mirror of
https://github.com/LCPQ/QUESTDB_website.git
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431 lines
13 KiB
JavaScript
431 lines
13 KiB
JavaScript
class excitationTypes {
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static get Valence() { return new excitationType(1<< 1, new description("Valence")) }
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static get Rydberg() { return new excitationType(1 << 2, new description("Rydberg")) }
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static get PiPis() { return new excitationType(1 << 3, new description(String.raw`\pi \rightarrow \pi^\star`,true)) }
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static get nPis() { return new excitationType(1 << 4, new description(String.raw`n \rightarrow \pi^\star`,true)) }
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static get Single() { return new excitationType(1 << 5, new description("Single")) }
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static get Double() { return new excitationType(1 << 6, new description("Double")) }
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static get SingletSinglet() { return new excitationType(1 << 7, new description(String.raw`\mathrm{Singlet} \rightarrow \mathrm{Singlet}`,true)) }
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static get SingletTriplet() { return new excitationType(1 << 8, new description(String.raw`\mathrm{Singlet} \rightarrow \mathrm{Triplet}`,true)) }
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// Max bit shifts is 31 because int are int32 So 1 << 31 are -2147483648
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static get Others() { return new excitationType(1 << 31, new description("Others"))}
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static get All() { return EnumUltils.getAll(this,excitationType)}
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static GetFlags(value){return EnumUltils.GetFlags(value,this,excitationType)}
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}
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class EnumUltils{
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static getAll(enumClass,valueType) {
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var lst = []
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for (const prop of Object.getOwnPropertyNames(enumClass)) {
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if (prop != "All") {
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const value = enumClass[prop]
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if (trueTypeOf(value) == valueType.name) {
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lst.push([prop, value])
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}
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}
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}
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return lst
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}
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static GetFlags(value,enumClass,valueType) {
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return this.getAll(enumClass,valueType).filter((x) => { value & x[1] })
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}
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}
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class description {
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constructor(string,isLaTeX=false) {
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this.string = string
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this.isLaTeX=isLaTeX
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}
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}
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class DescribedValueBase {
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constructor(value, description) {
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this.Value = value;
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this.description = description
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}
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valueOf() {
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return this.Value;
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}
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}
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class excitationType extends DescribedValueBase{
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}
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class VertExcitationKind extends DescribedValueBase{
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}
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class code {
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constructor(name, version) {
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this.name = name;
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this.version = version;
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};
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toString() {
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var str = this.name;
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if (this.version) {
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str = str + ' (' + this.version + ')';
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}
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return str;
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}
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static fromString(str) {
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var vals = str.split(",")
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if (vals.length >= 2) {
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return new code(vals[0], vals[1]);
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} else {
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return new code(vals[0], null);
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}
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}
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}
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class method {
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constructor(name, basis = null) {
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this.name = name;
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this.basis = basis;
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}
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static fromString(str) {
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var vals = str.split(",")
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if (vals.length == 2) {
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return new method(vals[0], vals[1]);
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}
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else {
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return new method(vals[0], null)
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}
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}
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toString(separator="/") {
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var str = this.name;
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if (this.basis) {
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str = str + separator + this.basis;
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}
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return str;
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}
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get isTBE() {
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return /^TBE/.test(this.name)
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}
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}
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class state {
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constructor(number, multiplicity, symetry) {
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this.number = number;
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this.multiplicity = multiplicity;
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this.symetry = symetry;
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};
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toString() {
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var str = this.number + ' ^' + this.multiplicity + this.symetry;
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return str;
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};
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toLaTeX() {
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var tex = String.raw`${this.number}\:^{${this.multiplicity}}\mathrm{${this.symetry}}`;
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return tex;
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};
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}
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class DOI {
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constructor(doistring,IsSupporting=false) {
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this.string = doistring
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this.IsSupporting = IsSupporting
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};
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static fromString(str){
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const vals=str.split(",")
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if (vals.length==1) {
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return new DOI(vals[0].toString())
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}
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else{
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return new DOI(vals[0].toString(),(true ? vals[1]=== true.toString() : false))
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}
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}
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toString() {
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var str=this.string;
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if (this.IsSupporting) {
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str+=" "+"(SI)"
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}
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return str
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};
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get url() {
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return new URL(this.string, 'https://doi.org').toString()
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}
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}
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class excitationBase {
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constructor(initial, final, type = '', T1 = null) {
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this.initial = initial;
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this.final = final
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this.type = new excitationType(0, new description(type,true))
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if (type !== "") {
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const tys = type.split(";")
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const arrow = String.raw`\rightarrow`
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for (const ty of tys) {
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if (ty.includes(arrow)) {
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const [initialt, finalt] = ty.split(arrow, 2)
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const initialts = initialt.split(",").map(x => x.trim())
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const finalts = finalt.split(",").map(x => x.trim())
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if (initialts.length == 2 && finalts.length == 2) {
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this.type.Value = this.type | excitationTypes.Double
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}
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else if (initialts.length == 1 && finalts.length == 1) {
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this.type.Value = this.type | excitationTypes.Single
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}
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if (initialts.includes("n") && finalts.includes(String.raw`\pi^\star`)) {
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this.type.Value = this.type | excitationTypes.nPis
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} else if (initialts.includes(String.raw`\pi`) && finalts.includes(String.raw`\pi^\star`)) {
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this.type.Value = this.type | excitationTypes.PiPis
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}
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} else if (ty.includes(String.raw`\mathrm{R}`)) {
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this.type.Value = this.type | excitationTypes.Rydberg
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} else if (ty.includes(String.raw`\mathrm{V}`)) {
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this.type.Value = this.type | excitationTypes.Valence
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}
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}
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}
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switch (final.multiplicity) {
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case 1:
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this.type.Value=this.type|excitationTypes.SingletSinglet
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break;
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case 3:
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this.type.Value=this.type|excitationTypes.SingletTriplet
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break;
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}
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if (this.type.Value==0) {
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this.type.Value=excitationTypes.Others.Value;
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}
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this.T1 = T1
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}
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}
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class excitationValue extends excitationBase {
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constructor(initial, final, type, value, oscilatorForces = null, T1 = null, isUnsafe = false) {
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super(initial, final, type, T1)
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this.value = value
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this.oscilatorForces = oscilatorForces
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this.isUnsafe = isUnsafe
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}
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}
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class excitation extends excitationBase {
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constructor(initial, final, Eabs, Efluo, EZPE) {
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super(initial, final)
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this.Eabs = Eabs
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this.Efluo = Efluo
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this.EZPE = EZPE
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}
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get Eadia() {
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return (this.Eabs + this.Efluo) / 2
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}
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get Ezz() {
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return this.Eadia - this.EZPE
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}
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toString() {
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return this.start + ', ' + this.end + ', ' + noNanPrecision(this.Eabs, 3);
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}
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}
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class dataFileBase {
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constructor() {
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this.molecule = ''
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this.comment = ""
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this.code = null
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this.method = null
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this.excitations = []
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this.DOI = null
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this.sourceFile = null
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}
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static _GetMetaRexEx() {
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//metadata RegExp (start with #; maybe somme spaces; : ; maybe somme space; datas)
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return /^#\s*([A-Za-z_]+)\s*:\s*(.*)$/;
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}
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CopyExcitationsTypeFrom(data) {
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for (const ex of this.excitations) {
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const ex2=data.excitations.find((e)=>{
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return (JSON.stringify(e.initial)===JSON.stringify(ex.initial)) && (JSON.stringify(e.final)===JSON.stringify(ex.final))
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})
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if(ex2!==undefined){
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console.assert(ex.type==0 || (ex2.type^(excitationTypes.Rydberg | excitationTypes.Valence)==ex.type^(excitationTypes.Rydberg | excitationTypes.Valence)),"Excitation type error",[ex,ex2,data.sourceFile])
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ex.type=ex2.type
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}
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}
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}
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static async loadAsync(file,kind=undefined) {
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switch (trueTypeOf(file)) {
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case String.name:
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file = getFullDataPath(file)
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var str = await getTextFromFileUrlAsync(file)
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break;
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case File.name:
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var str = await getTextFromUploadedFileAsync(file)
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break
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}
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var dat = this.loadString(str,kind);
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dat.sourceFile = new websiteFile(file)
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return dat
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}
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_OnReadMetaPair(key, value) {
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switch (key) {
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case "molecule":
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this.molecule = value
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break;
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case "comment":
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this.comment = value
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break;
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case "code":
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this.code = code.fromString(value)
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break;
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case "method":
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this.method = method.fromString(value)
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break;
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case "doi":
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this.DOI = DOI.fromString(value);
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break;
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default:
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}
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}
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_OnReadRow(line) {
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var vals = line.match(/\([^\)]+\)|\S+/g)
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var start = new state(parseInt(vals[0], 10), parseInt(vals[1], 10), vals[2]);
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var end = new state(parseInt(vals[3], 10), parseInt(vals[4],10), vals[5]);
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var hasType = vals.length >= 7 && isNaN(vals[6])
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var type = ((vals.length >= 7 && hasType) ? vals[6] : null)
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if (type) {
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const m = type.match(/^\(([^\)]*)\)$/)
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if (m) {
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type = m[1]
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}
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}
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var val = ((vals.length >= 7 + hasType) ? new stringNumber(vals[6 + hasType]) : NaN)
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var T1 = ((vals.length >= 8 + hasType) ? new stringNumber(vals[7 + hasType]) : NaN)
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var oscilatorForces = ((vals.length >= 9 + hasType) ? new stringNumber(vals[8 + hasType]) : NaN)
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var isUnsafe = ((vals.length >= 10 + hasType) ? vals[9 + hasType] === true.toString() : false)
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var ex = new excitationValue(start, end, type, val, oscilatorForces, T1, isUnsafe);
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if (this.VertExcitationKind) {
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ex.VertExcitationKind=this.VertExcitationKind
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}
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return ex;
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};
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_OnReadMeta(line) {
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// get key value
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var match = line.match(dataFileBase._GetMetaRexEx())
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// normalize key to lower
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var key = match[1].toLowerCase()
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//if data has value
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if (match.length == 3 && match[2]) {
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var val = match[2]
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this._OnReadMetaPair(key,val)
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}
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}
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static loadString(text,kind=null) {
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// for each line with metadata
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var ismetaArea = true;
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var dat = new VertDataFile()
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for (var line of text.split("\n")) {
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//if it's not empty line
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line = line.trim();
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if (line) {
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//if # may be metadata or comment
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if (line.charAt(0) == "#") {
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//if it's metadata
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if (ismetaArea && dataFileBase._GetMetaRexEx().test(line)) {
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dat._OnReadMeta(line);
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}
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} else { //else its row
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ismetaArea = false;
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dat.excitations.push(dat._OnReadRow(line,kind));
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}
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}
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}
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var stfy=dat.excitations.map(e=>JSON.stringify([e.initial,e.final]))
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var double=[]
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stfy.forEach(function(element, i) {
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// Find if there is a duplicate or not
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if (stfy.indexOf(element, i + 1) >= 0) {
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// Find if the element is already in the result array or not
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if (double.indexOf(element) === -1) {
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double.push(dat.excitations[i])
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}
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}
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});
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console.assert(double.length===0,"Double found",double,dat.molecule,dat.method.toString())
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if (dat.DOI.string!=="10.1021/acs.jctc.8b01205") {
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for (const ex of dat.excitations) {
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console.assert(Number.isNaN(ex.T1.valueOf()) | ex.T1>50 | ex.isUnsafe==true,"Must be unsafe",dat,ex)
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}
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}
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return dat
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}
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}
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class VertExcitationKinds{
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static get Absorbtion() {return new VertExcitationKind(1, new description("Absorption"))}
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static get Fluorescence() {return new VertExcitationKind(1<<1, new description("Fluorescence"))}
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static get All() { return EnumUltils.getAll(this,VertExcitationKind)}
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static GetFlags(value){return EnumUltils.GetFlags(value,this,VertExcitationKind)}
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}
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class VertDataFile extends dataFileBase {
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constructor(VertExcitationKind) {
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super()
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this.VertExcitationKind=VertExcitationKind
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this.geometry = null
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}
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_OnReadMetaPair(key, value) {
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if (key == "geom") {
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this.geometry = method.fromString(value)
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}
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else {
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super._OnReadMetaPair(key, value)
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}
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}
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_OnReadRow(line,kind) {
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var ex=super._OnReadRow(line)
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ex.VertExcitationKind=kind
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return ex
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}
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}
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class CombinedData {
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constructor() {
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this.Abs = null
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this.Fluo = null
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this.ZPE = null
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}
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get excitations() {
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var exs = []
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var dic = new Map()
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if (this.Abs != null) {
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for (const el of this.Abs.excitations) {
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var key = JSON.stringify([el.initial, el.final])
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if (!dic.has(key)) {
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dic.set(key, {})
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}
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dic.get(key)["abs"] = el.value
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}
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if (this.Fluo != null) {
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for (const el of this.Fluo.excitations) {
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var key = JSON.stringify([el.initial, el.final])
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if (!dic.has(key)) {
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dic.set(key, {})
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}
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dic.get(key)["fluo"] = el.value
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}
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}
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if (this.ZPE != null) {
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for (const el of this.ZPE.excitations) {
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var key = JSON.stringify([el.initial, el.final])
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if (!dic.has(key)) {
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dic.set(key, {})
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}
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dic.get(key)["ZPE"] = el.value
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}
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}
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dic.forEach((value, key) => {
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var eabs = NaN
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var efluo = NaN
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var eZPE = NaN
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var mykey = JSON.parse(key)
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for (var el of mykey) {
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Reflect.setPrototypeOf(el, state.prototype)
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}
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if ("abs" in value) {
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eabs = value["abs"]
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}
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if ("fluo" in value) {
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efluo = value["fluo"]
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}
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if ("ZPE" in value) {
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eZPE = value["ZPE"]
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}
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exs.push(new excitation(mykey[0], mykey[1], eabs, efluo, eZPE))
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})
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return exs
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}
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}
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} |