# Physics Simulation Setup

> Set up reproducible physics simulations — Monte Carlo (GEANT4), molecular dynamics (LAMMPS), DFT (VASP, Quantum ESPRESSO), quantum dynamics (QuTiP) — with containers, parameter files, and verification.

- Skill: `quantumquirkxyz/physics-simulation-setup` (Agent Skill)
- Install (CLI): `npx skillmds@latest add quantumquirkxyz/physics-simulation-setup`
- Raw SKILL.md: https://api.skillmd.com/api/skills/quantumquirkxyz/physics-simulation-setup/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: quantumquirkxyz (https://skillmd.com/u/quantumquirkxyz)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/quantumquirkxyz/physics-simulation-setup

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## Contract

- **Input:** physical system description and simulation goal.
- **Output:** parameter files + container + verification.
- **Side effects:** none.
- **Dependencies:** none.
- **Stop condition:** verification complete.
- **Risk:** low.
- **Boundary:** produces simulation setup; does not run long computations unless user executes container.

# Physics Simulation Setup

Prepare a **reproducible simulation** for a physics system — Monte Carlo, molecular dynamics, DFT, quantum dynamics — with exact parameters and a verification step.

## When to use

- A research question needs numerical simulation.
- A simulation result needs to be reproducible by reviewers or collaborators.
- A publication requires code and environment details.

## Process

### 1. Select the simulation family

- **Monte Carlo** — GEANT4 (particle physics), ROOT / Pythia.
- **Molecular dynamics** — LAMMPS (classical), GROMACS (biomolecules).
- **DFT** — VASP, Quantum ESPRESSO, ABINIT.
- **Quantum dynamics** — QuTiP (open quantum systems), Julia (DynamicalSystems.jl).

State choice and why.

**Completion criterion:** family and tool named; justification stated.

### 2. Define the system

- **Geometry / lattice / potential** — input file with exact parameters.
- **Initial conditions** — thermal, ground state, excited state.
- **Boundary conditions** — periodic, open, vacuum, fixed.
- **Physical units** — eV, K, angstrom, fs, with conversion notes.

**Completion criterion:** all parameters explicit; units consistent.

### 3. Configure the simulation

- **Timestep** — justified by stability criteria.
- **Integration length** — long enough for convergence, short enough for feasibility.
- **Sampling / statistics** — number of trajectories, statistical error target.
- **Output format** — HDF5 / CSV / ROOT with a schema description.

**Completion criterion:** configuration file complete; schema described.

### 4. Containerise

- **Docker:** base image with the simulation tool + dependencies.
- **Apptainer:** for HPC clusters.
- Include: parameter file, script, environment file with versions.

**Completion criterion:** container builds; runs and produces expected output.

### 5. Verify

Compare against:

- **Analytical limit** — e.g. ideal gas law, harmonic oscillator, free particle.
- **Benchmark** — known result from literature or standard test case.
- **Convergence** — result stable as parameter (timestep, grid size, trajectory count) changes.

Report agreement (percentage difference) and note any discrepancy.

**Completion criterion:** verification report saved; agreement stated.