Use a new format to separate data

content/_index.html

@@ -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")
+        window.Cite = require('citation-js');
-        getDataFilesName().forEach(function(element) {
+        window.dats=await loadAllData()
-          op=document.createElement("option");
+        window.data=new CombinedData()
-          op.value=element;
+        molecules=new Set(Object.values(window.dats).flat().map((d)=>d.molecule))
-          op.innerText=element.split('.')[0];
+        molecules.forEach(el=>{
-          fsel.appendChild(op);
+          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) {
+      async function reload() {
-        const Cite = require('citation-js');
-        // Start an async task to get publi data
-        let publiPromise = Cite.async(dat.doi.string)
         const LatexInline=['\\(','\\)']
         var par=document.getElementById("data_par")
         par.innerHTML='';
         var md=[];
         var els=[];
-        md.push(["Molecule",dat.molecule]);
+        var customRenderingProp=["excitations"]
-        md.push(["Comment",dat.comment])
+        for (const key of Object.keys(window.data)) {
-        var dict = {
+          if (window.data[key]!=null){
-          "Ground state": dat.GS,
+            md.push(key)
-          "Excited states": dat.ES,
+            for (const prop of Object.keys(window.data[key])) {
-        };
+              if(!(customRenderingProp.includes(prop)))
-        for (var key in dict){
+                md.push([prop,window.data[key][prop]])
-          md.push(key)
+            }
-          md.push(["Code",dict[key].code])
+            md.push(window.data[key].DOI)
-          md.push(["Method",dict[key].method])
+          }
-          md.push(["Geometry",dict[key].geometry])
         }
-        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"){
+          switch (trueTypeOf(element)) {
-            node= document.createElement("h2");
+            case "string":
-            node.innerText=element;
+              node= document.createElement("h2");
-          } else {
+              node.innerText=element;   
-            node = document.createElement("div");
+              break;
-            node.innerText= element[0]+': '+element[1]; 
+            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++) {
+        for (i = 0; i < window.data.excitations.length; i++) {
-          var ext=dat.excitations[i];
+          var ext=window.data.excitations[i];
-          var exexp=expdat.excitations[i]
+          var exexp=expAbsData.excitations[i]
-          plotdat[0].x.push(ext.end.toString())
+          plotdat[0].x.push(ext.final.toString())
-          plotdat[0].y.push(ext.Eabs-exexp.Eabs)
+          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>
-
+    <div>
-    <label>Select a data file name<br/>
+    <label>Select a molecule<br/>
-      <select id="fileSelect" onchange="onValueChange(event)">
+      <select id="select_mol" onchange="select_mol_onchange(event)">
-        <option value="" disabled=true selected=true>Select a file</option>
+        <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>

layouts/shortcodes/getDataFilesName.html

@@ -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 }})

static/data/abs/water_aug-cc-pVDZ.dat

@@ -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

static/data/abs/water_exp.dat

@@ -1,16 +1,13 @@
-# Molecule   : Water
+# Molecule : Water
-# Comment    : Water experimental
+# Comment  : Absorption energies of the water molecule from experimental datas
-# GS_code    : experimental
+# code     : experimental
-# GS_method  : experimental
+# method   : experimental
-# GS_geom    : experimental
+# geom     : experimental
-# ES_code    : experimental
+# DOI      : 10.1021/acs.jctc.8b00406
-# ES_method  : experimental
-# ES_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 

static/data/fluo/water_aug-cc-pVQZ_CCSD.dat

@@ -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   

static/data/zpe/water_6-31pGs_B3LYP.dat

@@ -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

static/scripts/data.js

@@ -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){
+class excitationBase{
-    this.start=start;
+  constructor(initial,final){
-    this.end=end;
+    this.initial=initial;
-    this.Eabs=Eabs;
+    this.final=final
-    this.Efluo=Efluo;
+  }
-    this.EZPE=EZPE;
+}
+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.molecule=''
-    this.method=null;
+    this.comment=null
-  }
+    this.code=null
-}
+    this.method=null
-class StateCalcParams extends CalcParams {
+    this.excitations=[]
-  constructor(){
+    this.DOI=null
-    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=[];
   }
   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 ${this.name}()`)
     function readmeta(line){
       // get key value
-      var match=line.match(meta);
+      var match=line.match(meta)
       // normalize key to lower
-      var key=match[1].toLowerCase();
+      var key=match[1].toLowerCase()
       //if data has value
       if(match.length==3 && match[2]) {
-        var val=match[2];
+        var val=match[2]
-        switch(key) {
+        eval(String.raw`${classname}.readmetaPair(key,val,dat)`)
-          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;
-        }
       }
     }
     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
+  };
+}

static/scripts/loadAllData.js

@@ -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;
+}

static/scripts/trueTypeOf.js

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