Team:BCCS-Bristol/Modeling-BSim Parameter File

BSim Parameter File

How To Use The File

Option Definitions

General Simulation Options

DT:	0.005

The time step (in seconds) used by the simulation. This should be small enough that you do not get objects moving through each other or that two objects get so close in a single time step that the reactive force pushes them too far apart.

VISCOSITY:	0.001 

The viscosity of the medium. This effects the speed of movement of the bacteria. The force of the bacteria should be selected based on this.

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
PHYSICS_REACT_FORCE:	15.0

All interactions between bacteria, particles and boundaries are handled by a potential function. Each of these options specifies the relevant options for the linear piece-wise function. The same reaction force (when objects overlap) is shared by all objects.

BACTERIA_RADIUS:	0.7

The default radius of a bacterium in microns.

BACTERIA_FORCE_DOWN:	0.41
BACTERIA_FORCE_UP:	0.4387

The force that a bacterium exerts when moving up and down a chemotactic gradient.

UP_RUN_LENGTH:	1.6
DOWN_RUN_LENGTH:	0.7
ISO_RUN_LENGTH:	0.86

The mean run length up and down a chemotatic gradient. Also the run length when in an isotropic region is given. This mean is for the exponential distribution used to model the run length distribution.

PARTICLE_RADIUS:	10.0

The default radius of a particle in microns.

Bacteria, Particle and 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)

Creates a set of uniformly random distributed bacteria within a rectangular region defined by an upper left point, p1, and a width and height. If you wish the bacteria to be the default size then the diameter value should be 0, otherwise enter the size in microns. There are 5 types of bacteria:

1. Basic -
2. Sensing -
3. Co-ordinated -
4. Recruit -
5. Dead -

CREATE_PARTICLE_SET: p1x	p1y	width	height	number	type	diameter(0=default)

Creates a set of uniformly random distributed particles within a rectangular region defined by an upper left point, p1, and a width and height. At present there is only one type of particle and so this should be left as 0. If you wish the particle to be the default size then the diameter value should be 0, otherwise enter the size in microns.

CREATE_BOUNDARY_SOLID:	p1x	p1y	p2x	p2y

Creates a straight solid boundary between two points.

CREATE_BOUNDARY_WRAP:	p1x	p1y	p2x	p2y	pOffsetX	pOffsetY

Creates a straight wrapping boundary between two points (p1, p2) with an offset vector that is used to place objects that cross the boundary.

Chemical Fields

***	**************************************
***	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 Aids
***	**************************************
VISUAL_AID_BACTERIA_TRACE:	StepsSkipped 
VISUAL_AID_AVG_BACTERIA_TRACE:	StepsSkipped
VISUAL_AID_PARTICLE_TRACE:	StepsSkipped
VISUAL_AID_CLOCK:	AlwaysLeaveAs1

Simulation View

***	**************************************
***	View
***	**************************************
SCREEN_HEIGHT:	pixels
SCREEN_WIDTH:	pixels
SCREEN_ZOOM:	xZoom(1Pixel=1Micron)1
SCREEN_MOVE:	xTrans	yTrans

Batch Settings

***	**************************************
***	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)