Adjust GUI to accept chemical formulae with floats instead of intigers

TrimSPlib.js

@@ -1,11 +1,14 @@
-// This file contains function that are Javascript generic
+// This file contains function that are generic Javascript for TrimSP
 
 function parse_formula (mf) {
     // This function takes a chemical formula and returns
     // an object that contains the atoms and their number
+
+    // replace all types of brackets into ()
     var mf = mf.replace(/\[/g,"(").replace(/\]/g,")").replace(/\{/g,"(").replace(/\}/g,")").replace(/\s+/g,"");
     if(/^\d+/.test(mf)) throw new SyntaxError("Molecular formula should not start with a number!");
     var mol = {};
+    // go into brackets and collect info
     while(mf.includes("(")){
 	var x = mf.lastIndexOf("(");
 	var y = mf.indexOf(")", mf.lastIndexOf("("));
@@ -14,7 +17,7 @@ function parse_formula (mf) {
 	var c = mf.substr(y+1);
 	c = /^\d+/.exec(c);
 	c=(c!= null)?Number(c[0]):1;
-			
+	// recursive
 	var a = this.parse_formula(z);
 	var b = "";
 	for(var k in a){
@@ -24,13 +27,19 @@ function parse_formula (mf) {
     }
 		
     var m = "";
-    while(m = /([A-Z]{1}[a-z]{0,}[0-9]{0,})/.exec(mf)){
+    // Separate element name from stoichiometry
+    //    while(m = /([A-Z]{1}[a-z]{0,}[0-9]{0,})/.exec(mf)){
+    while(m = /([A-Z]{1}[a-z]{0,}[0-9]{0,}\.?[0-9]{0,})/.exec(mf)){
+	// Element
 	var m1 = /([A-Z]{1,}[a-z]{0,})/.exec(m[0]);
-	var m2 = /\d+/.exec(m[0]);
+	// Stoichiometry
+	//var m2 = /\d+/.exec(m[0]);
+	var m2 = /\d+\.?\d{0,}/.exec(m[0]);
 	if(typeof mol[m1[0]] == 'undefined') mol[m1[0]]=(m2!=null)?Number(m2[0]):1;
 	else mol[m1[0]] += (m2!=null)?Number(m2[0]):1;
 	mf = mf.replace(m[0], "");
     }
+    console.log("mol=",mol);
     return mol;
 }
 
@@ -836,14 +845,15 @@ function CreateInpFile(All) {
 		Check++;
 	    }  
 	}
-	if (Comp == "") {Check++;}
+	if (Comp == "" || typeof Comp == 'undefined') {Check++;}
 	// Write composition to results file header
 
 	// Densities of layers
 	let Lrho="layer"+i+"rho";
 	let rho = 1*All[Lrho];
+	
 	// How to do this? All[Lrho]=sprintf("%6.2f",rho);
-	if (rho=="") {Check++;}
+	if (rho=="") {Check++;console.log("rho",rho);}
 	
 	// Thickness of layers
 	let Ld ="L"+i+"d";
@@ -853,8 +863,8 @@ function CreateInpFile(All) {
 	
 	// Sanity check, is the layer supposed to have value? are they all there?
 	if (Check!=0) {
-	    ErrMsg="Error: Bad chemical formula in Layer $i.\nPleach check!\n";
-	    //print STDERR $ErrMsg;
+	    ErrMsg="Error: Bad chemical formula in Layer $i.\nPlease check!\n";
+	    console.log($ErrMsg);
 	    return ErrMsg;
 	}
 	
@@ -866,6 +876,7 @@ function CreateInpFile(All) {
 	    Sum=Sum+LElComp[key];
 	}
 	if (Sum==0) {Sum=1;}
+	console.log("Sum=",Sum);
 	
 	let Els = Object.keys(LElComp);
 	

fortran/trimspNL.F

@@ -394,6 +394,7 @@ C     This part reads the input file (new format)
          OPEN(UNIT=99,file=errnam,STATUS='replace')
          OPEN(UNIT=11,file=innam,STATUS='unknown',ERR=1359)
 C     First line: properties of projectile
+C     Ordered as: Z, mass number (amu), imp. energy, dist. of imp. energy, angle, dist. angles,   
          READ(11,*) Z1,M1,E0,Esig,ALPHA,ALPHASIG,EF,ESB,SHEATH,ERC
 C     Second line: simulation related parameters
 C     Ordered as: Number of particles, seed, seed, seed, initial depth, RD, depth increment, CA, KK0, KDEE1,KDEE2,IPOT
@@ -406,13 +407,13 @@ C     Third line: Number of layers
 C     Here we read the NLayers structure
          DO I=1,NLayers
 C     Thickness (DX), density (RHO), and correction factor (CK, it is
-C     always 1.0??)  Atomic numbers
+C     always 1.0??)
             READ(11,*) DX(I),RHO(I),CK(I)
 C     Atomic numbers
             READ(11,*) ZT(I,1),ZT(I,2),ZT(I,3),ZT(I,4),ZT(I,5)
 C     Mass numbers (amu)
             READ(11,*) MT(I,1),MT(I,2),MT(I,3),MT(I,4),MT(I,5)
-C     Concentration
+C     Concentration (stoichiometry)
             READ(11,*) CO(I,1),CO(I,2),CO(I,3),CO(I,4),CO(I,5)
 C     Surface binding energy
             READ(11,*) SBE(I,1),SBE(I,2),SBE(I,3),SBE(I,4),SBE(I,5)