Clazz.declarePackage("J.adapter.readers.xtal");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.EspressoReader", ["JU.PT"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.cellParams = null;
this.totEnergy = null;
this.endFlag = false;
this.aPar = 0;
Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "EspressoReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.setSpaceGroupName("P1");
this.doApplySymmetry = true;
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (this.line.contains("lattice parameter (a_0)") || this.line.contains("lattice parameter (alat)")) {
this.readAparam();
} else if (this.line.contains("crystal axes:")) {
this.readCellParam(false);
} else if (this.line.contains("CELL_PARAMETERS (")) {
this.readCellParam(true);
} else if (this.line.contains("Cartesian axes")) {
this.discardLinesUntilContains("positions (");
if (this.doGetModel(++this.modelNumber, null)) this.readAtoms();
} else if (this.line.contains("POSITIONS (")) {
if (this.doGetModel(++this.modelNumber, null)) this.readAtoms();
} else if (this.line.contains("!    total energy")) {
this.readEnergy();
} else if (this.line.contains("A final scf")) {
this.endFlag = true;
}return true;
});
Clazz.defineMethod(c$, "readAparam", 
function(){
this.aPar = this.parseFloatStr(this.getTokens()[4]) * 0.5291772;
});
Clazz.defineMethod(c$, "readCellParam", 
function(andAPar){
var i0 = (andAPar ? 0 : 3);
if (this.line.contains("bohr")) this.aPar = 0.5291772;
if (andAPar && this.line.contains("=")) this.aPar = this.parseFloatStr(this.line.substring(this.line.indexOf("=") + 1)) * 0.5291772;
this.cellParams =  Clazz.newFloatArray (9, 0);
for (var n = 0, i = 0; n < 3; n++) {
var tokens = JU.PT.getTokens(this.rd());
this.cellParams[i++] = this.parseFloatStr(tokens[i0]) * this.aPar;
this.cellParams[i++] = this.parseFloatStr(tokens[i0 + 1]) * this.aPar;
this.cellParams[i++] = this.parseFloatStr(tokens[i0 + 2]) * this.aPar;
}
}, "~B");
Clazz.defineMethod(c$, "newAtomSet", 
function(){
this.asc.newAtomSet();
if (this.totEnergy != null) this.setEnergy();
});
Clazz.defineMethod(c$, "setCellParams", 
function(){
if (this.cellParams != null) {
this.addExplicitLatticeVector(0, this.cellParams, 0);
this.addExplicitLatticeVector(1, this.cellParams, 3);
this.addExplicitLatticeVector(2, this.cellParams, 6);
this.setSpaceGroupName("P1");
}});
Clazz.defineMethod(c$, "readAtoms", 
function(){
this.newAtomSet();
var isAlat = (this.line.contains("alat") || this.line.contains("a_0"));
var firstStr = (this.line.contains("site n."));
var isFractional = this.line.contains("crystal");
var isBohr = this.line.contains("bohr");
var isAngstrom = this.line.contains("angstrom");
if (isAlat || isFractional || isAngstrom) this.setCellParams();
this.setFractionalCoordinates(isFractional);
while (this.rd() != null && this.line.length > 45) {
var tokens = this.getTokens();
var atom = this.asc.addNewAtom();
atom.atomName = tokens[(isBohr || tokens.length == 4 || !firstStr ? 0 : 1)];
var i1 = (isBohr || tokens.length == 4 || !firstStr ? 1 : tokens.length - 4);
var x = this.parseFloatStr(tokens[i1++]);
var y = this.parseFloatStr(tokens[i1++]);
var z = this.parseFloatStr(tokens[i1++]);
atom.set(x, y, z);
if (isBohr) {
atom.scale(0.5291772);
} else if (isAlat) {
atom.scale(this.aPar);
}this.setAtomCoord(atom);
}
this.applySymmetryAndSetTrajectory();
if (this.endFlag) this.discardLinesUntilContains("Harris-Foulkes estimate");
});
Clazz.defineMethod(c$, "readEnergy", 
function(){
this.totEnergy = Double.$valueOf(Double.parseDouble(JU.PT.getTokens(this.line.substring(this.line.indexOf("=") + 1))[0]));
});
Clazz.defineMethod(c$, "setEnergy", 
function(){
this.asc.setAtomSetEnergy("" + this.totEnergy, this.totEnergy.floatValue());
this.asc.setInfo("Energy", this.totEnergy);
this.asc.setAtomSetName("E = " + this.totEnergy + " Ry");
});
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
