ConstantVolumeHeatCapacity

class mdhelper.analysis.thermodynamics.ConstantVolumeHeatCapacity(log_file: str | Path = None, log_format: str = None, *, energies: ndarray[float] | Quantity | Quantity = None, temperature: float | Quantity | Quantity = None, reduced: bool = False, sep: str = ',')

Bases: object

A serial implementation to caluclate the constant-volume heat capacity \(C_V\) for a canonical (\(NVT\)) system.

The constant-volume heat capacity is defined as

\[C_V=\frac{\langle U^2\rangle-\langle U\rangle^2} {k_\mathrm{B}T^2}\]

where \(U\) is the total potential energy of the system, \(\langle\cdot\rangle\) denotes the ensemble average, \(k_\mathrm{B}\) is the Boltzmann constant, and \(T\) is the system temperature.

Parameters:

log_filestr or pathlib.Path, optional

Log file generated by the simulation. If not provided, the potential energies must be provided directly in energy.

log_formatstr, optional

Format of the log file. If not provided, the format will be determined automatically (if possible).

Valid values: "lammps", "openmm".

energiesnumpy.ndarray or pint.Quantity, optional

Potential energies. If not provided, the log file must be provided in log_file.

temperaturefloat, openmm.unit.Quantity, or pint.Quantity, optional

System temperature. If not provided, the averaged temperature from the log file (if available) is used.

reducedbool, keyword-only, default: False

Specifies whether the data is in reduced units.

sepstr, keyword-only, default: ","

Delimiter for OpenMM log files.

Attributes:

results.unitsdict

Reference units for the results. For example, to get the reference units for results.temperature, call results.units["results.temperature"].

results.energiesnumpy.ndarray

Total (kinetic + potential) energy values.

Reference unit: \(\mathrm{kcal/mol}\) or \(\mathrm{kJ/mol}\).

results.temperaturefloat

System temperature.

Reference unit: \(\mathrm{K}\).

results.heat_capacityfloat

Constant-volume heat capacity.

Reference unit: \(\mathrm{kcal/K}\) or \(\mathrm{kJ/K}\).

Methods

run	Performs the calculation.

run(start: int = None, stop: int = None, step: int = None, frames: ndarray[int] | slice = None) → None

Performs the calculation.

Parameters:

startint, optional

Starting frame for analysis.

stopint, optional

Ending frame for analysis.

stepint, optional

Number of frames to skip between each analyzed frame.

framesslice or array-like, optional

Index or logical array of the desired trajectory frames.

verbosebool, optional

Determines whether detailed progress is shown.

**kwargs

Additional keyword arguments to pass to MDAnalysis.lib.log.ProgressBar.

Returns:

selfConstantVolumeHeatCapacity

Analysis object with results.