amep.evaluate.EkinTrans#

class amep.evaluate.EkinTrans(traj, mass: float | ndarray, mode: str = 'total', skip: float = 0.0, nav: int = 10, **kwargs)#

Bases: BaseEvaluation

Translational kinetic energy.

__init__(traj, mass: float | ndarray, mode: str = 'total', skip: float = 0.0, nav: int = 10, **kwargs)#

Calculate the translational kinetic energy of each particle.

Calculates energy over a whole trajectory.

Parameters:

traj (Traj) – Trajectory object with simulation data.
mass (float | np.ndarray) – Function to be used for analysis. Its signature should be func(frame, **kwargs)->float
mode ("total" or "particle") –

How to return the energy, c.f. thermo.py
total : sum over all particles particle : individual particle-energies
skip (float, default=0.0) – Skip this fraction at the beginning of the trajectory.
nav (int, default=10) – number of frames to consider for the time average.
**kwargs (Keyword Arguments) – General python keyword arguments to be forwarded to the function f

Examples

>>> import amep
>>> traj = amep.load.traj("../examples/data/lammps.h5amep")
>>> ekintrans = amep.evaluate.EkinTrans(
...     traj, mass=1.0, nav=traj.nframes
... )
>>> fig, axs = amep.plot.new()
>>> axs.plot(ekintrans.times, ekintrans.frames)
>>> axs.axhline(ekintrans.avg, ls="--", c="k")
>>> axs.set_xlabel(r'$t$')
>>> axs.set_ylabel(r'$E_{\rm trans}$')
>>> axs.semilogy()
>>> fig.savefig("./figures/evaluate/evaluate-EkinTrans.png")

Methods

`__init__`(traj, mass[, mode, skip, nav])	Calculate the translational kinetic energy of each particle.
`items`()
`keys`()
`save`(path[, backup, database, name])	Stores the evaluation result in an HDF5 file.
`values`()

Attributes

`avg`	Time-averaged translational kinetic energy (averaged over the given number of frames).
`frames`	Translational kinetic energy for each particle and in each frame.
`indices`	Indices of all frames for which the translational kinetic energy has been calculated.
`name`
`times`	Times at which the translational kinetic energy is evaluated.

property avg#

Time-averaged translational kinetic energy (averaged over the given number of frames).

Returns:: Time-averaged translational kinetic energy of each particle.
Return type:: np.ndarray

property frames#

Translational kinetic energy for each particle and in each frame.

Returns:: Translational kinetic energy for each frame.
Return type:: np.ndarray

property indices#

Indices of all frames for which the translational kinetic energy has been calculated.

Returns:: Frame indices.
Return type:: np.ndarray

save(path: str, backup: bool = True, database: bool = False, name: str | None = None) → None#

Stores the evaluation result in an HDF5 file.

Parameters:

path (str) – Path of the ‘.h5’ file in which the data should be stored. If only a directory is given, the filename is chosen as self.name. Raises an error if the given directory does not exist or if the file extension is not ‘.h5’.
backup (bool, optional) – If True, an already existing file is backed up and not overwritten. This keyword is ignored if database=True. The default is True.
database (bool, optional) – If True, the results are appended to the given ‘.h5’ file if it already exists. If False, a new file is created and the old is backed up. If False and the given ‘.h5’ file contains multiple evaluation results, an error is raised. In this case, database has to be set to True. The default is False.
name (str or None, optional) – Name under which the data should be stored in the HDF5 file. If None, self.name is used. The default is None.

Return type:

None.

property times#

Times at which the translational kinetic energy is evaluated.

Returns:: Times at which the translational kinetic energy is evaluated.
Return type:: np.ndarray