Logfile¶

The Logfile class is the base class you want to be using all the time. It is mainly meant to manipulate the output of a BigDFT calculation (written using the YAML format).

However, it might happen that the output actually contains many documents (for instance, one document per geometry optimization procedure). In such cases, the initialization of a Logfile actually gives another type of object, deriving from the MultipleLogfile class. Be careful: these objects behave as a list of Logfile instances, not as a Logfile instance (even though they are initialized via the Logfile class). To keep the same example as above, the output file of a geometry optimization calculation can be read via the Logfile.from_file() method of the Logfile class, returning a GeoptLogfile instance.

class mybigdft.iofiles.logfiles.Logfile(log=None)[source]¶

Bases: collections.abc.Mapping

Class allowing to initialize, read, write and interact with an output file of a BigDFT calculation.

Parameters: log (dict) – Output of the BigDFT code as a yaml dictionary.

classmethod from_file(filename)[source]¶

Initialize the Logfile from a file on disk.

Parameters: filename (str) – Name of the logfile.
Returns: Logfile initialized from a file on disk.
Return type: Logfile or GeoptLogfile or MultipleLogfile

>>> log = Logfile.from_file("tests/log.yaml")
>>> print(log.posinp)
2   angstroem
free
N   2.97630782434901e-23   6.87220595204354e-23   0.0107161998748779
N  -1.10434491945017e-23  -4.87342174483075e-23   1.10427379608154
<BLANKLINE>
>>> log.energy
-19.884659235401838

classmethod from_stream(stream)[source]¶

Initialize the Logfile from a stream.

Parameters: stream – Logfile as a stream.
Returns: Logfile initialized from a stream.
Return type: Logfile or GeoptLogfile or MultipleLogfile

property log¶

Returns: Yaml dictionary of the output of the BigDFT code.
Return type: Logfile

__dir__()[source]¶

The base attributes are not found when doing dir() on a Logfile instance, but their counterpart with a preceding underscore is. What is done here is a removal of the underscored names, replaced by the bare names (in order to avoid name repetition).

The bare attributes still behave as properties, while their value might be updated via the underscored attribute.

write(filename)[source]¶

Write the logfile on disk.

Parameters: filename (str) – Name of the logfile.

property posinp¶

Returns: Posinp used during the calculation.
Return type: Posinp

property inputparams¶

Returns: Input parameters used during the calculation.
Return type: InputParams

mybigdft.iofiles.logfiles.ATTRIBUTES Definition of the base attributes of a Logfile instance (and where to look for them in the logfile).¶

These attributes allow to get most of the relevant data contained in a Logfile. They provide simple shortcuts instead of having to know exactly where to look for them in the yaml output file, represented by the Logfile class. If some attributes do not appear in the BigDFT output, they default to None.

evals

Returns: Orbital energies and occupations.

forcemax_cv

Returns: Convergence criterion on forces.

kpts

Returns: Grid of k-points.

magnetization

Returns: Total magnetization of the system.

symmetry

Returns: Symmetry group.

energy

Returns: Energy (Hartree).

astruct

Returns: Atomic structure.

support_functions

Returns: Support functions.

electrostatic_multipoles

Returns: Electrostatic multipoles.

force_fluct

Returns: Threshold fluctuation of Forces.

n_at

Returns: Number of Atoms.

dipole

Returns: Electric Dipole Moment (AU).

cell

Returns: Cell size.

forces

Returns: Atomic Forces (Ha/Bohr).

WARNINGS

Returns: Warnings raised during the BigDFT run.

kpt_mesh

Returns: No. of Monkhorst-Pack grid points.

pressure

Returns: Pressure (GPa).

fermi_level

Returns: Fermi level.

atom_types

Returns: List of the atomic types present in the posinp.

walltime

Returns: Walltime since initialization.

boundary_conditions

Returns: Boundary Conditions.

forcemax

Returns: Maximum value of forces.

sdos

Returns: SDos files.

gnrm_cv

Returns: Convergence criterion on wavefunction residue.

class mybigdft.iofiles.logfiles.MultipleLogfile(logs)[source]¶

Bases: collections.abc.Sequence

Class allowing to initialize, read, write and interact with an output file of a BigDFT calculation containing multiple documents.

Parameters: logs (list) – List of the various documents contained in the logfile of a BigDFT calculation.

property logs¶

Returns: List of the documents read from a single output of a BigDFT calculation.
Return type: list

write(filename)[source]¶

Write the logfile on disk.

Parameters: filename (str) – Name of the logfile.

class mybigdft.iofiles.logfiles.GeoptLogfile(logs)[source]¶

Bases: mybigdft.iofiles.logfiles.MultipleLogfile

Class allowing to initialize, read, write and interact with an output file of a geometry optimization calculation.

Parameters: logs (list) – List of the various documents contained in the logfile of a geometry optimization calculation.

property inputparams¶

Returns: Input parameters used for each step of the geometry optimization procedure.
Return type: InputParams

property posinps¶

Returns: List of the input positions for each step of the geometry optimization procedure.
Return type: list