[Camino-users] Changing number of cylinders in MC simulation
Hall, Matt
matt.hall at ucl.ac.uk
Thu Sep 29 01:59:19 PDT 2016
Hi Lorenza,
Glad you're finding the simulation useful! If you're using a square packing, the arrangement is a regular grid of cylinders which extends periodically out to infinity. The number of cylinders in this case is just enough to define a unit cell with periodic boundaries -- spins leave one side and wander into an identical cell next door. Under these circumstances there's no option to change the number of cylinders since the packing is so regular.
This applies to the regular packings, but not the random packings. If you want to look at those you can specify the squashy inflammation substrate, a size (using -substratesize, a number of cylinders (-numcylinders) and paramters for the size distribution (-gamma <scale> <shape>). You'll need to watch out that the substrate is large enough to hold all the cylinders -- it'll generate a warning if it can't place them all.
Hope this helps,
Matt.
________________________________
From: camino-users-bounces at www.nitrc.org <camino-users-bounces at www.nitrc.org> on behalf of Lorenza Brusini <lorenza.brusini at univr.it>
Sent: 29 September 2016 09:50:11
To: camino-users at www.nitrc.org
Subject: [Camino-users] Changing number of cylinders in MC simulation
Hello, I'd like to ask a question about synthesis using Monte-Carlo diffusion simulator.
I did a simple simulation using:
datasynth -walkers 100000 -tmax 1000 -geometry cylinder -packing SQUARE -cylinderrad 0.5E-6 -cylindersep 1.1E-6 -p 0.0 -initial uniform -voxels 1 -schemefile scheme.scheme | float2txt > out.txt
Now I would like to change the number of the cylinders that, if I understood well when I read the documentation on the web site, is set to 20 as default. Moreover, I would like to keep constant the dimensions of the voxel thus to change the volume fractions only due to the number of cylinders.
How could I do? I tried with option -latticesize and -numcylinders that I found in the ActiveAx tutorial, but nothing seems function.
Another question is if is it possible to simulate myelinated cylinders or still not.
Thanks in advance. Regards.
Lorenza
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