mirror of
https://github.com/LCPQ/QUESTDB_website.git
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mveril
78fc5dd673
* Fix broken link * Fix bug in indexDB * Fix sourceFile for each geometry * Use valueOf in ex.type * Fix VertExcitationKind for custom files * Fix excitationType bug when value is set to Single by default * Remove the unnecessary valuOf() * Copy type of excitation from the reference for custom files * Remove sets dependency for %T1 to allow cross set %T1 reference data Co-authored-by: Mickaël Véril <mveril@irsamc.ups-tlse.fr>
437 lines
14 KiB
JavaScript
437 lines
14 KiB
JavaScript
class excitationTypes {
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static get Valence() { return new excitationType(1, new description("Valence")) }
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static get Rydberg() { return new excitationType(1 << 1, new description("Rydberg")) }
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static get PiPis() { return new excitationType(1 << 2, new description(String.raw`\pi \rightarrow \pi^\star`, true)) }
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static get nPis() { return new excitationType(1 << 3, new description(String.raw`n \rightarrow \pi^\star`, true)) }
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static get Single() { return new excitationType(1 << 4, new description("Single")) }
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static get Double() { return new excitationType(1 << 5, new description("Double")) }
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static get SingletSinglet() { return new excitationType(1 << 6, new description(String.raw`\mathrm{Singlet} \rightarrow \mathrm{Singlet}`, true)) }
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static get SingletTriplet() { return new excitationType(1 << 7, new description(String.raw`\mathrm{Singlet} \rightarrow \mathrm{Triplet}`, true)) }
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static get DoubletDoublet() { return new excitationType(1 << 8, new description(String.raw`\mathrm{Doublet} \rightarrow \mathrm{Doublet}`, 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, symmetry) {
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this.number = number;
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this.multiplicity = multiplicity;
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this.symmetry = symmetry;
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};
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toString() {
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var str = this.number + ' ^' + this.multiplicity + this.symmetry;
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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{${this.symmetry}}`;
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return tex;
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};
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}
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class exSet{
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constructor(name,index)
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{
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this.name = name
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this.index = index
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}
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static fromString(str) {
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var vals = str.split(",")
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var myset
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if (vals.length >= 2) {
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return new exSet(vals[0], parseInt(vals[1],10));
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} else {
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return new exSet(vals[0], 0);
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}
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}
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async getDOIAsync()
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{
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let db = await indexDB.loadAsync()
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if (db.sets.has(this.name)) {
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return db.sets.get(this.name)[this.index]
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}
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}
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toString()
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{
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return `${this.name},${this.index}`
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}
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isSameSet(set)
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{
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return this.name == set.name
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}
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async isSameArticleAsync(set)
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{
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if (this.name===set.name && this.index===set.index) {
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return true
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}
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else
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{
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return await this.getDOIAsync() === await set.getDOIAsync()
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}
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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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} else if (ty.toLowerCase()===excitationTypes.Double.description.string.toLowerCase()){
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this.type.Value = this.type | excitationTypes.Double
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}
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}
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}
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var m = new Map([
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[JSON.stringify([1, 1]), excitationTypes.SingletSinglet],
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[JSON.stringify([2, 2]), excitationTypes.DoubletDoublet],
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[JSON.stringify([1, 3]), excitationTypes.SingletTriplet],
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])
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const marray = JSON.stringify([initial.multiplicity, final.multiplicity])
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if (m.has(marray)) {
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this.type.Value = this.type.Value | m.get(marray)
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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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else if (!(this.type & (excitationTypes.Single.Value | excitationTypes.Double.Value))){
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this.type.Value += excitationTypes.Single.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 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.set = 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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async getGeometryAsync(state = null) {
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var site_url = "/"+window.location.pathname.split('/')[1];
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// var text = await getTextFromFileUrlAsync(`/data/structures/${this.set.name.replace("#", "")}/${this.molecule.toLowerCase()}.xyz`)
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var text = getTextFromFileUrl(site_url+`/data/structures/${this.set.name.replace("#", "")}/${this.molecule.toLowerCase()}.xyz`)
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var lines = text.split("\n")
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var indexes = lines.findAllIndexes((line) => {
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return line.match(/^\d+$/)
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})
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indexes.push(lines.length)
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var molsstr = []
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for (let i = 0; i < indexes.length - 1; i++) {
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molsstr.push(lines.slice(indexes[i], indexes[i + 1]).join('\n'))
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}
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molsstr.filter((molstr) => {
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var params = molstr.split("\n")[1].split(",")
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return (state === null || params[0] === `^${state.multiplicity}${state.symmetry}`) && params[1] == `${this.method.name},${this.method.basis}`
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})
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return molsstr.map((molstr) => {
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var params = molstr.split("\n")[1].split(",")
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var regex=/^\^(\d+)(.+)$/
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var m=params[1].match(regex)
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return {
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name: this.molecule,
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multiplicity:m[1],
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symmetry:m[2],
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method:this.geometry,
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geometry:ChemDoodle.readXYZ(molstr)
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}
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})
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}
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CopyExcitationsTypeFrom(data) {
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var exc_strings = data.excitations.map( e => [e, JSON.stringify(e.initial), JSON.stringify(e.final) ] )
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for (const ex of this.excitations) {
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const exi = JSON.stringify(ex.initial)
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const exf = JSON.stringify(ex.final)
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const ex2 = exc_strings.find((e) => {
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return (e[1]=== exi) && (e[2]=== exf)
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})
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if (ex2 !== undefined) {
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if (DebugMode.Enabled) {
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const restflag=ex.type.Value & ex2[0].type.Value
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const result=restflag==ex.type.Value
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console.assert(result, "Excitation type error", data.molecule, ex, ex2[0], this.sourceFile)
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}
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ex.type = ex2[0].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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// const maxAge= (DebugMode.Enabled,0,600)
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// var str = await getTextFromFileUrlAsync(file,{"Cache-Control":`max-age=${maxAge}`})
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var str = getTextFromFileUrl(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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static load(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 = getTextFromFileUrl(file)
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break;
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case File.name:
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var str = (async () => await getTextFromUploadedFileAsync(file))().then(x=>x)
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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 "set":
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this.set = exSet.fromString(value)
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break;
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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 type = ((vals.length >= 7) ? vals[6] : null)
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if (type === "_") {
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type = null
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}
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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 >= 8) ? new stringNumber(vals[7]) : NaN)
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var T1 = ((vals.length >= 9) ? new stringNumber(vals[8]) : NaN)
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var oscilatorForces = ((vals.length >= 10) ? new stringNumber(vals[9]) : NaN)
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var isUnsafe = ((vals.length >= 11) ? vals[10] === 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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if (DebugMode.Enabled) {
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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.set!== null && dat.set !== "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, "should be unsafe", dat, ex)
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}
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for (const ex of dat.excitations) {
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console.assert(JSON.stringify(ex.initial)!==JSON.stringify(ex.final),"Final must be different to initial", dat, ex)
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}
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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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