/**
* \brief Update the attachment, determining if an agent location crosses any boundaries
*
* <p>Update the attachment, determining if an agent location crosses any boundaries
*
* @return Boundary that has been crossed
*/
public AllBC updateAttachment() {
// Search a boundary which will be crossed
double distance;
for (AllBC aBoundary : getDomain().getAllBoundaries()) {
if (aBoundary.isSupport()) {
distance = aBoundary.getDistance(this._location);
_isAttached = distance <= (3 * this._totalRadius);
return aBoundary;
}
}
return null;
}
/**
* \brief Used by the move method to determine if an agents move crosses any of the domain's
* boundaries
*
* <p>Used by the move method to determine if an agents move crosses any of the domain's
* boundaries
*/
public void checkBoundaries() {
// Search a boundary which will be crossed
_newLoc.set(_location);
_newLoc.add(_movement);
AllBC aBoundary = getDomain().testCrossedBoundary(_newLoc);
int nDim = (_agentGrid.is3D ? 3 : 2);
boolean test = (aBoundary != null);
int counter = 0;
// Test all boundaries and apply corrections according to crossed
// boundaries
while (test) {
counter++;
aBoundary.applyBoundary(this, _newLoc);
aBoundary = getDomain().testCrossedBoundary(_newLoc);
test = (aBoundary != null) | (counter > nDim);
if (counter > nDim) System.out.println("LocatedAgent.move() : problem!");
}
}
/**
* \brief For self-attachment scenarios, determines whether a swimming agents move has taken it
* across a boundary, correcting the coordinate accordingly
*
* <p>For self-attachment scenarios, the agents are swimming through the domain, and we need to
* ensure that they perform the correct behaviour when the boundary is met. This method checks
* whether an agents move has taken it over the boundary and applies the relevant correction
* (either a bounce off the boundary or a reappearance on the other side). If the cell has hit the
* surface, the cell is deemed to have adhered to that surface and a relevant x coordinate
* generated to note that this is the case. The top of the domain is dealt with differently, as
* this is checked by the call to isNewCoordAboveBoundaryLayer, which determines if the agent has
* moved out of the boundary layer. If this is the case we assume this cell to have returned to
* the bulk and do no further action with that cell. An integer is returned noting the fate of
* this move - a 0 if the move is ok (after adjustment if required), a 1 if the agent has met the
* substratum and attached, and a 2 if the cell has returned to the bulk
*
* @param distanceMoving Distance the agent is moving (in microns) in this move
* @return Integer noting the fate of this move (0 move ok (after adjustment if required), 1 if
* attached to surface, 2 if returned to bulk
*/
public int agentMoveBorderCheck() {
// Simplest test to do first is to check if any boundaries have been crossed
AllBC boundaryCrossed = domain.testCrossedBoundary(swimmingAgentPosition);
// First is a simple test - has the cell returned to the bulk
// If this is the case, we can just forget this and have another go
// The cell will only have the capability to return to the bulk if the angle has it moving
// upwards or directly across
// (i.e 0-90 and 270-360 degrees)
if (isNewCoordAboveBoundaryLayer()) {
// The cell has returned into the bulk, and thus this try is over.
// Return 2 so the process starts with a new cell.
return 2;
} else {
// Now to see if the move takes the point outside any of the boundaries
if (boundaryCrossed == null) {
// No borders crossed, not back in the bulk.
return 0;
} else {
String boundaryCrossedName = boundaryCrossed.getSideName();
if (boundaryCrossedName.equals("y0z")) {
// Detected that the move has crossed the substratum, thus
// the cell has hit the biofilm. A return of 1 indicates
// that this is the case.
// Hit the biofilm, so set the species coordinates as required.
// We may have hit the biofilm but the Y and Z coordinates
// in this generated move may still be negative (as they
// may have gone over another boundary). So before we set
// the final x, we should check Y and Z.
// So firstly, set the X position onto the surface
swimmingAgentPosition.x = ExtraMath.getUniRandDbl();
// Now set the final X position.
// Do a new check on the boundary crossed.
boundaryCrossed = domain.testCrossedBoundarySelfAttach(swimmingAgentPosition);
if (boundaryCrossed != null) {
boundaryCrossedName = boundaryCrossed.getSideName();
if (boundaryCrossedName.equals("xNz") || boundaryCrossedName.equals("x0z"))
correctCrossedLeftRightBoundaries(boundaryCrossed);
else correctCrossedFrontBackBoundaries(boundaryCrossed);
}
return 1;
} else if (boundaryCrossedName.equals("xNz") || boundaryCrossedName.equals("x0z")) {
correctCrossedLeftRightBoundaries(boundaryCrossed);
return 0;
}
// Deal with 3D boundary too
else if (boundaryCrossedName.equals("x0y") || boundaryCrossedName.equals("xNy")) {
correctCrossedFrontBackBoundaries(boundaryCrossed);
return 0;
} else {
// This needs to be here so the function returns something.
// However this deals with the top boundary (yNz) and this
// has already been dealt with by the crossed bulk method.
// So it is highly doubtful we will ever end up here.
return 0;
}
}
}
}