Molecular Temperatures

Kinetic temperature decomposition for diatomic molecules into translational, rotational, and vibrational components.

Temperature Decomposition

For diatomic molecules:

Translational:

\[T_{\text{trans}} = \frac{2\langle KE_{\text{CM}}\rangle}{3Nk_B}\]

Rotational:

\[T_{\text{rot}} = \frac{\langle KE_{\text{rot}}\rangle}{Nk_B}\]

Vibrational:

\[T_{\text{vib}} = \frac{2\langle KE_{\text{vib}}\rangle}{Nk_B}\]

Implementation

from cavitymd.molecular_temperatures import DiatomicMolecularTemperatures

temp_tracker = DiatomicMolecularTemperatures(
    simulation=sim,
    time_tracker=time_tracker,
    output_period_ps=1.0,
    output_file='molecular_temps.csv'
)

sim.operations.writers.append(temp_tracker)

See Molecular Temperature Decomposition for Diatomic Molecules for detailed documentation.

Next: Correlation Analysis