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wavefunction.js
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wavefunction.js
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// To evauluate probability density at
function aoProb(x,y,z,AO){
//probability density at xyz
// of a particular AO
let n1 = 1;
let l1 = 0;
let m1 = 0;
let zeff = 25.0;
let n2 = AO[0];
let l2 = AO[1];
let m2 = AO[2];
let zeff2 = AO[3];
let x2 = AO[4];
let y2 = AO[5];
let z2 = AO[6];
// Center our ficticious orbital
// at origin
x2 -= x;
y2 -= y;
z2 -= z;
// conversion to spherical
r = Math.pow(x2*x2 +y2*y2 +z2*z2, 0.5 );
theta = Math.acos(z2 / r)//Math.atan(y2/x2);
if (r ==0.0){
theta = 0.0;
}
phi = Math.atan2(y2, x2);
// Calculate mooverlap
let thisSij;
if (zeff2[0][1] == 1.0){
thisSij = mooverlap(n1,l1,m1,n2,l2,m2,zeff,zeff2[0][0],r,theta,phi);
}
else {
thisSij = mooverlap(n1,l1,m1,n2,l2,m2,zeff,zeff2[0][0],r,theta,phi) * zeff2[0][1];
thisSij += mooverlap(n1,l1,m1,n2,l2,m2,zeff,zeff2[1][0],r,theta,phi) * zeff2[1][1];
}
return thisSij;
}
// get dimentions
// Center of Mass
// min max
function box(Mol){
allAtoms = Mol.atoms;
let Xt = 0.0 ;
let Yt = 0.0 ;
let Zt = 0.0 ;
let Xmax = allAtoms[0].x;
let Ymax = allAtoms[0].y;
let Zmax = allAtoms[0].z;
let Xmin = allAtoms[0].x;
let Ymin = allAtoms[0].y;
let Zmin = allAtoms[0].z;
for (var j=0; j< allAtoms.length;j++){
Xt += allAtoms[j].x;
Yt += allAtoms[j].y;
Zt += allAtoms[j].z;
// Max
if (Xmax < allAtoms[j].x){
Xmax = allAtoms[j].x;
}
if (Ymax < allAtoms[j].y){
Ymax = allAtoms[j].y;
}
if (Zmax < allAtoms[j].z){
Zmax = allAtoms[j].z;
}
//Min
if (Xmin > allAtoms[j].x){
Xmin = allAtoms[j].x;
}
if (Ymin > allAtoms[j].y){
Ymin = allAtoms[j].y;
}
if (Zmin > allAtoms[j].z){
Zmin = allAtoms[j].z;
}
}
let Xm = Xt/ allAtoms.length;
let Ym = Yt/ allAtoms.length;
let Zm = Zt/ allAtoms.length;
let f = 1.2;
//find biggest atom
let e = Mol.atoms[0].radius;
for (var i =1;i<Mol.atoms.length;i++){
e = Math.max(e, Mol.atoms[i].radius);
}
e *= 2;
e += 4;
return [[Xm,Ym,Zm],[Xmax*f +e ,Ymax*f + e,Zmax*f + e],[Xmin*f - e,Ymin*f - e,Zmin*f - e]];
}
function moProb(Mol,Nth,x,y,z){
let p =[];
let MOs = Mol.MOs;
let AOs = Mol.AOs;
for (var k =0;k<AOs.length;k++){
p.push(aoProb(x,y,z,AOs[k][0]));
}
// Now calculate for a specific Nth MO
P = 0.0
for (var k =0;k<MOs.length;k++){
P += MOs[k][Nth] * p[k];
}
return P;
}
// sample density of Nth MO of Molecule
async function sampleDensity(Mol,Nth,points =1000){
var prgwidth = 0;
updateProgress(prgwidth);
var suff = "th"
if (Nth===0){
suff = "st"
}
if (Nth===1){
suff = "nd"
}
if (Nth===2){
suff = "rd"
}
status("Computing " + String(Nth+1) + suff + " MO... (0% )");
document.getElementById("progressbar").className = "meter";
removeDensity();
let Box = box(Mol);
let scale = 1.0
// find scale by doing a sample of 100 points
// box dimension
let lx = Box[1][0]- Box[2][0];
let ly = Box[1][1]- Box[2][1];
let lz = Box[1][2]- Box[2][2];
let maxP = 0.0;
// Center Coordinate
let Xm = Box[0][0];
let Ym = Box[0][1];
let Zm = Box[0][2];
let MOs = Mol.MOs;
let AOs = Mol.AOs;
for (var i=0; i<110; i++){
// get a random point
let xp = (Math.random()-0.5)*lx + Xm;
let yp = (Math.random()-0.5)*ly + Ym;
let zp = (Math.random()-0.5)*lz + Zm;
let p = [];
for (var k =0;k<AOs.length;k++){
p.push(aoProb(xp,yp,zp,AOs[k][0]));
}
// Now calculate for a specific Nth MO
P = 0.0
for (var k =0;k<MOs.length;k++){
P += MOs[k][Nth] * p[k];
}
maxP = Math.max(Math.abs(P),maxP);
}
scale = 1.1/maxP
let boxSize = lx * ly * lz ;
//console.log(boxSize);
points = Math.min(5000,parseInt(boxSize * points/5000.0))
points = Math.max(points,400);
// DO the real one
i = 0;
let trials = 0
while (i<points){
// get a random point
let xp = (Math.random()-0.5)*lx*2.0 + Xm;
let yp = (Math.random()-0.5)*ly*2.0 + Ym;
let zp = (Math.random()-0.5)*lz*2.0 + Zm;
let p = [];
for (var k =0;k<AOs.length;k++){
p.push(aoProb(xp,yp,zp,AOs[k][0]));
}
// Now calculate for a specific Nth MO
P = 0.0
for (var k =0;k<MOs.length;k++){
P += MOs[k][Nth] * p[k];
}
showDensity(xp -Xm,yp -Ym ,zp-Zm ,P*scale);
if (P*scale>0.1){
prgwidth += 100/points;
updateProgress(prgwidth);
status("Computing " + String(Nth+1) + suff +" MO... (" + String(Math.round(prgwidth)) + "% )" );
await sleep(10);
i += 1;
}
if (trials%200 == 0){
await sleep(20);
}
trials++
}
document.getElementById("progressbar").className = "meterdone";
status("Showing " + String(Nth+1) + suff + " MO");
}