Clazz.declarePackage("J.adapter.readers.more");
Clazz.load(["J.adapter.readers.xtal.VaspPoscarReader", "java.util.Hashtable"], "J.adapter.readers.more.AFLOWReader", ["java.util.Arrays", "JU.BS", "$.Lst", "$.PT", "$.SB", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.aabb = null;
this.readPRE = false;
this.fracB = NaN;
this.compositions = null;
this.getComposition = false;
this.listKey = null;
this.listKeyCase = null;
this.fileModelNumber = 0;
this.havePRE = false;
this.titleMsg = null;
this.keyMap = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.more, "AFLOWReader", J.adapter.readers.xtal.VaspPoscarReader);
Clazz.prepareFields (c$, function(){
this.keyMap =  new java.util.Hashtable();
});
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.readPRE = this.checkFilterKey("PRE");
var s;
s = this.getFilter("CA=");
if (s != null) this.fracB = (1 - this.parseFloatStr(s));
s = this.getFilter("CB=");
if (s != null) this.fracB = this.parseFloatStr(s);
s = this.getFilter("LIST=");
this.listKey = (s == null ? "HF" : s);
this.listKeyCase = this.listKey;
this.getComposition = !Float.isNaN(this.fracB);
this.discardLinesUntilStartsWith("[");
this.aabb = this.line.substring(1, this.line.indexOf("]"));
var pt = (JU.PT.isUpperCase(this.aabb.charAt(1)) ? 1 : 2);
this.defaultLabels =  Clazz.newArray(-1, [this.aabb.substring(0, pt), this.aabb.substring(pt)]);
while (this.rd().indexOf("] REFERENCE:") >= 0) this.appendLoadNote(this.line);

this.compositions =  new java.util.Hashtable();
this.quiet = true;
this.asc.bsAtoms =  new JU.BS();
this.addJmolScript("unitcell off;axes off;");
this.havePRE = (this.line.indexOf("Structure PRE") >= 0);
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (!this.havePRE) this.discardLinesUntilContains("Structure PRE");
this.havePRE = false;
if (this.line == null) return false;
this.continuing = new Boolean (this.continuing & this.readPrePost()).valueOf();
return this.continuing;
});
Clazz.defineMethod(c$, "readPrePost", 
function(){
this.fileModelNumber++;
this.titleMsg = "#" + (this.modelNumber + 1) + (this.getComposition ? "," + this.fileModelNumber + ", Cb=" + this.fracB : "");
this.elementLabel = null;
var n0 = this.asc.bsAtoms.cardinality();
if (this.readPRE) {
this.readStructure(this.titleMsg);
} else {
this.readElementLabelsOnly();
this.discardLinesUntilContains("Structure POST");
this.readStructure(this.titleMsg);
}if (this.getData()) {
this.applySymmetryAndSetTrajectory();
} else {
this.asc.bsAtoms.clearBits(this.asc.getLastAtomSetAtomIndex(), this.asc.ac);
this.doCheckUnitCell = false;
}this.finalizeModel();
if (n0 != this.asc.bsAtoms.cardinality()) JU.Logger.info("AFLOW: file#, saved#, atoms: " + this.fileModelNumber + " " + this.modelNumber + " " + (this.asc.bsAtoms.cardinality() - n0));
return !this.haveModel || this.modelNumber != this.desiredModelNumber;
});
Clazz.defineMethod(c$, "finalizeModel", 
function(){
this.asc.removeLastUnselectedAtoms();
});
Clazz.defineMethod(c$, "readElementLabelsOnly", 
function(){
this.readLines(5);
this.rdline();
var n = this.getTokens().length;
this.elementLabel =  new Array(n);
this.rdline();
this.line = "";
var s = null;
var last = null;
for (var i = 0; i < n; i++) {
while (s == null || s.equals(last)) {
this.rdline();
var tokens = this.getTokens();
if (tokens.length != 4 || (s = this.elementLabel[i] = this.getElement(tokens[3])) == null) {
i = n + 1;
break;
}}
last = s;
}
if (s == null) this.elementLabel = this.defaultLabels;
});
Clazz.defineMethod(c$, "getData", 
function(){
this.discardLinesUntilContains("- DATA -");
var htAFLOW =  new java.util.Hashtable();
htAFLOW.put("fileModelNumber", Integer.$valueOf(this.fileModelNumber));
htAFLOW.put("modelNumber", Integer.$valueOf(this.modelNumber + 1));
htAFLOW.put("AaBb", this.aabb);
var pt = 0;
var sb =  new JU.SB();
var listVal = 3.4028235E38;
var strcb = "?";
var listValStr = null;
var cb = 0;
while (this.rdline() != null && (pt = this.line.indexOf(" # ")) >= 0) {
var key = this.line.substring(pt + 3).trim();
var val = this.line.substring(0, pt).trim();
sb.append(key).append("=").append(val).append(" | ");
if (key.toUpperCase().startsWith(this.listKey)) {
this.listKey = key.toUpperCase();
this.listKeyCase = key;
listValStr = val;
listVal = this.parseFloatStr(val);
}if (key.equals("Ca")) {
var ca = this.parseFloatStr(val);
if (this.getComposition && Math.abs((1 - ca) - this.fracB) > 0.01) return false;
} else if (key.equals("Cb")) {
cb = this.parseFloatStr(strcb = val);
if (this.getComposition && Math.abs(cb - this.fracB) > 0.01) return false;
} else if (key.equals("Hf_atom [eV] (VASP)")) {
var e = this.parseFloatStr(val);
this.asc.setAtomSetEnergy(val, e);
}}
this.asc.setAtomSetName(this.titleMsg + (this.getComposition ? "" : " Cb=" + cb) + " " + this.listKey + "=" + listValStr);
var count_min = this.compositions.get(strcb);
if (!this.doGetModel(++this.modelNumber, null)) return false;
if (count_min == null) this.compositions.put(strcb, count_min =  Clazz.newFloatArray(-1, [0, 3.4028235E38, 0]));
count_min[0]++;
if (listVal < count_min[1]) {
count_min[1] = listVal;
count_min[2] = this.fileModelNumber;
}while (this.line.indexOf("- URL -") < 0) this.rdline();

sb.append("URL=" + this.rdline() + "|");
while (this.line.indexOf("aurl=") < 0) this.rdline();

sb.append(this.line);
var pairs = JU.PT.split(sb.toString(), " | ");
for (var i = pairs.length; --i >= 0; ) {
var kv = pairs[i].$plit("=");
if (kv.length < 2) continue;
var f = this.parseFloatStr(kv[1]);
var o = Float.isNaN(f) ? kv[1] : Float.$valueOf(f);
htAFLOW.put(kv[0], o);
var kvclean = this.cleanKey(kv[0]);
if (kvclean !== kv[0]) htAFLOW.put(kvclean, o);
}
this.asc.setCurrentModelInfo("aflowInfo", htAFLOW);
return true;
});
Clazz.defineMethod(c$, "cleanKey", 
function(key){
var kclean = this.keyMap.get(key);
if (kclean != null) return kclean;
var chars = key.toCharArray();
for (var i = chars.length; --i >= 0; ) if (!JU.PT.isLetterOrDigit(chars[i])) chars[i] = '_';

this.keyMap.put(key, kclean = JU.PT.trim(JU.PT.rep( String.instantialize(chars), "__", "_"), "_"));
return kclean;
}, "~S");
Clazz.overrideMethod(c$, "finalizeSubclassReader", 
function(){
this.alignUnitCells();
this.listCompositions();
this.finalizeReaderASCR();
});
Clazz.defineMethod(c$, "listCompositions", 
function(){
var list =  new JU.Lst();
for (var e, $e = this.compositions.entrySet().iterator (); $e.hasNext()&& ((e = $e.next ()) || true);) {
var count_min = e.getValue();
list.addLast(e.getKey() + "\t" + (Clazz.floatToInt(count_min[0])) + "\t" + Clazz.floatToInt(count_min[2]) + "\t" + this.listKeyCase + "\t" + count_min[1]);
}
var a =  new Array(list.size());
list.toArray(a);
java.util.Arrays.sort(a);
for (var i = 0, n = a.length; i < n; i++) this.appendLoadNote(this.aabb + "\t" + a[i]);

});
Clazz.defineMethod(c$, "alignUnitCells", 
function(){
});
});
;//5.0.1-v7 Tue Jul 22 18:14:29 CDT 2025
