/**
* \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;
}
