Clazz.declarePackage("J.adapter.readers.xtal");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.AimsReader", ["JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.globalDoApplySymmetry = false;
this.isFractional = false;
this.nLatticeVectors = 0;
Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "AimsReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.globalDoApplySymmetry = this.doApplySymmetry;
this.doApplySymmetry = true;
this.isFractional = true;
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
var tokens = this.getTokens();
if (tokens.length == 0) return true;
if (tokens[0].equals("lattice_vector")) {
this.readLatticeVector(tokens);
return true;
}if (tokens[0].equals("atom")) {
this.readAtom(tokens, false);
return true;
}if (tokens[0].equals("atom_frac")) {
this.readAtom(tokens, true);
return true;
}if (tokens[0].equals("multipole")) {
this.readMultipole(tokens);
return true;
}return true;
});
Clazz.overrideMethod(c$, "finalizeSubclassReader", 
function(){
this.doApplySymmetry = this.globalDoApplySymmetry;
if (this.nLatticeVectors == 1 || this.nLatticeVectors == 2) {
JU.Logger.warn("ignoring translation symmetry for more or less than 3 dimensions(which is currently neither supported by FHI-aims");
}this.finalizeReaderASCR();
});
Clazz.defineMethod(c$, "readLatticeVector", 
function(tokens){
if (tokens.length < 4) {
JU.Logger.warn("cannot read line with FHI-aims lattice vector: " + this.line);
} else if (this.nLatticeVectors == 3) {
JU.Logger.warn("more than 3 FHI-aims lattice vectors found with line: " + this.line);
} else {
this.addExplicitLatticeVector(this.nLatticeVectors++,  Clazz.newFloatArray(-1, [this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[3])]), 0);
this.setFractionalCoordinates(this.nLatticeVectors == 3);
}}, "~A");
Clazz.defineMethod(c$, "readAtom", 
function(tokens, isFractional){
if (tokens.length < 5) {
JU.Logger.warn("cannot read line with FHI-aims line: " + this.line);
return;
}if (this.isFractional != isFractional) this.setFractionalCoordinates(this.isFractional = isFractional);
this.addAtomXYZSymName(tokens, 1, tokens[4], null);
}, "~A,~B");
Clazz.defineMethod(c$, "readMultipole", 
function(tokens){
if (tokens.length < 6) {
JU.Logger.warn("cannot read line with FHI-aims atom data: " + this.line);
return;
}var order = this.parseIntStr(tokens[4]);
if (order > 0) {
JU.Logger.warn("multipole line ignored since only monopoles are currently supported: " + this.line);
return;
}if (this.isFractional) this.setFractionalCoordinates(this.isFractional = false);
this.addAtomXYZSymName(tokens, 1, null, null).partialCharge = this.parseFloatStr(tokens[5]);
}, "~A");
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
