diff --git a/TrimSP.html b/TrimSP.html
index a24376c..53a8f1a 100644
--- a/TrimSP.html
+++ b/TrimSP.html
@@ -80,7 +80,7 @@
 		  <tr><td>Angle [deg]</td><td><input name="valAngle" id="valAngle" type="text" size="7" value="0"></td></tr>
 		  <tr><td>Angle sigma [deg]</td><td><input name="sigAngle" id="sigAngle" type="text" size="7" value="15"></td></tr>
 		  <tr><td>Random seed</td><td><input name="ranSeed" id="ranSeed" type="text" size="7" value="78741"></td></tr>
-		  <tr><td><button onclick="document.getElementById('btnPlots').click();tester();">Start</button></td><td></td></tr> 
+		  <tr><td><button onclick="startSim();">Start</button></td><td></td></tr> 
 		</table>
 	      </td>
 	    </tr>
@@ -313,7 +313,7 @@
 	    </tr>
 	    <tr>
 	      <td class="tooltip">
-		<input type="checkbox" id="flagICRU">
+		<input type="checkbox" id="flagICRU" checked>
 		<span class="tooltiptext">
 		  Force the TRIM.SP code to use stopping power
 		  parameters from the old ICRU tables. 
@@ -353,26 +353,16 @@
 	</div>
       </div>
   </td></tr>
-  <!tr>
-    <!td>
-      <!progress id="myBar" max=100 min=0><!/progress>
-    <!/td>
-  <!/tr>
+  <tr style="width: 100%;//visibility: hidden;">
+    <td>
+      <div class="w3-light-grey">
+	<div id="pBar" class="w3-container w3-green w3-center" style="width:0%">0%</div>
+      </div> 
+    </td>
+  </tr>
 </table>
 </body>
 <script>
-  document.getElementById("trimPath").value = remote.getGlobal('path');
-  
-  // Catch calls for open file
-  ipcRenderer.on('openFile', function(event, filename) {
-      console.log('Open file '+filename);
-      fs.readFile(filename.toString(), function read(err, data) {
-	  if (err) {
-	      throw err;
-	  }
-	  setValues(data);
-      });
-  });
 
   let workPath = document.getElementById("workPath");
   // If empty or undefined use local folder as default
@@ -381,53 +371,11 @@
             workPath.value = '/tmp';
       //app.setPath('temp',process.cwd());
   }
-
-  // Catch calls for selectfolder
-  ipcRenderer.on('selectFolder', function(event, foldername) {
-      if (foldername.length != 0) {
-	  document.getElementById("workPath").value = foldername[0];
-	  // Change process directory
-	  process.chdir(foldername[0]);
-      }
-      console.log("currentdir",process.cwd());
-   });
-  // Catch calls for save as
-  ipcRenderer.on('saveFile', function(event, filename) {
-      // If filename is empty use default value
-      if (filename == '') {filename='TrimSP.cfg';}
-      // Get values from all fields and prepare config file
-      let trimSPcfg=prep_cfg(0);
-      // Save file to filename
-      console.log('Save file to '+filename);
-      try { fs.writeFileSync(filename, trimSPcfg, 'utf-8'); }
-      catch(e) { alert('Failed to save the file !'); }
-  });
-  // Catch calls for plotProf
-  ipcRenderer.on('plotProf', function(event, filename) {
-      console.log("filename="+filename);
-      plotProfiles(filename);
-  });
-  // Catch calls for plotFrac
-  ipcRenderer.on('plotFrac', function(event, filename) {
-      console.log("filename="+filename);
-      plotFractions(filename);
-  });
-  // Catch calls for plotMean
-  ipcRenderer.on('plotMean', function(event, filename) {
-      console.log("filename="+filename);
-      plotMean(filename);
-  });
-  // Catch clicks for Browse button
-  ipcRenderer.on('browseFolder', function(event, foldername) {
-      if (foldername.length != 0) {
-	  document.getElementById("workPath").value = foldername[0];
-	  // Change process directory
-	  process.chdir(foldername[0]);
-      }
-  });
-  
-  // Get the element with id="defaultOpen" and click on it
+  // Open the default Layers tab
   document.getElementById("btnLayers").click();
 
+  // Set up after first load (electron specific menu calls)
+  firstLoad();
+
 </script>
 </html>
diff --git a/TrimSPelec.js b/TrimSPelec.js
index e19e46c..62dbc05 100644
--- a/TrimSPelec.js
+++ b/TrimSPelec.js
@@ -64,3 +64,62 @@ function fileExists(filename) {
     }
     return 0;
 }
+
+function firstLoad() {
+    document.getElementById("trimPath").value = remote.getGlobal('path');
+    
+    // Catch calls for open file
+    ipcRenderer.on('openFile', function(event, filename) {
+	console.log('Open file '+filename);
+	fs.readFile(filename.toString(), function read(err, data) {
+	    if (err) {
+		throw err;
+	    }
+	    setValues(data);
+	});
+    });
+    
+    // Catch calls for selectfolder
+    ipcRenderer.on('selectFolder', function(event, foldername) {
+	if (foldername.length != 0) {
+	    document.getElementById("workPath").value = foldername[0];
+	    // Change process directory
+	    process.chdir(foldername[0]);
+	}
+	console.log("currentdir",process.cwd());
+    });
+    // Catch calls for save as
+    ipcRenderer.on('saveFile', function(event, filename) {
+	// If filename is empty use default value
+	if (filename == '') {filename='TrimSP.cfg';}
+	// Get values from all fields and prepare config file
+	let trimSPcfg=prep_cfg(0);
+	// Save file to filename
+	console.log('Save file to '+filename);
+	try { fs.writeFileSync(filename, trimSPcfg, 'utf-8'); }
+	catch(e) { alert('Failed to save the file !'); }
+    });
+    // Catch calls for plotProf
+    ipcRenderer.on('plotProf', function(event, filename) {
+	console.log("filename="+filename);
+	plotProfiles(filename);
+    });
+    // Catch calls for plotFrac
+    ipcRenderer.on('plotFrac', function(event, filename) {
+	console.log("filename="+filename);
+	plotFractions(filename);
+    });
+    // Catch calls for plotMean
+    ipcRenderer.on('plotMean', function(event, filename) {
+	console.log("filename="+filename);
+	plotMean(filename);
+    });
+    // Catch clicks for Browse button
+    ipcRenderer.on('browseFolder', function(event, foldername) {
+	if (foldername.length != 0) {
+	    document.getElementById("workPath").value = foldername[0];
+	    // Change process directory
+	    process.chdir(foldername[0]);
+	}
+    });
+}
diff --git a/TrimSPlib.js b/TrimSPlib.js
index 51366b8..837badc 100644
--- a/TrimSPlib.js
+++ b/TrimSPlib.js
@@ -39,7 +39,6 @@ function parse_formula (mf) {
 	else mol[m1[0]] += (m2!=null)?Number(m2[0]):1;
 	mf = mf.replace(m[0], "");
     }
-    console.log("mol=",mol);
     return mol;
 }
 
@@ -517,11 +516,10 @@ function StoppingCoefficients(Element,flag)
     };
 
     if (flag) {
-	console.log("ICRU");
+	// Using stopping coefficients derived from ICRU Report 49
 	return StoppingCoefficientsICRU[Element];
     } else {
-	console.log("IAEA");
-	// prefer using stopping coefficients derived from data in the IAEA database;
+	// Using stopping coefficients derived from data in the IAEA database;
 	// however, if they are unavailable, return those from ICRU Report 49
 	return (Element in StoppingCoefficientsIAEA) ? StoppingCoefficientsIAEA[Element] : StoppingCoefficientsICRU[Element];
     }
@@ -698,7 +696,7 @@ function openTab(event, tabName) {
 
     // Show the current tab, and add an "active" class to the button that opened the tab
     document.getElementById(tabName).style.display = "block";
-    event.currentTarget.className += " active";
+    if (event) event.currentTarget.className += " active";
 }
 
 function adjust_table()
@@ -1047,26 +1045,25 @@ function sum(array){
 function startSequence(All) {
     let cmd = '';
     let trimBin = All['trimPath']+"/trimspNL";
-    console.log(trimBin);
     // Check if the trimspNL binary is found
     if (!fileExists(trimBin)) {
 	// if not found, try in PATH and hope for the best
 	trimBin = "trimspNL";
     }
-    console.log(trimBin);
     
     // Check if workPath exists otherwise create it
     checkDir(All['workPath']); // from TrimSPelec.js, Electron/Node specific
 
     let Progress =0;
-//    document.getElementById("myBar").style.width = Progress + "%";
-//    document.getElementById("myBar").innerHTML = Progress + "%";
+    document.getElementById("pBar").style.width = Progress + "%";
+    document.getElementById("pBar").innerHTML = Progress + "%";
 
     // This is a flag to indicate whether the lists of values and inclements are the same size
     All["SdzFlag"]=0;
     var SValues = [];
     let ScanName = "E";
     let ScanAttrib = "valEnergy";
+    // Generate an arry of scanned values (one element for a single run)
     if (All["scanSeq"]) {
 	// For multiple runs or a scan
 	if (All["scanType"]=="scanVals") {
@@ -1095,14 +1092,16 @@ function startSequence(All) {
 	    ScanName = "Ld"+All["scandL"];
 	    ScanAttrib = "L"+All["scandL"]+"d";
 	}
-
     } else {
 	// For single run, array with single value of valEnergy
 	SValues.push(parseInt(All["valEnergy"]));
     }
-	
+
+    // Now start the actual simulation
+    //setInterval(() => {
     let iScan=0;
     for (var SValue of SValues) {
+	// Update value in GUI
 	document.getElementById(ScanAttrib).value = SValue;
 	All[ScanAttrib]=SValue;
 	if ( All["SdzFlag"] == 1) {
@@ -1112,21 +1111,25 @@ function startSequence(All) {
 		document.getElementById(ScanAttrib).value = SdzValues[iScan];
 	    }
 	}
+	// Update GUI progress bar
+	Progress=Progress+90/SValues.length;
+	document.getElementById("pBar").style.width = Progress + "%";
+	document.getElementById("pBar").innerHTML = Progress + "%";
+	
+	// Single run: Start 
 	let eingabe1=CreateInpFile(All);
 	if (eingabe1=="ERROR") {return(0);}
 	let FILENAME=All["workPath"]+"/"+All["fileNamePrefix"]+"_"+ScanName+SValue;
 	writeAsciiFile(FILENAME+".inp",eingabe1)
-	// Update GUI progress bar
-	Progress=Progress+90/SValues.length;
 	// Prepare command and execute
-	cmd = "cd "+All["workPath"]+";cp "+FILENAME+".inp eingabe1.inp;"+trimBin;
+	cmd = "cd " + All["workPath"];
+	cmd += ";cp " + FILENAME + ".inp eingabe1.inp";
+	cmd += ";" + trimBin;
+	cmd += "; mv -f ausgabe1.rge " + FILENAME + ".reg";
+	cmd += "; mv -f ausgabe1.out " + FILENAME + ".out";
+	cmd += "; mv -f ausgabe1.err " + FILENAME + ".err";
 	execute(cmd);
-	
-	// Rename files to standarized format
-	for (let ext of [".err",".out",".rge"]) {
-	    cmd = "cd "+All["workPath"]+";mv -f ausgabe1"+ext+" "+FILENAME+ext;
-	    execute(cmd);
-	}
+	// Single run: End
 
 	// Read stopping profiels
 	let [cols,data]= readDatFile(FILENAME+".rge");
@@ -1161,7 +1164,7 @@ function startSequence(All) {
 	}
 	iScan++;
     }
-
+    //},1000);
     // An easy way to keep track of chemical formula is to replace impL_i by the corresponding chemical formula of layer i
     let data = readAsciiFile(All["workPath"]+"/"+"fort.33");
     let LComp = "";
@@ -1182,8 +1185,8 @@ function startSequence(All) {
     cmd="cd "+All["workPath"]+";rm -f eingabe1.inp; rm -f fort.33";
     execute(cmd);
     Progress=100;
-    //    document.getElementById("myBar").style.width = Progress + "%";
-    //    document.getElementById("myBar").innerHTML = Progress + "%";
+    document.getElementById("pBar").style.width = Progress + "%";
+    document.getElementById("pBar").innerHTML = Progress + "%";
     return(0);
 }
 
@@ -1198,7 +1201,6 @@ function readDatFile(filename,flag) {
     } else {
 	lines = readAsciiFile(filename);
     }
-	console.log(lines);
     let data = [];
     let i=0; // line counter
     for (let line of lines.trim().split('\n')) {
@@ -1236,14 +1238,9 @@ function plotProfiles(filenames) {
 	Es[i]=Number(filenames[i].substring(filenames[i].indexOf('_')+2,filenames[i].indexOf('.')));
 	files[Es[i]] = filenames[i];
     }
-//    console.log(Es,files);
-//    Es=Es.sort();
-//    console.log(Es,files);
-//    console.log("sortFiles=",files[Es]);
-    
+
     // loop on sorted values and plot
     for (let i=0;i<Es.length;i++) {
-	//console.log(Es[i],files[Es[i]]);
 	let [cols,data]= readDatFile(files[Es[i]]);
 	// convert depth to nm and normalize profile
 	let depth=data[0];
@@ -1309,7 +1306,8 @@ function plotMean(filename) {
     Plot_xy(plotDiv,cdata[0],strag,['E (keV)','Mean Depth/Stragg. (nm)',cfort[11]]);
 }
 
-function tester() {
+function startSim() {
+    // Collect data from GUI
     var All=prep_cfg(1);
     // Switch to plots tab
     document.getElementById("btnPlots").click();
@@ -1317,18 +1315,12 @@ function tester() {
     Plotly.purge("plotFrac")
     Plotly.purge("plotRge")
 
-   //var test = All["L1Comp"];
-    //console.log('test='+test);
+    // start simulation sequence
     startSequence(All)
     //CreateInpFile(All);
     //  document.location =
     //
     //  "http://musruser.psi.ch/cgi-bin/TrimSP.cgi?TrimSPcfg="+TrimSPcfg+'go=start';
-    //console.log(TrimSPcfg);
-    // call the function
-    //execute('ping -c 4 0.0.0.0', (output) => {
-    //	console.log(output);
-    //  });
 }
 
 // Function to load and ascii file