channel_worker.js

onmessage = function(e) {	
var atomInfo = e.data[0];
var triclinic = e.data[1];
var	cellMatrix = e.data[2];
var	inverseMatrix = e.data[3];
var cellSize = e.data[4];
var angles = e.data[7];
var unitResolution = parseFloat(e.data[5]);
var probeSize = parseFloat(e.data[6])/2;
var layerX = [];
var layerY = [];
var layerZ = [];
var adj = atomInfo.length + 1;


for (i=0;i<cellSize.length;i++) {
	cellSize[i] = parseFloat(cellSize[i]);
}


var atomDiameters = {
Ac:	3.098545742,
Ag:	2.804549165,
Al:	4.008153333,
Am:	3.012128566,
Ar:	3.445996242,
As:	3.768501578,
At:	4.231768911,
Au:	2.933729479,
B:	3.637539466,
Ba:	3.298997953,
Be:	2.445516981,
Bi:	3.893227398,
Bk:	2.97471082,
Br:	3.73197473,
C:	3.430850964,
Ca:	3.028164743,
Cd:	2.537279549,
Ce:	3.168035842,
Cf:	2.951547453,
Cl:	3.51637724,
Cm:	2.963129137,
Co:	2.558661118,
Cr:	2.693186825,
Cu:	3.11369102,
Cs:	4.02418951,
Dy:	3.054000806,
Eu:	3.111909222,
Er:	3.021037553,
Es:	2.939074871,
F:	2.996983288,
Fe:	2.594297067,
Fm:	2.927493188,
Fr:	4.365403719,
Ga:	3.904809082,
Ge:	3.813046514,
Gd:	3.000546883,
H:	2.571133701,
He:	2.571133701,
Hf:	2.798312874,
Hg:	2.409881033,
Ho:	3.03707373,
I:	4.009044232,
In:	3.976080979,
Ir:	2.53015236,
K:	3.396105914,
Kr:	3.689211592,
La:	3.137745285,
Li:	2.183592758,
Lu:	3.242871334,
Lr:	2.882948252,
Md:	2.916802403,
Mg:	2.691405028,
Mn:	2.637951104,
Mo:	2.719022888,
N:	3.260689308,
Na:	2.657550876,
Ne:	2.657550876,
Nb:	2.819694443,
Nd:	3.184962917,
No:	2.893639037,
Ni:	2.524806967,
Np:	3.050437211,
O:	3.118145513,
Os:	2.779604001,
P:	3.694556984,
Pa:	3.050437211,
Pb:	3.828191792,
Pd:	2.582715384,
Pm:	3.160017753,
Po:	4.195242064,
Pr:	3.212580778,
Pt:	2.45353507,
Pu:	3.050437211,
Ra:	3.275834587,
Rb:	3.665157326,
Re:	2.631714813,
Rh:	2.609442345,
Rn:	4.245132392,
Ru:	2.639732902,
S:	3.594776328,
Sb:	3.937772334,
Sc:	2.935511276,
Se:	3.74622911,
Si:	3.826409994,
Sm:	3.135963488,
Sn:	3.91282717,
Sr:	3.243762233,
Ta:	2.824148937,
Tb:	3.074491476,
Tc:	2.670914357,
Te:	3.98231727,
Th:	3.025492047,
Ti:	2.82860343,
TI:	3.872736728,
Tm:	3.005892275,
U:	3.024601148,
V:	2.80098557,
W:	2.734168166,
Xe:	3.923517955,
Y:	2.980056212,
Yb:	2.988965199,
Zn:	2.461553158,
Zr:	2.783167595,
}	

	var atomX = [];
	var atomY = [];
	var atomZ = [];
	for (l=0;l<atomInfo.length;l++) {
		atomX[l] = atomInfo[l]['x'];
		atomY[l] = atomInfo[l]['y'];
		atomZ[l] = atomInfo[l]['z'];
	}

var coords = [];

// a resolution of 2.0 A is made

//var unitResolution = 2.0;
var gridSize = [];
for (i=0;i<cellSize.length;i++) {
	gridSize[i] = Math.round(cellSize[i]/unitResolution);
}
var index = 0;
var counter = 0;
for (i=0;i<gridSize[0];i++) {
	for (j=0;j<gridSize[1];j++) {
		for (k=0;k<gridSize[2];k++) {
			//index = i + gridSize[1]*j + Math.pow(gridSize[2],2)*k; // index for an array describing a cube, a + bx + cx^2 			
			coords[counter] = [unitResolution*i/cellSize[0], unitResolution*j/cellSize[1], unitResolution*k/cellSize[2]]; // coordinates are fractional
			counter++;
		}
	}
}

//console.log(counter);
//console.log(index);
	for (i=0;i<coords.length;i++) {
		coords[i] = matrixDotVector(cellMatrix,coords[i]);
		coords[i][0] = coords[i][0].toFixed(3); 
		coords[i][1] = coords[i][1].toFixed(3); 
		coords[i][2] = coords[i][2].toFixed(3); 
	}



var noOverlapCoords = [];
index = 0;

for (i=0;i<coords.length;i++) {
	if (!checkOverlap(coords[i],probeSize)) {
		noOverlapCoords[i] = coords[i];
		index++;
	}
	else {
		noOverlapCoords[i] = '';
	}
}


//console.log(noOverlapCoords);

// needs fixing (only does square)
var ind = 0;

// needed?
for (i=0;i<gridSize[1];i++) {
	layerZ[i] = '';
}
for (i=0;i<gridSize[0];i++) {
	layerY[i] = '';
}
for (i=0;i<gridSize[2];i++) {
	layerX[i] = '';
}


ind = 0;
for (i=0;i<gridSize[2];i++) {
	for (j=0;j<gridSize[1];j++) {
		for (k=0;k<gridSize[0];k++) {
			ind = i*gridSize[1]*gridSize[0] + j*gridSize[0] + k;
			if (noOverlapCoords[ind] != null && noOverlapCoords[ind] != '') {
			//layerY[k] += noOverlapCoords[ind] + '\n'; // change k to j for layerZ, to i for layerX
			//~ adjusted = adj + ind;
			//~ layerY[k] += 'B' + adjusted + ',';
			//~ layerX[i] += 'B' + adjusted + ',';
			//~ layerZ[j] += 'B' + adjusted + ',';
			} 
		}	
	}
}




function checkOverlap(pt, r) {
	
		x = pt[0];
		y = pt[1];
		z = pt[2];
		
		var overlap = false;
		var flag = false;
		
		for (b=0;b<atomInfo.length;b++) {
			if (!flag) {
		xa = atomX[b];
		ya = atomY[b];
		za = atomZ[b];
			
		
		radius = atomDiameters[atomInfo[b]['sym']]/2;
		
		
		distR = distance(x,y,z,xa,ya,za);	
		distR = pbCond(distR,pt);	
		dr = Math.sqrt(Math.pow(distR[0],2) + Math.pow(distR[1],2) + Math.pow(distR[2],2));
		
			
			
			if (dr < (radius+r)) {
				overlap = true;
				flag = true;
			}
				else {
					overlap = false;
				}				
		}
		} 
		return overlap;
		} // end checkOverlap 


function pbCond(dist,probePt) {
	
			if (triclinic) {
		
	fractional = [0,0,0];	
	fractional = matrixDotVector(inverseMatrix, dist);
	xVect = [0,0,0];
	xVect[0] = fractional[0] - Math.round(fractional[0]);
	xVect[1] = fractional[1] - Math.round(fractional[1]);
	xVect[2] = fractional[2] - Math.round(fractional[2]);
	cartesian = matrixDotVector(cellMatrix,xVect);
	return cartesian;
			
				
				
			} // end if triclinic
			
			else {
			if (dist[0] > cellSize[0]/2) {
					dist[0] = dist[0] - cellSize[0]; 
			}
			if (dist[1] > cellSize[1]/2) {
					dist[1] = dist[1] - cellSize[1]; 
			}
			if (dist[2] > cellSize[2]/2) {
					dist[2] = dist[2] - cellSize[2]; 
			}
		return dist;
		}
			
}

function matrixDotVector(m,v) {
	sX = m[0]*v[0] + m[3]*v[1] + m[6]*v[2];
	sY = m[1]*v[0] + m[4]*v[1] + m[7]*v[2];
	sZ = m[2]*v[0] + m[5]*v[1] + m[8]*v[2];
	return [sX, sY, sZ];
}
function distance(x1,y1,z1,x2,y2,z2) {
	var distanceVector = [Math.abs(x1-x2),  Math.abs(y1-y2),   Math.abs(z1-z2)]; // return distance vector
	return distanceVector;
}	

var returnCoords = [];
index = 0;
for (i=0;i<noOverlapCoords.length;i++) {
	if (noOverlapCoords[i] && noOverlapCoords[i][0]) {
	returnCoords[index] = noOverlapCoords[i];
		index++;
	}
}
//var fileString = returnCoords.length + "\n" + "Probes\n";
var fileString = 'CRYST1 ' + cellSize[0].toFixed(3) + ' ' + cellSize[1].toFixed(3) + ' ' + cellSize[2].toFixed(3) + ' ' + angles[0].toFixed(2) + ' ' + angles[1].toFixed(2) + ' ' + angles[2].toFixed(2) + ' \n';
for (i=0;i<returnCoords.length;i++) {
	cur = returnCoords[i];
	num = i+1;
	fileString +='ATOM    ' + num + '  B  LIG           ' + cur[0] + '   ' + cur[1] + '   ' + cur[2] + '   1.00  0.00     B' +'\n';
}


postMessage([noOverlapCoords, fileString]);
}