quantum-spherifier 1.0.0

package/web/public/css/dashboard.css

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+/* quantum-spherifier v1.0 — Dashboard CSS
+ * Design language: quantum / scientific / dark-accent with quantum-blue + purple
+ */
+
+:root {
+  --bg:        #0a0e1a;
+  --bg-card:   #111729;
+  --bg-card-2: #1a2238;
+  --border:    #1f2a44;
+  --text:      #e6edf3;
+  --muted:     #8b949e;
+  --accent:    #4cc2ff;        /* quantum blue */
+  --accent-2:  #7c5cff;        /* quantum purple */
+  --green:     #3fb950;
+  --yellow:    #d29922;
+  --red:       #f85149;
+  --purple:    #bc8cff;
+  --cyan:      #39d0d8;
+  --pink:      #ff6ec7;
+  --radius:    10px;
+  --shadow:    0 4px 16px rgba(0,0,0,0.3);
+  --mono:      ui-monospace, "SF Mono", Menlo, Consolas, "Liberation Mono", monospace;
+  --sans:      -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif;
+}
+
+* { box-sizing: border-box; }
+
+body {
+  margin: 0;
+  background: var(--bg);
+  background-image: radial-gradient(circle at 20% 0%, rgba(124, 92, 255, 0.08) 0%, transparent 40%),
+                    radial-gradient(circle at 80% 100%, rgba(76, 194, 255, 0.06) 0%, transparent 40%);
+  color: var(--text);
+  font-family: var(--sans);
+  font-size: 14px;
+  line-height: 1.5;
+  min-height: 100vh;
+}
+
+/* Top bar */
+.topbar {
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+  padding: 16px 24px;
+  background: linear-gradient(180deg, #0f1626, #0a0e1a);
+  border-bottom: 1px solid var(--border);
+}
+
+.brand { display: flex; gap: 16px; align-items: center; }
+.brand .logo { font-size: 32px; line-height: 1; filter: drop-shadow(0 0 8px var(--accent-2)); }
+.brand h1 {
+  margin: 0;
+  font-size: 18px;
+  font-weight: 600;
+  letter-spacing: -0.02em;
+}
+.brand .alias { color: var(--accent-2); font-weight: 500; }
+.brand .version {
+  font-size: 11px;
+  font-weight: 400;
+  color: var(--accent);
+  padding: 2px 6px;
+  border: 1px solid var(--accent);
+  border-radius: 4px;
+  margin-left: 6px;
+}
+.brand p {
+  margin: 4px 0 0;
+  font-size: 12px;
+  color: var(--muted);
+  max-width: 720px;
+}
+
+.status-chips { display: flex; gap: 8px; flex-wrap: wrap; }
+.chip {
+  background: var(--bg-card);
+  border: 1px solid var(--border);
+  border-radius: 999px;
+  padding: 4px 12px;
+  font-size: 11px;
+  font-family: var(--mono);
+  color: var(--muted);
+}
+.chip-ok { color: var(--green); border-color: var(--green); }
+
+/* Tabs */
+.tabs {
+  display: flex;
+  gap: 0;
+  padding: 0 24px;
+  border-bottom: 1px solid var(--border);
+  background: var(--bg-card);
+  overflow-x: auto;
+}
+.tab {
+  background: none;
+  border: none;
+  border-bottom: 2px solid transparent;
+  color: var(--muted);
+  padding: 12px 16px;
+  cursor: pointer;
+  font-size: 13px;
+  font-weight: 500;
+  transition: color 0.15s, border-color 0.15s;
+  white-space: nowrap;
+}
+.tab:hover { color: var(--text); }
+.tab.active { color: var(--accent); border-bottom-color: var(--accent); }
+
+/* Layout */
+.layout { padding: 24px; }
+.panel { display: none; }
+.panel.active { display: block; }
+
+.panel-header {
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+  margin-bottom: 16px;
+  gap: 12px;
+  flex-wrap: wrap;
+}
+.panel-header h2 { margin: 0; font-size: 16px; font-weight: 600; }
+.filter-group { display: flex; gap: 8px; align-items: center; }
+
+/* Feed */
+.feed {
+  background: var(--bg-card);
+  border: 1px solid var(--border);
+  border-radius: var(--radius);
+  padding: 12px;
+  max-height: 70vh;
+  overflow-y: auto;
+  font-family: var(--mono);
+  font-size: 12px;
+}
+.feed-entry {
+  padding: 8px 10px;
+  border-bottom: 1px solid var(--border);
+  display: flex;
+  gap: 12px;
+}
+.feed-entry:last-child { border-bottom: none; }
+.feed-time { color: var(--muted); flex-shrink: 0; min-width: 80px; }
+.feed-tag {
+  font-weight: 600;
+  flex-shrink: 0;
+  min-width: 120px;
+}
+.feed-tag.cycle      { color: var(--accent); }
+.feed-tag.routed     { color: var(--cyan); }
+.feed-tag.hypothesis { color: var(--green); }
+.feed-tag.patent     { color: var(--purple); }
+.feed-tag.archive    { color: var(--yellow); }
+.feed-tag.error      { color: var(--red); }
+.feed-tag.safety     { color: var(--red); }
+.feed-tag.plan       { color: var(--accent); }
+.feed-tag.ann        { color: var(--muted); }
+.feed-tag.metrics    { color: var(--muted); }
+.feed-tag.clusters   { color: var(--pink); }
+.feed-tag.system     { color: var(--muted); }
+.feed-msg { color: var(--text); flex: 1; }
+
+/* Research Lines grid */
+.lines-grid {
+  display: grid;
+  grid-template-columns: repeat(auto-fill, minmax(320px, 1fr));
+  gap: 16px;
+}
+.line-card {
+  background: var(--bg-card);
+  border: 1px solid var(--border);
+  border-radius: var(--radius);
+  padding: 20px;
+  position: relative;
+  overflow: hidden;
+}
+.line-card::before {
+  content: '';
+  position: absolute;
+  top: 0; left: 0; right: 0;
+  height: 3px;
+}
+.line-card.qec::before    { background: var(--accent); }
+.line-card.qubits::before { background: var(--green); }
+.line-card.algo::before   { background: var(--purple); }
+.line-card.sim::before    { background: var(--cyan); }
+.line-card h3 {
+  margin: 0 0 8px;
+  font-size: 15px;
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+}
+.line-card .line-badge {
+  font-size: 10px;
+  padding: 2px 8px;
+  border-radius: 4px;
+  font-weight: 600;
+}
+.line-card.qec .line-badge    { background: rgba(76,194,255,0.15); color: var(--accent); }
+.line-card.qubits .line-badge { background: rgba(63,185,80,0.15); color: var(--green); }
+.line-card.algo .line-badge   { background: rgba(188,140,255,0.15); color: var(--purple); }
+.line-card.sim .line-badge    { background: rgba(57,208,216,0.15); color: var(--cyan); }
+.line-card .goal { font-size: 13px; color: var(--text); margin-bottom: 12px; }
+.line-card .metrics { font-size: 11px; color: var(--muted); }
+.line-card .metrics strong { color: var(--text); }
+.line-card .cycles {
+  margin-top: 12px;
+  padding-top: 12px;
+  border-top: 1px solid var(--border);
+  font-size: 12px;
+  font-family: var(--mono);
+  color: var(--accent);
+}
+
+/* Archive */
+.archive-list { display: grid; gap: 8px; }
+.archive-card {
+  background: var(--bg-card);
+  border: 1px solid var(--border);
+  border-radius: var(--radius);
+  padding: 14px 16px;
+  display: grid;
+  grid-template-columns: 80px 1fr auto;
+  gap: 16px;
+  align-items: center;
+}
+.archive-card .date { font-family: var(--mono); font-size: 11px; color: var(--muted); }
+.archive-card .title { font-weight: 600; }
+.archive-card .meta { font-size: 12px; color: var(--muted); margin-top: 4px; }
+.archive-card .tags { display: flex; gap: 6px; flex-wrap: wrap; }
+.tag {
+  font-size: 10px;
+  padding: 2px 8px;
+  border-radius: 4px;
+  background: var(--bg-card-2);
+  color: var(--muted);
+  font-family: var(--mono);
+}
+.tag.patent_ready { background: rgba(63, 185, 80, 0.15); color: var(--green); }
+.tag.patent_pending { background: rgba(210, 153, 34, 0.15); color: var(--yellow); }
+.tag.final_result { background: rgba(188, 140, 255, 0.15); color: var(--purple); }
+.tag.cross_linked { background: rgba(255, 110, 199, 0.15); color: var(--pink); }
+.tag.qec { background: rgba(76,194,255,0.15); color: var(--accent); }
+.tag.qubits { background: rgba(63,185,80,0.15); color: var(--green); }
+.tag.algorithms { background: rgba(188,140,255,0.15); color: var(--purple); }
+.tag.molecular_simulation { background: rgba(57,208,216,0.15); color: var(--cyan); }
+
+/* Patents */
+.patents-list { display: grid; gap: 12px; }
+.patent-card {
+  background: var(--bg-card);
+  border: 1px solid var(--border);
+  border-left: 4px solid var(--purple);
+  border-radius: var(--radius);
+  padding: 14px 16px;
+}
+.patent-card h3 { margin: 0 0 8px; font-size: 14px; color: var(--purple); }
+.patent-card .meta { font-size: 12px; color: var(--muted); margin-bottom: 8px; }
+.patent-card ol { margin: 0; padding-left: 20px; font-size: 12px; }
+.patent-card ol li { margin-bottom: 4px; }
+
+/* Clusters */
+.clusters-list { display: grid; gap: 16px; }
+.cluster-card {
+  background: var(--bg-card);
+  border: 1px solid var(--border);
+  border-radius: var(--radius);
+  padding: 20px;
+}
+.cluster-card.filing-ready {
+  border-left: 4px solid var(--green);
+  background: linear-gradient(90deg, rgba(63,185,80,0.05), var(--bg-card) 30%);
+}
+.cluster-card.filing-ready .cluster-title::before {
+  content: '★ ';
+  color: var(--green);
+}
+.cluster-card .cluster-title {
+  font-size: 15px;
+  font-weight: 600;
+  margin: 0 0 8px;
+  color: var(--text);
+}
+.cluster-card .cluster-meta {
+  font-size: 12px;
+  color: var(--muted);
+  margin-bottom: 12px;
+  display: flex;
+  gap: 12px;
+  flex-wrap: wrap;
+}
+.cluster-card .cluster-meta .status-filing { color: var(--green); font-weight: 600; }
+.cluster-card .cluster-summary {
+  font-size: 13px;
+  color: var(--text);
+  white-space: pre-wrap;
+  background: var(--bg-card-2);
+  border-radius: 6px;
+  padding: 12px;
+  margin-bottom: 12px;
+  font-family: var(--mono);
+}
+.cluster-card .cluster-members { font-size: 12px; color: var(--muted); }
+.cluster-card .cluster-members li { margin-bottom: 4px; }
+.cluster-card .cluster-concepts {
+  margin-top: 8px;
+  display: flex;
+  gap: 6px;
+  flex-wrap: wrap;
+}
+
+/* KG */
+.kg-source {
+  background: var(--bg-card);
+  border: 1px solid var(--border);
+  border-radius: var(--radius);
+  padding: 14px;
+  font-family: var(--mono);
+  font-size: 12px;
+  overflow: auto;
+  max-height: 60vh;
+  white-space: pre-wrap;
+  color: var(--text);
+}
+
+/* Metrics */
+.metrics-grid {
+  display: grid;
+  grid-template-columns: repeat(auto-fill, minmax(220px, 1fr));
+  gap: 12px;
+}
+.metric-card {
+  background: var(--bg-card);
+  border: 1px solid var(--border);
+  border-radius: var(--radius);
+  padding: 14px;
+}
+.metric-card .label { font-size: 11px; color: var(--muted); text-transform: uppercase; letter-spacing: 0.05em; }
+.metric-card .value { font-size: 24px; font-weight: 600; font-family: var(--mono); margin-top: 4px; }
+.metric-card .sub { font-size: 11px; color: var(--muted); margin-top: 4px; }
+
+/* Guidance */
+.guide-form textarea {
+  width: 100%;
+  background: var(--bg-card);
+  border: 1px solid var(--border);
+  border-radius: var(--radius);
+  padding: 12px;
+  color: var(--text);
+  font-family: var(--sans);
+  font-size: 14px;
+  resize: vertical;
+}
+.guide-actions {
+  display: flex;
+  gap: 12px;
+  align-items: center;
+  margin-top: 12px;
+}
+.btn-primary {
+  background: linear-gradient(135deg, var(--accent), var(--accent-2));
+  color: #001019;
+  border: none;
+  border-radius: 6px;
+  padding: 8px 20px;
+  font-size: 13px;
+  font-weight: 600;
+  cursor: pointer;
+}
+.btn-primary:hover { filter: brightness(1.15); }
+.btn-mini {
+  background: var(--bg-card-2);
+  color: var(--text);
+  border: 1px solid var(--border);
+  border-radius: 6px;
+  padding: 4px 12px;
+  font-size: 12px;
+  cursor: pointer;
+}
+.btn-mini:hover { background: var(--bg-card); }
+
+select, input[type="search"] {
+  background: var(--bg-card);
+  border: 1px solid var(--border);
+  border-radius: 6px;
+  color: var(--text);
+  padding: 6px 10px;
+  font-size: 13px;
+}
+
+.quick-directives { display: flex; flex-direction: column; gap: 8px; margin-top: 12px; }
+.btn-quick {
+  background: var(--bg-card);
+  border: 1px solid var(--border);
+  border-left: 3px solid var(--accent-2);
+  border-radius: 6px;
+  color: var(--text);
+  padding: 10px 14px;
+  text-align: left;
+  cursor: pointer;
+  font-size: 13px;
+}
+.btn-quick:hover { background: var(--bg-card-2); border-left-color: var(--accent); }
+
+/* Footer */
+.footer {
+  display: flex;
+  justify-content: space-between;
+  padding: 16px 24px;
+  border-top: 1px solid var(--border);
+  background: var(--bg-card);
+  font-size: 12px;
+  color: var(--muted);
+}
+
+/* Utilities */
+.muted { color: var(--muted); }
+.small { font-size: 12px; }
+a { color: var(--accent); }
+
+/* Responsive */
+@media (max-width: 768px) {
+  .topbar { flex-direction: column; gap: 12px; align-items: flex-start; }
+  .archive-card { grid-template-columns: 1fr; }
+  .feed-entry { flex-direction: column; gap: 4px; }
+  .feed-tag { min-width: 0; }
+  .lines-grid { grid-template-columns: 1fr; }
+}

package/web/public/index.html

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+<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <link rel="icon" type="image/png" href="favicon.png">
+  <title>quantum-spherifier (:qSpherifier) v1.0 — Autonomous Quantum Computing Research Agent</title>
+  <link rel="stylesheet" href="/css/dashboard.css" />
+</head>
+<body>
+  <header class="topbar">
+    <div class="brand">
+      <img class="logo" width="64px" src="qspherifier.png">
+      <div>
+        <h1>quantum-spherifier <span class="alias">:qSpherifier</span> <span class="version">v1.0</span></h1>
+        <p>Autonomous Scientific Research Agent for Quantum Computing — QEC · New Qubits · Algorithms · Molecular Simulation</p>
+      </div>
+    </div>
+    <div class="status-chips">
+      <span class="chip" id="chip-cycle">Cycle: —</span>
+      <span class="chip" id="chip-line">Line: —</span>
+      <span class="chip" id="chip-mode">Mode: —</span>
+      <span class="chip" id="chip-llm">LLM: —</span>
+      <span class="chip" id="chip-docs">Docs: 0</span>
+      <span class="chip" id="chip-clusters">Clusters: 0</span>
+      <span class="chip chip-ok" id="chip-ws">WS: connecting…</span>
+    </div>
+  </header>
+
+  <nav class="tabs">
+    <button class="tab active" data-tab="feed">Research Feed</button>
+    <button class="tab" data-tab="lines">Research Lines</button>
+    <button class="tab" data-tab="archive">Archive</button>
+    <button class="tab" data-tab="patents">Patent Queue</button>
+    <button class="tab" data-tab="clusters">Patent Clusters</button>
+    <button class="tab" data-tab="kg">Knowledge Graph</button>
+    <button class="tab" data-tab="metrics">Metrics</button>
+    <button class="tab" data-tab="guide">Owner Guidance</button>
+  </nav>
+
+  <main class="layout">
+
+    <!-- Research Feed -->
+    <section class="panel active" id="panel-feed">
+      <div class="panel-header">
+        <h2>Real-time Research Feed</h2>
+        <button id="btn-clear-feed" class="btn-mini">Clear</button>
+      </div>
+      <div id="feed" class="feed"></div>
+    </section>
+
+    <!-- Research Lines -->
+    <section class="panel" id="panel-lines">
+      <div class="panel-header">
+        <h2>Four Research Lines</h2>
+        <span class="muted">The agent cycles through these, cross-linking every 5th cycle.</span>
+      </div>
+      <div id="lines-grid" class="lines-grid"></div>
+    </section>
+
+    <!-- Archive -->
+    <section class="panel" id="panel-archive">
+      <div class="panel-header">
+        <h2>Document Archive</h2>
+        <div class="filter-group">
+          <select id="archive-filter">
+            <option value="">All lines</option>
+            <option value="quantum_error_correction">QEC</option>
+            <option value="new_qubit_modalities">New Qubits</option>
+            <option value="quantum_algorithms">Algorithms</option>
+            <option value="molecular_simulation">Molecular Simulation</option>
+          </select>
+          <input type="search" id="archive-search" placeholder="Search documents…" />
+        </div>
+      </div>
+      <div id="archive-list" class="archive-list"></div>
+    </section>
+
+    <!-- Patents -->
+    <section class="panel" id="panel-patents">
+      <div class="panel-header">
+        <h2>Patent Queue</h2>
+        <button id="btn-refresh-patents" class="btn-mini">Refresh</button>
+      </div>
+      <div id="patents-list" class="patents-list"></div>
+    </section>
+
+    <!-- Patent Clusters -->
+    <section class="panel" id="panel-clusters">
+      <div class="panel-header">
+        <h2>Patent Clusters — Coherent Grouped Solutions</h2>
+        <button id="btn-refresh-clusters" class="btn-mini">Refresh</button>
+      </div>
+      <p class="muted">
+        Clusters group patent-eligible documents into complete solutions that span
+        multiple research lines (hardware foundation + application layer). A cluster
+        is <strong>filing-ready</strong> when it combines QEC/Qubits with Algorithms/Simulation.
+      </p>
+      <div id="clusters-list" class="clusters-list"></div>
+    </section>
+
+    <!-- Knowledge Graph -->
+    <section class="panel" id="panel-kg">
+      <div class="panel-header">
+        <h2>Quantum Knowledge Graph</h2>
+        <div class="filter-group">
+          <select id="kg-filter">
+            <option value="">All lines</option>
+            <option value="quantum_error_correction">QEC</option>
+            <option value="new_qubit_modalities">New Qubits</option>
+            <option value="quantum_algorithms">Algorithms</option>
+            <option value="molecular_simulation">Molecular Simulation</option>
+          </select>
+          <span id="kg-stats" class="muted"></span>
+        </div>
+      </div>
+      <pre id="kg-mermaid" class="kg-source"></pre>
+      <p class="muted small">Tip: paste the above into <a href="https://mermaid.live" target="_blank" rel="noopener">mermaid.live</a> for an interactive view.</p>
+    </section>
+
+    <!-- Metrics -->
+    <section class="panel" id="panel-metrics">
+      <div class="panel-header"><h2>Live Metrics</h2></div>
+      <div id="metrics-grid" class="metrics-grid"></div>
+    </section>
+
+    <!-- Owner Guidance -->
+    <section class="panel" id="panel-guide">
+      <div class="panel-header"><h2>Owner Guidance</h2></div>
+      <p class="muted">
+        quantum-spherifier runs autonomously by default (AJN addiction property).
+        Use this panel to steer it toward a specific research target. The directive
+        is parsed by the Hierarchical Command Interpreter and injected as a new
+        addiction target into the AJN backbone.
+      </p>
+      <form id="guide-form" class="guide-form">
+        <textarea id="guide-input" rows="4"
+          placeholder="Example: Focus on surface code distance 11 with neutral atoms, targeting logical error rate 1e-9"></textarea>
+        <div class="guide-actions">
+          <select id="safety-select">
+            <option value="standard">Safety: standard</option>
+            <option value="strict">Safety: strict</option>
+            <option value="permissive">Safety: permissive</option>
+          </select>
+          <button type="submit" class="btn-primary">Send Directive</button>
+        </div>
+      </form>
+
+      <h3>Quick Directives</h3>
+      <div class="quick-directives">
+        <button class="btn-quick" data-directive="Focus on surface code distance 11 on neutral atoms, targeting logical error rate 1e-9">Surface code d=11 on neutral atoms</button>
+        <button class="btn-quick" data-directive="Investigate qLDPC codes on reconfigurable neutral-atom arrays for constant-rate encoding with 10x overhead reduction">qLDPC on neutral atoms</button>
+        <button class="btn-quick" data-directive="Explore fluxonium qubits with T1 = 1 ms and 99.9% 2-qubit gate fidelity for 100-qubit processors">Fluxonium long-coherence qubits</button>
+        <button class="btn-quick" data-directive="Design a QPE algorithm for FeMoco simulation requiring 3000 logical qubits and 1e11 T-gates">FeMoco via QPE</button>
+        <button class="btn-quick" data-directive="Evaluate cat-qubit Bacon-Shor codes for biased-noise error correction with 4x overhead reduction">Cat-qubit Bacon-Shor</button>
+        <button class="btn-quick" data-directive="Develop a VQE ansatz for Ni-catalyzed C-H activation on 80 NISQ qubits with 1 kcal/mol accuracy">VQE for transition-metal catalysis</button>
+        <button class="btn-quick" data-directive="Cross-link QSVT-based algorithms with qubitization for molecular simulation, targeting 100x T-gate reduction">QSVT + qubitization cross-link</button>
+        <button class="btn-quick" data-directive="Assess silicon spin qubits on Intel 3 CMOS nodes for 1000-qubit density scaling">Silicon spin qubits CMOS</button>
+      </div>
+    </section>
+  </main>
+
+  <footer class="footer">
+    <span>quantum-spherifier (:qSpherifier) v1.0 — based on AJN theory by Justo Tapiador Garcia (UA). MIT License.</span>
+    <span id="footer-uptime">Uptime: 0s</span>
+  </footer>
+
+  <script src="/js/dashboard.js"></script>
+</body>
+</html>