Clazz.declarePackage("J.adapter.readers.xtal");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader", "JU.Lst"], "J.adapter.readers.xtal.VaspOutcarReader", ["JU.DF", "$.PT"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.atomNames = null;
this.ac = 0;
this.inputOnly = false;
this.mDsimulation = false;
this.vaspVersion = 0;
this.elementNames = null;
this.gibbsEnergy = null;
this.gibbsEntropy = null;
this.electronEne = null;
this.kinEne = null;
this.totEne = null;
this.temp = 0;
Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "VaspOutcarReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.prepareFields (c$, function(){
this.elementNames =  new JU.Lst();
});
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.isPrimitive = true;
this.setSpaceGroupName("P1");
this.setFractionalCoordinates(true);
this.inputOnly = this.checkFilterKey("INPUT");
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (this.vaspVersion == 0 && this.line.contains(" vasp.")) {
this.readVersion();
if (this.vaspVersion > 0) this.appendLoadNote("VASP version " + this.vaspVersion + " " + this.line);
} else if (this.line.toUpperCase().startsWith(" POTCAR:")) {
this.readElementNames();
} else if (this.line.contains("ions per type")) {
this.readAtomCountAndSetNames();
} else if (this.line.contains("molecular dynamics for ions")) {
this.mDsimulation = true;
} else if (this.line.contains("direct lattice vectors")) {
this.readUnitCellVectors();
} else if (this.ac > 0 && this.line.contains("position of ions in fractional coordinates")) {
this.readInitialCoordinates();
if (this.inputOnly) this.continuing = false;
} else if (this.line.contains("POSITION")) {
this.readPOSITION();
return true;
} else if (this.line.startsWith("  FREE ENERGIE") && !this.mDsimulation) {
this.readEnergy();
} else if (this.line.contains("ENERGIE OF THE ELECTRON-ION-THERMOSTAT") && this.mDsimulation) {
this.readMdyn();
} else if (this.line.startsWith(" Eigenvectors and eigenvalues of the dynamical matrix")) {
this.readFrequency();
}return true;
});
Clazz.defineMethod(c$, "readVersion", 
function(){
var tokens = JU.PT.split(this.line, ".");
this.vaspVersion = JU.PT.parseInt(tokens[1]);
});
Clazz.overrideMethod(c$, "finalizeSubclassReader", 
function(){
this.setSymmetry();
});
Clazz.defineMethod(c$, "readElementNames", 
function(){
this.line = JU.PT.rep(this.line, " _ ", "_");
var tokens = this.getTokens();
var pt = tokens[1].indexOf(":");
var name = (pt >= 0 ? tokens[1].substring(0, pt) : tokens[2]);
this.elementNames.addLast(name);
});
Clazz.defineMethod(c$, "readAtomCountAndSetNames", 
function(){
var numofElement =  Clazz.newIntArray (100, 0);
var tokens = JU.PT.getTokens(this.line.substring(this.line.indexOf("=") + 1));
this.ac = 0;
for (var i = 0; i < tokens.length; i++) this.ac += (numofElement[i] = this.parseIntStr(tokens[i]));

this.atomNames =  new Array(this.ac);
var nElements = this.elementNames.size();
for (var pt = 0, i = 0; i < nElements; i++) for (var j = 0; j < numofElement[i] && pt < this.ac; j++) this.atomNames[pt++] = this.elementNames.get(i);


});
Clazz.defineMethod(c$, "readUnitCellVectors", 
function(){
if (this.asc.ac > 0) {
this.setSymmetry();
this.asc.newAtomSet();
this.setAtomSetInfo();
}var f =  Clazz.newFloatArray (3, 0);
for (var i = 0; i < 3; i++) this.addExplicitLatticeVector(i, this.fillFloatArray(this.fixMinus(this.rd()), 0, f), 0);

});
Clazz.defineMethod(c$, "fixMinus", 
function(line){
return JU.PT.rep(line, "-", " -");
}, "~S");
Clazz.defineMethod(c$, "setSymmetry", 
function(){
this.applySymmetryAndSetTrajectory();
this.setSpaceGroupName("P1");
this.setFractionalCoordinates(false);
});
Clazz.defineMethod(c$, "readInitialCoordinates", 
function(){
var counter = 0;
while (this.rd() != null && this.line.length > 10) {
this.addAtomXYZSymName(JU.PT.getTokens(this.fixMinus(this.line)), 0, null, this.atomNames[counter++]);
}
this.asc.setAtomSetName("Initial Coordinates");
});
Clazz.defineMethod(c$, "readPOSITION", 
function(){
var counter = 0;
this.readLines(1);
while (this.rd() != null && this.line.indexOf("----------") < 0) this.addAtomXYZSymName(this.getTokens(), 0, null, this.atomNames[counter++]);

});
Clazz.defineMethod(c$, "readEnergy", 
function(){
this.rd();
var tokens = JU.PT.getTokens(this.rd());
this.gibbsEnergy = Double.$valueOf(Double.parseDouble(tokens[4]));
this.rd();
tokens = JU.PT.getTokens(this.rd());
var enthalpy = Double.parseDouble(tokens[3]);
this.gibbsEntropy = Double.$valueOf(enthalpy - this.gibbsEnergy.doubleValue());
});
Clazz.defineMethod(c$, "setAtomSetInfo", 
function(){
if (this.gibbsEnergy == null) return;
this.asc.setAtomSetEnergy("" + this.gibbsEnergy, this.gibbsEnergy.floatValue());
this.asc.setCurrentModelInfo("Energy", this.gibbsEnergy);
this.asc.setCurrentModelInfo("Entropy", this.gibbsEntropy);
this.asc.setInfo("Energy", this.gibbsEnergy);
this.asc.setInfo("Entropy", this.gibbsEntropy);
this.asc.setAtomSetName("G = " + this.gibbsEnergy + " eV, T*S = " + this.gibbsEntropy + " eV");
});
Clazz.defineMethod(c$, "readMdyn", 
function(){
var tokens = this.getTokens();
this.rd();
tokens = JU.PT.getTokens(this.rd());
this.electronEne = Double.$valueOf(Double.parseDouble(tokens[4]));
tokens = JU.PT.getTokens(this.rd());
this.kinEne = Double.$valueOf(Double.parseDouble(tokens[4]));
this.temp = this.parseFloatStr(tokens[6]);
this.readLines(3);
tokens = JU.PT.getTokens(this.rd());
this.totEne = Double.$valueOf(Double.parseDouble(tokens[4]));
this.setAtomSetInfoMd();
});
Clazz.defineMethod(c$, "setAtomSetInfoMd", 
function(){
this.asc.setAtomSetName("Temp. = " + JU.DF.formatDecimal((this.temp), 2) + " K, Energy = " + this.totEne + " eV");
this.asc.setCurrentModelInfo("Energy", this.totEne);
this.asc.setInfo("Energy", this.totEne);
this.asc.setCurrentModelInfo("EleEnergy", this.kinEne);
this.asc.setInfo("EleEnergy", this.electronEne);
this.asc.setCurrentModelInfo("Kinetic", this.electronEne);
this.asc.setInfo("Kinetic", this.kinEne);
this.asc.setCurrentModelInfo("Temperature", JU.DF.formatDecimal((this.temp), 2));
this.asc.setInfo("Temperature", JU.DF.formatDecimal((this.temp), 2));
});
Clazz.defineMethod(c$, "readFrequency", 
function(){
var pt = this.asc.iSet;
this.asc.baseSymmetryAtomCount = this.ac;
if (this.vaspVersion >= 5) {
this.readLines(3);
} else {
this.discardLinesUntilContains("Eigenvectors after division by SQRT(mass)");
this.readLines(5);
}var ignore =  Clazz.newBooleanArray(1, false);
while (this.rd() != null && (this.line.contains("f  = ") || this.line.contains("f/i= "))) {
this.applySymmetryAndSetTrajectory();
var iAtom0 = this.asc.ac;
this.cloneLastAtomSet(this.ac, null);
if (!ignore[0]) {
this.asc.iSet = ++pt;
this.asc.setAtomSetFrequency(this.vibrationNumber, null, null, this.line.substring(this.line.indexOf("2PiTHz") + 6, this.line.indexOf("c") - 1).trim(), null);
}this.rd();
this.fillFrequencyData(iAtom0, this.ac, this.ac, ignore, true, 35, 12, null, 0, null);
this.rd();
}
});
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
