{
	"Notes": "Notes fields replace commenting, which is not standard in JSON.",
	"Description": "This configuration demonstrates the different ways that rectangular and
	spherical regions can be defined relative to each other. It is an arbitrarily complex
	toy example with many nested regions. Molecules are uniformly distributed and freely diffuse
	throughout, so the average observation at each passive actor should remain constant.
	There are 2 molecule types and their behavior should be independent.
	The definition of the actors is a blend of absolute (defined by geometry) and
	relative (defined by list of regions).
	In this version, all regions are microscopic.",
	"Output Filename": "accord_sample_all_shapes_micro",
	"Warning Override": false,
	"Simulation Control": {
		"Number of Repeats": 1,
		"Final Simulation Time": 1,
		"Global Microscopic Time Step": 1e-3,
		"Random Number Seed": 1,
		"Max Number of Progress Updates": 100
	},
	"Chemical Properties": {
		"Number of Molecule Types": 2,
		"Diffusion Coefficients": [2e-9, 5e-9],
		"Global Flow Type": "None",
		"Chemical Reaction Specification": []
	},
	"Environment":	{
		"Subvolume Base Size": 1e-6,
		"Region Specification": [
			{
				"Notes": "System parent region. Total volume 2.5e5 cubic microns",
				"Label": "A",
				"Parent Label": "",
				"Shape": "Rectangular Box",
				"Type": "Normal",
				"Anchor Coordinate": [0, 0, 0],
				"Integer Subvolume Size": 5,
				"Is Region Microscopic?": true,
				"Number of Subvolumes Per Dimension": [20, 10, 10]
			},
			{
				"Notes": "1st child of system parent.
					Volume 73500 cubic microns (29.4% of total)",
				"Label": "B",
				"Parent Label": "A",
				"Shape": "Rectangular Box",
				"Type": "Normal",
				"Anchor Coordinate": [10e-6, 10e-6, 10e-6],
				"Integer Subvolume Size": 5,
				"Is Region Microscopic?": true,
				"Number of Subvolumes Per Dimension": [12, 7, 7]
			},
			{
				"Notes": "2nd child of system parent. Adjacent to 1st child.
					Volume 18000 cubic microns (7.2% of total)",
				"Label": "C",
				"Parent Label": "A",
				"Shape": "Rectangular Box",
				"Type": "Normal",
				"Anchor Coordinate": [70e-6, 10e-6, 10e-6],
				"Integer Subvolume Size": 2,
				"Is Region Microscopic?": true,
				"Number of Subvolumes Per Dimension": [10, 15, 15]
			},
			{
				"Notes": "Neighbor to parent's neighbor.
					Volume 1000 cubic microns (0.4% of total)",
				"Label": "BChild1",
				"Parent Label": "B",
				"Shape": "Rectangular Box",
				"Type": "Normal",
				"Anchor Coordinate": [60e-6, 15e-6, 15e-6],
				"Integer Subvolume Size": 2,
				"Is Region Microscopic?": true,
				"Number of Subvolumes Per Dimension": [5, 5, 5]
			},
			{
				"Notes": "Neighbor to parent's neighbor. Uses
						bigger subvolumes than BChild1. 
						Volume 1000 cubic microns (0.4% of total)",
				"Label": "BChild2",
				"Parent Label": "B",
				"Shape": "Rectangular Box",
				"Type": "Normal",
				"Anchor Coordinate": [60e-6, 30e-6, 30e-6],
				"Integer Subvolume Size": 5,
				"Is Region Microscopic?": true,
				"Number of Subvolumes Per Dimension": [2, 2, 2]
			},
			{
				"Notes": "Spherical region nested in Rectangular region. Center is deliberately off-grid
				to show that spherical regions do not need to be flush with the coordinates used for the rectangular regions.
				Volume 8000 cubic microns (3.2% of total)",
				"Label": "D",
				"Parent Label": "B",
				"Shape": "Sphere",
				"Type": "Normal",
				"Anchor Coordinate": [30.1e-6, 27.55e-6, 27.5e-6],
				"Radius": 12.407e-6
			},
			{
				"Notes": "This region has a spherical parent.
					Volume 384 cubic microns (0.15% of total)",
				"Label": "DChild1",
				"Parent Label": "D",
				"Shape": "Rectangular Box",
				"Type": "Normal",
				"Anchor Coordinate": [23.6e-6, 21.1e-6, 21.2e-6],
				"Integer Subvolume Size": 1,
				"Is Region Microscopic?": true,
				"Number of Subvolumes Per Dimension": [8, 6, 8]
			},
			{
				"Notes": "This region has a spherical parent.
					Volume 192 cubic microns (0.0768% of total)",
				"Label": "DChild2",
				"Parent Label": "D",
				"Shape": "Rectangular Box",
				"Type": "Normal",
				"Anchor Coordinate": [23.6e-6, 27.1e-6, 21.2e-6],
				"Integer Subvolume Size": 1,
				"Is Region Microscopic?": true,
				"Number of Subvolumes Per Dimension": [8, 3, 8]
			},
			{
				"Notes": "Spherical region with a spherical parent.
				Volume 300 cubic microns (0.12% of total)",
				"Label": "DChild3",
				"Parent Label": "D",
				"Shape": "Sphere",
				"Type": "Normal",
				"Anchor Coordinate": [36.9e-6, 27.5e-6, 27.3e-6],
				"Radius": 4.1528e-6
			}
		],
		"Actor Specification": [
		{
				"Notes": "Observer of whole system",
				"Is Location Defined by Regions?": false,
				"Shape": "Rectangular Box",
				"Outer Boundary": [0, 100e-6, 0, 50e-6, 0, 50e-6],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e-2,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Observer of region B and its children",
				"Is Location Defined by Regions?": false,
				"Shape": "Rectangular Box",
				"Outer Boundary": [10e-6, 70e-6, 10e-6, 45e-6, 10e-6, 45e-6],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e-2,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Observer of region C and its children",
				"Is Location Defined by Regions?": false,
				"Shape": "Rectangular Box",
				"Outer Boundary": [70e-6, 90e-6, 10e-6, 40e-6, 10e-6, 40e-6],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e-2,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Observer of region BChild1",
				"Is Location Defined by Regions?": true,
				"List of Regions Defining Location": ["BChild1"],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e-2,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Observer of region BChild2",
				"Is Location Defined by Regions?": true,
				"List of Regions Defining Location": ["BChild2"],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e-2,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Observer of region D and its children",
				"Is Location Defined by Regions?": true,
				"List of Regions Defining Location": ["D", "DChild1", "DChild2", "DChild3"],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e-2,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Observer of region DChild1",
				"Is Location Defined by Regions?": true,
				"List of Regions Defining Location": ["DChild1"],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e-2,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Observer of region DChild2",
				"Is Location Defined by Regions?": true,
				"List of Regions Defining Location": ["DChild2"],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e-2,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Observer of region DChild3",
				"Is Location Defined by Regions?": false,
				"Shape": "Sphere",
				"Outer Boundary": [36.9e-6, 27.5e-6, 27.3e-6, 4.1528e-6],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e-2,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Transmitter 1. Releases 1 molecule per 100 cubic microns",
				"Is Location Defined by Regions?": false,
				"Shape": "Rectangular Box",
				"Outer Boundary": [0, 100e-6, 0, 50e-6, 0, 50e-6],
				"Is Actor Active?": true,
				"Start Time": 0,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1000000,
				"Is Actor Activity Recorded?": true,
				"Random Number of Molecules?": false,
				"Random Molecule Release Times?": false,
				"Release Interval": 0,
				"Slot Interval": 0,
				"Bits Random?": true,
				"Probability of Bit 1": 1,
				"Modulation Scheme": "CSK",
				"Modulation Bits": 1,
				"Modulation Strength": 2500,
				"Is Molecule Type Released?": [true, false]
		},
		{
				"Notes": "Transmitter 2. Releases 1000 molecules (i.e., 10 for every 1% of system volume).",
				"Is Location Defined by Regions?": false,
				"Shape": "Rectangular Box",
				"Outer Boundary": [0, 100e-6, 0, 50e-6, 0, 50e-6],
				"Is Actor Active?": true,
				"Start Time": 0,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1000000,
				"Is Actor Activity Recorded?": true,
				"Random Number of Molecules?": false,
				"Random Molecule Release Times?": false,
				"Release Interval": 0,
				"Slot Interval": 0,
				"Bits Random?": true,
				"Probability of Bit 1": 1,
				"Modulation Scheme": "CSK",
				"Modulation Bits": 1,
				"Modulation Strength": 1000,
				"Is Molecule Type Released?": [false, true]
		}
		]		
	}
}
