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<!-- Title -->
<text x="450" y="30" text-anchor="middle" font-size="16" font-weight="bold" fill="#e6edf3">CpptrajAI — Agent Execution Flow</text>
<!-- ═══ User Prompt ═══ -->
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<text x="450" y="65" text-anchor="middle" font-size="13" font-weight="bold" fill="#ffffff">User Prompt</text>
<text x="450" y="83" text-anchor="middle" font-size="11" fill="#cdd9e5">"Calculate RMSD of backbone..."</text>
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<!-- ═══ System Prompt Injection ═══ -->
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<text x="450" y="145" text-anchor="middle" font-size="13" font-weight="bold" fill="#e6edf3">System Prompt Injection</text>
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<text x="450" y="170" text-anchor="middle" font-size="11" fill="#8b949e">Topology info • File names • Execution rules • Workflow guidelines</text>
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<!-- ═══ LLM Decision Engine ═══ -->
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<text x="450" y="242" text-anchor="middle" font-size="13" font-weight="bold" fill="#79c0ff">LLM Decision Engine</text>
<text x="450" y="262" text-anchor="middle" font-size="11" fill="#8b949e">Decides next tool call or final answer</text>
<!-- ─── Fan-out via top bus ─── -->
<!-- Stem from LLM bottom center to top bus -->
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<!-- ═══ Tool Boxes (y=350, w=140, h=100) ═══ -->
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<text x="120" y="394" text-anchor="middle" font-size="10" fill="#8b949e">TF-IDF search over</text>
<text x="120" y="409" text-anchor="middle" font-size="10" fill="#8b949e">cpptraj syntax cache</text>
<text x="120" y="424" text-anchor="middle" font-size="10" fill="#8b949e">Returns top-2 chunks</text>
<text x="120" y="441" text-anchor="middle" font-size="9" fill="#484f58">on-demand / always for Ollama</text>
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<text x="285" y="394" text-anchor="middle" font-size="10" fill="#8b949e">Writes & executes</text>
<text x="285" y="409" text-anchor="middle" font-size="10" fill="#8b949e">cpptraj subprocess</text>
<text x="285" y="424" text-anchor="middle" font-size="10" fill="#8b949e">stdout + output files</text>
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<!-- run_python_script (center x=450) -->
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<text x="450" y="394" text-anchor="middle" font-size="10" fill="#8b949e">Executes Python</text>
<text x="450" y="409" text-anchor="middle" font-size="10" fill="#8b949e">pandas / numpy / scipy</text>
<text x="450" y="424" text-anchor="middle" font-size="10" fill="#8b949e">stdout + plot files</text>
<text x="450" y="441" text-anchor="middle" font-size="9" fill="#484f58">post-process & plotting</text>
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<text x="615" y="394" text-anchor="middle" font-size="10" fill="#8b949e">Reads .dat or any</text>
<text x="615" y="409" text-anchor="middle" font-size="10" fill="#8b949e">output file from disk</text>
<text x="615" y="424" text-anchor="middle" font-size="10" fill="#8b949e">Returns raw content</text>
<text x="615" y="441" text-anchor="middle" font-size="9" fill="#484f58">inspect results</text>
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<text x="780" y="394" text-anchor="middle" font-size="10" fill="#8b949e">Lists all files in</text>
<text x="780" y="409" text-anchor="middle" font-size="10" fill="#8b949e">session working dir</text>
<text x="780" y="424" text-anchor="middle" font-size="10" fill="#8b949e">Returns file list</text>
<text x="780" y="441" text-anchor="middle" font-size="9" fill="#484f58">check state</text>
<!-- ─── Fan-in via bottom bus ─── -->
<!-- Stems from tool bottoms (y=450) to bottom bus (y=490) -->
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<!-- ═══ Tool Result ═══ -->
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<text x="450" y="542" text-anchor="middle" font-size="13" font-weight="bold" fill="#e6edf3">Tool Result</text>
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<!-- Arrow down -->
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<!-- ═══ Tool Result → loop back to LLM (left side, green) ═══ -->
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<text x="16" y="410" text-anchor="middle" font-size="11" font-weight="bold" fill="#3fb950" transform="rotate(-90 16 410)">More tool calls needed — loop back</text>
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<text x="109" y="540" text-anchor="middle" font-size="9" fill="#e3b341">⚠ Safety limit: max 15 calls</text>
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<text x="884" y="440" text-anchor="middle" font-size="11" fill="#8b949e" transform="rotate(90 884 440)">Task complete — no tool needed</text>
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<!-- ═══ Final Response ═══ -->
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<!-- ═══ Legend ═══ -->
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<text x="782" y="717" font-size="10" fill="#8b949e">Task complete</text>
<text x="450" y="747" text-anchor="middle" font-size="10" fill="#484f58">Each run_cpptraj_script is a fresh process — write intermediates to disk, reload via readdata</text>
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