amep.base.BaseDatabase

class amep.base.BaseDatabase(path: str)

Bases: object

Evaluation database base class for storing and loading multiple evaluation results stored in a single HDF5 file.

__init__(path: str) → None

Loads/creates a database HDF5 file for storing data of multiple evaluate objects in a single file.

Parameters:

path (str) – Path of the HDF5 file. Raises an error if the path does not contain a filename with file extension ‘.h5’.

Return type:

None.

Examples

>>> import amep
>>> traj = amep.load.traj("../examples/data/lammps.h5amep")
>>> msd = amep.evaluate.MSD(traj)
>>> sf2d = amep.evaluate.SF2d(traj, nav=2)
>>> db = amep.base.BaseDatabase('./eval/database.h5')
>>> db.add('msd', msd)
>>> db.add('sf2d', sf2d)
>>> print(db.keys())
['msd', 'sf2d']
>>> print(db.msd)
<amep.base.BaseEvalData object at 0x0000025B7CB439A0>
>>> db.delete('msd')
>>> print(db.keys())
['sf2d']
>>> print(db.items())
[('sf2d', <amep.base.BaseEvalData object at 0x0000025B7A0A6E30>)]
>>>

Methods

__init__(path)	Loads/creates a database HDF5 file for storing data of multiple evaluate objects in a single file.
add(name, evaluation)	Adds the data of an evaluate object as a new group to the database HDF5 file.
delete(name)	Deletes a group/data from the database HDF5 file.
items()
keys()
values()

add(name: str, evaluation: BaseEvaluation) → None

Adds the data of an evaluate object as a new group to the database HDF5 file.

Parameters:

• name (str) – Name of the group/data.

• evaluation (BaseEvaluation) – Evaluate object of which the data should be stored in the database HDF5 file.

Return type:

None.

delete(name: str) → None

Deletes a group/data from the database HDF5 file.

Parameters:

name (str) – Name of the group that should be deleted.

Return type:

None.