# Loading default values
VALUE scale=0.1
VALUE TimeStep=0.01
VALUE scaleTimeStep=0.1*0.01
VALUE LogWriteFrequency=100 # The gap in frames between writing out log data
VALUE StartCountingMTsAt=0 # The start value at which to begin numbering MTs
VALUE DeadMicrotubules=0 # Count of the number of MTs which have died
VALUE LogLeftUp=False # If true write only MTs travelling in a certain direction
VALUE MaxFrameCount=2500 # The maximum number of frames to run the simulation for
VALUE ComputePPBFrame=False # Set to true in the frame you want to compute the PPB 
VALUE SplinePPB=True # Set to true to compute a spline for the PPB
VALUE OptimiseSpline=True # Set to true to minimise the curvature of the spline
VALUE SplineCurveWeight=0.1 # The weight to assign to spline curvature
VALUE NumberOfSimulations=1 # The number of simultaneous simulations to run
VALUE SpawnProbability=0.9 # Probability new MT will be created off anold one
VALUE SpontaneousNucleationProbability = 0.05 #Probability of spontaneous nucleation
VALUE CorticalSpawnProbability=0.05 #Prob per unit length of spawning an MT
VALUE SubCorticalSpawnProbability=0.1 #Prob per unit length of spawning an MT
VALUE StartMTCount=15 # The starting number of microtubules
VALUE MaximumLength=200000 # The maximum total microtubule length
VALUE MaximumIndividualLength=2000 # The maximum length of an individual MT
VALUE FlipForce=0 # Try to force a flip to look at rate of change
VALUE LayerFlipping=False # Nucleate MTs in lower layers at right angles
VALUE LayerFromWalls=False # Nucleate layers from walls
VALUE LayerOnEvenWalls=False # Layer on the even walls
ANGLE LayerDefault=0 # Default layer angle
VALUE LayerHysteresis=False # Deliver a payload into a face
VALUE WallRepel=True # Set to true to have MTs deliver a repelling payload to walls
VALUE LengthRepel=True # Amount of repellant delivered is proportional to MT length
VALUE BirthFromWalls=False # Birth new microtubules from walls based on repellant
VALUE BirthHysteresis=True # Implement hysteresis for wall births
VALUE BirthRange=0.0 # The range of angles (relative to normal) that MTs might be born
VALUE BirthProbability=0.5 # Probability that a microtubule with get born at a wall
VALUE BirthableIsTransmittable=False # The ability for an edge to transmit an mt is dependant upon the birthable value
ANGLE MinimumTransmissionAngle=0 # Min angle an MT will transmit at
ANGLE MaximumTransmissionAngle=180 # Max angle an MT will transmit at
VALUE PayloadSize=0.01 # The amount of payload an MT delivers to the wall for flipping
VALUE AreaDiffusion=False # Set to true to have repellant delivered to faces
VALUE PeriodicFromRepellant=True # MTs wrap based on wall repellant
VALUE SpontaneousCreationProbability=0.1 # Probability of spontaneously creating an MT
VALUE DestroyAllMicrotubules=False # Set to true to wipeout all the microtubules in the system
VALUE HorizontalArray=True # Set to true to creat a vertical array after DestroyAllMicrotubules
VALUE VerticalArray=False # Set to true to create a horizontal array after DestroyAllMicrotubules
VALUE ArrayDensityTimeDependent=True # Set True to make the arrays created dependent on frame number for density
VALUE MTCollisions=True # Set to true to perform MT-MT collision checks
VALUE TargetMTCount=150 # The target number of MTs the system will maintain
ANGLE MinAngle=-20 # The minimum angle a spawning MT will adopt
ANGLE MaxAngle=20 # The maximum angle a spawning MT will adopt
VALUE SpawnBothWays=True # If true spawn opposite to direction of motion
ANGLE ZipperAngle=40 # Critical angle under which zippering occurs
VALUE Severing=True # Set to true to enable severing
RATES CatastropheProbability=0.3 # Average catastrophes per MT per minute at the front
RATES MinusCatastropheProbability=0.3 # Average catastrophes per MT per minute at the rear
RATES RescueProbability=0.4 # Average rescues per MT per minute at the front
RATES MinusRescueProbability=0.0 # Average rescues per MT per minute at the rear
RATES PauseProbability=0.2 # Average pauses per MT per minute at the front
RATES MinusPauseProbability=0.2 # Average pauses per MT per minute at the rear
SPEED FrontGrowthVelocity=5.5 # The MT growth velocity at the front
SPEED RearGrowthVelocity=1.1 # The MT growth velocity at the rear
SPEED FrontShrinkVelocity=11.0 # The MT shrink (catastrophe) velocity at the front
SPEED RearShrinkVelocity=1.1 # The MT shrink (catastrophe) velocity at the rear
VALUE CatastropheOnCollision=True # Set to True to give MTs a chance of undergoing a catastrophe upon collision
VALUE StartCellFrameOffset=0 # The cell frame to start from when animating the geometry
VALUE CellVertexOffset=0 # Offset the first vertex index by this amount
VALUE CellFileOffset=1 # The cell number to take as cell 0 from a file created by Pierre's cell tracker.
VALUE CellFramesPerMinute=0.1 # Number of minutes it takes to transform to the next frame
VALUE MTOC=False # Set to True to turn on an MTOC
VALUE StabiliseMicrotubules=False # Setting true stabilises microtubules that span the nucleus-cell wall
VALUE UniformNucleation=True # If false used a look-up table to obtain nucleation angles
VALUE OmitZeroNucleation=False # If true use an alternate distribution to omit zero nucleations
VALUE NucleateToBelowLayer=False #If True then there's a finite probability of spontaneous nucleation on a lower layer
VALUE LowerLayerNucleationProbability=0.01 #Probability of nucleating onto a lower layer (also proportional to number of MTs)
VALUE DisplaySimulation=True # Not used yet but should put the simulation into silent mode
VALUE DisplayPlusEnds=False # Set to true if you want to see the plus ends
VALUE LineThickness=5 # The thickness in pixels to draw the lines
VALUE WallThickness=2 # The thickness to draw the cell walls
VALUE PeriodicBoundaryConditions=False # Specify whether to use periodic boundary conditions
VALUE DestructBoundaryConditions=False # Specify whether to use boundary conditions which catastrophise mts on contact
VALUE DisplayText=True # If false don't display the on-screen stats-Mette Mogensen
VALUE DisplayMicrotubules=True # If false don't show microtubues
VALUE MTOCinit=True # Set to true to position the MTOC at the cell centre prior to starting the simulation
VALUE MTOCRadius=0.241 # Set the radius of the nucleus or other MTOC
VALUE MTOCcentreX=0.0 # x-position of the MTOC centre
VALUE MTOCcentreY=0.0 # y-position of the MTOC centre
VALUE MTOCdiffusion=False # Set to true if the MTOC is able to experience Brownian motion
VALUE MTOCbrownianmu=0.0 # The average Brownian step size
VALUE MTOCbrowniansigma=0.001 # The brownian step-size sigma
VALUE MTOCpull=False # Set to true if microtubules should pull rather than push
VALUE MTOCExperimental=False # Set to true if experimental nuclear data exists
VALUE MTOCmatchRadius=True # Set to true to match the simulated nuclear radius to experiment
VALUE MTOCmatchPosition=False # Set to true to match simulated position to experimental
VALUE FlipExperimental=False # Set to true to change the order of experimental coordinates
VALUE BrownianMotion=False # If True have random Brownian motion-especially for Andrew
VALUE BrownianSideMotion=False # If True then sideways Brownian motion is different from length
SPEED BrownianStep=10.0 # The displacement to use during the Brownian step
SPEED BrownianHorizStep=10.0 # The displacement to use during the horizontal Brownian step
ANGLE BrownianAngle=5 # The displacement angle to use during theBrownian step
VALUE StericRestriction=False # Set to true to give the MTs thickness
VALUE MTWidth=0.05 # MT width if steric restruction is set to on
VALUE Depletion=False # If true have repellant on entire face
VALUE SetOddEmergence=False # Set true to have even edges emit MTs
VALUE SetEvenEmergence=False # Set true to have even edges emit MTs
VALUE SetNoEmergence=False # Set true to have even edges emit MTs
VALUE PlasmaMembrane=False # Set true to denote layer is attached toplasma membrane
VALUE StepsUntilTubulinRelease=500 #Frames until used tubulin becomes free
VALUE DisplayRosette=True # Set to true to display MT orientations ona rosette
VALUE CellList=['CellData/tracking.csv'] # List of cells that make up the geometry
VALUE NuclearList=['CellData/NONE.csv'] # List of experimental nuclear positions
VALUE LogFile='Logs/TestLog.txt' # Where to write the log file
VALUE MovieDir='Movies/movie' # Where to put the movies
VALUE Pause=0
VALUE Layer=0
VALUE LengthScale=-1
VALUE TimeScale=-1
VALUE ComputeEnergy=False # If true compute the energy of the configuration based on angles
VALUE StepsUntilTubulinRelease=300
VALUE SubCorticalMaxLength=25