Clazz.declarePackage("J.adapter.readers.quantum");
Clazz.load(["J.adapter.readers.quantum.MOReader"], "J.adapter.readers.quantum.QchemReader", ["java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "J.adapter.readers.quantum.BasisFunctionReader", "J.api.JmolAdapter", "J.quantum.QS", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.calculationNumber = 1;
this.isFirstJob = true;
this.alphas = null;
this.betas = null;
this.nBasis = 0;
this.dFixed = false;
this.fFixed = false;
this.dList = "";
this.fList = "";
this.dSpherical = false;
this.fSpherical = false;
if (!Clazz.isClassDefined("J.adapter.readers.quantum.QchemReader.MOInfo")) {
J.adapter.readers.quantum.QchemReader.$QchemReader$MOInfo$ ();
}
Clazz.instantialize(this, arguments);}, J.adapter.readers.quantum, "QchemReader", J.adapter.readers.quantum.MOReader);
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.energyUnits = "au";
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (this.line.indexOf("Standard Nuclear Orientation") >= 0) {
this.readAtoms();
this.moData = null;
return true;
}if (this.line.indexOf("Total energy") >= 0 || this.line.indexOf("total energy") >= 0 || this.line.indexOf("Energy is") >= 0) {
if (this.line.indexOf("Excitation") == -1) this.readEnergy();
return true;
}if (this.line.indexOf("Requested basis set is") >= 0) {
this.readCalculationType();
return true;
}if (this.line.indexOf("VIBRATIONAL FREQUENCIES") >= 0) {
this.readFrequencies();
return true;
}if (this.line.indexOf("Mulliken Net Atomic Charges") >= 0) {
this.readPartialCharges();
return true;
}if (this.line.startsWith("Job ") || this.line.startsWith("Running Job")) {
if (this.isFirstJob && this.line.startsWith("Running")) this.calculationNumber = 0;
this.calculationNumber++;
this.isFirstJob = false;
this.moData = null;
return true;
}if (this.line.indexOf("Basis set in general basis input format") >= 0) {
if (this.moData == null) {
this.readBasis();
}return true;
}if (this.moData == null) return true;
if (this.line.indexOf("Orbital Energies (a.u.) and Symmetries") >= 0) {
this.readESym(true);
return true;
}if (this.line.indexOf("Orbital Energies (a.u.)") >= 0) {
this.readESym(false);
return true;
}if (this.line.indexOf("MOLECULAR ORBITAL COEFFICIENTS") >= 0) {
if (this.filterMO()) this.readQchemMolecularOrbitals();
return true;
}return this.checkNboLine();
});
Clazz.defineMethod(c$, "readCalculationType", 
function(){
this.calculationType = this.line.substring(this.line.indexOf("set is") + 6).trim();
});
Clazz.defineMethod(c$, "readAtoms", 
function(){
this.asc.newAtomSet();
this.setMOData(true);
this.dFixed = this.fFixed = false;
this.readLines(2);
var tokens;
while (this.rd() != null && !this.line.startsWith(" --")) {
tokens = this.getTokens();
if (tokens.length < 5) continue;
var symbol = tokens[1];
if (J.api.JmolAdapter.getElementNumber(symbol) > 0) this.addAtomXYZSymName(tokens, 2, symbol, null);
}
this.asc.setAtomSetModelProperty(".PATH", "Job " + this.calculationNumber);
});
Clazz.defineMethod(c$, "readFrequencies", 
function(){
while (this.rd() != null && this.line.indexOf("STANDARD") < 0) {
if (!this.line.startsWith(" Frequency:")) this.discardLinesUntilStartsWith(" Frequency:");
var frequencies = this.getTokens();
var frequencyCount = frequencies.length - 1;
var ignore =  Clazz.newBooleanArray(frequencyCount, false);
var ac = this.asc.getLastAtomSetAtomCount();
var iAtom0 = this.asc.ac;
for (var i = 0; i < frequencyCount; ++i) {
ignore[i] = !this.doGetVibration(++this.vibrationNumber);
if (ignore[i]) continue;
this.asc.cloneLastAtomSet();
this.asc.setAtomSetFrequency(this.vibrationNumber, "Job " + this.calculationNumber, null, frequencies[i + 1], null);
}
this.discardLinesUntilStartsWith("               X");
this.fillFrequencyData(iAtom0, ac, ac, ignore, true, 0, 0, null, 0, null);
this.discardLinesUntilBlank();
}
});
Clazz.defineMethod(c$, "readPartialCharges", 
function(){
this.readLines(3);
var atoms = this.asc.atoms;
var ac = this.asc.getLastAtomSetAtomCount();
for (var i = 0; i < ac && this.rd() != null; ++i) atoms[i].partialCharge = this.parseFloatStr(this.getTokens()[2]);

});
Clazz.defineMethod(c$, "readEnergy", 
function(){
var ac = this.asc.getLastAtomSetAtomCount();
var tokens = this.getTokens();
var energyKey = "E(" + tokens[0] + ")";
var energyString = tokens[tokens.length - 1];
this.asc.setAtomSetEnergy(energyString, this.parseFloatStr(energyString));
this.asc.setAtomSetName(energyKey + " = " + energyString);
this.asc.setModelInfoForSet("name", energyKey + " " + energyString, ac);
});
Clazz.defineMethod(c$, "readBasis", 
function(){
this.moData =  new java.util.Hashtable();
var ac = 1;
var shellCount = 0;
var gaussianCount = 0;
this.shells =  new JU.Lst();
var gdata =  new JU.Lst();
var tokens;
this.discardLinesUntilStartsWith("$basis");
this.rd();
while (this.rd() != null) {
if (this.line.startsWith("****")) {
ac++;
if (this.rd() != null && this.line.startsWith("$end")) break;
continue;
}shellCount++;
var slater =  Clazz.newIntArray (4, 0);
tokens = this.getTokens();
slater[0] = ac;
slater[1] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID(tokens[0]);
slater[2] = gaussianCount + 1;
var nGaussians = this.parseIntStr(tokens[1]);
slater[3] = nGaussians;
this.shells.addLast(slater);
gaussianCount += nGaussians;
for (var i = 0; i < nGaussians; i++) {
gdata.addLast(JU.PT.getTokens(this.rd()));
}
}
this.gaussians = JU.AU.newFloat2(gaussianCount);
for (var i = 0; i < gaussianCount; i++) {
tokens = gdata.get(i);
this.gaussians[i] =  Clazz.newFloatArray (tokens.length, 0);
for (var j = 0; j < tokens.length; j++) this.gaussians[i][j] = this.parseFloatStr(tokens[j]);

}
if (this.debugging) {
JU.Logger.debug(shellCount + " slater shells read");
JU.Logger.debug(gaussianCount + " gaussian primitives read");
}this.discardLinesUntilStartsWith(" There are");
tokens = this.getTokens();
this.nBasis = this.parseIntStr(tokens[5]);
});
Clazz.defineMethod(c$, "readESym", 
function(haveSym){
this.alphas =  new Array(this.nBasis);
this.betas =  new Array(this.nBasis);
var moInfos;
var ne = 0;
var readBetas = false;
this.discardLinesUntilStartsWith(" Alpha");
var tokens = this.getTokens();
moInfos = this.alphas;
for (var e = 0; e < 2; e++) {
var nMO = 0;
while (this.rd() != null) {
if (this.line.startsWith(" -- ")) {
ne = 0;
if (this.line.indexOf("Vacant") < 0) {
if (this.line.indexOf("Occupied") > 0) ne = 1;
}this.rd();
}if (this.line.startsWith(" -------")) {
e = 2;
break;
}var nOrbs = this.getTokens().length;
if (nOrbs == 0 || this.line.startsWith(" Warning")) {
this.discardLinesUntilStartsWith(" Beta");
readBetas = true;
moInfos = this.betas;
break;
}if (haveSym) tokens = JU.PT.getTokens(this.rd());
for (var i = 0, j = 0; i < nOrbs; i++, j += 2) {
var info = Clazz.innerTypeInstance(J.adapter.readers.quantum.QchemReader.MOInfo, this, null);
info.ne = ne;
if (haveSym) info.moSymmetry = tokens[j] + tokens[j + 1] + " ";
moInfos[nMO] = info;
nMO++;
}
}
}
if (!readBetas) this.betas = this.alphas;
}, "~B");
Clazz.defineMethod(c$, "readQchemMolecularOrbitals", 
function(){
var orbitalType = this.getTokens()[0];
this.alphaBeta = "A";
this.readMOs(orbitalType.equals("RESTRICTED"), this.alphas);
if (orbitalType.equals("ALPHA")) {
this.discardLinesUntilContains("BETA");
this.alphaBeta = "B";
this.readMOs(false, this.betas);
}var isOK = true;
if (this.dList.length > 0) {
if (this.dSpherical) isOK = this.getDFMap("DS", this.dList, 3, J.adapter.readers.quantum.QchemReader.$DS_LIST, 2);
 else isOK = this.getDFMap("DC", this.dList, 4, J.adapter.readers.quantum.QchemReader.$DC_LIST, 3);
if (!isOK) {
JU.Logger.error("atomic orbital order is unrecognized -- skipping reading of MOs. dList=" + this.dList);
this.shells = null;
}}if (this.fList.length > 0) {
if (this.fSpherical) isOK = this.getDFMap("FS", this.fList, 5, J.adapter.readers.quantum.QchemReader.$FS_LIST, 2);
 else isOK = this.getDFMap("FC", this.fList, 6, J.adapter.readers.quantum.QchemReader.$FC_LIST, 3);
if (!isOK) {
JU.Logger.error("atomic orbital order is unrecognized -- skipping reading of MOs. fList=" + this.fList);
this.shells = null;
}}this.setMOData(this.shells == null);
this.shells = null;
});
Clazz.defineMethod(c$, "readMOs", 
function(restricted, moInfos){
var mos = JU.AU.createArrayOfHashtable(6);
var mocoef = JU.AU.newFloat2(6);
var moid =  Clazz.newIntArray (6, 0);
var tokens;
var energy;
var nMOs = 0;
while (this.rd().length > 2) {
tokens = this.getTokens();
var nMO = tokens.length;
energy = JU.PT.getTokens(this.rd().substring(13));
for (var i = 0; i < nMO; i++) {
moid[i] = this.parseIntStr(tokens[i]) - 1;
mocoef[i] =  Clazz.newFloatArray (this.nBasis, 0);
mos[i] =  new java.util.Hashtable();
}
for (var i = 0, pt = 0; i < this.nBasis; i++) {
tokens = JU.PT.getTokens(this.rd());
var s = this.line.substring(12, 17).trim();
var ch = s.charAt(0);
switch ((ch).charCodeAt(0)) {
case 100:
s = s.substring(s.length - 3).toUpperCase();
if (s.startsWith("D ")) {
if (!this.dFixed) this.fixSlaterTypes(4, 3);
s = "D" + s.charAt(2);
this.dSpherical = true;
}if (this.dList.indexOf(s) < 0) this.dList += s + " ";
this.dFixed = true;
break;
case 102:
s = s.substring(s.length - 3).toUpperCase();
if (s.startsWith("F ")) {
if (!this.fFixed) this.fixSlaterTypes(6, 5);
s = "F" + s.charAt(2);
this.fSpherical = true;
}if (this.fList.indexOf(s) < 0) this.fList += s + " ";
this.fFixed = true;
break;
default:
if (!J.quantum.QS.isQuantumBasisSupported(ch)) continue;
break;
}
for (var j = tokens.length - nMO, k = 0; k < nMO; j++, k++) mocoef[k][pt] = this.parseFloatStr(tokens[j]);

pt++;
}
for (var i = 0; i < nMO; i++) {
var moInfo = moInfos[moid[i]];
mos[i].put("energy", Float.$valueOf(energy[i]));
mos[i].put("coefficients", mocoef[i]);
var label = this.alphaBeta;
var ne = moInfo.ne;
if (restricted) ne = this.alphas[moid[i]].ne + this.betas[moid[i]].ne;
mos[i].put("occupancy", Float.$valueOf(ne));
switch (ne) {
case 2:
label = "AB";
break;
case 1:
break;
case 0:
if (restricted) label = "V";
 else label = "V" + label;
break;
}
mos[i].put("symmetry", moInfo.moSymmetry + label + "(" + (moid[i] + 1) + ")");
this.orbitals.addLast(mos[i]);
}
nMOs += nMO;
}
return nMOs;
}, "~B,~A");
c$.$QchemReader$MOInfo$ = function(){
/*if4*/;(function(){
var c$ = Clazz.decorateAsClass(function(){
Clazz.prepareCallback(this, arguments);
this.ne = 0;
this.moSymmetry = "";
Clazz.instantialize(this, arguments);}, J.adapter.readers.quantum.QchemReader, "MOInfo", null);
/*eoif4*/})();
};
c$.$DC_LIST = "DXX   DYY   DZZ   DXY   DXZ   DYZ";
c$.$DS_LIST = "D3    D4    D2    D5    D1";
c$.$FC_LIST = "XXX   YYY   ZZZ   XYY   XXY   XXZ   XZZ   YZZ   YYZ   XYZ";
c$.$FS_LIST = "F4    F5    F3    F6    F2    F7    F1";
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
