lammps-simulation

The Agentic Science Worker can:

• Run molecular dynamics simulations (LAMMPS) with literature-sourced parameters
• Perform DFT calculations (Quantum ESPRESSO) for electronic structure
• Search scientific literature and extract methodology/parameters
• Query materials databases (Materials Project) for structures and properties
• Analyze results and compare with published values
• Execute on HPC clusters for large-scale computations

The agent operates autonomously: given a scientific question, it researches the methodology, finds parameters, runs simulations, verifies results against literature, and iterates until achieving physically reasonable results.

```

┌─────────────────────────────────────────────────────────────┐

│ Coding Agent │

│ Claude Code │ Aider │ OpenAI Codex │ Cursor │

│ (AGENTS.md defines researcher behavior and methodology) │

└─────────────────────────────────────────────────────────────┘

│

▼

┌─────────────────────────────────────────────────────────────┐

│ Skills │

│ ┌──────────┐ ┌──────────┐ ┌──────────┐ ┌──────────┐ │

│ │ LAMMPS │ │ QE │ │ HPC │ │ MLIP │ │

│ │ Skill │ │ Skill │ │ Skill │ │ Skill │ │

│ └──────────┘ └──────────┘ └──────────┘ └──────────┘ │

│ ┌──────────┐ ┌──────────┐ ┌──────────┐ │

│ │Literature│ │Materials │ │ Data │ │

│ │ Search │ │ Database │ │ Analysis │ │

│ └──────────┘ └──────────┘ └──────────┘ │

└─────────────────────────────────────────────────────────────┘

│

▼

┌─────────────────────────────────────────────────────────────┐

│ External Tools │

│ LAMMPS │ Quantum ESPRESSO │ Python │ HPC Cluster │ Web │

└─────────────────────────────────────────────────────────────┘

```

| Agent | Status | Configuration |

|-------|--------|---------------|

| [Claude Code](https://claude.com/claude-code) | Full Support | AGENTS.md, .claude/ |

| [Aider](https://aider.chat) | Full Support | AGENTS.md, configs/aider/ |

| [OpenAI Codex](https://openai.com/codex) | Planned | AGENTS.md |

| [Cursor](https://cursor.com) | Full Support | AGENTS.md, .cursorrules |

All agents read AGENTS.md (the [industry standard](https://github.com/AgenticAI-Foundation/AGENTS.md)) as their primary context file.

Prerequisites

• A supported coding agent:

- [Claude Code CLI](https://claude.com/claude-code) with subscription, OR

- [Aider](https://aider.chat) with API key, OR

- [Cursor](https://cursor.com)

• Python 3.10+
• LAMMPS (with GPU support recommended)
• Quantum ESPRESSO (optional, for DFT)
• Materials Project API key

Installation

1. Clone the repository:

```bash

git clone https://github.com/yourusername/agentic-science-worker.git

cd agentic-science-worker

```

1. Copy and configure settings:

```bash

cp config.example.yaml config.yaml

cp .claude/settings.json.example .claude/settings.json

cp .mcp.json.example .mcp.json

```

1. Edit configuration files with your paths and API keys:

```yaml

# config.yaml

binaries:

lammps: "/path/to/your/lammps/bin/lmp"

qe_cpu: "/path/to/qe/bin"

api_keys:

materials_project: "YOUR_MP_API_KEY"

```

1. Verify infrastructure:

```bash

cd benchmarks/evaluation