Launch directory for runs and exports; Molden file check

CHANGELOG.md

@@ -7,6 +7,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+
+- Molden files are checked before loading. The g-xTB binary's molden writer (tblite) puts the valence electron count in the atomic-number column of `[Atoms]`, and JSmol trusts that column over the element label, so such files showed up as boron/beryllium/carbon with garbled bonds. A dialog now reports the problem and offers "Fix and load", "Fix, load and save…" (writes a `<name>-fixed.molden` copy through the save dialog) or "Load as is". The check also reports, without fixing, an MO coefficient count that does not match the basis size (the usual sign of a missing `[5D]` flag). Files given on the command line go through the same check.
+
+### Changed
+
+- ElemCo.jl and xtb calculations started from a terminal now run in the directory jlmol was started from, so exported files (`orbitals.molden` from an Export step, `xtbopt.xyz`, `xtbopt.log`, ...) and the generated `calculation.jl` / `coord.xyz` stay there. Previously every run used a temporary directory under the OS temp dir that was deleted when the run finished, so exports silently vanished. Launches without a terminal (desktop launcher, Finder, Start menu) keep the temporary directory. The output panel now prints which directory is used and whether it is deleted. The directory comes from `--workdir=PATH` (the `npm start` scripts pass the directory the command was typed in, also from WSL running the Windows binary) or, when started from a terminal, the current directory.
+- Image export and XYZ export in the desktop app now open a save dialog instead of dropping the file silently into the download folder. The dialog defaults to the launch directory when started from a terminal and to the download folder otherwise; the status line shows where the file was saved, or that the export was cancelled.
+- "Choose File" in the desktop app is replaced by an "Open File…" button with a native open dialog that starts in the launch directory when there is one (the browser file picker cannot be pointed at a directory, and its "No file chosen" label would stay stale). The loaded file's name is shown next to the button. Without a launch directory the OS chooses the folder as before. The browser build keeps the file input.
+
 ## [1.5.5] - 2026-09-07
 
 ### Fixed

README.md

@@ -115,6 +115,8 @@ npm install
 npm start
 ```
 
+`npm start` passes the directory you typed it in to the app as `--workdir` (npm itself changes to the package root), so calculations run there and the export dialog defaults to it. Under WSL this also works when `electron` resolves to the Windows binary: the script passes `$WSL_DISTRO_NAME` and the path is mapped to `\\wsl.localhost\<distro>\...` (or `C:\...` for `/mnt/c/...`). For any other start, pass `--workdir=/abs/path` explicitly, or start the app from a terminal, in which case the current directory is used.
+
 The terminal output is kept quiet by default. A full log is always written to `jsmol.log` in the app's user-data directory. To echo the detailed log to the terminal, run with verbose logging:
 
 ```bash
@@ -291,6 +293,7 @@ Run [xtb](https://github.com/grimme-lab/xtb) g-xTB calculations on the current s
 - Set charge, number of unpaired electrons (`--uhf`), and extra xtb flags
 - Configurable xtb command (supports WSL) in Settings → xtb
 - Browser mode shows a message to install jlmol locally; a clear message is shown if xtb is not accessible
+- Working directory: when jlmol is started from a terminal, xtb runs in the directory it was started from, so `coord.xyz`, `xtbopt.xyz`, `xtbopt.log` and the other xtb output files stay there. Started from a desktop launcher, xtb runs in a temporary directory that is deleted after the run. The output panel prints which one is used.
 - Requires the g-xTB binary from [grimme-lab/g-xtb](https://github.com/grimme-lab/g-xtb). At the moment that is all you need — download it, extract it, and make sure the `xtb` binary in its `bin` folder is on your `PATH` (e.g. a symbolic link in `~/bin`) or set its full path in Settings → xtb. No separate xtb installation or parameter-file download is required.
 
 ## ElemCo.jl Integration
@@ -340,6 +343,8 @@ jlmol now includes an integrated calculation runner that can execute ElemCo.jl c
 3. **Run Calculation**: Click "Run Calculation" to execute the calculation
 4. **View Results**: Monitor progress and view calculation output in real-time
 
+When jlmol is started from a terminal, the calculation runs in the directory it was started from: `calculation.jl` and every file the calculation writes (e.g. `orbitals.molden` from an Export step) stay there. Started from a desktop launcher, it runs in a temporary directory that is deleted after the run. The output panel prints which one is used. Image and XYZ exports open a save dialog; its default folder is the launch directory from a terminal and the download folder otherwise, and the status line shows where the file was saved. "Open File…" opens in the launch directory as well.
+
 #### WSL (Windows Subsystem for Linux) Support
 
 For Windows users running Julia under WSL, jlmol provides seamless integration:

css/styles.css

@@ -461,6 +461,26 @@
             margin-bottom: 8px;  /* Add space below the file input */
             display: block;  /* Ensure it's on its own line */
         }
+        #structureFile[hidden] {
+            display: none;  /* the id rule above would beat the hidden attribute */
+        }
+        /* Desktop app: replaces the file input (see js/search.js) */
+        #structureFileNative {
+            margin-bottom: 8px;
+            display: flex;
+            align-items: center;
+            gap: 8px;
+        }
+        #structureFileNative[hidden] {
+            display: none;
+        }
+        #structureFileName {
+            font-size: 12px;
+            color: #666;
+            overflow: hidden;
+            text-overflow: ellipsis;
+            white-space: nowrap;
+        }
         .sample-buttons {
             margin-top: 4px;  /* Add space above the sample buttons */
         }
@@ -1342,7 +1362,7 @@
         }
 
         /* ---- Update-available dialog (js/updater.js) ---- */
-        #updateOverlay {
+        #updateOverlay, #moldenCheckOverlay {
             position: fixed;
             top: 0;
             left: 0;
@@ -1355,7 +1375,7 @@
             z-index: 100000;
         }
 
-        #updateDialog {
+        #updateDialog, #moldenCheckDialog {
             background: white;
             border: 1px solid #ccc;
             border-radius: 8px;
@@ -1423,6 +1443,17 @@
             text-decoration: underline;
         }
 
+        .molden-check-issues {
+            margin: 8px 0 0;
+            padding-left: 20px;
+            font-size: 13px;
+            line-height: 1.4;
+            color: #333;
+        }
+        .molden-check-issues li {
+            margin-bottom: 6px;
+        }
+
         .update-dialog-footer {
             padding: 12px 18px;
             border-top: 1px solid #eee;

index.html

@@ -37,6 +37,7 @@
     <script type="text/javascript" src="js/image-export.js"></script>
     <script type="text/javascript" src="js/molecule-data.js"></script>
     <script type="text/javascript" src="js/viewer-controls.js"></script>
+    <script type="text/javascript" src="js/molden-check.js"></script>
     <script type="text/javascript" src="js/search.js"></script>
     <script type="text/javascript" src="js/orbitals.js"></script>
     <script type="text/javascript" src="js/xyz-editor.js"></script>
@@ -62,6 +63,10 @@
             <div id="version-display" style="font-size: 12px; color: #666; margin-bottom: 16px; padding: 4px 8px; background: #f5f5f5; border-radius: 4px; text-align: center;">jlmol v<span id="version-number">loading...</span></div>
             <h3>Load Structure</h3>
             <input type="file" id="structureFile" accept=".xyz,.pdb,.mol,.cif,.molden" onChange="handleFileSelect(event)" title="Select a molecular structure file">
+            <div id="structureFileNative" hidden>
+                <button id="structureFileButton" title="Select a molecular structure file">Open File…</button>
+                <span id="structureFileName"></span>
+            </div>
             <div class="sample-buttons">
                 <button onclick="loadSample('caffeine.mol')" title="Load a caffeine molecule structure">Caffeine</button>
                 <button onclick="loadSample('buckyball.mol')" title="Load a buckminsterfullerene (C60) structure">Buckyball</button>

js/elemco.js

@@ -1234,12 +1234,16 @@ async function runJuliaInElectron(juliaCode) {
     const prefs = getPreferences();
     const juliaCommand = prefs.juliaCommand || 'julia';
 
+    // Started from a terminal: run in that directory, so @export_molden and
+    // friends write next to the user and nothing is deleted afterwards.
+    // Otherwise a temp work dir, removed after the run.
     let workDir = null;
+    let ownsWorkDir = false;
     function cleanupTempFile() {
-        if (workDir) {
+        if (workDir && ownsWorkDir) {
             native.removeWorkDir(workDir);   // main also reaps on quit
-            workDir = null;
         }
+        workDir = null;
     }
 
     try {
@@ -1273,8 +1277,14 @@ async function runJuliaInElectron(juliaCode) {
         const commandParts = parseCommand(juliaCommand.trim());
         const isWSL = commandParts[0].toLowerCase() === 'wsl';
 
-        // Julia code goes into a scoped work directory
-        workDir = await native.mkWorkDir('jlmol_julia_');
+        // Julia code goes into the work directory
+        const launch = await native.launchDir();
+        if (launch) {
+            workDir = launch.token;
+        } else {
+            workDir = await native.mkWorkDir('jlmol_julia_');
+            ownsWorkDir = true;
+        }
         const workDirPath = await native.workDirPath(workDir);
         await native.writeFile(workDir, 'calculation.jl', juliaCode);
         const sep = native.platform === 'win32' ? '\\' : '/';
@@ -1283,15 +1293,23 @@ async function runJuliaInElectron(juliaCode) {
         // For WSL, convert Windows path to WSL path
         let filePathForCommand = tempFile;
         if (isWSL) {
-            if (/^[A-Za-z]:/.test(tempFile)) {
+            const unc = /^\\\\(?:wsl\.localhost|wsl\$)\\[^\\]+(\\.*)$/.exec(tempFile);
+            if (unc) {
+                // \\wsl.localhost\<distro>\home\... is the distro's own tree
+                // (the launch dir when started from WSL): drop the share.
+                filePathForCommand = unc[1].replace(/\\/g, '/');
+            } else if (/^[A-Za-z]:/.test(tempFile)) {
                 const driveLetter = tempFile.charAt(0).toLowerCase();
                 filePathForCommand = tempFile.replace(/^[A-Za-z]:/, `/mnt/${driveLetter}`).replace(/\\/g, '/');
             } else {
                 filePathForCommand = tempFile.replace(/\\/g, '/');
             }
         }
 
-        outputTextarea.value = `=== JLMol Julia Calculation ===\nTimestamp: ${new Date().toISOString()}\nJulia command: ${juliaCommand}\nTemporary file: ${tempFile}\n${isWSL ? `WSL path: ${filePathForCommand}\n` : ''}Full command: ${juliaCommand} "${filePathForCommand}"\n\n--- Starting calculation ---\n`;
+        const workDirNote = ownsWorkDir
+            ? `Working directory (temporary, deleted after the run): ${workDirPath}`
+            : `Working directory (started from here; exported files stay here): ${workDirPath}`;
+        outputTextarea.value = `=== JLMol Julia Calculation ===\nTimestamp: ${new Date().toISOString()}\nJulia command: ${juliaCommand}\n${workDirNote}\nInput file: ${tempFile}\n${isWSL ? `WSL path: ${filePathForCommand}\n` : ''}Full command: ${juliaCommand} "${filePathForCommand}"\n\n--- Starting calculation ---\n`;
         setStatusText('Starting Julia process...');
 
         // Prepare command and arguments for version check
@@ -1375,8 +1393,11 @@ async function runJuliaInElectron(juliaCode) {
                 close: (code) => {
                     updateOutput();
                     const elapsed = ((Date.now() - startTime) / 1000).toFixed(1);
+                    const cleanupNote = ownsWorkDir
+                        ? '--- Cleanup: temporary work directory deleted ---'
+                        : `--- Files written by the calculation are in ${workDirPath} ---`;
                     cleanupTempFile();
-                    outputTextarea.value += `\n--- Cleanup: Temporary file deleted ---\n`;
+                    outputTextarea.value += `\n${cleanupNote}\n`;
                     if (code === 0) {
                         outputTextarea.value += `\n=== CALCULATION COMPLETED SUCCESSFULLY ===\nElapsed time: ${elapsed} seconds\nExit code: ${code}`;
                         setStatusText(`Julia calculation completed successfully (${elapsed}s)`);

js/image-export.js

@@ -149,3 +149,13 @@ function downloadImage(imageData, filename, format, transparent) {
     const transparencyNote = (format === 'png' && transparent) ? ' with transparent background' : '';
     setStatusText(`${format.toUpperCase()} image exported successfully${transparencyNote}`);
 }
+
+// Desktop app: exports go through a save dialog and main reports the
+// outcome; show the real path (or the cancel) instead of the guess above.
+if (window.jlmolNative && window.jlmolNative.onDownloadDone) {
+    window.jlmolNative.onDownloadDone((state, savedPath) => {
+        if (state === 'completed') setStatusText(`Saved ${savedPath}`);
+        else if (state === 'cancelled') setStatusText('Export cancelled');
+        else setStatusText(`Export failed (${state})`);
+    });
+}