Quick Reference¶

This page provides quick reference tables, command-line flags, units, and a glossary for Cavity HOOMD.

Command-Line Flags ¶

05_advanced_run.py Options ¶

Basic Parameters:

Flag	Default	Description
`--coupling VALUE`	1e-3	Coupling strength (atomic units)
`--temperature VALUE`	100	Temperature in Kelvin
`--frequency VALUE`	2000	Cavity frequency in cm⁻¹
`--runtime VALUE`	500	Simulation time in ps

Thermostats:

Flag	Default	Description
`--molecular-bath`	bussi	Molecular thermostat: bussi, langevin, none
`--cavity-bath`	langevin	Cavity thermostat: bussi, langevin, none

Modes:

Flag	Default	Description
`--finite-q`	False	Enable finite-q cavity mode
`--no-cavity`	False	Run without cavity (control)

Time-Varying:

Flag	Default	Description
`--switch-time VALUE`	None	Time to switch coupling on (ps)

Execution:

Flag	Default	Description
`--device`	auto	Device: GPU, CPU, auto
`--replicas`	1	Replica IDs (e.g., “1-5” or “1,3,5”)

Parameter Tables ¶

Typical Values ¶

Parameter	Range	Notes
Coupling strength	10⁻⁵ - 10⁻³	Atomic units; strong coupling > 10⁻³
Temperature	50-500 K	Typical molecular simulations
Cavity frequency	1000-4000 cm⁻¹	Match molecular vibrations
Timestep	0.0005-0.002 ps	Smaller for high frequencies
Runtime	100-10000 ps	Depends on observable

Unit Conversions ¶

Energy ¶

Unit	Conversion
1 Hartree	27.2 eV = 627 kcal/mol = 4.36×10⁻¹⁸ J
1 eV	0.0367 Hartree = 23.06 kcal/mol
1 kcal/mol	0.00159 Hartree = 0.043 eV

Temperature ¶

Temperature	Reduced Units
50 K	0.00016 Hartree/k_B
100 K	0.00032 Hartree/k_B
300 K	0.00095 Hartree/k_B

Length ¶

Unit	Conversion
1 Bohr	0.529 Å = 0.0529 nm
1 Å	1.889 Bohr
1 nm	18.89 Bohr

Time ¶

Unit	Conversion
1 atomic time unit	0.024 fs = 2.42×10⁻¹⁷ s
1 fs	41.34 atomic time units
1 ps	41,341 atomic time units

Frequency ¶

Unit	Conversion
1 cm⁻¹	4.556×10⁻⁶ Hartree/ℏ = 0.030 meV
1000 cm⁻¹	0.00456 Hartree/ℏ = 124 meV
2000 cm⁻¹	0.00916 Hartree/ℏ = 248 meV

Output Files ¶

File Formats ¶

trajectory.gsd:

Binary GSD format
Contains: positions, velocities, forces, box
Read with: gsd.hoomd.open()

energy_tracker.txt:

Tab-separated values
Columns: time, kinetic, potential, cavity, coupling, self, total
Units: ps for time, reduced units for energy

cavity_mode.txt:

Tab-separated values
Columns: time, q_x, q_y, v_x, v_y
Units: ps for time, reduced units for positions/velocities

molecular_temps.csv:

Comma-separated values
Columns: time, T_trans, T_rot, T_vib, T_total
Units: ps for time, Kelvin for temperatures

Glossary ¶

Cavity Mode¶: Quantized electromagnetic field mode confined in optical cavity
Coupling Strength¶: Parameter g controlling interaction between molecular dipoles and cavity field
Collective Coupling¶: Enhanced coupling \(g_{\text{eff}} = g\sqrt{N}\) for N molecules
Finite-q Mode¶: Cavity mode with non-zero wave vector, spatial phase variation
FDR¶: Fluctuation-Dissipation Ratio, measures effective temperature
Polariton¶: Hybrid light-matter quasi-particle from strong coupling
Rabi Splitting¶: Energy splitting \(\Omega_R\) between upper and lower polaritons
q=0 Mode¶: Uniform cavity mode with zero wave vector, all molecules couple in phase
Self-Energy¶: Dipole-dipole interaction energy term \(g^2 D^2/2K\)
Strong Coupling¶: Regime where \(\Omega_R > \sqrt{\gamma\kappa}\), polaritons form

Symbol Reference ¶

Mathematical Symbols ¶

Symbol	Meaning
\(g\)	Coupling strength parameter
\(\omega_c\)	Cavity angular frequency
\(q_\lambda\)	Cavity mode coordinate (polarization λ)
\(D_\lambda\)	Total molecular dipole moment (direction λ)
\(d_n\)	Dipole moment of molecule n
\(K\)	Cavity spring constant \(m\omega^2\)
\(\tilde{\varepsilon}\)	Effective coupling strength
\(N\)	Number of molecules
\(\Omega_R\)	Rabi splitting / Rabi frequency
\(\gamma\)	Molecular dephasing rate
\(\kappa\)	Cavity photon loss rate
\(\tau\)	Thermostat coupling time
\(T\)	Temperature
\(k_B\)	Boltzmann constant

Citations ¶

If you use Cavity HOOMD, please cite:

@software{cavity_hoomd_2025,
  title={Cavity HOOMD: Molecular Dynamics with Optical Cavity Coupling},
  author={Development Team},
  year={2025},
  url={https://github.com/muhammadhasyim/cav-hoomd}
}

Also cite HOOMD-blue:

@article{anderson2020hoomd,
  title={HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations},
  author={Anderson, Joshua A and Glaser, Jens and Glotzer, Sharon C},
  journal={Computational Materials Science},
  volume={173},
  pages={109363},
  year={2020},
  publisher={Elsevier}
}