Team:BCCS-Bristol/Modeling-BSim Parameter File

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BSim Parameter File

How To Use The File

Definition

***	**************************************
***	General Simulation
***	**************************************
DT:	0.005

The time step used by the simulation. Value is in seconds.

VISCOSITY: 0.001

PHYSICS_WELL_WIDTH_BACT_BACT:	0.0
PHYSICS_WELL_DEPTH_BACT_BACT:	0.0
PHYSICS_WELL_WIDTH_BACT_PART:	0.0
PHYSICS_WELL_DEPTH_BACT_PART:	0.0
PHYSICS_WELL_WIDTH_PART_PART:	0.0
PHYSICS_WELL_DEPTH_PART_PART:	0.0
PHYSICS_WELL_WIDTH_PART_BDRY:	0.0
PHYSICS_WELL_DEPTH_PART_BDRY:	0.0
PHYSICS_WELL_WIDTH_BACT_BDRY:	0.0
PHYSICS_WELL_DEPTH_BACT_BDRY:	0.0
BACTERIA_RADIUS:	0.7
BACTERIA_FORCE:	0.4
BACTERIA_SPEED:	50.0
UP_RUN_LENGTH:	1.6
DOWN_RUN_LENGTH:	0.7
ISO_RUN_LENGTH:	0.86
PARTICLE_RADIUS:	10.0
***	**************************************
***	Bacteria/Particle/Boundary Sets
***	**************************************
CREATE_BACTERIUM_SINGLE:	x	y	diameter(0=default)
CREATE_PARTICLE_SINGLE:	x	y	diameter(0=default)
CREATE_BACTERIA_SET: p1x	p1y	width	height	number	type	diameter(0=default)
CREATE_PARTICLE_SET: p1x	p1y	width	height	number	type	diameter(0=default)
CREATE_BOUNDARY_SOLID:	p1x	p1y	p2x	p2y
CREATE_BOUNDARY_WRAP:	p1x	p1y	p2x	p2y	pOffsetX	pOffsetY
***	**************************************
***	Chemical Field Settings (These should be defined for every simulation)
***	**************************************
FIELD_GOAL_DEFINE:	p1x	p1y	width	height	xboxes	yboxes	threshold	type	boundary	rate
FIELD_GOAL_SETUP:	visible	type(1=LINEAR_X,2=LINEAR_Y)	startCon	endCon	unUsed(setToZero)	unUsed(setToZero)
FIELD_COORD_DEFINE:	p1x	p1y	width	height	xboxes	yboxes	threshold	type	boundary	rate
FIELD_COORD_SETUP:	visible	type(1=LINEAR_X,2=LINEAR_Y)	startCon	endCon	unUsed(setToZero)	unUsed(setToZero)
FIELD_RECRUIT_DEFINE:	p1x	p1y	width	height	xboxes	yboxes	threshold	type	boundary	rate
FIELD_GOAL_SETUP:	visible	type(1=LINEAR_X,2=LINEAR_Y)	startCon	endCon	unUsed(setToZero)	unUsed(setToZero)
***	**************************************
***	Visual Aids
***	**************************************
VISUAL_AID_BACTERIA_TRACE:	StepsSkipped 
VISUAL_AID_AVG_BACTERIA_TRACE:	StepsSkipped
VISUAL_AID_PARTICLE_TRACE:	StepsSkipped
VISUAL_AID_CLOCK:	AlwaysLeaveAs1
***	**************************************
***	View
***	**************************************
SCREEN_HEIGHT:	pixels
SCREEN_WIDTH:	pixels
SCREEN_ZOOM:	xZoom(1Pixel=1Micron)1
SCREEN_MOVE:	xTrans	yTrans
***	**************************************
***	Batch Settings
***	**************************************
VIDEO_FRAMES_SKIP:	FramesToSkipInVideo(OnlyUsedWhenRunByBSimBatch)
RECORD_VIDEO:	FlagToRecordVideo(1=true)(OnlyUsedWhenRunByBSimBatch)
DATA_FRAMES_SKIP:	FramesToSkipInTextOutput(OnlyUsedWhenRunByBSimBatch)
SIMULATION_LENGTH:	NumberOfTimeSteps(OnlyUsedWhenRunByBSimBatch)
SIMULATION_RUNS:	NumberOfRuns(OnlyUsedWhenRunByBSimBatch)
EXPORT_DIR:	DirectoryPath(MustExist)(OnlyUsedWhenRunByBSimBatch)