[Camino-users] ply files in Monte Carlo simulations

[Damien McHugh]

Hi Matt,
Many thanks for your reply. I had thought the intracellular walker placement may be an issue, but even setting up simulations with very few walkers doesn't appear to help - none of them progress. I will start by taking a look at the checks you suggest!

Best wishes,
Damien
________________________________
From: camino-users-bounces at www.nitrc.org [camino-users-bounces at www.nitrc.org] on behalf of Matt Budde [matt.budde at yahoo.com]
Sent: 16 July 2012 19:56
To: Damien McHugh; camino-users at www.nitrc.org
Subject: Re: [Camino-users] ply files in Monte Carlo simulations

Hi Damien,

I spent considerable time a couple of years ago running some simulations with ply files.  I can give you my insights, but recognize that things could have changed since then.

Regarding intra/extra cellular spaces with mesh substrates: Whether a point within the substrate is intracellular or extracellular is determined by whether a vector passing through the point crosses the mesh an even (intracellular) or odd/zero (extracellular) number of times.  The complication is that if there are odd edges, overlaps, or gaps in your mesh, things can get very complicated.  With the '-initial intra' flag, an initial position is selected at random within the entire substrate, and if it happens to be intracellular according to the vector crossing, it is kept, if it is extracellular, it is discarded and the process continues until all your initial points are determined.  If only a small portion of your substrate is intracellular, it can take considerably longer to randomly select points within this space.  Hence, that might be the situation you are seeing. If you start with a much smaller number of walkers, does the intra condition eventually get going?

I also did several checks along the way to ensure that things were working appropriately.  The first was to plot the initial positions of the walkers compared to the mesh to ensure that these were in the right locations.  (I wrote some matlab routines to read and plot my ply files and overlay the walker data stored in the trajectory files from camino). Early on, I had issues with units and visualizing the data helped me get things scaled appropriately, including resolving an issue with intra/extra points.  The second check was to plot the full random walk history for at least a small number of walkers to ensure that they stayed within their compartment for the duration of the simulation (with permeability set to zero).  I did have the problem initially that sometimes a walker would cross over the mesh instead of being reflected by it.  The exact solution escapes me now, but I think it had to do with either a rounding or floating point precision issue.  In any case, I had modified and recompiled the code to resolve that issue.  For what it's worth, I was using camino version 841.

Feel free to email me directly if you have any followup questions,

-matt



________________________________
From: Damien McHugh <damien.mchugh-2 at postgrad.manchester.ac.uk>
To: "camino-users at www.nitrc.org" <camino-users at www.nitrc.org>
Sent: Monday, July 16, 2012 9:14 AM
Subject: [Camino-users] ply files in Monte Carlo simulations

Hello all,
I am having trouble running simulations of intra-cellular diffusion when using .ply files as substrates. If I set '-initial extra' the simulation will run, with the terminal output showing, for example:

Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation <init>
INFO: running simulation: 100000 walkers, 1000 timesteps, p= 0.0
Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation <init>
INFO: dynamics duration 0.13
Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation initialiseWalkers
INFO: writing initial walker positions
Jul 10, 2012 2:53:34 PM simulation.DiffusionSimulation initialiseWalkers
INFO: walkr positions written
0.0%

However, if I use '-initial intra' I get the following:

INFO: running simulation: 100000 walkers, 1000 timesteps, p= 0.0
Jul 10, 2012 3:08:52 PM simulation.DiffusionSimulation <init>
INFO: dynamics duration 0.13

The simulation does not progress from here and 0.0% doesn't print to the terminal. Any advice regarding the use of ply files is much appreciated.

Many thanks,
Damien


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