Apply titou format

content/_index.html

@@ -38,35 +38,50 @@ draft: false
         par.innerHTML='';
         var md=[];
         var els=[];
-        md.push(["Title",dat.title]);
+        md.push(["Molecule",dat.molecule]);
-        md.push(["Code",dat.code]);
+        md.push(["Comment",dat.comment])
-        md.push(["ZPE geometry",dat.ZPE])
+        var dict = {
-        md.push(["Method",dat.method])
+          "Ground state": dat.GS,
-        md.push(["Basis",dat.basis]);
+          "exited 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])
+        }
+        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")
         md.forEach(function(element){
-          var node = document.createElement("div");
+          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]; 
-          par.appendChild(node);
+          }
+          div.appendChild(node);
+        });
+        var t=document.getElementById("ex_table")
+        dat.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]}`)
+          var e=[el.Eabs,el.Efluo,el.EZPE,el.Ezz]
+          e.forEach((val)=>rowd.push(val.toFixed(2)))
+          rowd.forEach((d)=>{
+            td=document.createElement("td")
+            td.innerText=d
+            row.appendChild(td)
+          })
+          t.appendChild(row)
         });
-        var exDiv= document.createElement("div");
-        par.appendChild(exDiv);
-        var exTitle = document.createElement("h2");
-        exTitle.innerText= "Excitations";
-        exDiv.appendChild(exTitle);
-        var exPar= document.createElement("p");
-        exDiv.appendChild(exPar);
-        await dat.excitations.reduce(async (promise,el)=> {
-          await promise;
-          var node = document.createElement("div");
-          node.innerHTML= String.raw`${LatexInline[0]} ${el.start.toLaTeX()} \rightarrow ${el.end.toLaTeX()}${LatexInline[1]}, ${LatexInline[0]}${el.Eabs.toPrecision(3)}\:\mathrm{eV}${LatexInline[1]}`;
-          node.hidden=true
-          exPar.appendChild(node);
         await MathJax.typesetPromise();
-          node.hidden=false;
+        document.getElementById("ex_div").hidden=false
-        });
-        
-        
         var lnkdoi = document.createElement("a");
         // Wait for the value of publi when required
         let publi=await publiPromise;
@@ -93,5 +108,19 @@ draft: false
       </select>
     </label><br/>
     <h1>Data</h1>
-    <p id=data_par></p>
+    <p id=data_par>
+      <div id="meta_div"></div>
+      <div id="ex_div" hidden=true>
+      <h2>exitation</h2>
+      <table id="ex_table">
+        <tr>
+          <th>Transition</th>
+          <th>\(E_{abs}\)</th>
+          <th>\(E_{fluo}\)</th>
+          <th>\(\Delta E_{ZPE}\)</th>
+          <th>\(E_{00}\)</th>
+        </tr>
+      </table>
+    </div>
+    </p>
     <a target="_blank" id='lnk_file'>Go to file</a>

static/data/water_aug-cc-pVDZ_CCpVQZ_CC3.dat

@@ -0,0 +1,21 @@
+# Molecule   : Water
+# Comment    : 0-0 energies of the water molecule
+# GS_code    : Dalton
+# GS_method  : CC3,aug-cc-pVDZ
+# GS_geom    : CC3,aug-cc-pVTZ 
+# ES_code    : Molpro
+# ES_method  : CCSD,aug-cc-pVQZ
+# ES_geom    : CC2,cc-pVDZ 
+# ZPE_code   : Gaussian16
+# ZPE_method : B3LYP,6-31+G*
+# DOI        : 10.1021/acs.jctc.8b00406
+
+# Initial state            Final state               Energies (eV)
+#######################  #######################   #######################
+# Spin  Number  Symm       Spin  Number  Symm        E_abs  E_fluo  E_zpe
+  1     1       A_1        1     1       B_1         7.51   0.23    0.01
+  1     1       A_1        1     1       A_2         9.29   4.23    -0.02
+  1     1       A_1        1     2       A_1         9.92   8.38    -0.03
+  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/scripts/data.js

@@ -10,12 +10,24 @@ class code {
     }
     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){
     this.name=name;
     this.basis=basis;
   }
+  static fromString(str) {
+    var vals=str.split(",")            
+    return new method(vals[0],vals[1]);
+  }
   toString() { 
     var str=this.name;
     if (this.name) {
@@ -24,22 +36,12 @@ class method {
     return str;
   }
 }
-class geometry {
-  constructor(symetry,method){
-    this.symetry=method
-    this.symetry=method
-  }
-  toString(){
-    return String.raw `${this.symetry}-${this.method}`
-  }
-}
 
 class state{
-  constructor(number,multiplicity,symetry,geometry){
+  constructor(number,multiplicity,symetry){
     this.number=number;
     this.multiplicity=multiplicity;
     this.symetry=symetry;
-    this.geometry=geometry
   };
   toString() { 
     var str=this.number+ ' ^'+this.multiplicity+this.symetry;
@@ -62,22 +64,41 @@ class doi{
   };
 }
 class excitation{
-  constructor(start,end,Eabs){
+  constructor(start,end,Eabs,Efluo,EZPE){
     this.start=start;
     this.end=end;
     this.Eabs=Eabs;
+    this.Efluo=Efluo;
+    this.EZPE=EZPE;
+  }
+  get Ezz() {
+     return this.Eabs-this.Efluo+this.EZPE
   }
   toString() {
     return this.start+ ', ' + this.end +', '+ this.Eabs.toPrecision(3);
   }
 }
 
+class CalcParams {
+  constructor(){
+    this.code=null;
+    this.method=null;
+  }
+}
+class StateCalcParams extends CalcParams {
+  constructor(){
+    super()
+    this.geometry;
+  }
+}
+
 class data {
   constructor(){
-    this.title='';
+    this.molecule='';
-    this.code=null;
+    this.comment;
-    this.ZPE=null;
+    this.GS=new StateCalcParams();
-    this.method=null;
+    this.ES=new StateCalcParams();
+    this.ZPE=new CalcParams();
     this.doi=null;
     this.excitations=[];
   }
@@ -88,7 +109,7 @@ class data {
     // 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*(.*)$/;
+    var meta=/^#\s*([A-Za-z_]+)\s*:\s*(.*)$/;
     var dat=new data();
     function readmeta(line){
       // get key value
@@ -99,24 +120,35 @@ class data {
       if(match.length==3 && match[2]) {
         var val=match[2];
         switch(key) {
-          case "title":
+          case "molecule":
-            dat.title=val;
+            dat.molecule=val
             break;
-          case "code":
+          case "comment":
-            var vals=val.split(",")
+            dat.comment=val
-            if(vals.length>=2){
-              dat.code=new code(vals[0],vals[1]);
-            } else {
-              dat.code=new code(vals[0],null);
-            }
             break;
-          case "method":
+          case "gs_code":
-            var vals=val.split(",")            
+            dat.GS.code=code.fromString(val)
-            dat.method=new method(vals[0],vals[1]);
             break;
-          case "zpe":
+          case "gs_method":
-            var vals=val.split(",")            
+            dat.GS.method=method.fromString(val)
-            dat.ZPE=new method(vals[0],vals[1]);
+            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);
@@ -126,11 +158,12 @@ class data {
     }
     function readrow(line){
       var vals=line.split(/\s+/);
-      var geom=vals[3].split(",")
+      while (vals.length<8){
-      var start=new state(parseInt(vals[0],10),parseInt(vals[1],10),vals[2], new geometry(geom[0],new method(geom[1],geom[2])));
+        vals.push(null);
-      geom=vals[7].split(",")
+      }
-      var end=new state(parseInt(vals[4],10),vals[5],vals[6], new geometry(geom[0],new method(geom[1],geom[2])));
+      var start=new state(parseInt(vals[0],10),parseInt(vals[1],10),vals[2]);
-      var ex=new excitation(start,end,parseFloat(vals[8],10));
+      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));
       dat.excitations.push(ex);
     };