{
	"Notes": "Notes fields replace commenting, which is not standard in JSON.",
	"Description": "This configuration consider a simple communications scenario where both
		the transmitter and receiver have chemical processes.
		This configuration was arranged to demonstrate the following functionality:
		- CSK transmission with more than one bit per symbol
		- transmission of modulated signal over finite interval with molecules randomly generated.
		- reversible chemical conversion at the receiver surface		
		One repeat of this simulation should take less than a minute to execute on a personal computer.
		The differences in run time compared to the non-chemical version of this simulation are due
		to the definition of 2 regions and not the chemical reactions themselves. A second region is
		required here in order to define where the receiver chemical reactions take place. Most
		computational resources are spent on determining whether the molecules have transitioned
		between the two regions.",
	"Output Filename": "accord_sample_communication_chemical",
	"Warning Override": false,
	"Simulation Control": {
		"Number of Repeats": 1,
		"Final Simulation Time": 0.1,
		"Global Microscopic Time Step": 1e-4,
		"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?": true,
				"Reverse Reaction Label": "Reverse",
				"Surface Reaction?": true,
				"Surface Reaction Type": "Absorbing",
				"Surface Transition Probability": "Steady State",
				"Default Everywhere?": false,
				"Exception Regions": ["Receiver"],
				"Reactants": [1, 0],
				"Products": [0, 1],
				"Products Released?": [false, false],
				"Reaction Rate": 40
			},
			{							
				"Notes": "Reverse reaction. Can only occur at the receiver.",
				"Label": "Reverse",
				"Is Reaction Reversible?": true,
				"Reverse Reaction Label": "Conversion",
				"Surface Reaction?": true,
				"Surface Reaction Type": "Desorbing",
				"Surface Transition Probability": "Steady State",
				"Default Everywhere?": false,
				"Exception Regions": ["Receiver"],
				"Reactants": [0, 1],
				"Products": [1, 0],
				"Products Released?": [true, false],
				"Release Placement Type": "Steady State Diffusion",
				"Reaction Rate": 200
			}
		]
	},
	"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, 2e-6, 0],
				"Radius": 0.5e-6
			}
		],
		"Actor Specification": [
		{
				"Notes": "Point Transmitter at origin with 10ms symbol length. Molecules are
					generated at random times at an expected rate that depends on the current symbol.",
				"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": 10e-3,
				"Is Actor Activity Recorded?": true,
				"Random Number of Molecules?": true,
				"Random Molecule Release Times?": true,
				"Release Interval": 1e-3,
				"Bits Random?": true,
				"Probability of Bit 1": 0.5,
				"Modulation Scheme": "CSK",
				"Modulation Bits": 2,
				"Modulation Strength": 120000,
				"Is Molecule Type Released?": [true, false]
		},
		{
				"Notes": "Observer at molecule source. Demonstrates that molecules quickly
					leave the source. Observations here are much lower than in the
					non-chemical version of this simulation because molecules get created
					at any time and are able to diffuse away between observations",
				"Is Location Defined by Regions?": false,
				"Shape": "Sphere",
				"Outer Boundary": [0, 0, 0, 1e-7],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e-4,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, false],
				"Is Molecule Position Observed?": [false, 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": 1e-4,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [false, true],
				"Is Molecule Position Observed?": [false, false]
		},
		{
				"Notes": "Global observer.",
				"Is Location Defined by Regions?": false,
				"Shape": "Sphere",
				"Outer Boundary": [0, 0, 0, 1e9999],
				"Is Actor Active?": false,
				"Start Time": 1e-10,
				"Is There Max Number of Actions?": false,
				"Is Actor Independent?": true,
				"Action Interval": 1e-4,
				"Is Actor Activity Recorded?": true,
				"Is Time Recorded with Activity?": false,
				"Is Molecule Type Observed?": [true, false],
				"Is Molecule Position Observed?": [false, false]
		}
		]		
	}
}
