{
	"Notes": "Notes fields replace commenting, which is not standard in JSON.",
	"Description": "Sample function that uses the A Priori Monte Carlo (APMC) algorithm
		for simulating surface absorption. System has a point transmitter that releases
		molecules instantaneously and an absorbing sphere. The APMC algorithm performs
		a die roll for every molecule in every time step, using the probability of the
		molecule being absorbed in the current time step. This approach, which is only
		suitable when this probability can be accurately calculated, enables much
		larger time steps (orders of magnitude) without a loss of accuracy.",
	"Output Filename": "accord_sample_a_priori_absorption",
	"Warning Override": false,
	"Simulation Control": {
		"Number of Repeats": 1,
		"Final Simulation Time": 50,
		"Global Microscopic Time Step": 0.5,
		"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 at the receiver.",
				"Label": "Conversion",
				"Is Reaction Reversible?": false,
				"Surface Reaction?": true,
				"Surface Reaction Type": "A Priori Absorbing",
				"Surface Transition Probability": "A Priori Sphere",
				"Surface Reaction Threshold Type": "None",
				"Surface Reaction Threshold Value": 0,
				"Default Everywhere?": false,
				"Exception Regions": ["Receiver"],
				"Reactants": [1, 0],
				"Products": [0, 1],
				"Products Released?": [false, false],
				"Reaction Rate": 1e9999
			}
		]
	},
	"Environment":	{
		"Subvolume Base Size": 1e-12,
		"Region Specification": [
			{
				"Notes": "Single spherical region with infinite radius. If any other region were
					added here then it should be defined as a child of this region.",
				"Label": "A",
				"Parent Label": "",
				"Shape": "Sphere",
				"Type": "Normal",
				"Anchor Coordinate": [0, 0, 0],
				"Radius": 1e9999
			},
			{
				"Notes": "Region at receiver defined so that it can have a local chemical reaction.
				Its location must match that of receiver.",
				"Label": "Receiver",
				"Parent Label": "A",
				"Shape": "Sphere",
				"Type": "3D Surface",
				"Surface Type": "Outer",
				"Anchor Coordinate": [0, 50e-6, 0],
				"Radius": 5e-6
			}
		],
		"Actor Specification": [
		{
				"Notes": "Point Transmitter at origin.",
				"Is Location Defined by Regions?": false,
				"Shape": "Point",
				"Outer Boundary": [0, 0, 0],
				"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,
				"Release Interval": 0,
				"Slot Interval": 0,
				"Modulation Scheme": "Burst",
				"Modulation Strength": 1e4,
				"Is Molecule Type Released?": [true, false]
		},
		{
				"Notes": "Spherical observer at receiver",
				"Is Location Defined by Regions?": true,
				"List of Regions Defining Location": ["Receiver"],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 0.5,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [false, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Observer of propagation environment",
				"Is Location Defined by Regions?": true,
				"List of Regions Defining Location": ["A"],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 0.5,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, false],
				"Is Molecule Position Observed?": [false, false]
		}
		]		
	}
}
