Remove binaries.

fix typo in file extension

.gitignore

@@ -118,4 +118,5 @@ dist
 .pnp.*
 
 # my additions
+package-lock.json
 *~

Readme.md

@@ -10,7 +10,7 @@ an application for performing [Monte Carlo] simulations of ion implantation.
 * The code is maintained by the Low Energy Muons ([LEM]) group at the Paul Scherrer Institute ([PSI]). 
 * The [GUI] is written in [Node.js], [JavaScript] and [Electron]. 
 * The binary (statically linked) from the [Fortran] code is also included.
-* Linux packages can be generated locally from the current source tree.
+* [RPM] and [DEB] packages are also included.
 
 Further information can be found in the following publications:
 
@@ -39,8 +39,7 @@ Further information can be found in the following publications:
 
 ### Installation ###
 
-Packages are not stored in this repository. You can either run the application
-directly from source or build Linux packages locally as described below.
+For a simple installation you may use the included RPM or Debian packages which come with statically linked binaries. See instructions below if you prefer a manual installation. 
 
 ###### Fortran code compilation ######
 
@@ -49,18 +48,11 @@ Install the `gfortran` compiler, then:
 ```bash
 cd trimsp/fortran
 make
+make install
 ```
-
-This creates the `trimspNL` binary in the repository root. For packaged
-Electron builds, copy or rebuild it into:
-
-```text
-resources/bin/trimspNL
-```
-
-The application will prefer that bundled copy when running from a packaged
-install. During development it can still use a local checkout copy or a
-`trimspNL` binary found in the configured path or in `PATH`.
+    
+This will install the `trimspNL` binary in `/usr/local/bin`,
+but it can be moved to any other directory in your `PATH`.
 
 ###### Running the GUI ######
 
@@ -76,114 +68,6 @@ npm start
 Note: you do not need to run `npm install` every time.
 Next time you can simply run `npm start` only. 
 
-###### Building RPM and DEB packages ######
-
-Install [Node.js] (`nodejs`, `nodejs-libs` and `npm`), then run:
-
-```bash
-cd trimsp
-cp trimspNL resources/bin/trimspNL
-npm install
-npm run make
-```
-
-This uses Electron Forge to build Linux packages from the current checkout.
-The packaged application bundles `resources/bin/trimspNL` inside the app
-resources, so make sure that file exists and is up to date before packaging.
-
-The generated files are written under:
-
-```text
-out/make/deb/x64/
-out/make/rpm/x64/
-```
-
-Typical output files are:
-
-```text
-out/make/deb/x64/trimsp_<version>_amd64.deb
-out/make/rpm/x64/TrimSP-<version>-1.x86_64.rpm
-```
-
-To generate matching checksum sidecar files for each generated package, run:
-
-```bash
-npm run checksums
-```
-
-This creates files next to each package, for example:
-
-```text
-out/make/rpm/x64/TrimSP-<version>-1.x86_64.rpm.md5
-out/make/rpm/x64/TrimSP-<version>-1.x86_64.rpm.sha256
-```
-
-If you only want one checksum type, you can also run:
-
-```bash
-npm run checksums:md5
-npm run checksums:sha256
-```
-
-Depending on the host system, additional packaging tools may be required for
-the RPM/DEB build chain.
-
-###### Building a Flatpak ######
-
-Install the Flatpak build tools in addition to [Node.js]:
-
-```bash
-flatpak
-flatpak-builder
-elfutils
-```
-
-Then run:
-
-```bash
-cd trimsp
-cp fortran/trimspNL resources/bin/trimspNL
-npm install
-npm run make:flatpak
-```
-
-This uses Electron Forge's Flatpak maker and writes the resulting `.flatpak`
-under:
-
-```text
-out/make/flatpak/x86_64/
-```
-
-Checksum sidecar files can be generated afterward with:
-
-```bash
-npm run checksums
-```
-
-The current Flatpak config grants access to the home directory and `/tmp`,
-which matches how the packaged app currently handles simulation input/output.
-
-###### Deploying on a web server ######
-
-The browser version requires a server-side setup in addition to the static
-HTML/JavaScript files.
-
-In particular:
-
-* the browser build uses `TrimSPweb.js` rather than the Electron-specific
-  `TrimSPelec.js`
-* the simulation backend must be available on the server
-* a web-exposed helper/CGI layer is required to create input files, run the
-  backend, and return the generated output
-
-Notes:
-
-* this repository does not currently include the CGI/backend helper used by
-  the online deployment
-* a plain static web server is therefore not sufficient for running web
-  simulations from this checkout
-* static hosting can still be used to test page loading only
-
 ### Contact ###
 
 Zaher Salman <zaher.salman@psi.ch>

TrimSP.html

@@ -9,7 +9,7 @@
   <script src="TrimSPlib.js"></script>
   <script src="myplots.js"></script>
   <!script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
-  <title>TRIM.SP</title>
+  <title>Trim.SP</title>
 </head>
 <body onresize="resizePl()" onload="adjust_table();adjust_scans();">
 <table style="width: 100%;">
@@ -30,16 +30,15 @@
 		    <td><label>File name prefix:</label></td>
 		    <td>
 		      <input name="fileNamePrefix" id="fileNamePrefix" type="text" style="width:70%" value="SrTiO3"/>
-		      <input name="trimPath" id="trimPath" type="hidden"/>
+		      <input name="trimPath" id="trimPath" type="text" style="width:70%;visibility:hidden;"/>
 		    </td>
 		  </tr>
 		  <tr id="FolderRow">
 		    <td><label>Save folder:</label></td>
 		    <td>
-		      <input type="text" disabled style="width:70%" id="workPath" name="workPath" title="Use Browse to select the save folder" />
+		      <input type="text" style="width:70%" id="workPath" name="workPath" readonly/>
 		      <input type="button" value="Browse"
-			     id="browseFolde" onclick="browseForFolder();">
-		      <input type="file" id="folderPicker" style="display:none" webkitdirectory directory>
+			     id="browseFolde" onclick="ipcRenderer.send('browseFolder');">
 		    </td>
 		  </tr>
 		  <tr>
@@ -60,7 +59,6 @@
 		    <td><select name="ProjType" id="ProjType" onchange="ProjSmartDefaults()" onload="ProjSmartDefaults()">
 			<option selected="selected" value="muon">muon</option>
 			<option value="Li-8">Li-8</option>
-			<option value="Be-11">Be-11</option>
 			<option value="B-12">B-12</option>
 			<option value="Mg-31">Mg-31</option>
 			<option value="H">H</option>
@@ -312,23 +310,14 @@
 	    </tr>
 	    <tr>
 	      <td class="tooltip">
-	        Stopping Power<br>Coefficients
+		<input type="checkbox" id="flagICRU" checked>
 		<span class="tooltiptext">
-	          Data source for the Varelas-Biersack parameterization of electronic
-	          stopping cross-sections for proton-like projectiles implanted in
-	          elemental targets:
-	          <ol>
-	            <li value="1">Table 1 in Anderson & Ziegler (1977).</li>
-	            <li value="2">Table 3.1 in ICRU Report 49 (1993).</li>
-	            <li value="3">Table II in McFadden et al. (2023) and McFadden et al. (unpublished).</li>
-	          </ol>
-	          Note: While option 3 contains the most up-to-date values, it currently
-	          does not contain entries for every target element. For elements with
-	          missing data, values from option 2 are taken instead.
-	        </span>
+		  Force the TRIM.SP code to use stopping power
+		  parameters from the old ICRU tables. 
+		</span>
 	      </td>
 	      <td>
-		<input name="flagSPC" id="flagSPC" type="number" step="1" min="1" max="3" value="2">
+		Use ICRU parameters
 	      </td>
 	      <td class="tooltip">
 	        IRL
@@ -349,7 +338,9 @@
 	    </tr>
           </table>
 	  <p>
-	    For further details see:<br>
+	    For further details see:
+	  </p>
+	  <p>
 	    W. Eckstein, <i>Computer Simulation of Ion-Solid Interactions</i>,<br>
 	    Springer Series in Materials Science, Vol. 10 (Springer-Verlag, Berlin, 1991).<br>
 	    <a href="https://doi.org/10.1007/978-3-642-73513-4">
@@ -359,36 +350,28 @@
 	</div>
       </div>
   </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>
-<div id="statusBar" class="status-bar">
-  <span class="status-item"><strong>Folder:</strong> <span id="statusWorkPath">-</span></span>
-  <span class="status-item"><strong>Backend:</strong> <span id="statusBackend">-</span></span>
-  <span class="status-item"><strong>Last save:</strong> <span id="statusLastSave">Not saved yet</span></span>
-  <span class="status-item"><strong>Run:</strong> <span id="statusRun">Idle</span></span>
-  <div class="status-progress">
-    <div class="status-progress-track">
-      <div id="pBar" class="status-progress-fill">0%</div>
-    </div>
-  </div>
-</div>
 </body>
 <script>
 
   let workPath = document.getElementById("workPath");
-  let webOrApp = amIWeb();
   // If empty or undefined use local folder as default
   if (workPath.value == '' || workPath.value == undefined ) {
-      if (webOrApp) {
-          workPath.value = '/tmp';
-      } else {
-          workPath.value = process.cwd();
-      }
-  }
-  if (typeof syncStatusBar === 'function') {
-      syncStatusBar();
+       //     workPath.value = process.cwd();
+            workPath.value = '/tmp';
+      //app.setPath('temp',process.cwd());
   }
   // Open the default Layers tab
   document.getElementById("btnLayers").click();
+
+  let webOrApp = amIWeb();
   
   if (webOrApp) {
       console.log('this script is not running in Node.js');

TrimSPelec.js

@@ -5,7 +5,7 @@ const Plotly = require('plotly.js-dist');
 const ipcRenderer = require('electron').ipcRenderer;
 const fs = require('fs');
 const exec = require('child_process').execSync;
-const path = require('path');
+const remote = require('electron').remote;
 
 function getFiles(dir, filelist){
     fileList = [];
@@ -73,70 +73,8 @@ function fileExists(filename) {
     return 0;
 }
 
-function getTrimBinaryPath(configuredPath) {
-    const candidates = [];
-    if (configuredPath) {
-	candidates.push(path.join(configuredPath, "trimspNL"));
-    }
-    if (process.resourcesPath) {
-	candidates.push(path.join(process.resourcesPath, "bin", "trimspNL"));
-	candidates.push(path.join(process.resourcesPath, "trimspNL"));
-    }
-    candidates.push(path.join(process.cwd(), "trimspNL"));
-
-    for (const candidate of candidates) {
-	if (fileExists(candidate)) {
-	    return candidate;
-	}
-    }
-    return "trimspNL";
-}
-
-function setWorkFolder(foldername) {
-    const folder = Array.isArray(foldername) ? foldername[0] : foldername;
-    if (folder) {
-	document.getElementById("workPath").value = folder;
-	if (typeof updateStatusBar === 'function') {
-	    updateStatusBar({ workPath: folder });
-	}
-	ipcRenderer.send('updateWorkPath', folder);
-	try {
-	    // Change process directory
-	    process.chdir(folder);
-	} catch (err) {
-	    console.log('Failed to change directory:', err);
-	}
-    }
-}
-
-function browseForFolder() {
-    ipcRenderer.send('browseFolder');
-}
-
-function fallbackBrowseForFolder() {
-    const picker = document.getElementById("folderPicker");
-    if (!picker) { return; }
-    picker.value = '';
-    picker.click();
-}
-
 function firstLoad() {
-    document.getElementById("trimPath").value = process.cwd();
-    if (typeof syncStatusBar === 'function') {
-	syncStatusBar();
-    }
-
-    const folderPicker = document.getElementById("folderPicker");
-    if (folderPicker) {
-	folderPicker.addEventListener('change', function(event) {
-	    const files = event.target.files;
-	    if (!files || files.length === 0) {
-		return;
-	    }
-	    const folder = path.dirname(files[0].path);
-	    setWorkFolder([folder]);
-	});
-    }
+    document.getElementById("trimPath").value = remote.getGlobal('path');
     
     // Catch calls for open file
     ipcRenderer.on('openFile', function(event, filename) {
@@ -151,31 +89,22 @@ function firstLoad() {
     
     // Catch calls for selectfolder
     ipcRenderer.on('selectFolder', function(event, foldername) {
-	setWorkFolder(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) {
-	const workPath = document.getElementById("workPath").value || process.cwd();
-	if (filename === undefined || filename === null) { return; }
-	// If filename is empty use default value in the selected work folder
-	if (filename == '') {filename = path.join(workPath, 'TrimSP.cfg');}
-	if (path.extname(filename) === '') {
-	    filename += '.cfg';
-	}
+	// 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');
-	    if (typeof updateStatusBar === 'function') {
-		updateStatusBar({ lastSave: filename });
-	    }
-	    if (typeof showTransientWarning === 'function') {
-		showTransientWarning('Saved configuration to ' + filename, document.getElementById('workPath'), 4000);
-	    }
-	}
+	try { fs.writeFileSync(filename, trimSPcfg, 'utf-8'); }
 	catch(e) { alert('Failed to save the file !'); }
     });
     // Catch calls for plotProf
@@ -195,11 +124,10 @@ function firstLoad() {
     });
     // Catch clicks for Browse button
     ipcRenderer.on('browseFolder', function(event, foldername) {
-	console.log('browseFolder reply', foldername);
-	setWorkFolder(foldername);
-    });
-
-    ipcRenderer.on('browseFolderFallback', function() {
-	fallbackBrowseForFolder();
+	if (foldername.length != 0) {
+	    document.getElementById("workPath").value = foldername[0];
+	    // Change process directory
+	    process.chdir(foldername[0]);
+	}
     });
 }

ZGUI.css

@@ -19,27 +19,21 @@ td {
     margin-top: 0.5em;
     margin-bottom: 0.5em;
 }
-
 .guitable tr:last-child td:first-child {
     border-bottom-left-radius: 12px;
 }
-
 .guitable tr:last-child td:last-child {
     border-bottom-right-radius: 12px;
 }
-
 .guitable tr:first-child td:first-child {
     border-top-left-radius: 12px;
 }
-
 .guitable tr:first-child td:last-child {
     border-top-right-radius: 12px;
 }
-
 .guitable tr:nth-child(odd) {
     background-color: #DDDDDD;
 }
-
 .guitable tr:nth-child(even) {
     background-color: #DDDDDD;
 }
@@ -50,323 +44,161 @@ td {
 }
 
 @media only screen and (min-width: 700px) {
-
     /* For tablets: */
-    .col-s-1 {
-        width: 50%;
-        background-color: #DDDDDD;
-    }
-
-    .col-s-2 {
-        width: 50%;
-        background-color: #DDDDDD;
-    }
-
-    .col-s-full {
-        width: 100%;
-        background-color: #F2F2F2;
-    }
-
+    .col-s-1 {width: 50%;background-color: #DDDDDD;}
+    .col-s-2 {width: 50%;background-color: #DDDDDD;}
+    .col-s-full {width: 100%;background-color: #F2F2F2;} 
     [class*="col-"] {
-        width: 100%;
+	width: 100%;
     }
+    
+@media only screen and (min-width: 990px) {
+    /* For desktop: */
+    .col-1 {width: 50%;background-color: #F2F2F2;}
+    .col-2 {width: 50%;background-color: #F2F2F2;}
+    .col-full {width: 100%;background-color: #F2F2F2;}
+} 
 
-    @media only screen and (min-width: 990px) {
+[class*="col-"] {
+    float: left;
+    padding: 5px;
+    border: none;
+}
 
-        /* For desktop: */
-        .col-1 {
-            width: 50%;
-            background-color: #F2F2F2;
-        }
+.row::after {
+    content: "";
+    clear: both;
+    display: table;
+}
 
-        .col-2 {
-            width: 50%;
-            background-color: #F2F2F2;
-        }
+.group_name {
+    padding-left:1em;
+    padding-right:1em;
+    font-size:105%;
+    font-weight:bold;
+    width: 1%;
+    white-space: nowrap;
+    /* text-align: center; */
+}
+.yellow_td {
+    padding-left:1em;
+    padding-right:1em;
+    background-color: yellow;
+    width: 1%;
+    white-space: nowrap;
+}
+.gray_td {
+    padding-left:1em;
+    padding-right:1em;
+    background-color: gray;
+    width: 1%;
+    white-space: nowrap;
+}
+.nocol_td {
+    padding-left:1em;
+    padding-right:1em;
+    width: 1%;
+    white-space: nowrap;
+}
 
-        .col-full {
-            width: 100%;
-            background-color: #F2F2F2;
-        }
-    }
+/* Style the tab */
+.tab {
+    overflow: hidden;
+    border: 1px solid #ccc;
+    background-color: #f1f1f1;
+}
 
-    [class*="col-"] {
-        float: left;
-        padding: 5px;
-        border: none;
-    }
+/* Style the buttons that are used to open the tab content */
+.tab button {
+    background-color: inherit;
+    float: left;
+    border: none;
+    outline: none;
+    cursor: pointer;
+    padding: 14px 16px;
+    transition: 0.3s;
+    font-size:105%;
+    font-weight:bold;
+}
 
-    .row::after {
-        content: "";
-        clear: both;
-        display: table;
-    }
+/* Change background color of buttons on hover */
+.tab button:hover {
+    background-color: #ddd;
+}
+    
+/* Create an active/current tablink class */
+.tab button.active {
+    background-color: #ccc;
+}
 
-    .transient-warning {
-        position: fixed;
-        max-width: 360px;
-        padding: 10px 14px;
-        background-color: #fff4cc;
-        border: 1px solid #c5a100;
-        border-radius: 8px;
-        color: #4d3b00;
-        box-shadow: 0 6px 18px rgba(0, 0, 0, 0.18);
-        font-size: 0.95rem;
-        line-height: 1.35;
-        opacity: 0;
-        pointer-events: none;
-        transition: opacity 0.25s ease;
-        z-index: 1000;
-    }
+/* Style the tab content */
+.tabcontent {
+    display: none;
+    padding: 6px 12px;
+    border: 1px solid #ccc;
+    border-top: none;
+}
+    
+.tabcontent {
+/*    animation: fadeEffect 1s; /* Fading effect takes 1 second */
+}
+    
+/* Go from zero to full opacity */
+@keyframes fadeEffect {
+    from {opacity: 0;}
+    to {opacity: 1;}
+}
 
-    .transient-warning.visible {
-        opacity: 1;
-    }
+/* Chrome, Safari, Opera */
+@-webkit-keyframes example {
+    0%   {background-color:red; left:20px; top:0px;}
+    25%  {background-color:orange; left:25px; top:0px;}
+    50%  {background-color:green; left:30px; top:0px;}
+    75%  {background-color:orange; left:25px; top:0px;}
+    100% {background-color:red; left:20px; top:0px;}
+}
 
-    .estimated-density {
-        background-color: #fff4cc;
-        border: 1px solid #c5a100;
-    }
+/* Standard syntax */
+@keyframes example {
+    0%   {background-color:red; left:20px; top:0px;}
+    25%  {background-color:orange; left:25px; top:0px;}
+    50%  {background-color:green; left:30px; top:0px;}
+    75%  {background-color:orange; left:25px; top:0px;}
+    100% {background-color:red; left:20px; top:0px;}
+}
 
-    .status-bar {
-        position: fixed;
-        left: 0;
-        right: 0;
-        bottom: 0;
-        display: flex;
-        flex-wrap: wrap;
-        gap: 8px 16px;
-        align-items: center;
-        padding: 8px 14px;
-        background-color: #eef2f5;
-        border-top: 1px solid #b8c3cc;
-        color: #23313d;
-        font-size: 0.88rem;
-        box-shadow: 0 -2px 8px rgba(0, 0, 0, 0.08);
-        z-index: 900;
-    }
+#myBar {
+    width: 10%;
+    height: 30px;
+    background-color: #4CAF50;
+    text-align: center; /* To center it horizontally (if you want) */
+    line-height: 30px; /* To center it vertically */
+    color: white;
+}
 
-    .status-item {
-        min-width: 180px;
-        overflow: hidden;
-        text-overflow: ellipsis;
-        white-space: nowrap;
-    }
+/* Tooltip container */
+.tooltip {
+  position: relative;
+  display: inline-block;
+  /* border-bottom: 1px dotted black; /* If you want dots under the hoverable text */
+}
 
-    .status-item strong {
-        color: #10202c;
-    }
+/* Tooltip text */
+.tooltip .tooltiptext {
+  visibility: hidden;
+  width: 320px;
+  background-color: black;
+  color: #fff;
+  text-align: left;
+  padding: 5px;
+  border-radius: 6px;
+ 
+  /* Position the tooltip text - see examples below! */
+  position: absolute;
+  z-index: 1;
+}
 
-    .status-progress {
-        flex: 1 1 260px;
-        min-width: 220px;
-    }
-
-    .status-progress-track {
-        width: 100%;
-        height: 22px;
-        background-color: #d7dee5;
-        border-radius: 8px;
-        overflow: hidden;
-        border: 1px solid #b8c3cc;
-    }
-
-    .status-progress-fill {
-        width: 0%;
-        height: 100%;
-        background-color: #2e8b57;
-        color: black;
-        padding-left: 3px;
-        text-align: center;
-        line-height: 20px;
-        font-size: 0.78rem;
-        font-weight: 600;
-        transition: width 0.2s ease;
-    }
-
-    .group_name {
-        padding-left: 1em;
-        padding-right: 1em;
-        font-size: 105%;
-        font-weight: bold;
-        width: 1%;
-        white-space: nowrap;
-        /* text-align: center; */
-    }
-
-    .yellow_td {
-        padding-left: 1em;
-        padding-right: 1em;
-        background-color: yellow;
-        width: 1%;
-        white-space: nowrap;
-    }
-
-    .gray_td {
-        padding-left: 1em;
-        padding-right: 1em;
-        background-color: gray;
-        width: 1%;
-        white-space: nowrap;
-    }
-
-    .nocol_td {
-        padding-left: 1em;
-        padding-right: 1em;
-        width: 1%;
-        white-space: nowrap;
-    }
-
-    /* Style the tab */
-    .tab {
-        overflow: hidden;
-        border: 1px solid #ccc;
-        background-color: #f1f1f1;
-    }
-
-    /* Style the buttons that are used to open the tab content */
-    .tab button {
-        background-color: inherit;
-        float: left;
-        border: none;
-        outline: none;
-        cursor: pointer;
-        padding: 14px 16px;
-        transition: 0.3s;
-        font-size: 105%;
-        font-weight: bold;
-    }
-
-    /* Change background color of buttons on hover */
-    .tab button:hover {
-        background-color: #ddd;
-    }
-
-    /* Create an active/current tablink class */
-    .tab button.active {
-        background-color: #ccc;
-    }
-
-    /* Style the tab content */
-    .tabcontent {
-        display: none;
-        padding: 6px 12px;
-        border: 1px solid #ccc;
-        border-top: none;
-    }
-
-    /* Go from zero to full opacity */
-    @keyframes fadeEffect {
-        from {
-            opacity: 0;
-        }
-
-        to {
-            opacity: 1;
-        }
-    }
-
-    /* Chrome, Safari, Opera */
-    @-webkit-keyframes example {
-        0% {
-            background-color: red;
-            left: 20px;
-            top: 0px;
-        }
-
-        25% {
-            background-color: orange;
-            left: 25px;
-            top: 0px;
-        }
-
-        50% {
-            background-color: green;
-            left: 30px;
-            top: 0px;
-        }
-
-        75% {
-            background-color: orange;
-            left: 25px;
-            top: 0px;
-        }
-
-        100% {
-            background-color: red;
-            left: 20px;
-            top: 0px;
-        }
-    }
-
-    /* Standard syntax */
-    @keyframes example {
-        0% {
-            background-color: red;
-            left: 20px;
-            top: 0px;
-        }
-
-        25% {
-            background-color: orange;
-            left: 25px;
-            top: 0px;
-        }
-
-        50% {
-            background-color: green;
-            left: 30px;
-            top: 0px;
-        }
-
-        75% {
-            background-color: orange;
-            left: 25px;
-            top: 0px;
-        }
-
-        100% {
-            background-color: red;
-            left: 20px;
-            top: 0px;
-        }
-    }
-
-    #myBar {
-        width: 10%;
-        height: 30px;
-        background-color: #4CAF50;
-        text-align: center;
-        /* To center it horizontally (if you want) */
-        line-height: 30px;
-        /* To center it vertically */
-        color: white;
-    }
-
-    /* Tooltip container */
-    .tooltip {
-        position: relative;
-        display: inline-block;
-        /* border-bottom: 1px dotted black; /* If you want dots under the hoverable text */
-    }
-
-    /* Tooltip text */
-    .tooltip .tooltiptext {
-        visibility: hidden;
-        width: 320px;
-        background-color: black;
-        color: #fff;
-        text-align: left;
-        padding: 5px;
-        border-radius: 6px;
-
-        /* Position the tooltip text - see examples below! */
-        position: absolute;
-        z-index: 1;
-    }
-
-    /* Show the tooltip text when you mouse over the tooltip container */
-    .tooltip:hover .tooltiptext {
-        visibility: visible;
-    }
-}
+/* Show the tooltip text when you mouse over the tooltip container */
+.tooltip:hover .tooltiptext {
+  visibility: visible;
+}

forge.config.js

@@ -1,97 +0,0 @@
-const path = require('path');
-const redhatDependencies = require('electron-installer-redhat/src/dependencies');
-
-const linuxIconSet = {
-  '16x16': 'appicons/icons/png/16x16.png',
-  '24x24': 'appicons/icons/png/24x24.png',
-  '32x32': 'appicons/icons/png/32x32.png',
-  '48x48': 'appicons/icons/png/48x48.png',
-  '64x64': 'appicons/icons/png/64x64.png',
-  '128x128': 'appicons/icons/png/128x128.png',
-  '256x256': 'appicons/icons/png/256x256.png',
-  '512x512': 'appicons/icons/png/512x512.png',
-};
-
-const linuxDesktopTemplate = path.resolve(__dirname, 'packaging/linux/trimsp.desktop.ejs');
-
-// The upstream RPM maker assumes Fedora-style package names. Mageia provides
-// GTK 3 under lib64gtk+3_0, so allow either name in the generated Requires.
-redhatDependencies.dependencyMap.gtk3 = '(gtk3 or lib64gtk+3_0)';
-
-module.exports = {
-  packagerConfig: {
-    icon: 'appicons/icons/png/1024x1024.png',
-    extraResource: ['resources/bin'],
-    ignore: [
-      'Readme.md',
-      'ToDo.txt',
-      'TrimSP.cfg',
-      'fortran/*',
-      '\\.flatpak-builder($|/)',
-      '\\.tmp-flatpak-manual($|/)',
-      'out-flatpak-test($|/)',
-    ],
-  },
-  makers: [
-    {
-      name: '@electron-forge/maker-squirrel',
-      config: {
-        name: 'TrimSP',
-      },
-    },
-    {
-      name: '@electron-forge/maker-zip',
-      platforms: ['darwin'],
-    },
-    {
-      name: '@electron-forge/maker-deb',
-      config: {
-        name: 'trimsp',
-        productName: 'TrimSP',
-        genericName: 'Ion implantation simulator',
-        description: 'TRIM.SP simulation GUI for ion implantation studies.',
-        categories: ['Science'],
-        icon: linuxIconSet,
-        desktopTemplate: linuxDesktopTemplate,
-      },
-    },
-    {
-      name: '@electron-forge/maker-rpm',
-      config: {
-        name: 'trimsp',
-        productName: 'TrimSP',
-        genericName: 'Ion implantation simulator',
-        description: 'TRIM.SP simulation GUI for ion implantation studies.',
-        categories: ['Science'],
-        icon: linuxIconSet,
-        desktopTemplate: linuxDesktopTemplate,
-      },
-    },
-    {
-      name: '@electron-forge/maker-flatpak',
-      config: {
-        options: {
-          id: 'ch.psi.lem.TrimSP',
-          productName: 'TrimSP',
-          genericName: 'Ion implantation simulator',
-          description: 'TRIM.SP simulation GUI for ion implantation studies.',
-          baseVersion: '24.08',
-          runtimeVersion: '24.08',
-          extraFlatpakBuilderArgs: ['--state-dir=.flatpak-builder'],
-          icon: linuxIconSet,
-          modules: [],
-          categories: ['Science'],
-          finishArgs: [
-            '--share=ipc',
-            '--share=network',
-            '--socket=x11',
-            '--socket=wayland',
-            '--device=dri',
-            '--filesystem=home',
-            '--filesystem=/tmp',
-          ],
-        },
-      },
-    },
-  ],
-};

fortran/trimspNL.F

@@ -401,9 +401,7 @@ C     LMAX is maximum number of layers and JMAX is maximum number of
 C     elements per layer.
       JMAX=5
 
-C     This part reads the input file (new format).
-C     The JavaScript/Electron frontend writes this sequential block layout,
-C     so the READ order below must stay in sync with CreateInpFile().
+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
@@ -816,9 +814,6 @@ C
       ENDDO
 C
 C     PROJECTILE LOOP
-C     Each pass transports one projectile history. The state vectors
-C     X/Y/Z, E, direction cosines, current layer index, etc. are updated
-C     in-place until the particle stops, backscatters or transmits.
 C
  1    CONTINUE
       NPROJ=NPROJ+1
@@ -834,10 +829,6 @@ C
       KK1=KK0
 C
 C     COLLISION LOOP (INCLUDES WEAK SIMULTANEOUS COLL. FOR KK1.LT.4)
-C     KK controls the treatment of weak simultaneous collisions.
-C     For every active projectile we choose a collision partner, sample an
-C     impact parameter, solve the scattering geometry for the selected
-C     interatomic potential and then update the projectile state.
 C
       DO 245 KK=KK1,0,-1
 C
@@ -3383,10 +3374,6 @@ C     &     I0,3x))
      &     ,1x))
 
       inquire(FILE='fort.33',EXIST=FORT33)
-C     fort.33 is the compact per-run summary consumed by the GUI for scan
-C     plots (fractions stopped in each layer, backscattering, transmission,
-C     mean depth, etc.). The header line is written once, then each run
-C     appends a single summary row.
       if (.not.FORT33) then
          open(33)
          WRITE(33,7802)  (chem(k),k=1,NLayers)
@@ -3933,10 +3920,6 @@ C
       REAL*8 X1SY,X2SY,X3SY,X4SY,X5SY,X6SY,X1S,X2S,X3S,X4S,X5S,X6S,Y
       LOGICAL EQUAL
 
-C     Convert accumulated raw sums into per-particle moments by dividing
-C     through the population size Y. The higher-level MOMENTS/MOMENTN
-C     routines use these normalized values to build means, spreads and
-C     uncertainties for the reported observables.
       IF(EQUAL(Y,0.D0))GOTO 10
       X1SY=X1S/Y
       X2SY=X2S/Y
@@ -3954,9 +3937,6 @@ C     uncertainties for the reported observables.
      &     ,SPHI(N)
       REAL*8 SRAT,CX2,CY2,CZ2,UNIT
 
-C     Rotate the current direction cosines by the sampled scattering
-C     angles (psi,phi). The output direction is explicitly renormalized
-C     because repeated collisions amplify small floating-point drift.
       DO IV=1,N
          SRAT=SPSI(IV)/SINE(IV)
          CX2=CPSI(IV)*COSX(IV)+SPSI(IV)*SINE(IV)*CPHI(IV)
@@ -3979,8 +3959,6 @@ C     MAKE SURE COSZ.NE.0.
       INTEGER n,I
 C     
 C     FETCH A NEW VELOCITY FROM A MAXWELLIAN FLUX AT A SURFACE
-C     Vectorized version used when multiple projectiles are initialized
-C     together with thermal surface velocities.
 C     
       REAL*8 FG(2*N),FFG(N),E(N),COSX(N),COSY(N),COSZ(N),SINE(N)
 C     DIMENSIOM E(N),COSX(N),COSY(N),COSZ(N),SINE(N)
@@ -4008,7 +3986,6 @@ C     DIMENSIOM E(N),COSX(N),COSY(N),COSZ(N),SINE(N)
       SUBROUTINE VELOC(E,COSX,COSY,COSZ,SINE)
 C
 C     FETCH A NEW VELOCITY FROM A MAXWELLIAN FLUX AT A SURFACE
-C     Scalar version that reuses Gaussian deviates generated by FGAUSS.
 C     
       IMPLICIT NONE
       INTEGER INIV1,INIV3
@@ -4051,8 +4028,6 @@ C     ZA=0.
 C     ZS=1.
 C     
 C     IT IS THE BOX-MUELLER METHOD
-C     FG returns symmetric normal deviates, while FFG stores the positive
-C     half-space distribution used for Maxwellian flux sampling.
 C     
       IMPLICIT NONE
       INTEGER IND,IND2,IANZ,JJ
@@ -4228,9 +4203,6 @@ C     why is it needed??
       INTEGER I,N,J,INC
       REAL*8 ARRAY(N),TARGT
 
-C     Return the first index whose value is strictly greater than TARGT.
-C     This is used to map a continuous coordinate/depth onto the current
-C     layer or histogram bin in monotonic arrays.
       J=1
       IF(INC.LT.0) J=N*(-INC)
       DO I=1,N
@@ -4248,8 +4220,6 @@ C     layer or histogram bin in monotonic arrays.
       REAL*8 p1,p2,p3,pi
       real*4 random(2)
       DATA pi/3.14159265358979D0/
-C     Sample a Gaussian-distributed incident energy around E0 using a
-C     Box-Mueller transform. Epar is the per-projectile starting energy.
       call ranlux(random, 2)
       p1  = Esig*DSQRT(-2.D0*DLOG(1.D0-DBLE(random(1)))) 
       p2  = 2.D0*pi*DBLE(random(2))
@@ -4267,8 +4237,6 @@ C     Box-Mueller transform. Epar is the per-projectile starting energy.
       REAL*8 p1,p2,p3,pi
       real*4 random(2)
       DATA pi/3.14159265358979D0/
-C     Sample a Gaussian-distributed incidence angle around ALPHA and
-C     return both the angle in radians (ALFA) and its sine/cosine.
       call ranlux(random, 2)	
       p1  = ALPHASIG*DSQRT(-2.D0*DLOG(1.D0-DBLE(random(1)))) 
       p2  = 2.D0*pi*DBLE(random(2))
@@ -4288,8 +4256,6 @@ C     return both the angle in radians (ALFA) and its sine/cosine.
       REAL*8 F1,F2
       REAL*8 TINY
       PARAMETER  (TINY = 1.0D-10)
-C     Centralized floating-point comparison used throughout the transport
-C     code to avoid exact equality checks on derived real-valued quantities.
       IF (DABS(F1-F2).LE.TINY) THEN
          EQUAL = .TRUE.
       ELSE

main.js

@@ -1,64 +1,9 @@
-const path = require('path');
 const { app, BrowserWindow, Menu, dialog, ipcMain, fs } = require('electron');
-
-let currentWorkPath = process.cwd();
-
-app.setName('TrimSP');
-
-function showAboutDialog(parentWindow) {
-    const detail = [
-	'TRIM.SP simulation GUI for low-energy ion implantation studies.',
-	`Version: ${app.getVersion()}`,
-	'License: GNU General Public License v2 (GPL-2.0).',
-	'Maintained by the Low Energy Muons group at the Paul Scherrer Institute.',
-	'Main contributor: Zaher Salman.',
-	'',
-	'Key references:',
-	'J. P. Biersack and W. Eckstein, Appl. Phys. A 34, 73-94 (1984).',
-	'W. Eckstein, Computer Simulation of Ion-Solid Interactions (1991).',
-	'E. Morenzoni et al., NIM B 192, 245-266 (2002).',
-	'',
-	'Project repositories:',
-	'Bitbucket: bitbucket.org/zaher-salman/trimsp',
-	'Gitea: gitea.psi.ch/LMU/TRIMSP'
-    ].join('\n');
-
-    dialog.showMessageBox(parentWindow, {
-	type: 'info',
-	title: 'About TrimSP',
-	message: 'TrimSP',
-	detail: detail,
-	buttons: ['OK'],
-	icon: parentWindow ? undefined : undefined
-    });
-}
-
-// Some Linux/remote desktop setups expose a broken GPU context to Electron.
-// Fall back to software rendering instead of crashing on startup.
-app.disableHardwareAcceleration();
-
-if (process.platform === 'linux') {
-    // The XDG portal dialog backend ignores defaultPath on some systems and
-    // may cancel folder selection entirely in X11/SSH sessions.
-    app.commandLine.appendSwitch('xdg-portal-required-version', '999');
-}
-
-function getDefaultDialogPath() {
-    return currentWorkPath || process.cwd();
-}
-
-function getWindowIconPath() {
-    if (app.isPackaged) {
-        return path.join(process.resourcesPath, 'app.asar', 'icon.png');
-    }
-    return path.join(__dirname, 'icon.png');
-}
-
 function createWindow () {
     const win = new BrowserWindow({
-	width: 1000,
-	height: 610,
-	icon: getWindowIconPath(),
+	width: 950,
+	height: 580,
+	icon: "/usr/lib/TrimSP/resources/app/icon.png",
 	webPreferences: {
 	    contextIsolation: false,
 	    nodeIntegration: true,
@@ -79,7 +24,7 @@ function createWindow () {
 		    click () {
 			dialog.showOpenDialog(win,
 					      { title : "Load configuration file", 
-						defaultPath : getDefaultDialogPath(),
+						defaultPath : app.getPath('temp'),
 						//buttonLabel : "Custom button",
 						filters :[
 						    {name: 'Config file type', extensions: ['cfg']},
@@ -100,12 +45,12 @@ function createWindow () {
 		    }
 		},
 		{
-		    label: 'Save Folder...',
+		    label: 'Select Folder...',
 		    accelerator: 'CmdOrCtrl+F',
 		    click () {
 			dialog.showOpenDialog(win,
 					      { title: "Select folder",
-						defaultPath :  getDefaultDialogPath(),
+						defaultPath :  app.getPath('temp'),
 						properties:["openDirectory"]}
 					     ).then(result => {
 						 setImmediate(function() {
@@ -134,16 +79,13 @@ function createWindow () {
 		    click () {
 			dialog.showSaveDialog(win,
 					      { title : "Save configuration file", 
-						defaultPath : path.join(getDefaultDialogPath(), 'TrimSP.cfg'),
+						defaultPath : app.getPath('temp'),
 						filters :[
 						    {name: 'Config file type', extensions: ['cfg']},
 						    {name: 'All Files', extensions: ['*']}
 						],
 						properties: ['showOverwriteConfirmation']}
 					     ).then(result => {
-						 if (result.canceled || !result.filePath) {
-						     return;
-						 }
 						 setImmediate(function() {
 						     var focusedWindow = BrowserWindow.getFocusedWindow();
 						     focusedWindow.webContents.send('saveFile',result.filePath);
@@ -257,12 +199,18 @@ function createWindow () {
 	{
 	    role: 'viewMenu'
 	},
+	{
+	    role: 'windowMenu'
+	},
 	{
 	    role: 'help',
 	    submenu: [
 		{
-		    label: 'About TrimSP',
-		    click () { showAboutDialog(win); }
+		    role: 'about'
+		},
+		{
+		    label: 'Learn More',
+		    click () { require('electron').shell.openExternal('http://electron.atom.io') }
 		}
 	    ]
 	}
@@ -294,27 +242,19 @@ app.on('activate', () => {
 // Reply to calls from browser button
 ipcMain.on('browseFolder', (event, args) => {
     console.log('received a message: '+args);
-    const senderWindow = BrowserWindow.fromWebContents(event.sender);
-    dialog.showOpenDialog(senderWindow, { title: "Select folder",
-					  defaultPath : getDefaultDialogPath(),
-					  properties:["openDirectory"]}
-			       ).then(result => {
-				     console.log(result)
-				     if (result.canceled || result.filePaths.length === 0) {
-					 event.reply('browseFolderFallback');
-					 return;
-				     }
-				     event.reply('browseFolder', result.filePaths);
-				     app.setPath('temp',result.filePaths[0]);
-				 }).catch(err => {
-				     console.log(err);
-				 })
-});
-
-ipcMain.on('updateWorkPath', (event, folder) => {
-    if (folder) {
-	currentWorkPath = folder;
-    }
+    dialog.showOpenDialog({ title: "Select folder",
+			    defaultPath : app.getPath('temp'),
+			    properties:["openDirectory"]}
+			 ).then(result => {
+			     console.log(result)
+			     setImmediate(function() {
+				 var focusedWindow = BrowserWindow.getFocusedWindow();
+				 focusedWindow.webContents.send('browseFolder',result.filePaths);
+				 app.setPath('temp',result.filePaths[0]);
+			     });
+			 }).catch(err => {
+			     console.log(err);
+			 })
 });
 
 //ipcMain.on('browseFolder-send', (event, args) => {

package.json

@@ -1,16 +1,12 @@
 {
   "name": "TrimSP",
-  "version": "1.0.5",
+  "version": "1.0.2",
   "description": "Trim.SP simulation to calculate stopping profile of implanted probes.",
   "main": "main.js",
   "scripts": {
     "start": "electron-forge start",
     "package": "electron-forge package",
-    "make": "electron-forge make",
-    "make:flatpak": "FORGE_FLATPAK=1 electron-forge make --targets=@electron-forge/maker-flatpak",
-    "checksums:md5": "sh -c 'for d in out/make/deb/x64 out/make/rpm/x64 out/make/flatpak/x86_64; do [ -d \"$d\" ] || continue; for f in \"$d\"/*; do [ -f \"$f\" ] || continue; case \"$f\" in *.deb|*.rpm|*.flatpak) base=$(basename \"$f\"); (cd \"$d\" && md5sum \"$base\" > \"$base.md5\");; esac; done; done'",
-    "checksums:sha256": "sh -c 'for d in out/make/deb/x64 out/make/rpm/x64 out/make/flatpak/x86_64; do [ -d \"$d\" ] || continue; for f in \"$d\"/*; do [ -f \"$f\" ] || continue; case \"$f\" in *.deb|*.rpm|*.flatpak) base=$(basename \"$f\"); (cd \"$d\" && sha256sum \"$base\" > \"$base.sha256\");; esac; done; done'",
-    "checksums": "npm run checksums:md5 && npm run checksums:sha256"
+    "make": "electron-forge make"
   },
   "keywords": [
     "TRIM",
@@ -21,14 +17,47 @@
   "devDependencies": {
     "@electron-forge/cli": "^6.0.0-beta.57",
     "@electron-forge/maker-deb": "^6.0.0-beta.57",
-    "@electron-forge/maker-flatpak": "^7.11.1",
     "@electron-forge/maker-rpm": "^6.0.0-beta.57",
     "@electron-forge/maker-squirrel": "^6.0.0-beta.57",
     "@electron-forge/maker-zip": "^6.0.0-beta.57",
-    "electron": "40.6.0"
+    "electron": "^11.2.1"
   },
   "dependencies": {
     "plotly.js-dist": "^1.58.4"
   },
-  "config": {}
+  "config": {
+    "forge": {
+      "packagerConfig": {
+        "icon": "appicons/icons/png/1024x1024.png",
+        "ignore": [
+          "Readme.md",
+          "ToDo.txt",
+          "TrimSP.cfg",
+          "fortran/*"
+        ]
+      },
+      "makers": [
+        {
+          "name": "@electron-forge/maker-squirrel",
+          "config": {
+            "name": "TrimSP"
+          }
+        },
+        {
+          "name": "@electron-forge/maker-zip",
+          "platforms": [
+            "darwin"
+          ]
+        },
+        {
+          "name": "@electron-forge/maker-deb",
+          "config": {}
+        },
+        {
+          "name": "@electron-forge/maker-rpm",
+          "config": {}
+        }
+      ]
+    }
+  }
 }

packaging/linux/trimsp.desktop.ejs

@@ -1,10 +0,0 @@
-[Desktop Entry]
-Name=<%= productName %>
-<% if (description) { print(`Comment=${description}\n`) } %>GenericName=<%= genericName %>
-Exec=<%= name %> %U<% if (execArguments && execArguments.length) { %> <%= execArguments.join(' ') %><% } %>
-Icon=<%= name %>
-Type=Application
-StartupNotify=true
-StartupWMClass=TrimSP
-Categories=<%= categories.join(';') %>;
-<% if (mimeType && mimeType.length) { %>MimeType=<%= mimeType.join(';') %>;<% } %>