[Camino-users] ArrayIndexOutOfBoundsException when running datasynth command.

[Rajalekshmi Deepu]

Dear Camino users,

  I came across the following ArrayIndexOutOfBoundsException when 
running datasynth command for montecarlo simulations.


Oct 18, 2019 12:39:15 PM simulation.dynamics.StepGeneratorFactory 
getStepGenerator
INFO: instantiating fixed length step generator
Oct 18, 2019 12:39:16 PM 
simulation.geometry.substrates.SquashyInflammationSubstrate <init>
INFO: arranging cylinders
Oct 18, 2019 12:39:16 PM 
simulation.geometry.substrates.SquashyInflammationSubstrate <init>
INFO: initialising dynamic spatial optimisation
Oct 18, 2019 12:39:16 PM 
simulation.geometry.substrates.SquashyInflammationSubstrate <init>
INFO: arranging cylinders
Oct 18, 2019 12:39:16 PM 
simulation.geometry.substrates.SquashyInflammationSubstrate <init>
INFO: cylinder 0 (0% complete)
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 
-1845339287
         at 
simulation.geometry.substrates.SquashyInflammationSubstrate.checkIntersections(SquashyInflammationSubstrate.java:1157)
         at 
simulation.geometry.substrates.SquashyInflammationSubstrate.<init>(SquashyInflammationSubstrate.java:256)
         at 
simulation.geometry.substrates.SubstrateFactory.getSubstrate(SubstrateFactory.java:80)
         at 
simulation.DiffusionSimulation.<init>(DiffusionSimulation.java:143)
         at 
tools.CL_Initializer.initDataSynthesizerFromSimulation(CL_Initializer.java:2160)
         at 
tools.CL_Initializer.initDataSynthesizer(CL_Initializer.java:2191)
         at apps.SyntheticData.initOptions(SyntheticData.java:55)
         at apps.Executable.<init>(Executable.java:24)
         at apps.SyntheticData.<init>(SyntheticData.java:34)
         at apps.EntryPoint.getExecutable(EntryPoint.java:234)
         at apps.EntryPoint.main(EntryPoint.java:291)

Example command is given below: (just to save the time, I have used less 
number of walkers and timesteps in this run)

datasynth -walkers 25000 -tmax 500 -geometry inflammation -numcylinders 
100 -p 0.0 -initial uniform -voxels 1 -increments 1 -separateruns 
*-latticesize 1.4E-5 *-seed <<random_number>> -schemefile %s -*g**amma 
%f %f *-diffusivity 1.5E-9 -cylfile testcyls.csv -drawcrosssection 
LamDlaSubstrate.gray

Shape and scale of the gamma distribution are  random values in the 
following ranges  which are calculated from the mean and standard deviation.

Range of mean (random_mean)--> (0.2E-6 , 5.0E-6)
Range of standard deviation (std) ---> [ (0.1E-6, random_mean/5),  
random_mean/2) ]
  Shape_k = (random_mean / std) ** 2

  Scale_theta =  (std ** 2) / random_mean

Could someone help me to fix this?

Thanks and regards,

Lekshmi




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