9צxNLpB"aGXuPנxc"5,.]^QlνVI Xʒ+}|nwu"^jbQaDxpD* _ [ћSxFkyV80P\SR̟]&E'GL)˟*|Kn- yIJ틧fn*-^vA i)Ĩc${ Bhlc?ljƹWqz{^/O֧"DqAK !vPmpR\2-v5V;e[}V(L'x^U[ j4FPצJ%N;^.o)*dՄƠYir}
-Lˎ
- IHX>$LGg _'% 2ީlC31\\_[Mz}Gōyv?\!]:kEzQ[G :w?F4%,
-\ No newline at end of file
+xڭXMO1+"נ"nH"@CM ;4;Zz ?̼ye-o')G+vѤz E.ݛey3tpnGtSS4X?0{>HUuEwTI7cv2g B|b%X|]v`r{$aBjKvHN_zň'^Y;i6lE3YӐTh:r$v)8E&2z.sIY D|]!&]\V!džVpԪ0PPr.C>%z֖pIv F0I59yB<rJuV-4` bInjo)j}E92CٓC4l
+-@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 @@
-Search.setIndex({objects:{"":{sphere:[5,0,1,""]},sphere:{status:[5,2,1,""],convert:[5,2,1,""],visualize:[5,2,1,""],run:[5,2,1,""],render:[5,2,1,""],thinsectionVideo:[5,2,1,""],torqueScriptParallel3:[5,2,1,""],V_sphere:[5,2,1,""],vector_norm:[5,2,1,""],cleanup:[5,2,1,""],video:[5,2,1,""],sim:[5,3,1,""]},"sphere.sim":{consolidate:[5,1,1,""],forcechains:[5,1,1,""],initGridAndWorldsize:[5,1,1,""],initGrid:[5,1,1,""],render:[5,1,1,""],energy:[5,1,1,""],disableFluidPressureModulation:[5,1,1,""],totalMomentum:[5,1,1,""],shearVel:[5,1,1,""],porosities:[5,1,1,""],initRandomPos:[5,1,1,""],readfirst:[5,1,1,""],writeVTKall:[5,1,1,""],setTolerance:[5,1,1,""],readstep:[5,1,1,""],generateBimodalRadii:[5,1,1,""],defaultParams:[5,1,1,""],plotFluidDiffAdvPresZ:[5,1,1,""],readbin:[5,1,1,""],randomBondPairs:[5,1,1,""],periodicBoundariesX:[5,1,1,""],porosity:[5,1,1,""],initRandomGridPos:[5,1,1,""],writebin:[5,1,1,""],setBeta:[5,1,1,""],bondsRose:[5,1,1,""],cleanup:[5,1,1,""],addParticle:[5,1,1,""],currentNormalStress:[5,1,1,""],plotConvergence:[5,1,1,""],periodicBoundariesXY:[5,1,1,""],triaxial:[5,1,1,""],shear:[5,1,1,""],status:[5,1,1,""],acceleration:[5,1,1,""],thinsection_x1x3:[5,1,1,""],run:[5,1,1,""],setFluidPressureModulation:[5,1,1,""],voidRatio:[5,1,1,""],zeroKinematics:[5,1,1,""],initFluid:[5,1,1,""],setGamma:[5,1,1,""],plotFluidVelocitiesZ:[5,1,1,""],writeFluidVTK:[5,1,1,""],plotFluidVelocitiesY:[5,1,1,""],normalBoundariesXY:[5,1,1,""],defineWorldBoundaries:[5,1,1,""],forcechainsRose:[5,1,1,""],bulkPorosity:[5,1,1,""],createBondPair:[5,1,1,""],setTheta:[5,1,1,""],torqueScript:[5,1,1,""],adjustUpperWall:[5,1,1,""],generateRadii:[5,1,1,""],uniaxialStrainRate:[5,1,1,""],adjustWall:[5,1,1,""],initGridPos:[5,1,1,""],shearStrain:[5,1,1,""],plotFluidPressuresY:[5,1,1,""],plotFluidPressuresZ:[5,1,1,""],readlast:[5,1,1,""],plotPrescribedFluidPressures:[5,1,1,""],writeVTK:[5,1,1,""],video:[5,1,1,""],readsecond:[5,1,1,""],bond:[5,1,1,""],initTemporal:[5,1,1,""],sheardisp:[5,1,1,""],setMaxIterations:[5,1,1,""],contactModel:[5,1,1,""]}},terms:{prefix:3,whose:[],s_law:[],"const":3,under:[1,0,5],everi:2,"void":[3,5],readbin:[3,5],scalar:[3,2,5],vector:[3,2,4,5],bulkporos:5,p_f:5,seper:3,direct:[4,5],second:[3,2,4,5],even:[3,4],supervis:0,hide:5,neg:[2,4,5],lundbek:0,"new":[2,4,5],net:3,topolog:3,abov:[1,2,4,5],here:2,path:[1,5],interpret:1,dry:[3,5],initgridandworlds:5,precis:[3,5],linearli:2,releas:1,instabl:5,total:[3,2,4,5],univ:[],unit:1,plot:5,describ:[2,4],initfluid:5,call:[3,5],recommend:5,type:[1,3,4,5],relax:5,successful:1,relat:3,warn:5,exce:[2,5],loss:[4,5],must:5,setup:[1,5],work:[1,0,5],coalesc:3,root:[1,3,5],unnam:5,kinet:[4,5],give:3,img_width:3,indic:0,want:2,readstep:5,david:0,unsign:3,end:[3,2,5],mu_w:5,travel:3,mu_r:5,how:[3,5],env:5,place:[1,3,5],mu_d:5,updat:[1,0,2,3],after:[1,3,2,5],befor:[3,5],wrong:[],law:[3,2,4],parallel:[1,2,5],averag:[2,5],third:[0,2,5],maintain:1,environ:1,incorpor:2,enter:2,exclus:5,order:[1,3,2,4,5],oper:[1,0,2,3],over:4,visc_n_rat:5,pascal:5,flexibl:[1,2],img:[],fix:5,welcome_:[],fig:3,hidden:[],shear:[2,5],them:5,anim:5,thei:[3,2],choic:[],include_cod:[],arrow:5,each:[3,2,4,5],angvel:[3,5],side:[2,5],mean:[1,2,5],pdflatex:1,logn:5,euler_method:[],network:4,gradient:2,content:0,rewrit:2,gov:[],linear:[2,4,5],slipscal:5,situat:2,free:[1,2],configuraion:3,angl:5,filter:5,isn:[2,5],rang:[2,5],render:[1,3,5],restrict:1,hook:[],instruct:1,sort_by_kei:3,advect:[2,5],top:[2,5],evolut:[3,5],addparticl:5,tool:1,lower:[3,5],max_val:5,somewhat:[4,5],conserv:[2,5],target:[3,5],provid:1,zero:[3,2,4,5],project:[0,2,5],matter:4,rad:5,setfluidpressuremodul:5,xdisp:[3,5],ram:3,rai:[1,5],raw:4,seed:4,increment:4,ldot:3,latter:4,blue:5,though:[3,4],object:[1,5],regular:5,phase:[2,5],prematur:5,don:3,doc:1,flow:[1,0,2,5],vector_norm:5,section:[3,2,4,5],dot:4,radix:3,opposit:2,random:[3,5],radiu:[2,4,5],radii:5,pkg:1,involv:3,consolid:5,layout:3,menu:5,explain:[3,0],configur:[1,3,5],settheta:5,folder:[1,3,5],loopstart:3,stop:5,fluid:[0,2,4,5],symmetr:2,bar:5,cuda_sdk_root_dir:1,"public":[1,3],mu_:5,datatyp:3,result:[1,3,2,4,5],elasto:5,fail:[],best:[1,5],tensor:2,wikipedia:5,figur:3,simplest:4,angpo:[3,5],approach:2,attribut:2,extend:[],cfdem:[],toler:[2,5],subfold:3,howev:[3,4],against:5,uni:5,seri:3,com:[1,3,5],height:5,summat:3,assum:[2,5],gamma_n:5,numpi:[1,5],three:[1,3,2,4,5],been:4,spherebin:5,interest:[0,5],gamma_t:5,gamma_r:5,suppress:3,gidaspow:2,emploi:3,ident:2,cudamemcheck:5,plotconverg:5,gnu:[1,3],properti:[1,2,5],aim:[1,0],euclidean:5,calcul:[3,2,4,5],seven:2,conv:5,tabl:0,toolkit:1,shami:2,sever:[3,5],perform:[1,3,5],make:[1,3,5],transpar:5,complex:[],split:[0,2],dimensionless:2,complet:5,hang:5,hand:[3,2,4],kin:5,"0e3f":3,thu:3,contact:[3,0,2,4,5],thi:[0,1,2,3,4,5],left:5,identifi:[3,4,5],savefig:5,newton:[3,2,4],yet:4,previous:[2,5],expos:1,character:[2,4],save:5,applic:[3,5],dissip:4,mennu:5,background:[3,2],maxval:3,specif:[1,3],initcuda:3,www:[],right:[2,5],old:[2,5],deal:2,interv:[3,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