[Camino-users] Mesh substrates

[Damien McHugh]

To all,

I'm having some problems running datasynth simulations using mesh substrates specified by a .ply file - my bash script is:

#! /bin/bash

echo DEL_9

datasynth -walkers 1000000 -tmax 5000 -voxels 1 -p 0.0 -schemefile DEL_9.scheme -initial uniform -substrate mesh -plyfile sphere_1.ply  > sphere_1_1000000_walkers_DEL_9_Ghigh_290_seed1.Bfloat

The output in the terminal is:

DEL_9
Sep 20, 2011 10:54:04 AM tools.CL_Initializer CL_init
WARNING: unrecognised geometry type 'mesh' will use default (CYL_1_FIXED)
Sep 20, 2011 10:54:04 AM tools.CL_Initializer checkParsing
WARNING: WARNING: couldn't parse arg 13: 'mesh'
Sep 20, 2011 10:54:04 AM simulation.dynamics.StepGeneratorFactory getStepGenerator
INFO: instantiating fixed length step generator
Sep 20, 2011 10:54:04 AM simulation.geometry.substrates.ParallelCylinderSubstrate <init>
INFO: constructing hexagonally packed cylinder substrate, radius= 1.0E-5 separation= 3.0E-5
Sep 20, 2011 10:54:04 AM simulation.geometry.substrates.ParallelCylinderSubstrate <init>
INFO: intracellular vol frac = 0.40306652538538185
Sep 20, 2011 10:54:04 AM simulation.DiffusionSimulation <init>
INFO: running simulation: 1000000 walkers, 5000 timesteps, p= 0.0
Sep 20, 2011 10:54:04 AM simulation.DiffusionSimulation <init>
INFO: dynamics duration 0.035

Here it proceeds with the simulation, but uses the default CYL_1_FIXED substrate. Any help with what I need to do in order for the simulation to run in the mesh substrate is much appreciated.

Thanks,
Damien
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