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adamjgnoel / AcCoRD

Actor-based Communication via Reaction-Diffusion. A molecular communication simulator. Simulates stochastic reaction-diffusion systems.
https://warwick.ac.uk/adamnoel/software/accord/
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Problem with a Sphere child region #35

Closed ModarHalimeh closed 8 years ago

ModarHalimeh commented 8 years ago

Here are the configs i'm using to create 2 spheres as child region, each one is placed inside a rectangular one: %%%%%%%%%%%%%%%%%Parent Regions%%%%%%%%%%%%%%%%%%%%%%%% "Number of Dimensions": 3, "Subvolume Base Size": 1e-6, "Region Specification": [ { "Notes": "", "Label": "A", "Parent label": "", "Shape": "Rectangular Box", "Anchor X Coordinate": 0, "Anchor Y Coordinate": 0,
"Anchor Z Coordinate": 0,
"Integer Subvolume Size": 1, "Is Region Microscopic?": true, "Number of Subvolumes Along X": 4, "Number of Subvolumes Along Y": 5, "Number of Subvolumes Along Z": 4 }, { "Notes": "", "Label": "B", "Parent label": "", "Shape": "Rectangular Box", "Anchor X Coordinate": 4e-6, "Anchor Y Coordinate": 0, "Anchor Z Coordinate": 0, "Integer Subvolume Size": 1, "Is Region Microscopic?": true, "Number of Subvolumes Along X": 4, "Number of Subvolumes Along Y": 5, "Number of Subvolumes Along Z": 4 }, %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%Child Regions%%%%%%%%%%%%%%%%%%%%%%% "Notes": "", "Label": "C", "Parent label": "A", "Shape": "Sphere", "Anchor X Coordinate": 2e-6, "Anchor Y Coordinate": 2e-6, "Anchor Z Coordinate": 2e-6, "Radius": 1e-6 }, { "Notes": "", "Label": "D", "Parent label": "B", "Shape": "Sphere", "Anchor X Coordinate": 6e-6, "Anchor Y Coordinate": 2e-6, "Anchor Z Coordinate": 2e-6, "Radius": 1e-6 } %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

It's outputting an error that the nested regions are not properly within their parents. Which i assume is not right ?!

adamjgnoel commented 8 years ago

Can you attach the original config file? At first glance this shouldn't generate an error, but it could be that the 2 radii are "just" too big. It should work with radii 0.99999e-6 instead of 1e-6.

ModarHalimeh commented 8 years ago

sure i posted this part just for compactness.

Config.txt

Note: Your solution worked :) 'the 0.999999e-6'

adamjgnoel commented 8 years ago

Ok, I won't need to run the configuration myself then.

Posting the excerpt as you did was helpful without needing the whole file.

I will fix this by adding (or in this case subtracting) the subvolume resolution value (which is about 1%) from the clearance size, so that 1e-6 will work.

adamjgnoel commented 8 years ago

The clearance distance between spherical and rectangular subvolumes has been modified from the ("rectangular subvolume size") to ("rectangular subvolume size" - "epsilon distance"), where the epsilon distance is currently defined as 1% of the base subvolume size.

With this change, your config file runs fine. The correction will be in the next code commit.