pyiron_atomistics.project.AtomisticsLocalMaintenance#
- class pyiron_atomistics.project.AtomisticsLocalMaintenance(project)[source]#
Bases:
LocalMaintenance- __init__(project)#
Methods
__init__(project)defragment_storage([recursive, progress])Rewrite the hdf5 files of jobs.
update_hdf_types([recursive, progress])Rewrite TYPE fields in hdf5 files for renamed modules.
update_pyiron_tables([recursive, progress])vasp_correct_energy_kin([recursive, progress])Ensure kinetic and potential energy are correctly parsed for AIMD Vasp jobs.
vasp_energy_pot_as_free_energy([recursive, ...])Ensure generic potential energy is the electronic free energy.
- defragment_storage(recursive: bool = True, progress: bool = True, **kwargs: dict)#
Rewrite the hdf5 files of jobs. This can free up unused space.
By default iterate recursively over the jobs within the current project. This can be controlled with recursive and kwargs.
- Parameters:
recursive (bool) – search subprojects [True/False] - True by default
progress (bool) – if True (default), add an interactive progress bar to the iteration
**kwargs (dict) – Optional arguments for filtering with keys matching the project database column name (eg. status=”finished”). Asterisk can be used to denote a wildcard, for zero or more instances of any character
- update_hdf_types(recursive: bool = True, progress: bool = True, **kwargs: dict)#
Rewrite TYPE fields in hdf5 files for renamed modules.
New module conversions can be added with
add_module_conversion(old, new)(). This method will then consider all objects previously imported from old to be imported from new.- Parameters:
recursive (bool) – search subprojects [True/False] - True by default
progress (bool) – if True (default), add an interactive progress bar to the iteration
**kwargs (dict) – Optional arguments for filtering with keys matching the project database column name (eg. status=”finished”). Asterisk can be used to denote a wildcard, for zero or more instances of any character
- vasp_correct_energy_kin(recursive: bool = True, progress: bool = True, **kwargs)[source]#
Ensure kinetic and potential energy are correctly parsed for AIMD Vasp jobs.
Version 0.1.0 of the Vasp job (pyiron_atomistics<=0.3.10) incorrectly parsed the kinetic energy during MD runs, such that it only reported the kinetic energy of the final ionic step and subtracted it from the electronic energy instead of adding it.
- Parameters:
recursive (bool) – search subprojects [True/False] - True by default
progress (bool) – if True (default), add an interactive progress bar to the iteration
**kwargs (dict) – Optional arguments for filtering with keys matching the project database column name (eg. status=”finished”). Asterisk can be used to denote a wildcard, for zero or more instances of any character
- vasp_energy_pot_as_free_energy(recursive: bool = True, progress: bool = True, **kwargs)[source]#
Ensure generic potential energy is the electronic free energy.
This ensures that the energy is consistent with the forces and stresses. In version 0.1.0 of the Vasp job (pyiron_atomistics<=0.3.10) a combination of bugs in Vasp and pyiron caused the potential energy reported to be the internal energy of electronic system extrapolated to zero smearing instead.
- Parameters:
recursive (bool) – search subprojects [True/False] - True by default
progress (bool) – if True (default), add an interactive progress bar to the iteration
**kwargs (dict) – Optional arguments for filtering with keys matching the project database column name (eg. status=”finished”). Asterisk can be used to denote a wildcard, for zero or more instances of any character