Clazz.declarePackage("J.adapter.readers.quantum");
Clazz.load(["J.adapter.readers.quantum.SlaterReader", "java.util.Hashtable"], "J.adapter.readers.quantum.DgridReader", ["JU.PT", "$.SB", "J.quantum.SlaterData", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.title = null;
this.htExponents = null;
this.htFuncMap = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.quantum, "DgridReader", J.adapter.readers.quantum.SlaterReader);
Clazz.prepareFields (c$, function(){
this.htExponents =  new java.util.Hashtable();
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (this.line.indexOf(":title") == 0) {
this.title = this.rd().substring(2);
return true;
}if (this.line.indexOf("basis:  CARTESIAN  STO") >= 0) {
this.readSlaterBasis();
return true;
}if (this.line.indexOf(":atom") == 0) {
this.readCoordinates();
return true;
}if (this.line.indexOf(" MO  DATA ") >= 0) {
if (this.doReadMolecularOrbitals) this.readMolecularOrbitals();
return true;
}return true;
});
Clazz.defineMethod(c$, "readCoordinates", 
function(){
this.asc.newAtomSet();
this.asc.setAtomSetName(this.title);
this.discardLinesUntilContains("----");
while (this.rd() != null && !this.line.startsWith(":-----")) {
var tokens = this.getTokens();
if (tokens.length < 5) break;
this.setAtomCoordScaled(null, tokens, 2, 0.5291772).elementSymbol = tokens[0];
}
});
Clazz.defineMethod(c$, "readSlaterBasis", 
function(){
this.discardLinesUntilContains(":-");
var ch = 'a';
while (this.rd() != null && this.line.indexOf(":-") < 0) {
var atomSymbol = this.line.substring(3, 6).trim();
var xyz = this.line.substring(19, 21);
var code = atomSymbol + xyz;
if (this.htExponents.get(code) == null) {
ch = 'a';
} else {
code += "_" + ($c$ = ch, ch = String.fromCharCode(ch.charCodeAt(0)+1), $c$);
}var exp = this.line.substring(34);
this.htExponents.put(code, Float.$valueOf(this.parseFloatStr(exp)));
}
});
Clazz.defineMethod(c$, "readMolecularOrbitals", 
function(){
this.htFuncMap =  new java.util.Hashtable();
this.readLines(3);
this.getSlaters();
while (this.line != null && this.line.indexOf(":") != 0) {
this.discardLinesUntilContains("sym: ");
var symmetry = this.line.substring(4, 10).trim();
if (symmetry.indexOf("_FC") >= 0) break;
var data =  new JU.SB();
data.append(this.line.substring(15));
while (this.rd() != null && this.line.length >= 15) data.append(this.line);

var tokens = JU.PT.getTokens(data.toString());
var nFuncs = Clazz.doubleToInt(tokens.length / 2);
var ptSlater =  Clazz.newIntArray (nFuncs, 0);
var atoms = this.asc.atoms;
for (var i = 0, pt = 0; i < tokens.length; ) {
var iAtom = this.parseIntStr(tokens[i++]) - 1;
var code = tokens[i++];
var key = iAtom + "_" + code;
if (this.htFuncMap.containsKey(key)) {
ptSlater[pt++] = this.htFuncMap.get(key).intValue();
} else {
var n = this.slaters.size();
ptSlater[pt++] = n;
this.htFuncMap.put(key, Integer.$valueOf(n));
this.addSlater(this.createSlaterData(iAtom + 1, atoms[iAtom].elementSymbol, code), n);
}}
this.discardLinesUntilContains(":-");
this.rd();
while (this.line != null && this.line.length >= 20) {
var iOrb = this.parseIntRange(this.line, 0, 10);
var energy = this.parseFloatRange(this.line, 10, 20);
var cData =  new JU.SB();
cData.append(this.line.substring(20));
while (this.rd() != null && this.line.length >= 10) {
if (this.line.charAt(3) != ' ') break;
cData.append(this.line);
}
var list =  Clazz.newFloatArray (this.slaters.size(), 0);
tokens = JU.PT.getTokens(cData.toString());
if (tokens.length != nFuncs) JU.Logger.error("DgridReader: number of coefficients (" + tokens.length + ") does not equal number of functions (" + nFuncs + ")");
for (var i = 0; i < tokens.length; i++) {
var pt = ptSlater[i];
list[pt] = this.parseFloatStr(tokens[i]);
}
var mo =  new java.util.Hashtable();
mo.put("energy", Float.$valueOf(energy));
mo.put("coefficients", list);
mo.put("symmetry", symmetry + "_" + iOrb);
this.setMO(mo);
}
}
this.discardLinesUntilContains(":  #  symmetry");
this.rd();
for (var i = 0; i < this.orbitals.size(); i++) {
this.rd();
var occupancy = this.parseFloatRange(this.line, 31, 45) + this.parseFloatRange(this.line, 47, 61);
this.orbitals.get(i).put("occupancy", Float.$valueOf(occupancy));
}
this.sortOrbitals();
this.setSlaters(true);
this.setMOs("eV");
});
Clazz.defineMethod(c$, "createSlaterData", 
function(iAtom, atomSymbol, xyz){
var ch;
var abc = ' ';
var type = ' ';
var exp = 1;
var el = 0;
var x = 0;
var y = 0;
var z = 0;
for (var i = xyz.length; --i >= 0; ) {
switch ((ch = xyz.charAt(i)).charCodeAt(0)) {
case 95:
type = abc;
break;
case 49:
case 50:
case 51:
case 52:
exp = ch.charCodeAt(0) - 48;
break;
case 120:
x = exp;
el += exp;
exp = 1;
break;
case 121:
y = exp;
el += exp;
exp = 1;
break;
case 122:
z = exp;
el += exp;
exp = 1;
break;
case 115:
case 112:
case 100:
case 102:
default:
abc = ch;
}
}
var r = (exp - el - 1);
var code = atomSymbol + xyz.substring(0, 2);
if (type != ' ') code += "_" + type;
var f = this.htExponents.get(code);
var zeta = 0;
if (f == null) JU.Logger.error("Exponent for " + code + " not found");
 else zeta = f.floatValue();
return  new J.quantum.SlaterData(iAtom, x, y, z, r, zeta, 1);
}, "~N,~S,~S");
});
;//5.0.1-v7 Mon May 12 16:54:26 CDT 2025
