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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hiya,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Let me see if I can answer these:</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Dear all,<o:p></o:p></p>
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<p class="MsoNormal">I am a new user of Camino. I would like to use Camino to generate the trajectories (inside the closed cylinder PLY mesh).<o:p></o:p></p>
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<p class="MsoNormal">1. From Camino tutorial: The simple command to generate trajectories is:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">datasynth -walkers 100000 -tmax 1000 -p 0.0 -voxels 1 -initial uniform -duration 0.2 -trajfile mytraj.traj</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#505050">I am wondering about the particles stepping size in this case. The particles stepping size should be sigma = sqrt(6*D0*dt), where D0 is diffusivity coefficient and dt is time step.
But in the above command, there is no D0 value. So, how it works? Is there specify defaults value for D0?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">The step length is indeed set via the time increment and the diffusivity (sqrt[6D0dt]). The diffusivity can be set from the commandline with the –diffusivity
switch – like everything in camino it should be specified in SI units. The default value is 2.1E-9 and is given in tools/CL_Initializer.java (the variable’s called DIFF_CONST)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#505050">2. Now, I would like to generate trajectories inside
<b>only one closed cylinder</b> (defined by PLY mesh). The command is:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">datasynth -walkers ${WALKERS} -tmax ${TVAL} -p 0.0 -voxels 1 -initial intra -voxelsizefrac 1 -diffusivity 0.5E-9 -duration 0.05 -substrate ply -plyfile ${plyfile} -trajfile ${mytrajfile}</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I would not recommend using a ply file for a single cylinder. There are default cylinder substrates which will do the job more efficiently. First of all, are
you wanting to simulate spins inside the cylinder only or also outside? If it’s the latter the packing of the cylinders in space will make a difference – square or hex both use cylindes of a fixed size. If you are only simulating inside a cylinder, then you
can use any parallel cylinder substrate and it will give you results from a single cylinder. You can specify these options with –initial intra or –initial uniform.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#505050">Where </span><span style="font-family:"Courier New";color:#505050">${WALKERS}=</span><span style="font-family:"Arial",sans-serif;color:#505050">131072 and </span><span style="font-family:"Courier New";color:#505050">${TVAL}=</span><span style="font-family:"Arial",sans-serif;color:#505050">1000.
The header of my plyfile is </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">ply</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">comment closed surface</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">format ascii 1.0</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">element vertex
<b>8071</b></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">property float x</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">property float y</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">property float z</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">element face
<b>16138</b></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">property list uchar uint vertex_indices</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New";color:#505050">end_header</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#505050">The question are:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#505050">2.a. Is this command correct?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#505050">2.b. Why is the generation running very very slowly? (just 1% finished for more than 12 hours running)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Your command looks about right, although see above about not using PLY files. It is possible that your performance is poor because of network latency. If you
are writing your PLY file to a network drive this will be very slow. Try writing to a local drive and then copying it over when it’s finished.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#505050">Thank you so much.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hope this helps,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Matt.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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