/**
* \brief Defines a region of the computation domain where a new species may be created, using
* restrictions in the protocol file
*
* <p>Defines a region of the computation domain where a new species may be created, using
* restrictions in the protocol file. These restrictions for a particular species are specified in
* 'coordinates' tags. There should be two such tags where this is used - one to start the
* restriction and one to end it. Example of use: \<coordinates x="0" y="0" z="0"/\> \<coordinates
* x="1" y="264" z="0"/\>. This method will read these in and create an array that represents this
* area
*
* @param spRoot The information within the 'initArea' tags of the protocol file
* @return A continuous vector representing the area of the domain specified in these tags
*/
public ContinuousVector[] defineSquareArea(XMLParser spRoot) {
List<XMLParser> area = spRoot.getChildrenParsers("coordinates");
ContinuousVector[] initArea = new ContinuousVector[2];
initArea[0] = new ContinuousVector();
initArea[1] = new ContinuousVector();
// KA NOV 13 - CHANGED THIS, AS WE'RE GOING TO LET THE USER NOT DECLARE AN INITIAL AREA IF THEY
// WANT THE CELLS SPREAD ACROSS
// THE WHOLE DOMAIN. THUS THIS NEEDS CHECKING AND FIXING
if (area.size() > 0) {
// First Coordinate Tag
ContinuousVector cc1 = new ContinuousVector(area.get(0));
// Second Coordinate Tag
ContinuousVector cc2 = new ContinuousVector(area.get(1));
// Set each point
initArea[0].x = Math.min(cc1.x, cc2.x);
initArea[1].x = Math.max(cc1.x, cc2.x);
initArea[0].y = Math.min(cc1.y, cc2.y);
initArea[1].y = Math.max(cc1.y, cc2.y);
// In the case of 2D simulation, the agent's z-coordinate is 0.
if (domain.is3D) {
initArea[0].z = Math.min(cc1.z, cc2.z);
initArea[1].z = Math.max(cc1.z, cc2.z);
} else {
initArea[0].z = initArea[1].z = 0.0;
}
} else {
// NO INITIAL AREA HAS BEEN DECLARED, USE THE WHOLE SUBSTRATUM. NOTE THAT THE X (HEIGHT)
// COORDINATE IS SET TO 1 SO THE
// CELLS ARE PLACED NEAR THE SUBSTRATUM
// Set each point
initArea[0].x = 0.0;
initArea[0].y = 0.0;
initArea[0].z = 0.0;
initArea[1].x = 1.0;
initArea[1].y = domain.length_Y;
initArea[1].z = domain.length_Z;
}
return initArea;
}
/**
* \brief For self-attachment scenarios, performs the run and tumble motion of a swimming cell,
* and the required position checks and corrections
*
* <p>For self-attachment scenarios, the agents enter the system on top of the boundary layer and
* perform a run and tumble motion, swimming through the biofilm. This method captures that
* motion. A random angle is chosen and the cell moves at a certain distance, set by cell tumble
* speed in the protocol file. The agent may move back into the bulk, where we assume it will go
* back into the mix and thus we take no further action with it. The aim is for that cell to swim
* around until it either hits the substratum surface or biofilm surface, where it will attach. If
* the agent does not attach in this distance, a new angle is chosen (a 'tumble') and this is
* repeated. This method takes care of all checks to the coordinates (such as a crossed boundary
* and hitting the surface/biofilm). An integer value is returned that states the fate of this
* move - the cell has either not attached anywhere (0), and thus needs to tumble, the cell has
* attached (1), or the cell has returned to the bulk (2).
*
* @author Kieran Alden
* @param spRoot The Species markup from the protocol file for one particular species being
* initialised
* @return Integer value noting the fate of this move (0 no attachment, 1 attachment, 2 returned
* to bulk)
*/
public int performRunAndTumble(XMLParser spRoot) {
// To clarify how Jan has designed this to work:
// The moving cell has a speed, measured in microns a second, and this is specified in the
// protocol file.
// You would thus think that the cell would move at a speed that this related to this and the
// global timestep.
// However, it has been decided that this is not to be the case, and the cell will run and
// tumble continuously this timestep
// until it has attached to a surface or to the biofilm.
// Thus this speed is only used to calculate how far the cell will move before tumbling, and the
// speed at which the cell moves
// has no relation to the global timestep (and thus no relation to real time)
// Now the distance the cell will move in a particular direction is calculated from the tumble
// interval (specified in the protocol file)
// and the cell run speed (also in the protocol file). The cell will move away at a random angle
// for that distance, and will then
// tumble (changing the angle). This continues until this cell has either returned into the bulk
// or has attached to the surface
// or biofilm
// Eventually we will look to change this tumble interval, as this can be used to alter cell
// movement when under chemotaxis
Double distanceEachTumble = getLocatedParam().cellRunSpeed * getLocatedParam().tumbleInterval;
Double distanceToMoveThisTumble = 0.0;
Double distanceAgentMoves = 0.0;
Double distanceSeekingAgent = getLocatedParam().getStickinessRadius();
// We will use a integer flag system to determine what has happened to the cell after a run
// 0 - no attachment, must do another run
// 1 - cell has attached and thus movement is over
// 2 - cell has returned into the bulk (and thus is discarded)
int cellRunResult = 0;
while (true)
// for ( int i = 0; i < 1000000; i++ )
{
/*
* Now work out the new position of the cell based on the distance
* covered this tumble. Firstly calculate that direction - generate
* a random angle between 0 and 360.
*/
setAgentAngleOfMovement();
/*
* Now we're going to break the move down into chunks such that
* collision or move over the boundary can be detected. The size of
* the chunk is going to be the resolution of the agent grid.
*/
distanceToMoveThisTumble = distanceEachTumble;
while (distanceToMoveThisTumble > 0.0) {
/*
* If the cell has less distance to move remaining that the
* resolution, should only move that much.
*/
distanceAgentMoves = Math.min(distanceToMoveThisTumble, distanceSeekingAgent);
calculateNewAgentPosition(distanceAgentMoves);
/*
* Now need to check for collision on any point of that path.
*/
cellRunResult = checkAgentMove(distanceAgentMoves);
// Add the distance moved in this mini move to the tally.
distanceToMoveThisTumble -= distanceAgentMoves;
// If the cell has finished moving, we can return the result.
if (cellRunResult != 0) return cellRunResult;
}
}
// return cellRunResult;
}