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Use a new format to separate data

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This commit is contained in:
Mickaël Véril 2019-09-26 09:32:03 +02:00
parent b50de34cb6
commit cff3f653c7
9 changed files with 385 additions and 145 deletions
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183
content/_index.html
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@ -4,8 +4,10 @@ date: 2019-08-29 09:00
draft: false
---
<script src="/scripts/data.js" type="text/javascript"></script>
<script src="/scripts/loadAllData.js" type="text/javascript"></script>
<script src="/scripts/getFullDataPath.js" type="text/javascript"></script>
<script src="/scripts/getTextFromFile.js" type="text/javascript"></script>
<script src="/scripts/trueTypeOf.js" type="text/javascript"></script>
<script src="https://cdn.rawgit.com/larsgw/citation.js/archive/citation.js/citation-0.4.0-9.js" type="text/javascript"></script>
<script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script>
<script type="text/javascript" id="MathJax-script" async
@ -14,15 +16,58 @@ draft: false
<script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
{{< getDataFilesName >}}
<script>
window.onload=function()
window.onload=async function()
{
fsel=document.getElementById("fileSelect")
getDataFilesName().forEach(function(element) {
op=document.createElement("option");
op.value=element;
op.innerText=element.split('.')[0];
fsel.appendChild(op);
});
window.Cite = require('citation-js');
window.dats=await loadAllData()
window.data=new CombinedData()
molecules=new Set(Object.values(window.dats).flat().map((d)=>d.molecule))
molecules.forEach(el=>{
op=document.createElement("option")
op.value=el
op.innerText=el
document.getElementById("select_mol").appendChild(op)
})
}
function select_mol_onchange(event){
update_mol(event.target.value)
}
function select_abs_onchange(event){
update_abs(window.dats["abs"][event.target.value])
}
function select_fluo_onchange(event){
update_fluo(window.dats["fluo"][event.target.value])
}
function select_ZPE_onchange(event){
update_ZPE(window.dats["ZPE"][event.target.value])
}
async function update_mol(molecule){
Object.keys(window.dats).forEach((key)=>{
var s=document.getElementById(String.raw`select_${key}`)
while (s.options[s.options.length-1].value!= "") {
s.options.remove(s.options[s.options.length-1])
}
window.dats[key].forEach(val=>{
if(val.molecule==molecule){
var op=document.createElement("option")
op.value=window.dats[key].indexOf(val)
op.innerText=val.method.toString()
s.appendChild(op)
}
})
})
}
async function update_abs(abs){
window.data.Abs=abs
reload()
}
async function update_fluo(fluo){
window.data.Fluo=fluo
reload()
}
async function update_ZPE(ZPE){
window.data.ZPE=ZPE
reload()
}
async function update_file(file) {
var lnk_file=document.getElementById('lnk_file');
@ -30,50 +75,61 @@ draft: false
dat= await data.loadAsync(file);
await applyData(dat);
}
async function applyData(dat) {
const Cite = require('citation-js');
// Start an async task to get publi data
let publiPromise = Cite.async(dat.doi.string)
async function reload() {
const LatexInline=['\\(','\\)']
var par=document.getElementById("data_par")
par.innerHTML='';
var md=[];
var els=[];
md.push(["Molecule",dat.molecule]);
md.push(["Comment",dat.comment])
var dict = {
"Ground state": dat.GS,
"Excited states": dat.ES,
};
for (var key in dict){
md.push(key)
md.push(["Code",dict[key].code])
md.push(["Method",dict[key].method])
md.push(["Geometry",dict[key].geometry])
var customRenderingProp=["excitations"]
for (const key of Object.keys(window.data)) {
if (window.data[key]!=null){
md.push(key)
for (const prop of Object.keys(window.data[key])) {
if(!(customRenderingProp.includes(prop)))
md.push([prop,window.data[key][prop]])
}
md.push(window.data[key].DOI)
}
}
md.push("ZPE")
md.push(["Code",dat.ZPE.code])
md.push(["Method",dat.ZPE.method])
md.push(["DOI",dat.doi]);
div=document.getElementById("meta_div")
div.innerHTML=""
md.forEach(function(element){
for (element of md) {
var node =null;
if(typeof element==="string"){
node= document.createElement("h2");
node.innerText=element;
} else {
node = document.createElement("div");
node.innerText= element[0]+': '+element[1];
switch (trueTypeOf(element)) {
case "string":
node= document.createElement("h2");
node.innerText=element;
break;
case "doi":
var doi=element
var publi=await Cite.async(element.string)
var output = publi.format('bibliography', {
format: 'html',
template: 'apa',
lang: 'en-US'
})
node=document.createElement("a")
node.innerHTML=output
node.target='_blank'
node.href=element.url
break
case "Array":
k=element[0]
v=element[1]
k=k.charAt(0).toUpperCase() + k.slice(1)
node = document.createElement("div");
node.innerText= k+': '+v;
break;
}
div.appendChild(node);
});
}
var tb=document.getElementById("ex_table_b");
tb.innerHTML=''
dat.excitations.forEach(el=> {
window.data.excitations.forEach(el=> {
var row=document.createElement("tr")
var rowd=[]
rowd.push(String.raw`${LatexInline[0]} ${el.start.toLaTeX()} \rightarrow ${el.end.toLaTeX()}${LatexInline[1]}`)
rowd.push(String.raw`${LatexInline[0]} ${el.initial.toLaTeX()} \rightarrow ${el.final.toLaTeX()}${LatexInline[1]}`)
var e=[el.Eabs,el.Efluo,el.EZPE,el.Eadia,el.Ezz]
e.forEach((val)=>rowd.push(val.toFixed(2)))
rowd.forEach((d)=>{
@ -90,30 +146,18 @@ draft: false
y: [],
type: 'bar'
}];
var expdat= await data.loadAsync("/"+dat.molecule.toLowerCase()+"_exp.dat")
var expAbsData= await AbsDataFile.loadAsync("/abs/"+window.data.Abs.molecule.toLowerCase()+"_exp.dat")
var i;
for (i = 0; i < dat.excitations.length; i++) {
var ext=dat.excitations[i];
var exexp=expdat.excitations[i]
plotdat[0].x.push(ext.end.toString())
plotdat[0].y.push(ext.Eabs-exexp.Eabs)
for (i = 0; i < window.data.excitations.length; i++) {
var ext=window.data.excitations[i];
var exexp=expAbsData.excitations[i]
plotdat[0].x.push(ext.final.toString())
plotdat[0].y.push(ext.Eabs-exexp.value)
}
await MathJax.typesetPromise();
var layout={title: "Absorption theory deviation"}
Plotly.newPlot('abs_plot', plotdat,layout);
document.getElementById("graph_div").hidden=false
var lnkdoi = document.createElement("a");
// Wait for the value of publi when required
let publi=await publiPromise;
let output = publi.format('bibliography', {
format: 'html',
template: 'apa',
lang: 'en-US'
})
lnkdoi.innerHTML=output
lnkdoi.setAttribute('target','_blank');
lnkdoi.setAttribute('href',dat.doi.url);
par.appendChild(lnkdoi);
}
</script>
<script>
@ -121,12 +165,31 @@ draft: false
update_file(e.target.value);
}
</script>
<label>Select a data file name<br/>
<select id="fileSelect" onchange="onValueChange(event)">
<option value="" disabled=true selected=true>Select a file</option>
<div>
<label>Select a molecule<br/>
<select id="select_mol" onchange="select_mol_onchange(event)">
<option value="" disabled=true selected=true>Select a molecule</option>
</select>
</label><br/>
</label>
</div>
<div>
<label>Select an absorption method<br/>
<select id="select_abs" onchange="select_abs_onchange(event)">
<option value="" disabled=true selected=true>Select an absorption method</option>
</select>
</label>
<label>Select a fluorescence method<br/>
<select id="select_fluo" onchange="select_fluo_onchange(event)">
<option value="" disabled=true selected=true>Select a fluorescence method</option>
</select>
</label>
<label>Select a ZPE method<br/>
<select id="select_ZPE" onchange="select_ZPE_onchange(event)">
<option value="" disabled=true selected=true>Select a ZPE method</option>
</select>
</label>
</div>
<h1>Data</h1>
<p id=data_par>
<div id="meta_div"></div>

30
layouts/shortcodes/getDataFilesName.html
View File

@ -1,11 +1,35 @@
<script>
{{- $files := readDir "/static/data" }}
{{- $files := readDir "/static/data/abs" }}
{{- $list := slice }}
function getDataFilesName(){
function getAbsFilesName(){
{{- range $files }}
{{- $ext := path.Ext .Name}}
{{- if eq $ext ".dat" }}
{{- $list = $list | append .Name }}
{{- $list = $list | append (print "abs/" .Name) }}
{{- end }}
{{- end }}
var files=JSON.parse({{ jsonify $list }})
return files
}
{{- $files := readDir "/static/data/fluo" }}
{{- $list := slice }}
function getFluoFilesName(){
{{- range $files }}
{{- $ext := path.Ext .Name}}
{{- if eq $ext ".dat" }}
{{- $list = $list | append (print "fluo/" .Name) }}
{{- end }}
{{- end }}
var files=JSON.parse({{ jsonify $list }})
return files
}
{{- $files := readDir "/static/data/zpe" }}
{{- $list := slice }}
function getZPEFilesName(){
{{- range $files }}
{{- $ext := path.Ext .Name}}
{{- if eq $ext ".dat" }}
{{- $list = $list | append (print "zpe/" .Name )}}
{{- end }}
{{- end }}
var files=JSON.parse({{ jsonify $list }})

16
static/data/abs/water_aug-cc-pVDZ.dat Normal file
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@ -0,0 +1,16 @@
# Molecule : Water
# Comment : Absorption energies of the water molecule
# code : Dalton
# method : CC3,aug-cc-pVDZ
# geom : CC3,aug-cc-pVTZ
# DOI : 10.1021/acs.jctc.8b00406
# Initial state Final state Energies (eV)
####################### ####################### ############
# Spin Number Symm Spin Number Symm E_abs
1 1 A_1 1 1 B_1 7.51
1 1 A_1 1 1 A_2 9.29
1 1 A_1 1 2 A_1 9.92
1 1 A_1 1 3 B_1 7.13
1 1 A_1 3 1 A_2 9.12
1 1 A_1 3 1 A_1 9.47

19
static/data/water_exp.dat → static/data/abs/water_exp.dat
View File

@ -1,16 +1,13 @@
# Molecule : Water
# Comment : Water experimental
# GS_code : experimental
# GS_method : experimental
# GS_geom : experimental
# ES_code : experimental
# ES_method : experimental
# ES_geom : experimental
# DOI : 10.1021/acs.jctc.8b00406
# Molecule : Water
# Comment : Absorption energies of the water molecule from experimental datas
# code : experimental
# method : experimental
# geom : experimental
# DOI : 10.1021/acs.jctc.8b00406
# Initial state Final state Energies (eV)
####################### ####################### #######################
# Spin Number Symm Spin Number Symm E_abs E_fluo E_zpe
####################### ####################### ###############
# Spin Number Symm Spin Number Symm E_abs
1 1 A_1 1 1 B_1 7.41
1 1 A_1 1 1 A_2 9.20
1 1 A_1 1 2 A_1 9.67

13
static/data/fluo/water_aug-cc-pVQZ_CCSD.dat Normal file
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@ -0,0 +1,13 @@
# Molecule : Water
# Comment : 0-0 energies of the water molecule
# code : Molpro
# method : CCSD,aug-cc-pVQZ
# geom : CC2,cc-pVDZ
# DOI : 10.1021/acs.jctc.8b00406
# Initial state Final state Energies (eV)
####################### ####################### #############
# Spin Number Symm Spin Number Symm E_fluo
1 1 A_1 1 1 B_1 0.23
1 1 A_1 1 1 A_2 4.23
1 1 A_1 1 2 A_1 8.38

14
static/data/zpe/water_6-31pGs_B3LYP.dat Normal file
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@ -0,0 +1,14 @@
# Molecule : Water
# Comment : 0-0 energies of the water molecule
# code : Gaussian16
# GS : CC3,aug-cc-pVTZ
# ES : CC2,cc-pVDZ
# method : B3LYP,6-31+G*
# DOI : 10.1021/acs.jctc.8b00406
# Initial state Final state Energies (eV)
####################### ####################### ###############
# Spin Number Symm Spin Number Symm E_zpe
1 1 A_1 1 1 B_1 0.01
1 1 A_1 1 1 A_2 -0.02
1 1 A_1 1 2 A_1 -0.03

235
static/scripts/data.js
View File

@ -26,7 +26,12 @@ class method {
}
static fromString(str) {
var vals=str.split(",")
return new method(vals[0],vals[1]);
if(vals.length==2){
return new method(vals[0],vals[1]);
}
else{
return new method(vals[0],null)
}
}
toString() {
var str=this.name;
@ -63,13 +68,26 @@ class doi{
return 'https://doi.org/'+this.string;
};
}
class excitation{
constructor(start,end,Eabs,Efluo,EZPE){
this.start=start;
this.end=end;
this.Eabs=Eabs;
this.Efluo=Efluo;
this.EZPE=EZPE;
class excitationBase{
constructor(initial,final){
this.initial=initial;
this.final=final
}
}
class excitationValue extends excitationBase{
constructor(initial,final,value){
super(initial,final)
this.value=value
}
}
class excitation extends excitationBase{
constructor(initial,final,Eabs,Efluo,EZPE){
super(initial,final)
this.Eabs=Eabs
this.Efluo=Efluo
this.EZPE=EZPE
}
get Eadia() {
return (this.Eabs+this.Efluo)/2
@ -82,81 +100,54 @@ class excitation{
}
}
class CalcParams {
class dataFileBase {
constructor(){
this.code=null;
this.method=null;
}
}
class StateCalcParams extends CalcParams {
constructor(){
super()
this.geometry;
}
}
class data {
constructor(){
this.molecule='';
this.comment;
this.GS=new StateCalcParams();
this.ES=new StateCalcParams();
this.ZPE=new CalcParams();
this.doi=null;
this.excitations=[];
this.molecule=''
this.comment=null
this.code=null
this.method=null
this.excitations=[]
this.DOI=null
}
static async loadAsync(file) {
return data.loadString(await getTextFromFileAsync(getFullDataPath(file)));
return this.loadString(await getTextFromFileAsync(getFullDataPath(file)));
}
static readmetaPair(key, value,dat){
switch(key) {
case "molecule":
dat.molecule=value
break;
case "comment":
dat.comment=value
break;
case "code":
dat.code=code.fromString(value)
break;
case "method":
dat.method=method.fromString(value)
break;
case "doi":
dat.DOI=new doi(value);
break;
default:
}
}
static loadString(text) {
// for each line with metadata
var ismetaArea=true;
//metadata RegExp (start with #; maybe somme spaces; : ; maybe somme space; datas)
var meta=/^#\s*([A-Za-z_]+)\s*:\s*(.*)$/;
var dat=new data();
var classname=this.name
var dat=eval(String.raw`new ${this.name}()`)
function readmeta(line){
// get key value
var match=line.match(meta);
var match=line.match(meta)
// normalize key to lower
var key=match[1].toLowerCase();
var key=match[1].toLowerCase()
//if data has value
if(match.length==3 && match[2]) {
var val=match[2];
switch(key) {
case "molecule":
dat.molecule=val
break;
case "comment":
dat.comment=val
break;
case "gs_code":
dat.GS.code=code.fromString(val)
break;
case "gs_method":
dat.GS.method=method.fromString(val)
break;
case "gs_geom":
dat.GS.geometry=method.fromString(val)
break;
case "es_code":
dat.ES.code=code.fromString(val)
break
case "es_method":
dat.ES.method=method.fromString(val)
break;
case "es_geom":
dat.ES.geometry=method.fromString(val)
break;
case "zpe_code":
dat.ZPE.code=code.fromString(val)
break
case "zpe_method":
dat.ZPE.method=method.fromString(val)
break;
case "doi":
dat.doi=new doi(val);
break;
}
var val=match[2]
eval(String.raw`${classname}.readmetaPair(key,val,dat)`)
}
}
function readrow(line){
@ -164,9 +155,10 @@ class data {
while (vals.length<8){
vals.push(null);
}
var start=new state(parseInt(vals[0],10),parseInt(vals[1],10),vals[2]);
var end=new state(parseInt(vals[3],10),vals[4],vals[5]);
var ex=new excitation(start,end,parseFloat(vals[6],10),parseFloat(vals[7],10),parseFloat(vals[8],10));
var ex= new excitationValue(start,end,parseFloat(vals[6],10));
dat.excitations.push(ex);
};
@ -189,3 +181,106 @@ class data {
return dat
}
}
class oneStateDataFile extends dataFileBase {
constructor(){
super()
this.geometry=null
}
static readmetaPair(key,value,dat)
{
if(key=="geom")
{
dat.geometry=method.fromString(value)
}
else{
dataFileBase.readmetaPair(key,value,dat)
}
}
}
class AbsDataFile extends oneStateDataFile {
}
class FluoDataFile extends oneStateDataFile {
}
class twoStateDataFileBase extends dataFileBase{
constructor(){
super()
this.GS=null
this.ES=null
}
static readmetaPair(key,value,dat){
switch(key) {
case "gs":
dat.GS=method.fromString(value)
break;
case "es":
dat.ES=method.fromString(value)
break;
default:
dataFileBase.readmetaPair(key,value,dat)
}
}
}
class ZPEDataFile extends twoStateDataFileBase {
}
class CombinedData{
constructor(){
this.Abs=null
this.Fluo=null
this.ZPE=null
}
get excitations() {
var exs=[]
var dic=new Map()
if(this.Abs!=null){
this.Abs.excitations.forEach((el)=>{
var key=JSON.stringify([el.initial,el.final])
if(!dic.has(key)){
dic.set(key,{})
}
dic.get(key)["abs"]=el.value
})
}
if(this.Fluo!=null){
this.Fluo.excitations.forEach((el)=>{
var key=JSON.stringify([el.initial,el.final])
if(!dic.has(key)){
dic.set(key,{})
}
dic.get(key)["fluo"]=el.value
})
}
if(this.ZPE!=null){
this.ZPE.excitations.forEach((el)=>{
var key=JSON.stringify([el.initial,el.final])
if(!dic.has(key)){
dic.set(key,{})
}
dic.get(key)["ZPE"]=el.value
})
}
dic.forEach((value,key)=>{
var eabs=NaN
var efluo=NaN
var eZPE=NaN
var mykey=JSON.parse(key)
mykey.forEach(el=>{
Reflect.setPrototypeOf(el,state.prototype)
})
if("abs" in value){
eabs=value["abs"]
}
if("fluo" in value){
efluo=value["fluo"]
}
if("ZPE" in value){
eZPE=value["ZPE"]
}
exs.push(new excitation(mykey[0],mykey[1],eabs,efluo,eZPE))
})
return exs
};
}

11
static/scripts/loadAllData.js Normal file
View File

@ -0,0 +1,11 @@
async function loadAllData() {
dic = {
abs: [],
fluo: [],
ZPE: []
};
dic.abs = await Promise.all(getAbsFilesName().map((f) => AbsDataFile.loadAsync(f)))
dic.fluo = await Promise.all(getFluoFilesName().map((f) => FluoDataFile.loadAsync(f)))
dic.ZPE = await Promise.all(getZPEFilesName().map((f) => ZPEDataFile.loadAsync(f)));
return dic;
}

7
static/scripts/trueTypeOf.js Normal file
View File

@ -0,0 +1,7 @@
function trueTypeOf(object){
result=typeof object
if(result==typeof({})) {
result= object.constructor.name
}
return result
}