Clazz.declarePackage("J.adapter.readers.spartan");
Clazz.load(null, "J.adapter.readers.spartan.SpartanArchive", ["java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "$.V3", "J.adapter.smarter.AtomSetCollectionReader", "$.Bond", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.modelCount = 0;
this.modelAtomCount = 0;
this.ac = 0;
this.bondData = null;
this.moCount = 0;
this.coefCount = 0;
this.shellCount = 0;
this.gaussianCount = 0;
this.endCheck = null;
this.isSMOL = false;
this.r = null;
this.line = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.spartan, "SpartanArchive", null);
Clazz.makeConstructor(c$, 
function(r, bondData, endCheck, smolAtomCount){
this.initialize(r, bondData);
this.modelAtomCount = smolAtomCount;
this.endCheck = endCheck;
this.isSMOL = (endCheck != null);
}, "J.adapter.readers.quantum.BasisFunctionReader,~S,~S,~N");
Clazz.defineMethod(c$, "initialize", 
function(r, bondData){
this.r = r;
r.moData.put("isNormalized", Boolean.TRUE);
r.moData.put("energyUnits", "");
this.bondData = bondData;
}, "J.adapter.readers.quantum.BasisFunctionReader,~S");
Clazz.defineMethod(c$, "readArchive", 
function(infoLine, haveGeometryLine, ac0, doAddAtoms){
this.modelAtomCount = this.setInfo(infoLine);
this.line = (haveGeometryLine ? "GEOMETRY" : "");
var haveMOData = false;
var skipping = false;
while (this.line != null) {
if (this.line.equals("GEOMETRY")) {
if (!this.isSMOL && !this.r.doGetModel(++this.modelCount, null)) {
this.readLine();
skipping = true;
continue;
}skipping = false;
this.readAtoms(ac0, doAddAtoms);
if (doAddAtoms && this.bondData.length > 0) this.addBonds(this.bondData, ac0);
} else if (this.line.indexOf("BASIS") == 0) {
if (this.r.doReadMolecularOrbitals) {
this.readBasis();
} else {
this.r.discardLinesUntilContains("ENERGY");
this.line = this.r.line;
continue;
}} else if (this.line.indexOf("WAVEFUNC") == 0 || this.line.indexOf("BETA") == 0) {
if (this.r.doReadMolecularOrbitals && !skipping) {
this.readMolecularOrbital();
haveMOData = true;
} else {
this.r.discardLinesUntilContains("GEOM");
this.line = this.r.line;
}} else if (this.line.indexOf("ENERGY") == 0 && !skipping) {
this.readEnergy();
} else if (this.line.equals("ENDARCHIVE") || this.isSMOL && this.line.indexOf(this.endCheck) == 0) {
break;
}this.readLine();
}
if (haveMOData) this.r.finalizeMOData(this.r.moData);
return this.modelAtomCount;
}, "~S,~B,~N,~B");
Clazz.defineMethod(c$, "readEnergy", 
function(){
var tokens = JU.PT.getTokens(this.readLine());
var value = this.parseFloat(tokens[0]);
this.r.asc.setCurrentModelInfo("energy", Float.$valueOf(value));
if (this.isSMOL) (this.r).setEnergy(value);
this.r.asc.setAtomSetEnergy(tokens[0], value);
});
Clazz.defineMethod(c$, "setInfo", 
function(info){
var tokens = JU.PT.getTokens(info);
if (JU.Logger.debugging) {
JU.Logger.debug("reading Spartan archive info :" + info);
}this.modelAtomCount = this.parseInt(tokens[0]);
this.coefCount = this.parseInt(tokens[1]);
this.shellCount = this.parseInt(tokens[2]);
this.gaussianCount = this.parseInt(tokens[3]);
this.moCount = this.parseInt(tokens[6]);
this.r.calculationType = tokens[9];
var s = this.r.moData.get("calculationType");
if (s == null) s = this.r.calculationType;
 else if (s.indexOf(this.r.calculationType) < 0) s = this.r.calculationType + s;
this.r.moData.put("calculationType", this.r.calculationType = s);
return this.modelAtomCount;
}, "~S");
Clazz.defineMethod(c$, "readAtoms", 
function(ac0, doAddAtoms){
for (var i = 0; i < this.modelAtomCount; i++) {
var tokens = JU.PT.getTokens(this.readLine());
var atom = (doAddAtoms ? this.r.asc.addNewAtom() : this.r.asc.atoms[ac0 - this.modelAtomCount + i]);
atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol(this.parseInt(tokens[0]));
this.r.setAtomCoordScaled(atom, tokens, 1, 0.5291772);
}
if (doAddAtoms && JU.Logger.debugging) {
JU.Logger.debug(this.r.asc.ac + " atoms read");
}}, "~N,~B");
Clazz.defineMethod(c$, "addBonds", 
function(data, ac0){
var tokens = JU.PT.getTokens(data);
for (var i = this.modelAtomCount; i < tokens.length; ) {
var sourceIndex = this.parseInt(tokens[i++]) - 1 + ac0;
var targetIndex = this.parseInt(tokens[i++]) - 1 + ac0;
var bondOrder = this.parseInt(tokens[i++]);
if (bondOrder > 0) {
this.r.asc.addBond( new J.adapter.smarter.Bond(sourceIndex, targetIndex, bondOrder < 4 ? bondOrder : bondOrder == 5 ? 515 : 1));
}}
var bondCount = this.r.asc.bondCount;
if (JU.Logger.debugging) {
JU.Logger.debug(bondCount + " bonds read");
}}, "~S,~N");
Clazz.defineMethod(c$, "readBasis", 
function(){
var shells =  new JU.Lst();
var gaussians = JU.AU.newFloat2(this.gaussianCount);
var typeArray =  Clazz.newIntArray (this.gaussianCount, 0);
for (var i = 0; i < this.shellCount; i++) {
var tokens = JU.PT.getTokens(this.readLine());
var isSpherical = (tokens[4].charAt(0) == '1');
var slater =  Clazz.newIntArray (4, 0);
slater[0] = this.parseInt(tokens[3]);
var iBasis = this.parseInt(tokens[0]);
switch (iBasis) {
case 0:
iBasis = 0;
break;
case 1:
iBasis = (isSpherical ? 1 : 2);
break;
case 2:
iBasis = (isSpherical ? 3 : 4);
break;
case 3:
iBasis = (isSpherical ? 5 : 6);
break;
}
slater[1] = iBasis;
slater[2] = this.parseInt(tokens[2]);
var gaussianPtr = slater[2] - 1;
var nGaussians = slater[3] = this.parseInt(tokens[1]);
for (var j = 0; j < nGaussians; j++) typeArray[gaussianPtr + j] = iBasis;

shells.addLast(slater);
}
for (var i = 0; i < this.gaussianCount; i++) {
var alpha = this.parseFloat(this.readLine());
var tokens = JU.PT.getTokens(this.readLine());
var nData = tokens.length;
var data =  Clazz.newFloatArray (nData + 1, 0);
data[0] = alpha;
switch (typeArray[i]) {
case 0:
data[1] = this.parseFloat(tokens[0]);
break;
case 1:
data[1] = this.parseFloat(tokens[1]);
break;
case 2:
data[1] = this.parseFloat(tokens[0]);
data[2] = this.parseFloat(tokens[1]);
if (data[1] == 0) {
data[1] = data[2];
typeArray[i] = 2;
}break;
case 4:
case 3:
data[1] = this.parseFloat(tokens[2]);
break;
case 6:
case 5:
data[1] = this.parseFloat(tokens[3]);
break;
}
gaussians[i] = data;
}
var nCoeff = 0;
for (var i = 0; i < this.shellCount; i++) {
var slater = shells.get(i);
switch (typeArray[slater[2] - 1]) {
case 0:
nCoeff++;
break;
case 1:
slater[1] = 1;
nCoeff += 3;
break;
case 2:
nCoeff += 4;
break;
case 3:
nCoeff += 5;
break;
case 4:
nCoeff += 6;
break;
case 5:
nCoeff += 7;
break;
case 6:
nCoeff += 10;
break;
}
}
var isD5F7 = (nCoeff < this.coefCount);
if (isD5F7) for (var i = 0; i < this.shellCount; i++) {
var slater = shells.get(i);
switch (typeArray[i]) {
case 4:
slater[1] = 3;
break;
case 6:
slater[1] = 5;
break;
}
}
this.r.moData.put("shells", shells);
this.r.moData.put("gaussians", gaussians);
if (JU.Logger.debugging) {
JU.Logger.debug(shells.size() + " slater shells read");
JU.Logger.debug(gaussians.length + " gaussian primitives read");
}});
Clazz.defineMethod(c$, "readMolecularOrbital", 
function(){
var tokenPt = 0;
this.r.orbitals =  new JU.Lst();
var tokens = JU.PT.getTokens("");
var energies =  Clazz.newFloatArray (this.moCount, 0);
var coefficients =  Clazz.newFloatArray (this.moCount, this.coefCount, 0);
for (var i = 0; i < this.moCount; i++) {
if (tokenPt == tokens.length) {
tokens = JU.PT.getTokens(this.readLine());
tokenPt = 0;
}energies[i] = this.parseFloat(tokens[tokenPt++]);
}
for (var i = 0; i < this.moCount; i++) {
for (var j = 0; j < this.coefCount; j++) {
if (tokenPt == tokens.length) {
tokens = JU.PT.getTokens(this.readLine());
tokenPt = 0;
}coefficients[i][j] = this.parseFloat(tokens[tokenPt++]);
}
}
for (var i = 0; i < this.moCount; i++) {
var mo =  new java.util.Hashtable();
mo.put("energy", Float.$valueOf(energies[i]));
mo.put("coefficients", coefficients[i]);
this.r.setMO(mo);
}
if (JU.Logger.debugging) {
JU.Logger.debug(this.r.orbitals.size() + " molecular orbitals read");
}this.r.moData.put("mos", this.r.orbitals);
});
Clazz.defineMethod(c$, "readProperties", 
function(){
if (JU.Logger.debugging) JU.Logger.debug("Reading PROPARC properties records...");
while (this.readLine() != null && !this.line.startsWith("ENDPROPARC") && !this.line.startsWith("END Directory Entry ")) {
if (this.line.startsWith("PROP")) this.readProperty();
 else if (this.line.startsWith("DIPOLE")) this.readDipole();
 else if (this.line.startsWith("VIBFREQ")) this.readVibFreqs();
}
this.setVibrationsFromProperties();
});
Clazz.defineMethod(c$, "readDipole", 
function(){
this.setDipole(JU.PT.getTokens(this.readLine()));
});
Clazz.defineMethod(c$, "setDipole", 
function(tokens){
if (tokens.length != 3) return;
var dipole = JU.V3.new3(this.parseFloat(tokens[0]), this.parseFloat(tokens[1]), this.parseFloat(tokens[2]));
this.r.asc.setCurrentModelInfo("dipole", dipole);
}, "~A");
Clazz.defineMethod(c$, "readProperty", 
function(){
var tokens = JU.PT.getTokens(this.line);
if (tokens.length == 0) return;
var isString = (tokens[1].startsWith("STRING"));
var keyName = tokens[2];
var isDipole = (keyName.equals("DIPOLE_VEC"));
var value =  new Clazz._O();
var vector =  new JU.Lst();
if (tokens[3].equals("=")) {
if (isString) {
value = this.getQuotedString(tokens[4].substring(0, 1));
} else {
value = Float.$valueOf(this.parseFloat(tokens[4]));
}} else if (tokens[tokens.length - 1].equals("BEGIN")) {
var nValues = this.parseInt(tokens[tokens.length - 2]);
if (nValues == 0) nValues = 1;
var isArray = (tokens.length == 6);
var atomInfo =  new JU.Lst();
var ipt = 0;
while (this.readLine() != null && !this.line.substring(0, 3).equals("END")) {
if (isString) {
value = this.getQuotedString("\"");
vector.addLast(value);
} else {
var tokens2 = JU.PT.getTokens(this.line);
if (isDipole) this.setDipole(tokens2);
for (var i = 0; i < tokens2.length; i++, ipt++) {
if (isArray) {
atomInfo.addLast(Float.$valueOf(this.parseFloat(tokens2[i])));
if ((ipt + 1) % nValues == 0) {
vector.addLast(atomInfo);
atomInfo =  new JU.Lst();
}} else {
value = Float.$valueOf(this.parseFloat(tokens2[i]));
vector.addLast(value);
}}
}}
value = null;
} else {
if (JU.Logger.debugging) {
JU.Logger.debug(" Skipping property line " + this.line);
}}if (value != null) this.r.asc.setInfo(keyName, value);
if (vector.size() != 0) this.r.asc.setInfo(keyName, vector);
});
Clazz.defineMethod(c$, "readVibFreqs", 
function(){
this.readLine();
var label = "";
var frequencyCount = this.parseInt(this.line);
var vibrations =  new JU.Lst();
var freqs =  new JU.Lst();
if (JU.Logger.debugging) {
JU.Logger.debug("reading VIBFREQ vibration records: frequencyCount = " + frequencyCount);
}var ignore =  Clazz.newBooleanArray(frequencyCount, false);
for (var i = 0; i < frequencyCount; ++i) {
var ac0 = this.r.asc.ac;
ignore[i] = !this.r.doGetVibration(++this.r.vibrationNumber);
if (!ignore[i] && this.r.desiredVibrationNumber <= 0) {
this.r.asc.cloneLastAtomSet();
this.addBonds(this.bondData, ac0);
}this.readLine();
var info =  new java.util.Hashtable();
var freq = this.parseFloat(this.line);
info.put("freq", Float.$valueOf(freq));
if (this.line.length > 15 && !(label = this.line.substring(15, this.line.length)).equals("???")) info.put("label", label);
freqs.addLast(info);
if (!ignore[i]) {
this.r.asc.setAtomSetFrequency(this.r.vibrationNumber, null, label, "" + freq, null);
}}
this.r.asc.setInfo("VibFreqs", freqs);
var ac = this.r.asc.getAtomSetAtomCount(0);
var vib =  new JU.Lst();
var vibatom =  new JU.Lst();
var ifreq = 0;
var iatom = ac;
var nValues = 3;
var atomInfo =  Clazz.newFloatArray (3, 0);
while (this.readLine() != null) {
var tokens2 = JU.PT.getTokens(this.line);
for (var i = 0; i < tokens2.length; i++) {
var f = this.parseFloat(tokens2[i]);
atomInfo[i % nValues] = f;
vibatom.addLast(Float.$valueOf(f));
if ((i + 1) % nValues == 0) {
if (!ignore[ifreq]) {
this.r.asc.addVibrationVector(iatom, atomInfo[0], atomInfo[1], atomInfo[2]);
vib.addLast(vibatom);
vibatom =  new JU.Lst();
}++iatom;
}}
if (iatom % ac == 0) {
if (!ignore[ifreq]) {
vibrations.addLast(vib);
}vib =  new JU.Lst();
if (++ifreq == frequencyCount) {
break;
}}}
this.r.asc.setInfo("vibration", vibrations);
});
Clazz.defineMethod(c$, "setVibrationsFromProperties", 
function(){
var freq_modes = this.r.asc.atomSetInfo.get("FREQ_MODES");
if (freq_modes == null) {
return;
}var freq_lab = this.r.asc.atomSetInfo.get("FREQ_LAB");
var freq_val = this.r.asc.atomSetInfo.get("FREQ_VAL");
var frequencyCount = freq_val.size();
var vibrations =  new JU.Lst();
var freqs =  new JU.Lst();
if (JU.Logger.debugging) {
JU.Logger.debug("reading PROP VALUE:VIB FREQ_MODE vibration records: frequencyCount = " + frequencyCount);
}var v;
for (var i = 0; i < frequencyCount; ++i) {
var ac0 = this.r.asc.ac;
this.r.asc.cloneLastAtomSet();
this.addBonds(this.bondData, ac0);
var info =  new java.util.Hashtable();
info.put("freq", (v = freq_val.get(i)));
var freq = v.floatValue();
var label = freq_lab.get(i);
if (!label.equals("???")) {
info.put("label", label);
}freqs.addLast(info);
this.r.asc.setAtomSetName(label + " " + freq + " cm^-1");
this.r.asc.setAtomSetModelProperty("Frequency", freq + " cm^-1");
this.r.asc.setAtomSetModelProperty(".PATH", "Frequencies");
}
this.r.asc.setInfo("VibFreqs", freqs);
var ac = this.r.asc.getAtomSetAtomCount(0);
var iatom = ac;
for (var i = 0; i < frequencyCount; i++) {
if (!this.r.doGetVibration(i + 1)) continue;
var ipt = 0;
var vib =  new JU.Lst();
var mode = freq_modes.get(i);
for (var ia = 0; ia < ac; ia++, iatom++) {
var vibatom =  new JU.Lst();
var vx = (v = mode.get(ipt++)).floatValue();
vibatom.addLast(v);
var vy = (v = mode.get(ipt++)).floatValue();
vibatom.addLast(v);
var vz = (v = mode.get(ipt++)).floatValue();
vibatom.addLast(v);
this.r.asc.addVibrationVector(iatom, vx, vy, vz);
vib.addLast(vibatom);
}
vibrations.addLast(vib);
}
this.r.asc.setInfo("vibration", vibrations);
});
Clazz.defineMethod(c$, "getQuotedString", 
function(strQuote){
var i = this.line.indexOf(strQuote);
var j = this.line.lastIndexOf(strQuote);
return (j == i ? "" : this.line.substring(i + 1, j));
}, "~S");
Clazz.defineMethod(c$, "parseInt", 
function(info){
return this.r.parseIntStr(info);
}, "~S");
Clazz.defineMethod(c$, "parseFloat", 
function(info){
return this.r.parseFloatStr(info);
}, "~S");
Clazz.defineMethod(c$, "readLine", 
function(){
return (this.line = this.r.rd());
});
});
;//5.0.1-v7 Mon May 12 16:54:26 CDT 2025
