{
	"Notes": "Notes fields replace commenting, which is not standard in JSON.",
	"Description": "This configuration demonstrates reaction-diffusion in the mesoscopic
		regime. We define a chain of subvolumes that form a pipe. Molecules are added
		by an active actor at one end of the chamber and can convert into an immobile product molecule at the other end. This file has no 2nd order reactions so it can be done in the microscopic regime. 1 repeat of this simulation should less than 10 seconds to
		execute on a personal computer.",
	"Output Filename": "accord_sample_pipe_reaction_diffusion_microscopic",
	"Warning Override": false,
	"Simulation Control": {
		"Number of Repeats": 1,
		"Final Simulation Time": 100,
		"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": [1e-9, 0],
		"Global Flow Type": "None",
		"Chemical Reaction Specification": [
			{							
				"Notes": "Conversion. Can only occur in the destination region.",
				"Label": "Conversion",
				"Is Reaction Reversible?": false,
				"Surface Reaction?": false,
				"Default Everywhere?": false,
				"Exception Regions": ["Destination"],
				"Reactants": [1, 0],
				"Products": [0, 1],
				"Reaction Rate": 0.1			
			}
		]
	},
	"Environment":	{
		"Subvolume Base Size": 1e-6,
		"Region Specification": [
			{
				"Notes": "Primary region",
				"Label": "Pipe",
				"Parent Label": "",
				"Shape": "Rectangular Box",
				"Type": "Normal",
				"Anchor Coordinate": [0, 0, 0],
				"Integer Subvolume Size": 1,
				"Is Region Microscopic?": true,
				"Number of Subvolumes Per Dimension": [10, 1, 1]
			},
			{
				"Notes": "Region where conversion reaction can occur.",
				"Label": "Destination",
				"Parent Label": "",
				"Shape": "Rectangular Box",
				"Type": "Normal",
				"Anchor Coordinate": [10e-6, 0, 0],
				"Integer Subvolume Size": 1,
				"Is Region Microscopic?": true,
				"Number of Subvolumes Per Dimension": [1, 1, 1]
			}
		],
		"Actor Specification": [
		{
				"Notes": "Molecule source. Release molecules at start.",
				"Is Location Defined by Regions?": false,
				"Shape": "Rectangular Box",
				"Outer Boundary": [0, 1e-6, 0, 1e-6, 0, 1e-6],
				"Is Actor Active?": true,
				"Start Time": 0,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e9999,
				"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": 50,
				"Is Molecule Type Released?": [true, false]
		},
		{
				"Notes": "Destination observer",
				"Is Location Defined by Regions?": true,
				"List of Regions Defining Location": ["Destination"],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Source observer",
				"Is Location Defined by Regions?": false,
				"Shape": "Rectangular Box",
				"Outer Boundary": [0e-6, 1e-6, 0e-6, 1e-6, 0e-6, 1e-6],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, false],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "System observer (to show conservation of molecules)",
				"Is Location Defined by Regions?": false,
				"Shape": "Rectangular Box",
				"Outer Boundary": [0e-6, 11e-6, 0e-6, 1e-6, 0e-6, 1e-6],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, true],
				"Is Molecule Position Observed?": [false, false]
		}
		]		
	}
}
