class excitationTypes { static get Valence() { return new excitationType(1, new description("Valence")) } static get Rydberg() { return new excitationType(1 << 1, new description("Rydberg")) } static get PiPis() { return new excitationType(1 << 2, new description(String.raw`\pi \rightarrow \pi^\star`, true)) } static get nPis() { return new excitationType(1 << 3, new description(String.raw`n \rightarrow \pi^\star`, true)) } static get Single() { return new excitationType(1 << 4, new description("Single")) } static get Double() { return new excitationType(1 << 5, new description("Double")) } static get SingletSinglet() { return new excitationType(1 << 6, new description(String.raw`\mathrm{Singlet} \rightarrow \mathrm{Singlet}`, true)) } static get SingletTriplet() { return new excitationType(1 << 7, new description(String.raw`\mathrm{Singlet} \rightarrow \mathrm{Triplet}`, true)) } static get DoubletDoublet() { return new excitationType(1 << 8, new description(String.raw`\mathrm{Doublet} \rightarrow \mathrm{Doublet}`, true)) } // Max bit shifts is 31 because int are int32 So 1 << 31 are -2147483648 static get Others() { return new excitationType(1 << 31, new description("Others")) } static get All() { return EnumUltils.getAll(this, excitationType) } static GetFlags(value) { return EnumUltils.GetFlags(value, this, excitationType) } } class EnumUltils { static getAll(enumClass, valueType) { var lst = [] for (const prop of Object.getOwnPropertyNames(enumClass)) { if (prop != "All") { const value = enumClass[prop] if (trueTypeOf(value) == valueType.name) { lst.push([prop, value]) } } } return lst } static GetFlags(value, enumClass, valueType) { return this.getAll(enumClass, valueType).filter(x => value & x[1]) } } class description { constructor(string, isLaTeX = false) { this.string = string this.isLaTeX = isLaTeX } } class DescribedValueBase { constructor(value, description) { this.Value = value; this.description = description } valueOf() { return this.Value; } } class excitationType extends DescribedValueBase { } class VertExcitationKind extends DescribedValueBase { } class code { constructor(name, version) { this.name = name; this.version = version; }; toString() { var str = this.name; if (this.version) { str = str + ' (' + this.version + ')'; } return str; } static fromString(str) { var vals = str.split(",") if (vals.length >= 2) { return new code(vals[0], vals[1]); } else { return new code(vals[0], null); } } } class method { constructor(name, basis = null) { this.name = name; this.basis = basis; } static fromString(str) { var vals = str.split(",") if (vals.length == 2) { return new method(vals[0], vals[1]); } else { return new method(vals[0], null) } } toString(separator = "/") { var str = this.name; if (this.basis) { str = str + separator + this.basis; } return str; } get isTBE() { return /^TBE/.test(this.name) } } class state { constructor(number, multiplicity, symmetry) { this.number = number; this.multiplicity = multiplicity; this.symmetry = symmetry; }; toString() { var str = this.number + ' ^' + this.multiplicity + this.symmetry; return str; }; toLaTeX() { var tex = String.raw`${this.number}\:^{${this.multiplicity}}\mathrm{${this.symmetry}}`; return tex; }; } class exSet{ constructor(name,index) { this.name = name this.index = index } static fromString(str) { var vals = str.split(",") var myset if (vals.length >= 2) { return new exSet(vals[0], parseInt(vals[1],10)); } else { return new exSet(vals[0], 0); } } async getDOIAsync() { let db = await indexDB.loadAsync() if (db.sets.has(this.name)) { return db.sets.get(this.name)[this.index] } } toString() { return `${this.name},${this.index}` } isSameSet(set) { return this.name == set.name } async isSameArticleAsync(set) { if (this.name===set.name && this.index===set.index) { return true } else { return await this.getDOIAsync() === await set.getDOIAsync() } } } class excitationBase { constructor(initial, final, type = '', T1 = null) { this.initial = initial; this.final = final this.type = new excitationType(0, new description(type, true)) if (type) { const tys = type.split(";") const arrow = String.raw`\rightarrow` for (const ty of tys) { if (ty.includes(arrow)) { const [initialt, finalt] = ty.split(arrow, 2) const initialts = initialt.split(",").map(x => x.trim()) const finalts = finalt.split(",").map(x => x.trim()) if (initialts.length == 2 && finalts.length == 2) { this.type.Value = this.type | excitationTypes.Double } else if (initialts.length == 1 && finalts.length == 1) { this.type.Value = this.type | excitationTypes.Single } if (initialts.includes("n") && finalts.includes(String.raw`\pi^\star`)) { this.type.Value = this.type | excitationTypes.nPis } else if (initialts.includes(String.raw`\pi`) && finalts.includes(String.raw`\pi^\star`)) { this.type.Value = this.type | excitationTypes.PiPis } } else if (ty.includes(String.raw`\mathrm{R}`)) { this.type.Value = this.type | excitationTypes.Rydberg } else if (ty.includes(String.raw`\mathrm{V}`)) { this.type.Value = this.type | excitationTypes.Valence } else if (ty.toLowerCase()===excitationTypes.Double.description.string.toLowerCase()){ this.type.Value = this.type | excitationTypes.Double } } } var m = new Map([ [JSON.stringify([1, 1]), excitationTypes.SingletSinglet], [JSON.stringify([2, 2]), excitationTypes.DoubletDoublet], [JSON.stringify([1, 3]), excitationTypes.SingletTriplet], ]) const marray = JSON.stringify([initial.multiplicity, final.multiplicity]) if (m.has(marray)) { this.type.Value = this.type.Value | m.get(marray) } if (this.type.Value == 0) { this.type.Value = excitationTypes.Others.Value; } this.T1 = T1 } } class excitationValue extends excitationBase { constructor(initial, final, type, value, oscilatorForces = null, T1 = null, isUnsafe = false) { super(initial, final, type, T1) this.value = value this.oscilatorForces = oscilatorForces this.isUnsafe = isUnsafe } } class dataFileBase { constructor() { this.molecule = '' this.comment = "" this.code = null this.method = null this.excitations = [] this.set = null this.sourceFile = null } static _GetMetaRexEx() { //metadata RegExp (start with #; maybe somme spaces; : ; maybe somme space; datas) return /^#\s*([A-Za-z_]+)\s*:\s*(.*)$/; } async getGeometryAsync(state = null) { var text = await getTextFromFileUrlAsync(`/data/structures/${this.set.name.replace("#", "")}/${this.molecule.toLowerCase()}.xyz`) var lines = text.split("\n") var indexes = lines.findAllIndexes((line) => { return line.match(/^\d+$/) }) indexes.push(lines.length) var molsstr = [] for (let i = 0; i < indexes.length - 1; i++) { molsstr.push(lines.slice(indexes[i], indexes[i + 1]).join('\n')) } molsstr.filter((molstr) => { var params = molstr.split("\n")[1].split(",") return (state === null || params[0] === `^${state.multiplicity}${state.symmetry}`) && params[1] == `${this.method.name},${this.method.basis}` }) return molsstr.map((molstr) => { var params = molstr.split("\n")[1].split(",") var regex=/^\^(\d+)(.+)$/ var m=params[1].match(regex) return { name: this.molecule, multiplicity:m[1], symmetry:m[2], method:this.geometry, geometry:ChemDoodle.readXYZ(molstr) } }) } CopyExcitationsTypeFrom(data) { for (const ex of this.excitations) { const ex2 = data.excitations.find((e) => { return (JSON.stringify(e.initial) === JSON.stringify(ex.initial)) && (JSON.stringify(e.final) === JSON.stringify(ex.final)) }) if (ex2 !== undefined) { if (DebugMode.Enabled) { const restflag=ex.type.Value & ex2.type.Value const result=restflag==ex.type.Value console.assert(result, "Excitation type error", data.molecule, ex, ex2, this.sourceFile) } ex.type = ex2.type } } } static async loadAsync(file, kind = undefined) { switch (trueTypeOf(file)) { case String.name: file = getFullDataPath(file) var str = await getTextFromFileUrlAsync(file) break; case File.name: var str = await getTextFromUploadedFileAsync(file) break } var dat = this.loadString(str, kind); dat.sourceFile = new websiteFile(file) return dat } _OnReadMetaPair(key, value) { switch (key) { case "molecule": this.molecule = value break; case "comment": this.comment = value break; case "code": this.code = code.fromString(value) break; case "method": this.method = method.fromString(value) break; case "set": this.set = exSet.fromString(value) break; } } _OnReadRow(line) { var vals = line.match(/\([^\)]+\)|\S+/g) var start = new state(parseInt(vals[0], 10), parseInt(vals[1], 10), vals[2]); var end = new state(parseInt(vals[3], 10), parseInt(vals[4], 10), vals[5]); var type = ((vals.length >= 7) ? vals[6] : null) if (type === "_") { type = null } if (type) { const m = type.match(/^\(([^\)]*)\)$/) if (m) { type = m[1] } } var val = ((vals.length >= 8) ? new stringNumber(vals[7]) : NaN) var T1 = ((vals.length >= 9) ? new stringNumber(vals[8]) : NaN) var oscilatorForces = ((vals.length >= 10) ? new stringNumber(vals[9]) : NaN) var isUnsafe = ((vals.length >= 11) ? vals[10] === true.toString() : false) var ex = new excitationValue(start, end, type, val, oscilatorForces, T1, isUnsafe); if (this.VertExcitationKind) { ex.VertExcitationKind = this.VertExcitationKind } return ex; }; _OnReadMeta(line) { // get key value var match = line.match(dataFileBase._GetMetaRexEx()) // normalize key to lower var key = match[1].toLowerCase() //if data has value if (match.length == 3 && match[2]) { var val = match[2] this._OnReadMetaPair(key, val) } } static loadString(text, kind = null) { // for each line with metadata var ismetaArea = true; var dat = new VertDataFile() for (var line of text.split("\n")) { //if it's not empty line line = line.trim(); if (line) { //if # may be metadata or comment if (line.charAt(0) == "#") { //if it's metadata if (ismetaArea && dataFileBase._GetMetaRexEx().test(line)) { dat._OnReadMeta(line); } } else { //else its row ismetaArea = false; dat.excitations.push(dat._OnReadRow(line, kind)); } } } if (DebugMode.Enabled) { var stfy = dat.excitations.map(e => JSON.stringify([e.initial, e.final])) var double = [] stfy.forEach(function (element, i) { // Find if there is a duplicate or not if (stfy.indexOf(element, i + 1) >= 0) { // Find if the element is already in the result array or not if (double.indexOf(element) === -1) { double.push(dat.excitations[i]) } } }); console.assert(double.length === 0, "Double found", double, dat.molecule, dat.method.toString()) if (dat.set!== null && dat.set !== "10.1021/acs.jctc.8b01205") { for (const ex of dat.excitations) { console.assert(Number.isNaN(ex.T1.valueOf()) | ex.T1 > 50 | ex.isUnsafe == true, "should be unsafe", dat, ex) } for (const ex of dat.excitations) { console.assert(JSON.stringify(ex.initial)!==JSON.stringify(ex.final),"Final must be different to initial", dat, ex) } } } return dat } } class VertExcitationKinds { static get Absorbtion() { return new VertExcitationKind(1, new description("Absorption")) } static get Fluorescence() { return new VertExcitationKind(1 << 1, new description("Fluorescence")) } static get All() { return EnumUltils.getAll(this, VertExcitationKind) } static GetFlags(value) { return EnumUltils.GetFlags(value, this, VertExcitationKind) } } class VertDataFile extends dataFileBase { constructor(VertExcitationKind) { super() this.VertExcitationKind = VertExcitationKind this.geometry = null } _OnReadMetaPair(key, value) { if (key == "geom") { this.geometry = method.fromString(value) } else { super._OnReadMetaPair(key, value) } } _OnReadRow(line, kind) { var ex = super._OnReadRow(line) ex.VertExcitationKind = kind return ex } }