Clazz.declarePackage("J.adapter.readers.xtal");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.DmolReader", ["JU.DF", "$.PT", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.unitCellData = null;
this.totE = null;
this.geomOpt = false;
Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "DmolReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (this.line.contains("** GEOMETRY OPTIMIZATION IN DELOCALIZED COORDINATES **")) {
this.geomOpt = true;
} else if (this.line.contains("INCOOR, atomic coordinates")) {
this.geomOpt = false;
} else if (!this.geomOpt ? this.line.contains("$cell vectors") : this.line.contains("Lattice:")) {
this.readCellParam();
} else if (!this.geomOpt ? this.line.contains("$coordinates") : this.line.contains("Input Coordinates")) {
this.readCoord();
} else if (this.line.contains(" Total Energy")) {
this.readEnergy();
} else if (this.line.contains("Frequencies (cm-1)")) {
this.readFreq();
}return true;
});
Clazz.defineMethod(c$, "readCellParam", 
function(){
this.unitCellData =  Clazz.newFloatArray (9, 0);
for (var n = 0, i = 0; n < 3; n++) {
var tokens = JU.PT.getTokens(this.rd());
this.unitCellData[i++] = this.parseFloatStr(!this.geomOpt ? tokens[0] : tokens[4]) * 0.5291772;
this.unitCellData[i++] = this.parseFloatStr(!this.geomOpt ? tokens[1] : tokens[5]) * 0.5291772;
this.unitCellData[i++] = this.parseFloatStr(!this.geomOpt ? tokens[2] : tokens[6]) * 0.5291772;
}
});
Clazz.defineMethod(c$, "newAtomSet", 
function(){
this.applySymmetryAndSetTrajectory();
this.asc.newAtomSet();
if (this.totE != null) this.setEnergy();
this.doApplySymmetry = true;
if (this.unitCellData != null) {
this.addExplicitLatticeVector(0, this.unitCellData, 0);
this.addExplicitLatticeVector(1, this.unitCellData, 3);
this.addExplicitLatticeVector(2, this.unitCellData, 6);
this.setSpaceGroupName("P1");
}this.setFractionalCoordinates(false);
});
Clazz.defineMethod(c$, "readCoord", 
function(){
this.newAtomSet();
if (this.geomOpt) this.readLines(2);
while (this.rd() != null && !this.geomOpt ? !this.line.contains("$end") : !this.line.contains("-----")) {
var tokens = this.getTokens();
var atom = this.asc.addNewAtom();
atom.atomName = !this.geomOpt ? tokens[0] : tokens[1];
var factor = (!this.geomOpt ? 0.5291772 : 1.00);
var x = this.parseFloatStr(!this.geomOpt ? tokens[1] : tokens[2]) * factor;
var y = this.parseFloatStr(!this.geomOpt ? tokens[2] : tokens[3]) * factor;
var z = this.parseFloatStr(!this.geomOpt ? tokens[3] : tokens[4]) * factor;
atom.set(x, y, z);
this.setAtomCoord(atom);
}
});
Clazz.defineMethod(c$, "readEnergy", 
function(){
this.rd();
if (this.line.contains("Ef")) this.totE = Double.$valueOf(Double.parseDouble(JU.PT.getTokens(this.line.substring(this.line.indexOf("Ef") + 1, this.line.indexOf("Ha")))[1]));
});
Clazz.defineMethod(c$, "setEnergy", 
function(){
this.asc.setAtomSetEnergy("" + this.totE, this.totE.floatValue());
this.asc.setInfo("Energy", this.totE);
this.asc.setAtomSetName("E = " + this.totE + " Hartree");
});
Clazz.defineMethod(c$, "readFreq", 
function(){
var lastAtomCount = 0;
var ac = this.asc.getLastAtomSetAtomCount();
while (this.rd() != null && this.line.charAt(1) == ' ') {
var tokens = this.getTokens();
var frequencyCount = Clazz.doubleToInt(tokens.length / 2);
var frequencies =  Clazz.newFloatArray (frequencyCount, 0);
for (var i = 1, n = 0; i < tokens.length; i += 2, n++) {
frequencies[n] = this.parseFloatStr(tokens[i]);
if (this.debugging) JU.Logger.debug((this.vibrationNumber + n) + " frequency=" + frequencies[n]);
}
var ignore =  Clazz.newBooleanArray(frequencyCount, false);
var iAtom0 = 0;
for (var i = 0; i < frequencyCount; i++) {
ignore[i] = (!this.doGetVibration(++this.vibrationNumber));
if (ignore[i]) continue;
this.applySymmetryAndSetTrajectory();
lastAtomCount = this.cloneLastAtomSet(ac, null);
if (i == 0) iAtom0 = this.asc.getLastAtomSetAtomIndex();
this.asc.setAtomSetFrequency(this.vibrationNumber, null, null, String.valueOf(frequencies[i]), null);
this.asc.setAtomSetName(JU.DF.formatDecimal(frequencies[i], 2) + " cm-1");
}
this.rd();
this.fillFrequencyData(iAtom0, ac, lastAtomCount, ignore, false, 5, 13, null, 0, null);
this.readLines(2);
}
});
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
