Clazz.declarePackage("J.adapter.readers.quantum");
Clazz.load(["J.adapter.readers.quantum.MOReader", "java.util.Hashtable", "JU.Lst"], "J.adapter.readers.quantum.PsiReader", ["JU.AU", "$.PT", "J.adapter.readers.quantum.BasisFunctionReader", "J.api.JmolAdapter", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.atomNames = null;
this.shellsByUniqueAtom = null;
this.uniqueAtomMap = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.quantum, "PsiReader", J.adapter.readers.quantum.MOReader);
Clazz.prepareFields (c$, function(){
this.atomNames =  new JU.Lst();
this.shellsByUniqueAtom =  new JU.Lst();
this.uniqueAtomMap =  new java.util.Hashtable();
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (this.line.indexOf("-Geometry after Center-of-Mass shift and reorientation (a.u.):") >= 0) {
this.readAtoms(true);
this.doProcessLines = true;
return true;
}if (this.line.indexOf("-Unique atoms in the canonical coordinate system (a.u.):") >= 0) {
this.readUniqueAtoms();
this.doProcessLines = true;
return true;
}if (!this.doProcessLines) return true;
if (this.line.indexOf("New Cartesian Geometry in a.u.") >= 0) {
this.readAtoms(false);
return true;
}if (this.line.startsWith("  label        = ")) {
this.moData.put("calculationType", this.calculationType = this.line.substring(17).trim());
return true;
}if (this.line.startsWith("molecular orbitals for ")) {
this.moData.put("energyUnits", "");
return true;
}if (this.line.startsWith("  -BASIS SETS:")) {
this.readBasis();
return true;
}if (this.line.indexOf("Molecular Orbital Coefficients") >= 0) {
if (this.filterMO()) this.readPsiMolecularOrbitals();
return true;
}if (this.line.indexOf("SCF total energy   =") >= 0) {
this.readSCFDone();
return true;
}if (this.line.indexOf("Normal Modes") >= 0) {
this.readFrequencies();
return true;
}return this.checkNboLine();
});
Clazz.defineMethod(c$, "readSCFDone", 
function(){
this.asc.setAtomSetName(this.line);
});
Clazz.defineMethod(c$, "readAtoms", 
function(isInitial){
if (isInitial) {
this.asc.newAtomSet();
this.asc.setAtomSetName("");
this.discardLinesUntilContains("----");
}var atomPt = 0;
while (this.rd() != null && this.line.length > 0) {
var tokens = this.getTokens();
var atom = (isInitial ? this.asc.addNewAtom() : this.asc.atoms[atomPt++]);
if (isInitial) {
this.atomNames.addLast(tokens[0]);
if (tokens[0].length <= 2) atom.elementNumber = J.api.JmolAdapter.getElementNumber(tokens[0]);
} else {
atom.elementNumber = this.parseIntStr(tokens[0]);
}if (atom.elementNumber < 0) atom.elementNumber = 0;
this.setAtomCoordScaled(atom, tokens, 1, 0.5291772);
}
}, "~B");
Clazz.defineMethod(c$, "readBasis", 
function(){
var gdata =  new JU.Lst();
this.gaussianCount = 0;
this.shellCount = 0;
var tokens;
var slater = null;
var slatersByUniqueAtom = null;
this.rd();
while (this.rd() != null && this.line.startsWith("   -Basis set on")) {
slatersByUniqueAtom =  new JU.Lst();
var nGaussians = 0;
while (this.rd() != null && !this.line.startsWith("       )")) {
this.line = this.line.$replace('(', ' ').$replace(')', ' ');
tokens = this.getTokens();
var ipt = 0;
switch (tokens.length) {
case 3:
if (slater != null) {
slatersByUniqueAtom.addLast(slater);
}ipt = 1;
slater =  Clazz.newIntArray (3, 0);
slater[0] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID(tokens[0]);
slater[1] = this.gaussianCount;
this.shellCount++;
break;
case 2:
break;
}
nGaussians++;
gdata.addLast( Clazz.newArray(-1, [tokens[ipt], tokens[ipt + 1]]));
slater[2] = nGaussians;
}
if (slater != null) {
slatersByUniqueAtom.addLast(slater);
}this.shellsByUniqueAtom.addLast(slatersByUniqueAtom);
this.gaussianCount += nGaussians;
this.rd();
}
var garray = JU.AU.newFloat2(this.gaussianCount);
for (var i = 0; i < this.gaussianCount; i++) {
tokens = gdata.get(i);
garray[i] =  Clazz.newFloatArray (tokens.length, 0);
for (var j = 0; j < tokens.length; j++) garray[i][j] = this.parseFloatStr(tokens[j]);

}
this.moData.put("gaussians", garray);
if (this.debugging) {
JU.Logger.debug(this.shellCount + " slater shells read");
JU.Logger.debug(this.gaussianCount + " gaussian primitives read");
}});
Clazz.defineMethod(c$, "readUniqueAtoms", 
function(){
var sdata =  new JU.Lst();
this.discardLinesUntilContains("----");
var n = 0;
while (this.rd() != null && this.line.length > 0) {
var tokens = this.getTokens();
this.uniqueAtomMap.put(tokens[0], Integer.$valueOf(n++));
}
var ac = this.atomNames.size();
for (var i = 0; i < ac; i++) {
var atomType = this.atomNames.get(i);
var iUnique = this.uniqueAtomMap.get(atomType).intValue();
var slaters = this.shellsByUniqueAtom.get(iUnique);
if (slaters == null) {
JU.Logger.error("slater for atom " + i + " atomType " + atomType + " was not found in listing. Ignoring molecular orbitals");
return;
}for (var j = 0; j < slaters.size(); j++) {
var slater = slaters.get(j);
sdata.addLast( Clazz.newIntArray(-1, [i + 1, slater[0], slater[1], slater[2]]));
}
}
this.moData.put("shells", sdata);
});
Clazz.defineMethod(c$, "readPsiMolecularOrbitals", 
function(){
var mos = JU.AU.createArrayOfHashtable(5);
var data = JU.AU.createArrayOfArrayList(5);
var nThisLine = 0;
while (this.rd() != null && this.line.toUpperCase().indexOf("DENS") < 0) {
var tokens = this.getTokens();
var ptData = (this.line.charAt(5) == ' ' ? 2 : 4);
if (this.line.indexOf("                    ") == 0) {
this.addMOData(nThisLine, data, mos);
nThisLine = tokens.length;
tokens = JU.PT.getTokens(this.rd());
for (var i = 0; i < nThisLine; i++) {
mos[i] =  new java.util.Hashtable();
data[i] =  new JU.Lst();
mos[i].put("symmetry", tokens[i]);
}
tokens = J.adapter.smarter.AtomSetCollectionReader.getStrings(this.rd().substring(21), nThisLine, 10);
for (var i = 0; i < nThisLine; i++) {
mos[i].put("energy", Float.$valueOf(tokens[i]));
}
continue;
}try {
for (var i = 0; i < nThisLine; i++) {
data[i].addLast(tokens[i + ptData]);
}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
JU.Logger.error("Error reading Psi3 file molecular orbitals at line: " + this.line);
break;
} else {
throw e;
}
}
}
this.addMOData(nThisLine, data, mos);
this.moData.put("mos", this.orbitals);
this.finalizeMOData(this.moData);
});
Clazz.defineMethod(c$, "readFrequencies", 
function(){
this.rd();
var ac = this.asc.getLastAtomSetAtomCount();
var tokens;
while (this.rd() != null && this.line.indexOf("Frequency") >= 0) {
tokens = this.getTokens();
var iAtom0 = this.asc.ac;
var ignore =  Clazz.newBooleanArray(1, false);
if (!this.doGetVibration(++this.vibrationNumber)) continue;
this.asc.cloneLastAtomSet();
this.asc.setAtomSetFrequency(this.vibrationNumber, null, null, tokens[1], null);
this.readLines(2);
this.fillFrequencyData(iAtom0, ac, ac, ignore, true, 0, 0, null, 0, null);
this.rd();
}
});
});
;//5.0.1-v7 Mon May 12 16:54:26 CDT 2025
