Clazz.declarePackage("J.adapter.readers.cif");
Clazz.load(null, "J.adapter.readers.cif.Subsystem", ["JU.Lst", "$.Matrix", "$.V3", "JU.Logger", "$.SimpleUnitCell"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.msRdr = null;
this.code = null;
this.d = 0;
this.w = null;
this.symmetry = null;
this.modMatrices = null;
this.isFinalized = false;
Clazz.instantialize(this, arguments);}, J.adapter.readers.cif, "Subsystem", null);
Clazz.makeConstructor(c$, 
function(msRdr, code, w){
this.msRdr = msRdr;
this.code = code;
this.w = w;
this.d = w.getArray().length - 3;
}, "J.adapter.readers.cif.MSRdr,~S,JU.Matrix");
Clazz.defineMethod(c$, "getSymmetry", 
function(){
if (!this.isFinalized) this.setSymmetry(true);
return this.symmetry;
});
Clazz.defineMethod(c$, "getModMatrices", 
function(){
if (!this.isFinalized) this.setSymmetry(true);
return this.modMatrices;
});
Clazz.defineMethod(c$, "setSymmetry", 
function(setOperators){
var a;
JU.Logger.info("[subsystem " + this.code + "]");
var winv = this.w.inverse();
JU.Logger.info("w=" + this.w);
JU.Logger.info("w_inv=" + winv);
var w33 = this.w.getSubmatrix(0, 0, 3, 3);
var wd3 = this.w.getSubmatrix(3, 0, this.d, 3);
var w3d = this.w.getSubmatrix(0, 3, 3, this.d);
var wdd = this.w.getSubmatrix(3, 3, this.d, this.d);
var sigma = this.msRdr.getSigma();
var sigma_nu = wdd.mul(sigma).add(wd3).mul(w3d.mul(sigma).add(w33).inverse());
var tFactor = wdd.sub(sigma_nu.mul(w3d));
JU.Logger.info("sigma_nu = " + sigma_nu);
var s0 = this.msRdr.cr.asc.getSymmetry();
var vu43 = s0.getUnitCellVectors();
var vr43 = JU.SimpleUnitCell.getReciprocal(vu43, null, 1);
var mard3 =  new JU.Matrix(null, 3 + this.d, 3);
var mar3 =  new JU.Matrix(null, 3, 3);
var mard3a = mard3.getArray();
var mar3a = mar3.getArray();
for (var i = 0; i < 3; i++) mard3a[i] = mar3a[i] =  Clazz.newDoubleArray(-1, [vr43[i + 1].x, vr43[i + 1].y, vr43[i + 1].z]);

var sx = sigma.mul(mar3);
a = sx.getArray();
for (var i = 0; i < this.d; i++) mard3a[i + 3] = a[i];

a = this.w.mul(mard3).getArray();
var uc_nu =  new Array(4);
uc_nu[0] = vu43[0];
for (var i = 0; i < 3; i++) uc_nu[i + 1] = JU.V3.new3(a[i][0], a[i][1], a[i][2]);

uc_nu = JU.SimpleUnitCell.getReciprocal(uc_nu, null, 1);
(this.symmetry = this.msRdr.cr.asc.newFileSymmetry()).getUnitCell(uc_nu, false, null);
this.modMatrices =  Clazz.newArray(-1, [sigma_nu, tFactor]);
if (!setOperators) return;
this.isFinalized = true;
JU.Logger.info("unit cell parameters: " + this.symmetry.getUnitCellInfo(true));
this.symmetry.createSpaceGroup(-1, "[subsystem " + this.code + "]",  new JU.Lst(), this.d);
var nOps = s0.getSpaceGroupOperationCount();
for (var iop = 0; iop < nOps; iop++) {
var rv = s0.getOperationRsVs(iop);
var r0 = rv.getRotation();
var v0 = rv.getTranslation();
var r = this.cleanMatrix(this.w.mul(r0).mul(winv));
var v = this.cleanMatrix(this.w.mul(v0));
var code = this.code;
if (this.isMixed(r)) {
for (var e, $e = this.msRdr.htSubsystems.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var ss = e.getValue();
if (ss === this) continue;
var rj = this.cleanMatrix(ss.w.mul(r0).mul(winv));
if (!this.isMixed(rj)) {
r = rj;
v = ss.w.mul(v0);
code = ss.code;
break;
}}
}var jf = this.symmetry.addSubSystemOp(code, r, v, sigma_nu);
JU.Logger.info(this.code + "." + (iop + 1) + (this.code.equals(code) ? "   " : ">" + code + " ") + jf);
}
}, "~B");
Clazz.defineMethod(c$, "cleanMatrix", 
function(m){
var a = m.getArray();
var d1 = a.length;
var d2 = a[0].length;
for (var i = d1; --i >= 0; ) for (var j = d2; --j >= 0; ) if (J.adapter.readers.cif.Subsystem.approxZero(a[i][j])) a[i][j] = 0;


return m;
}, "JU.Matrix");
c$.approxZero = Clazz.defineMethod(c$, "approxZero", 
function(d){
return d < 1e-7 && d > -1.0E-7;
}, "~N");
Clazz.defineMethod(c$, "isMixed", 
function(r){
var a = r.getArray();
for (var i = 3; --i >= 0; ) for (var j = 3 + this.d; --j >= 3; ) if (a[i][j] != 0) return true;


return false;
}, "JU.Matrix");
Clazz.overrideMethod(c$, "toString", 
function(){
return "Subsystem " + this.code + "\n" + this.w;
});
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
