Clazz.declarePackage("J.adapter.readers.quantum");
Clazz.load(["J.adapter.readers.quantum.MopacSlaterReader", "java.util.Hashtable"], "J.adapter.readers.quantum.CsfReader", ["JU.AU", "$.Lst", "$.PT", "J.adapter.readers.quantum.BasisFunctionReader", "J.adapter.smarter.Atom", "$.Bond", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.nAtoms = 0;
this.strAtomicNumbers = "";
this.fieldCount = 0;
this.nVibrations = 0;
this.nGaussians = 0;
this.nSlaters = 0;
this.htBonds = null;
this.propertyItemCounts = null;
this.fieldTypes = null;
this.connectors = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.quantum, "CsfReader", J.adapter.readers.quantum.MopacSlaterReader);
Clazz.prepareFields (c$, function(){
this.propertyItemCounts =  new java.util.Hashtable();
this.fieldTypes =  Clazz.newIntArray (100, 0);
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (this.line.equals("local_transform")) {
this.processLocalTransform();
return true;
}if (this.line.startsWith("object_class")) {
if (this.line.equals("object_class connector")) {
this.processConnectorObject();
return false;
}if (this.line.equals("object_class atom")) {
this.processAtomObject();
return false;
}if (this.line.equals("object_class bond")) {
this.processBondObject();
return false;
}if (this.line.equals("object_class vibrational_level")) {
this.processVibrationObject();
return false;
}if (this.line.equals("object_class mol_orbital")) {
this.processMolecularOrbitalObject();
return false;
}if (this.line.equals("object_class sto_basis_fxn")) {
this.processBasisObject("sto");
return false;
}if (this.line.equals("object_class gto_basis_fxn")) {
this.processBasisObject("gto");
return false;
}}return true;
});
Clazz.defineMethod(c$, "processLocalTransform", 
function(){
var tokens = JU.PT.getTokens(this.rd() + " " + this.rd() + " " + this.rd() + " " + this.rd());
this.setTransform(this.parseFloatStr(tokens[0]), this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[4]), this.parseFloatStr(tokens[5]), this.parseFloatStr(tokens[6]), this.parseFloatStr(tokens[8]), this.parseFloatStr(tokens[9]), this.parseFloatStr(tokens[10]));
});
Clazz.defineMethod(c$, "getPropertyCount", 
function(what){
var count = this.propertyItemCounts.get(what);
return (what.equals("ID") ? 1 : count == null ? 0 : count.intValue());
}, "~S");
Clazz.defineMethod(c$, "parseLineParameters", 
function(fields, fieldMap){
for (var i = 0; i < this.fieldCount; i++) this.fieldTypes[i] = 0;

this.fieldCount = -1;
if (this.line == null || this.line.startsWith("property_flags:")) this.rd();
if (this.line == null || this.line.startsWith("object_class")) return this.fieldCount;
var tokens =  new Array(0);
while (this.line != null) {
tokens = this.getTokens();
if (this.line.indexOf("property ") == 0) this.propertyItemCounts.put(tokens[1], Integer.$valueOf((tokens[6].equals("STRING") ? 1 : this.parseIntStr(tokens[5]))));
 else if (this.line.indexOf("ID") == 0) break;
this.rd();
}
for (var ipt = 0, fpt = 0; ipt < tokens.length; ipt++) {
var field = tokens[ipt];
for (var i = fields.length; --i >= 0; ) if (field.equals(fields[i])) {
this.fieldTypes[fpt] = fieldMap[i];
this.fieldCount = fpt + 1;
break;
}
fpt += this.getPropertyCount(field);
}
return this.fieldCount;
}, "~A,~A");
Clazz.defineMethod(c$, "fillCsfArray", 
function(property, tokens, i0, f, isInteger){
var n = this.getPropertyCount(property);
var ioffset = i0;
for (var i = 0; i < n; i++) {
var ipt = ioffset + i;
if (ipt == tokens.length) {
tokens = JU.PT.getTokens(this.rd());
ioffset -= ipt - i0;
ipt = i0;
}if (isInteger) (f)[i] = this.parseIntStr(tokens[ipt]);
 else (f)[i] = this.parseFloatStr(tokens[ipt]);
}
}, "~S,~A,~N,~O,~B");
Clazz.defineMethod(c$, "processConnectorObject", 
function(){
this.connectors =  new java.util.Hashtable();
this.rd();
this.parseLineParameters(J.adapter.readers.quantum.CsfReader.connectorFields, J.adapter.readers.quantum.CsfReader.connectorFieldMap);
out : for (; this.rd() != null; ) {
if (this.line.startsWith("property_flags:")) break;
var thisAtomID = null;
var thisBondID = null;
var tokens = this.getTokens();
var field2 = "";
var isVibration = false;
for (var i = 0; i < this.fieldCount; ++i) {
var field = tokens[i];
switch (this.fieldTypes[i]) {
case 1:
if (!field.equals("atom")) continue out;
break;
case 3:
field2 = field;
if (field.equals("sto_basis_fxn")) this.nSlaters++;
 else if (field.equals("gto_basis_fxn")) this.nGaussians++;
 else if (field.equals("vibrational_level")) isVibration = true;
 else if (!field.equals("bond")) continue out;
break;
case 2:
thisAtomID = field;
break;
case 4:
thisBondID = field2 + field;
if (isVibration) this.nVibrations = Math.max(this.nVibrations, this.parseIntStr(field));
break;
default:
}
}
if (thisAtomID != null && thisBondID != null) {
if (this.connectors.containsKey(thisBondID)) {
var connect = this.connectors.get(thisBondID);
connect[1] = thisAtomID;
if (this.htBonds != null) this.setBond(this.htBonds.get(thisBondID), connect);
} else {
var connect =  new Array(2);
connect[0] = thisAtomID;
this.connectors.put(thisBondID, connect);
}}}
});
Clazz.defineMethod(c$, "setBond", 
function(bond, connect){
bond.atomIndex1 = this.asc.getAtomIndex(connect[0]);
bond.atomIndex2 = this.asc.getAtomIndex(connect[1]);
this.asc.addBond(bond);
}, "J.adapter.smarter.Bond,~A");
Clazz.defineMethod(c$, "processAtomObject", 
function(){
this.rd();
this.parseLineParameters(J.adapter.readers.quantum.CsfReader.atomFields, J.adapter.readers.quantum.CsfReader.atomFieldMap);
this.nAtoms = 0;
for (; this.rd() != null; ) {
if (this.line.startsWith("property_flags:")) break;
var tokens = this.getTokens();
var atom =  new J.adapter.smarter.Atom();
var field;
for (var i = 0; i < this.fieldCount; i++) {
var type = this.fieldTypes[i];
if (type == 0) continue;
if ((field = tokens[i]) == null) JU.Logger.warn("field == null in " + this.line);
switch (type) {
case -1:
atom.atomSerial = JU.PT.parseInt(field);
break;
case 1:
atom.elementSymbol = field;
atom.atomName = field + atom.atomSerial;
break;
case 2:
this.strAtomicNumbers += field + " ";
break;
case 3:
atom.formalCharge = this.parseIntStr(field);
break;
case 5:
atom.partialCharge = this.parseFloatStr(field);
break;
case 4:
this.setAtomCoordTokens(atom, tokens, i);
i += 2;
break;
}
}
if (Float.isNaN(atom.x) || Float.isNaN(atom.y) || Float.isNaN(atom.z)) {
JU.Logger.warn("atom " + atom.atomName + " has invalid/unknown coordinates");
} else {
this.nAtoms++;
this.asc.addAtomWithMappedSerialNumber(atom);
}}
});
Clazz.defineMethod(c$, "processBondObject", 
function(){
this.rd();
this.parseLineParameters(J.adapter.readers.quantum.CsfReader.bondFields, J.adapter.readers.quantum.CsfReader.bondFieldMap);
for (; this.rd() != null; ) {
if (this.line.startsWith("property_flags:")) break;
var thisBondID = null;
var tokens = this.getTokens();
for (var i = 0; i < this.fieldCount; ++i) {
var field = tokens[i];
switch (this.fieldTypes[i]) {
case -1:
thisBondID = "bond" + field;
break;
case 1:
var order = 1;
if (field.equals("single")) order = 1;
 else if (field.equals("double")) order = 2;
 else if (field.equals("triple")) order = 3;
 else JU.Logger.warn("unknown CSF bond order: " + field);
var bond =  new J.adapter.smarter.Bond(-1, -1, 1);
bond.order = order;
if (this.connectors == null) {
if (this.htBonds == null) this.htBonds =  new java.util.Hashtable();
this.htBonds.put(thisBondID, bond);
} else {
this.setBond(bond, this.connectors.get(thisBondID));
}break;
}
}
}
});
Clazz.defineMethod(c$, "processVibrationObject", 
function(){
var vibData =  Clazz.newFloatArray (this.nVibrations, this.nAtoms * 3, 0);
var energies =  new Array(this.nVibrations);
this.rd();
while (this.line != null && this.parseLineParameters(J.adapter.readers.quantum.CsfReader.vibFields, J.adapter.readers.quantum.CsfReader.vibFieldMap) > 0) {
while (this.rd() != null && !this.line.startsWith("property_flags:")) {
var tokens = this.getTokens();
var thisvib = -1;
for (var i = 0; i < this.fieldCount; ++i) {
var field = tokens[i];
switch (this.fieldTypes[i]) {
case -1:
thisvib = this.parseIntStr(field) - 1;
break;
case 1:
this.fillCsfArray("normalMode", tokens, i, vibData[thisvib], false);
break;
case 2:
energies[thisvib] = field;
break;
}
}
}
}
for (var i = 0; i < this.nVibrations; i++) {
if (!this.doGetVibration(++this.vibrationNumber)) continue;
this.asc.cloneAtomSetWithBonds(false);
this.asc.setAtomSetFrequency(this.vibrationNumber, null, null, energies[i], null);
var ipt = 0;
var baseAtom = this.nAtoms * (i + 1);
for (var iAtom = 0; iAtom < this.nAtoms; iAtom++) this.asc.addVibrationVector(baseAtom + iAtom, vibData[i][ipt++], vibData[i][ipt++], vibData[i][ipt++]);

}
});
Clazz.defineMethod(c$, "processMolecularOrbitalObject", 
function(){
if (this.nSlaters == 0 && this.nGaussians == 0 || !this.doReadMolecularOrbitals) {
this.rd();
return;
}this.nOrbitals = (this.nSlaters + this.nGaussians);
JU.Logger.info("Reading CSF data for " + this.nOrbitals + " molecular orbitals");
var energy =  Clazz.newFloatArray (this.nOrbitals, 0);
var occupancy =  Clazz.newFloatArray (this.nOrbitals, 0);
var list =  Clazz.newFloatArray (this.nOrbitals, this.nOrbitals, 0);
var listCompressed = null;
var coefIndices = null;
var ipt = 0;
var isCompressed = false;
this.rd();
while (this.line != null && this.parseLineParameters(J.adapter.readers.quantum.CsfReader.moFields, J.adapter.readers.quantum.CsfReader.moFieldMap) > 0) while (this.rd() != null && !this.line.startsWith("property_flags:")) {
var tokens = this.getTokens();
for (var i = 0; i < this.fieldCount; ++i) {
switch (this.fieldTypes[i]) {
case -1:
ipt = this.parseIntStr(tokens[i]) - 1;
break;
case 1:
energy[ipt] = this.parseFloatStr(tokens[i]);
break;
case 2:
occupancy[ipt] = this.parseFloatStr(tokens[i]);
break;
case 3:
this.fillCsfArray("eig_vec", tokens, i, list[ipt], false);
break;
case 4:
isCompressed = true;
if (listCompressed == null) listCompressed =  Clazz.newFloatArray (this.nOrbitals, this.nOrbitals, 0);
this.fillCsfArray("eig_vec_compressed", tokens, i, listCompressed[ipt], false);
break;
case 5:
if (coefIndices == null) coefIndices =  Clazz.newIntArray (this.nOrbitals, this.nOrbitals, 0);
this.fillCsfArray("coef_indices", tokens, i, coefIndices[ipt], true);
break;
}
}
}

for (var iMo = 0; iMo < this.nOrbitals; iMo++) {
if (isCompressed) {
for (var i = 0; i < coefIndices[iMo].length; i++) {
var pt = coefIndices[iMo][i] - 1;
if (pt < 0) break;
list[iMo][pt] = listCompressed[iMo][i];
}
}for (var i = 0; i < this.nOrbitals; i++) if (Math.abs(list[iMo][i]) < 1.0E-4) list[iMo][i] = 0;

var mo =  new java.util.Hashtable();
mo.put("energy", Float.$valueOf(energy[iMo]));
mo.put("occupancy", Float.$valueOf(occupancy[iMo]));
mo.put("coefficients", list[iMo]);
this.setMO(mo);
}
this.setMOs("eV");
});
Clazz.defineMethod(c$, "processBasisObject", 
function(sto_gto){
var atomNos = JU.PT.getTokens(this.strAtomicNumbers);
this.atomicNumbers =  Clazz.newIntArray (atomNos.length, 0);
for (var i = 0; i < this.atomicNumbers.length; i++) this.atomicNumbers[i] = this.parseIntStr(atomNos[i]);

this.nOrbitals = (this.nSlaters + this.nGaussians);
var isGaussian = (sto_gto.equals("gto"));
var zetas = JU.AU.newFloat2(this.nOrbitals);
var contractionCoefs = null;
var types =  new Array(this.nOrbitals);
var shells =  Clazz.newIntArray (this.nOrbitals, 0);
var nZetas = 0;
this.rd();
while (this.line != null && this.parseLineParameters(J.adapter.readers.quantum.CsfReader.moFields, J.adapter.readers.quantum.CsfReader.moFieldMap) > 0) {
if (nZetas == 0) nZetas = this.getPropertyCount(sto_gto + "_exp");
var ipt = 0;
while (this.rd() != null && !this.line.startsWith("property_flags:")) {
var tokens = this.getTokens();
for (var i = 0; i < this.fieldCount; ++i) {
var field = tokens[i];
switch (this.fieldTypes[i]) {
case -1:
ipt = this.parseIntStr(field) - 1;
break;
case 6:
types[ipt] = field;
break;
case 7:
case 9:
zetas[ipt] =  Clazz.newFloatArray (nZetas, 0);
this.fillCsfArray(sto_gto + "_exp", tokens, i, zetas[ipt], false);
break;
case 10:
shells[ipt] = this.parseIntStr(field);
break;
case 8:
if (contractionCoefs == null) contractionCoefs =  Clazz.newFloatArray (this.nOrbitals, nZetas, 0);
this.fillCsfArray("contractions", tokens, i, contractionCoefs[ipt], false);
}
}
}
}
if (isGaussian) {
var sdata =  new JU.Lst();
var gdata =  new JU.Lst();
var iShell = 0;
var gaussianCount = 0;
for (var ipt = 0; ipt < this.nGaussians; ipt++) {
if (shells[ipt] != iShell) {
iShell = shells[ipt];
var slater =  Clazz.newIntArray (4, 0);
var iAtom = this.asc.getAtomIndex(this.connectors.get(sto_gto + "_basis_fxn" + (ipt + 1))[0]);
slater[0] = iAtom + 1;
slater[1] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID(types[ipt].substring(0, 1));
var nZ = 0;
while (++nZ < nZetas && zetas[ipt][nZ] != 0) {
}
slater[2] = gaussianCount;
slater[3] = nZ;
sdata.addLast(slater);
gaussianCount += nZ;
for (var i = 0; i < nZ; i++) gdata.addLast( Clazz.newFloatArray(-1, [zetas[ipt][i], contractionCoefs[ipt][i]]));

}}
var garray = JU.AU.newFloat2(gaussianCount);
for (var i = 0; i < gaussianCount; i++) garray[i] = gdata.get(i);

this.moData.put("shells", sdata);
this.moData.put("gaussians", garray);
} else {
for (var ipt = 0; ipt < this.nSlaters; ipt++) {
var iAtom = this.asc.getAtomIndex(this.connectors.get(sto_gto + "_basis_fxn" + (ipt + 1))[0]);
for (var i = 0; i < nZetas; i++) {
if (zetas[ipt][i] == 0) break;
this.createSphericalSlaterByType(iAtom, this.atomicNumbers[iAtom], types[ipt], zetas[ipt][i] * (i == 0 ? 1 : -1), contractionCoefs == null ? 1 : contractionCoefs[ipt][i]);
}
}
this.setSlaters(false);
}}, "~S");
c$.connectorFields =  Clazz.newArray(-1, ["objCls1", "objID1", "objCls2", "objID2"]);
c$.connectorFieldMap =  Clazz.newByteArray(-1, [1, 2, 3, 4]);
c$.atomFields =  Clazz.newArray(-1, ["ID", "sym", "anum", "chrg", "xyz_coordinates", "pchrg"]);
c$.atomFieldMap =  Clazz.newByteArray(-1, [-1, 1, 2, 3, 4, 5]);
c$.bondFields =  Clazz.newArray(-1, ["ID", "type"]);
c$.bondFieldMap =  Clazz.newByteArray(-1, [-1, 1]);
c$.vibFields =  Clazz.newArray(-1, ["ID", "normalMode", "Energy", "transitionDipole"]);
c$.vibFieldMap =  Clazz.newByteArray(-1, [-1, 1, 2, 3]);
c$.moFields =  Clazz.newArray(-1, ["ID", "eig_val", "mo_occ", "eig_vec", "eig_vec_compressed", "coef_indices", "bfxn_ang", "sto_exp", "contractions", "gto_exp", "shell"]);
c$.moFieldMap =  Clazz.newByteArray(-1, [-1, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]);
});
;//5.0.1-v7 Mon May 12 16:54:26 CDT 2025
