ClickFF · AxiEj · May 15, 2026 · May 16, 2026 · May 16, 2026 · May 16, 2026
diff --git a/about.html b/about.html
@@ -5,6 +5,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
     <title>About MAPLE</title>
     <link rel="stylesheet" href="assets/css/styles.css">
+    <link rel="icon" href="favicon.ico">
 </head>
 <body>
     <header class="top-nav">
@@ -17,7 +18,7 @@
                 <ul>
                     <li><a href="index.html">Home</a></li>
                     <li><a href="general.html">About MAPLE</a></li>
-                    <li><a href="documentation.html">User Guide</a></li>
+                    <li><a href="tutorials/installation.html">User Guide</a></li>
                     <li><a href="articles.html">Articles</a></li>
                     <li><a href="downloads.html">Downloads</a></li>
                     <li><a href="issues.html">Report an issue</a></li>
@@ -58,4 +59,3 @@ <h2>Features</h2>
     </footer>
 </body>
 </html>
-
diff --git a/articles.html b/articles.html
@@ -5,6 +5,7 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>Articles &amp; News — MAPLE</title>
   <link rel="stylesheet" href="assets/css/styles.css">
+  <link rel="icon" href="favicon.ico">
 </head>
 <body>
   <header class="top-nav">
@@ -43,11 +44,11 @@ <h2 id="maple-papers">MAPLE Publications</h2>
       </div>
 
       <div class="card-grid">
-        <a class="card" id="paper-maple" href="https://chemrxiv.org/doi/10.26434/chemrxiv-2026-k7znx" target="_blank" rel="noopener noreferrer">
-          <div class="card-tag">Framework &mdash; January 3, 2026 &middot; ChemRxiv</div>
-          <h3>MAPLE: A General Framework for Automated Molecular Modeling Across Machine Learning Potentials</h3>
-          <p>Presents MAPLE as a comprehensive framework for automated molecular modeling that works seamlessly across different machine learning potentials, providing a unified interface for diverse computational chemistry applications.</p>
-          <p class="mt-1 card-cta">Read on ChemRxiv &rarr;</p>
+        <a class="card" id="paper-maple" href="https://doi.org/10.1039/D6SC01279E" target="_blank" rel="noopener noreferrer">
+          <div class="card-tag">Framework &mdash; April 30, 2026 &middot; Chemical Science</div>
+          <h3>MAPLE: A Machine-Learning Force-Field-Native Platform for Automated Reaction Modeling and Enzyme Design</h3>
+          <p>Presents MAPLE as an MLFF-native molecular modeling platform with a tailored software framework and parallelized algorithms for large-scale, versatile reaction modeling and enzyme design.</p>
+          <p class="mt-1 card-cta">Read in Chemical Science &rarr;</p>
         </a>
       </div>
 

diff --git a/assets/css/styles.css b/assets/css/styles.css
@@ -635,7 +635,7 @@ pre .section { color: #267f99; font-weight: 600; }
 .admonition.note .admonition-title { background: rgba(0, 176, 255, 0.08); color: #0077b3; }
 
 .admonition.tip { border-left-color: var(--color-tip); }
-.admonition.tip .admonition-title { background: rgba(0, 200, 82, 0.08); color: #00873e; }
+.admonition.tip .admonition-title { background: rgba(0, 200, 82, 0.08); color: #007a38; }
 
 .admonition.warning { border-left-color: var(--color-warning); }
 .admonition.warning .admonition-title { background: rgba(255, 145, 0, 0.08); color: #b36500; }

diff --git a/assets/images/scan/cg/butane_torsion_scan_visual_lab_traj_energy.gif b/assets/images/scan/cg/butane_torsion_scan_visual_lab_traj_energy.gif
diff --git a/assets/images/scan/lbfgs/ethanol_torsion_scan_visual_lab_traj_energy.gif b/assets/images/scan/lbfgs/ethanol_torsion_scan_visual_lab_traj_energy.gif
diff --git a/assets/images/scan/rfo/methanol_oh_torsion_scan_visual_lab_traj_energy.gif b/assets/images/scan/rfo/methanol_oh_torsion_scan_visual_lab_traj_energy.gif
diff --git a/assets/images/scan/sd/dimethyl_peroxide_torsion_scan_visual_lab_traj_energy.gif b/assets/images/scan/sd/dimethyl_peroxide_torsion_scan_visual_lab_traj_energy.gif
diff --git a/assets/images/scan/sdcg/glycine_backbone_torsion_scan_visual_lab_traj_energy.gif b/assets/images/scan/sdcg/glycine_backbone_torsion_scan_visual_lab_traj_energy.gif
diff --git a/development.html b/development.html
@@ -5,6 +5,7 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>Development &amp; Releases — MAPLE</title>
   <link rel="stylesheet" href="assets/css/styles.css">
+  <link rel="icon" href="favicon.ico">
 </head>
 <body>
   <header class="top-nav">
@@ -71,7 +72,7 @@ <h3 id="v0-1-0">Version 0.1.0 <span class="text-muted">&mdash; December 31, 2025
         <li><strong>Geometry optimization</strong> &mdash; L-BFGS, RFO, steepest descent, conjugate gradient, DIIS, and bracketing L-BFGS methods.</li>
         <li><strong>Transition state search</strong> &mdash; NEB, CI-NEB, P-RFO, Dimer, and Growing String methods.</li>
         <li><strong>IRC</strong> &mdash; Intrinsic reaction coordinate with GS, LQA, HPC, and EulerPC integrators.</li>
-        <li><strong>PES scan</strong> &mdash; 1D relaxed and rigid scans along bonds, angles, and dihedrals.</li>
+        <li><strong>PES scan</strong> &mdash; 1D, 2D, and 3D relaxed or rigid scans along bonds, angles, and dihedrals.</li>
         <li><strong>Solvation</strong> &mdash; GBSA implicit solvation and explicit solvent models.</li>
         <li><strong>Constraints</strong> &mdash; Fix atoms, bonds, angles, and dihedral angles during optimization.</li>
         <li><strong>GPU acceleration</strong> &mdash; Full CUDA support for all ML potential evaluations.</li>

diff --git a/downloads.html b/downloads.html
@@ -5,6 +5,7 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>Downloads — MAPLE</title>
   <link rel="stylesheet" href="assets/css/styles.css">
+  <link rel="icon" href="favicon.ico">
 </head>
 <body>
   <header class="top-nav">
@@ -38,9 +39,10 @@ <h1>Downloads</h1>
   <div class="page-body">
     <article>
       <h2 id="source-code">Source Code</h2>
-      <p>MAPLE is hosted on GitHub. Clone the repository to get the latest development version (see the <a href="#license">license terms</a> below).</p>
+      <p>MAPLE is hosted on GitHub. Clone the public source repository for the published code line (see the <a href="#license">license terms</a> below).</p>
       <p><a href="https://github.com/ClickFF/MAPLE" target="_blank" rel="noopener noreferrer" class="btn btn-primary">Source Code on GitHub &rarr;</a></p>
       <pre><code>git clone https://github.com/ClickFF/MAPLE.git</code></pre>
+      <p><strong>Documentation note:</strong> The SCAN method pages are synchronized with the MAPLE <code>debug/OPT</code> development snapshot verified at commit <code>85a39ca</code>. The public upstream link may lag until those changes are merged.</p>
 
       <h2 id="installation">Installation</h2>
       <p>Follow the step-by-step guide to set up Python, PyTorch, and the ML potential dependencies.</p>

diff --git a/favicon.ico b/favicon.ico
diff --git a/functions/constrain.html b/functions/constrain.html
@@ -5,6 +5,7 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>Constraints - MAPLE Documentation</title>
   <link rel="stylesheet" href="../assets/css/styles.css">
+  <link rel="icon" href="../favicon.ico">
 </head>
 <body>
   <header class="top-nav">
@@ -75,6 +76,8 @@
                     <li><a href="../tasks/opt/opt_lbfgs.html">L-BFGS</a></li>
                     <li><a href="../tasks/opt/opt_rfo.html">RFO</a></li>
                     <li><a href="../tasks/opt/opt_sd.html">SD</a></li>
+                    <li><a href="../tasks/opt/opt_cg.html">CG</a></li>
+                    <li><a href="../tasks/opt/opt_sdcg.html">SD/CG</a></li>
                   </ul>
                 </li>
                 <li>
@@ -92,6 +95,9 @@
                   <ul class="children">
                     <li><a href="../tasks/scan/scan_lbfgs.html">L-BFGS</a></li>
                     <li><a href="../tasks/scan/scan_rfo.html">RFO</a></li>
+                    <li><a href="../tasks/scan/scan_sd.html">SD</a></li>
+                    <li><a href="../tasks/scan/scan_cg.html">CG</a></li>
+                    <li><a href="../tasks/scan/scan_sdcg.html">SD/CG</a></li>
                   </ul>
                 </li>
                 <li>
@@ -225,7 +231,7 @@ <h2 id="dihedral-constraints">Dihedral Constraints (D Command)</h2>
 
         <h2 id="scan-coordinates">Scan Coordinates (S Command)</h2>
 
-        <p>The <code>S</code> command defines an internal coordinate to be scanned over a range of values. It is used exclusively with <code>#scan</code> tasks. The scan systematically varies the specified coordinate from its initial value, stepping by a fixed increment for a given number of steps. At each step, the remaining degrees of freedom are optimized.</p>
+        <p>The <code>S</code> command defines an internal coordinate to be scanned over a range of values. It is used exclusively with <code>#scan</code> tasks. The scan systematically varies the specified coordinate from its initial value, stepping by a fixed increment for the requested number of steps. Relaxed scans optimize the remaining degrees of freedom at each scan point; rigid scans move the detected connected fragment to satisfy the target coordinate without optimization.</p>
 
         <table>
           <thead>
@@ -254,17 +260,17 @@ <h2 id="scan-coordinates">Scan Coordinates (S Command)</h2>
           </tbody>
         </table>
 
-        <p>The <code>step</code> parameter specifies the increment per step (in Angstroms for bond lengths, degrees for angles), and <code>nsteps</code> is the number of steps to take.</p>
+        <p>The <code>step</code> parameter specifies the increment per step (in Angstroms for bond lengths, degrees for angles and dihedrals). MAPLE writes the initial point plus each requested step, so one <code>S</code> line produces <code>nsteps + 1</code> scan points.</p>
 
         <pre><code>S 1 2 0.05 10</code></pre>
-        <p>This scans the bond length between atoms 1 and 2, increasing it by 0.05 Angstroms at each of 10 steps.</p>
+        <p>This scans the bond length between atoms 1 and 2 over 11 points: the initial geometry plus 10 increments of 0.05 Angstroms.</p>
 
         <pre><code>S 2 1 3 10.0 6</code></pre>
-        <p>This scans the bond angle at atom 1 (between atoms 2, 1, and 3), increasing it by 10 degrees at each of 6 steps.</p>
+        <p>This scans the bond angle at atom 1 (between atoms 2, 1, and 3) over 7 points: the initial angle plus 6 increments of 10 degrees.</p>
 
         <div class="admonition tip">
           <p class="admonition-title">Tip</p>
-          <p>You can define multiple <code>S</code> commands to perform a multi-dimensional scan. MAPLE will systematically vary all scan coordinates, creating a grid of geometries across the combined coordinate space.</p>
+          <p>You can define up to three <code>S</code> commands for 1D, 2D, or 3D scans. MAPLE varies all scan coordinates as a Cartesian-product grid across the combined coordinate space.</p>
         </div>
 
         <h2 id="post-command">POST Command</h2>
@@ -285,7 +291,7 @@ <h2 id="examples">Examples</h2>
         <h3>Constrained optimization: freeze atoms and fix a bond</h3>
         <pre><code>#model = uma
 #device = gpu0
-#opt(method=lbfgs, convergence=tight)
+#opt(method=lbfgs, level=tight)
 
 0 1
 C    0.000000    0.000000    0.000000
@@ -325,36 +331,27 @@ <h3>Constrained optimization: fix a dihedral angle</h3>
         <p>The dihedral angle along H(5)-C(1)-C(2)-C(3) is fixed at its initial value while the rest of the geometry relaxes.</p>
 
         <h3>1D bond scan</h3>
-        <pre><code>#model = uma
-#device = gpu0
-#scan(method=lbfgs)
+        <p>Checked-in MAPLE example: <code>example/scan/C18.inp</code>. The full coordinate block is kept in the source example; the scan command belongs after that coordinate block:</p>
+        <pre><code>#model=aimnet2nse
+#scan(mode=rigid)
+#device=gpu0
 
-0 1
-C    0.000000    0.000000    0.000000
-C    1.540000    0.000000    0.000000
-H   -0.392000    1.011000    0.000000
-H   -0.392000   -0.506000    0.875000
-H   -0.392000   -0.506000   -0.875000
-H    1.932000    0.506000    0.875000
-H    1.932000    0.506000   -0.875000
-H    1.932000   -1.011000    0.000000
+[XYZ coordinates from example/scan/C18.inp]
 
-S 1 2 0.05 10</code></pre>
-        <p>Scans the C-C bond in 10 increments of 0.05 Angstroms.</p>
+S 1 36 0.1 50</code></pre>
+        <p>Scans the atom 1&ndash;36 distance over 51 points: the initial geometry plus 50 increments of 0.1 Angstroms.</p>
 
-        <h3>2D scan: bond length + bond angle</h3>
-        <pre><code>#model = uma
-#device = gpu0
-#scan(method=lbfgs)
+        <h3>2D scan: two distance coordinates</h3>
+        <p>Checked-in MAPLE example: <code>example/scan/da.inp</code>. It defines a two-coordinate relaxed scan with the default L-BFGS method. The long coordinate block is omitted here, but the <code>S</code> commands must remain after it:</p>
+        <pre><code>#model=ANI-1xnr
+#scan
+#device=gpu0
 
-0 1
-O    0.000000    0.000000    0.117300
-H    0.000000    0.757160   -0.469200
-H    0.000000   -0.757160   -0.469200
+[XYZ coordinates from example/scan/da.inp]
 
-S 1 2 0.05 5
-S 2 1 3 5.0 6</code></pre>
-        <p>Simultaneously scans the O-H bond length (5 steps of 0.05 Angstroms) and the H-O-H bond angle (6 steps of 5 degrees), producing a 2D potential energy surface.</p>
+S 11 52 -0.1 15
+S 14 51 -0.1 15</code></pre>
+        <p>Each coordinate gives 16 values, producing a 256-point 2D potential energy surface.</p>
 
         <h3>Using the POST command for external constraints</h3>
         <pre><code>#model = uma

diff --git a/functions/solvent.html b/functions/solvent.html
@@ -5,6 +5,7 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>Solvation - MAPLE Documentation</title>
   <link rel="stylesheet" href="../assets/css/styles.css">
+  <link rel="icon" href="../favicon.ico">
 </head>
 <body>
   <header class="top-nav">
@@ -75,6 +76,8 @@
                     <li><a href="../tasks/opt/opt_lbfgs.html">L-BFGS</a></li>
                     <li><a href="../tasks/opt/opt_rfo.html">RFO</a></li>
                     <li><a href="../tasks/opt/opt_sd.html">SD</a></li>
+                    <li><a href="../tasks/opt/opt_cg.html">CG</a></li>
+                    <li><a href="../tasks/opt/opt_sdcg.html">SD/CG</a></li>
                   </ul>
                 </li>
                 <li>
@@ -92,6 +95,9 @@
                   <ul class="children">
                     <li><a href="../tasks/scan/scan_lbfgs.html">L-BFGS</a></li>
                     <li><a href="../tasks/scan/scan_rfo.html">RFO</a></li>
+                    <li><a href="../tasks/scan/scan_sd.html">SD</a></li>
+                    <li><a href="../tasks/scan/scan_cg.html">CG</a></li>
+                    <li><a href="../tasks/scan/scan_sdcg.html">SD/CG</a></li>
                   </ul>
                 </li>
                 <li>
@@ -262,7 +268,7 @@ <h2 id="usage-example">Usage Example</h2>
         <pre><code>#model = uma
 #device = gpu0
 #solv(implicit=gbsa)
-#opt(method=lbfgs, convergence=tight)
+#opt(method=lbfgs, level=tight)
 
 0 1
 C    0.000000    0.000000    0.000000
@@ -278,7 +284,7 @@ <h2 id="usage-example">Usage Example</h2>
         <pre><code>#model = uma
 #device = gpu0
 #solv(explicit=water, radius=10.0, clash_cutoff=1.5, fix_dis=8.0)
-#opt(method=lbfgs, convergence=medium)
+#opt(method=lbfgs, level=medium)
 
 0 1
 C    0.000000    0.000000    0.000000

diff --git a/general.html b/general.html
@@ -5,6 +5,7 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>About MAPLE — Machine-learning Potential for Landscape Exploration</title>
   <link rel="stylesheet" href="assets/css/styles.css">
+  <link rel="icon" href="favicon.ico">
 </head>
 <body>
   <header class="top-nav">
@@ -126,7 +127,7 @@ <h3>Transition State</h3>
         <a class="card" href="tasks/scan/scan.html">
           <div class="card-tag">scan</div>
           <h3>PES Scan</h3>
-          <p>1D to N-dimensional relaxed or rigid scans along chosen internal coordinates.</p>
+          <p>1D, 2D, or 3D relaxed or rigid scans along chosen internal coordinates.</p>
         </a>
         <a class="card" href="tasks/irc/irc.html">
           <div class="card-tag">irc</div>

diff --git a/home1.html b/home1.html
@@ -5,6 +5,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
     <title>MAPLE User Guide</title>
     <link rel="stylesheet" href="assets/css/styles.css">
+    <link rel="icon" href="favicon.ico">
 </head>
 <body>
     <main>
@@ -85,11 +86,13 @@ <h3><a href="tasks/ts/ts.html">Transition State Search</a></h3>
                     <p style="color: #30c0b4;"><strong>II. Input Structure Requirements</strong></p>
 
                     <h3><a href="tasks/scan/scan.html">PES Scan</a></h3>
-                    <p style="color: #00b0f0;">Sweeps selected bonds, angles, or dihedrals to build a relaxed potential-energy map along chosen coordinates.</p>
+                    <p style="color: #00b0f0;">Sweeps selected bonds, angles, or dihedrals to build 1D, 2D, or 3D relaxed/rigid potential-energy maps.</p>
                     <p style="color: #30c0b4;"><strong>I. Input Parameters</strong></p>
                     <p><a href="tasks/scan/scan_lbfgs.html">→ method: L-BFGS</a></p>
-                    <p style="color: #ee822f; margin-left: 0.75in;"><strong>I. Adjustable Parameters</strong></p>
                     <p><a href="tasks/scan/scan_rfo.html">→ method: RFO</a></p>
+                    <p><a href="tasks/scan/scan_sd.html">→ method: SD</a></p>
+                    <p><a href="tasks/scan/scan_cg.html">→ method: CG</a></p>
+                    <p><a href="tasks/scan/scan_sdcg.html">→ method: SD/CG</a></p>
                     <p style="color: #ee822f; margin-left: 0.75in;"><strong>I. Adjustable Parameters</strong></p>
                     <p style="color: #30c0b4;"><strong>II. Output File Contents</strong></p>
 

diff --git a/index.html b/index.html
@@ -5,6 +5,7 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>MAPLE — Machine-learning Potential for Landscape Exploration</title>
   <link rel="stylesheet" href="assets/css/styles.css">
+  <link rel="icon" href="favicon.ico">
 </head>
 <body>
   <header class="top-nav">
@@ -77,7 +78,7 @@ <h3>Vibrational Analysis</h3>
           <a class="feature-card" href="tasks/scan/scan.html">
             <div class="icon">&#128506;&#65039;</div>
             <h3>PES Scanning</h3>
-            <p>1D to N-dimensional relaxed or rigid scans. Map energy landscapes along chosen coordinates.</p>
+            <p>1D, 2D, or 3D relaxed or rigid scans. Map energy landscapes along chosen coordinates.</p>
           </a>
           <a class="feature-card" href="functions/solvent.html">
             <div class="icon">&#127754;</div>
@@ -100,6 +101,10 @@ <h3>More Coming Soon</h3>
 
       <aside class="news-sidebar">
         <h2><a href="articles.html#news">Articles &amp; News</a></h2>
+        <a class="news-item" href="https://doi.org/10.1039/D6SC01279E" target="_blank" rel="noopener noreferrer">
+          <div class="date">April 30, 2026 &middot; Chemical Science</div>
+          <p>MAPLE published in Chemical Science as an MLFF-native platform for automated reaction modeling and enzyme design.</p>
+        </a>
         <a class="news-item" href="https://github.com/ClickFF/MAPLE/releases/tag/v.0.1.3" target="_blank" rel="noopener noreferrer">
           <div class="date">April 1, 2026</div>
           <p>MAPLE v0.1.3 released with expanded MD workflows, UMA/MACEPol updates, and IRC/debug cleanup.</p>
@@ -108,10 +113,6 @@ <h2><a href="articles.html#news">Articles &amp; News</a></h2>
           <div class="date">February 7, 2026</div>
           <p>MAPLE v0.1.1 released with AutoNEB, NVE MD, SDCG, and new IRC integrators.</p>
         </a>
-        <a class="news-item" href="https://chemrxiv.org/doi/10.26434/chemrxiv-2026-k7znx" target="_blank" rel="noopener noreferrer">
-          <div class="date">January 3, 2026 &middot; ChemRxiv</div>
-          <p>MAPLE: A General Framework for Automated Molecular Modeling Across Machine Learning Potentials.</p>
-        </a>
         <a class="news-item" href="https://github.com/ClickFF/MAPLE/releases/tag/v.0.1.0" target="_blank" rel="noopener noreferrer">
           <div class="date">December 31, 2025</div>
           <p>MAPLE v0.1.0 marked the first public release with core optimization, TS, IRC, and frequency tools.</p>

diff --git a/issues.html b/issues.html
@@ -5,6 +5,7 @@
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>Report an Issue — MAPLE</title>
   <link rel="stylesheet" href="assets/css/styles.css">
+  <link rel="icon" href="favicon.ico">
 </head>
 <body>
   <header class="top-nav">