mirror of
https://github.com/LCPQ/QUESTDB_website.git
synced 2024-12-26 14:23:42 +01:00
440 lines
14 KiB
JavaScript
440 lines
14 KiB
JavaScript
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 CT() { return new excitationType(1 << 2, new description("CT")) }
|
|
static get PiPis() { return new excitationType(1 << 3, new description(String.raw`\pi \rightarrow \pi^\star`, true)) }
|
|
static get nPis() { return new excitationType(1 << 4, new description(String.raw`n \rightarrow \pi^\star`, true)) }
|
|
static get Single() { return new excitationType(1 << 5, new description("Single")) }
|
|
static get Double() { return new excitationType(1 << 6, new description("Double")) }
|
|
static get SingletSinglet() { return new excitationType(1 << 7, new description(String.raw`\mathrm{Singlet} \rightarrow \mathrm{Singlet}`, true)) }
|
|
static get SingletTriplet() { return new excitationType(1 << 8, new description(String.raw`\mathrm{Singlet} \rightarrow \mathrm{Triplet}`, true)) }
|
|
static get DoubletDoublet() { return new excitationType(1 << 9, 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.includes(String.raw`\mathrm{CT}`)) {
|
|
this.type.Value = this.type | excitationTypes.CT
|
|
} 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;
|
|
}
|
|
else if (!(this.type & (excitationTypes.Single.Value | excitationTypes.Double.Value))){
|
|
this.type.Value += excitationTypes.Single.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 site_url = "/"+window.location.pathname.split('/')[1];
|
|
// var text = await getTextFromFileUrlAsync(`/data/structures/${this.set.name.replace("#", "")}/${this.molecule.toLowerCase()}.xyz`)
|
|
var text = getTextFromFileUrl(site_url+`/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) {
|
|
var exc_strings = data.excitations.map( e => [e, JSON.stringify(e.initial), JSON.stringify(e.final) ] )
|
|
for (const ex of this.excitations) {
|
|
const exi = JSON.stringify(ex.initial)
|
|
const exf = JSON.stringify(ex.final)
|
|
const ex2 = exc_strings.find((e) => {
|
|
return (e[1]=== exi) && (e[2]=== exf)
|
|
})
|
|
if (ex2 !== undefined) {
|
|
if (DebugMode.Enabled) {
|
|
const restflag=ex.type.Value & ex2[0].type.Value
|
|
const result=restflag==ex.type.Value
|
|
console.assert(result, "Excitation type error", data.molecule, ex, ex2[0], this.sourceFile)
|
|
}
|
|
ex.type = ex2[0].type
|
|
}
|
|
}
|
|
}
|
|
static async loadAsync(file, kind = undefined) {
|
|
switch (trueTypeOf(file)) {
|
|
case String.name:
|
|
file = getFullDataPath(file)
|
|
// const maxAge= (DebugMode.Enabled,0,600)
|
|
// var str = await getTextFromFileUrlAsync(file,{"Cache-Control":`max-age=${maxAge}`})
|
|
var str = getTextFromFileUrl(file)
|
|
break;
|
|
case File.name:
|
|
var str = await getTextFromUploadedFileAsync(file)
|
|
break
|
|
}
|
|
var dat = this.loadString(str, kind);
|
|
dat.sourceFile = new websiteFile(file)
|
|
return dat
|
|
}
|
|
static load(file, kind = undefined) {
|
|
switch (trueTypeOf(file)) {
|
|
case String.name:
|
|
file = getFullDataPath(file)
|
|
var str = getTextFromFileUrl(file)
|
|
break;
|
|
case File.name:
|
|
var str = (async () => await getTextFromUploadedFileAsync(file))().then(x=>x)
|
|
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
|
|
}
|
|
}
|