This module is useful to process a logfile of BigDFT run, in yaml format. It also provides some tools to extract typical informations about the run, like the energy, the eigenvalues and so on.
- class Energies(filename, units='AU', disp=None, strict=True)¶
Find the energy terms from a BigDFT logfile. May also accept malformed logfiles that are issued, for instance, from a badly terminated run that had I/O error.
- property to_dict¶
- class Logfile(*args, **kwargs)¶
Import a Logfile from a filename in yaml format, a list of filenames, an archive (compressed tar file), a dictionary or a list of dictionaries.
*args – sequence of logfiles to be parsed. If it is longer than one item, the logfiles are considered as belonging to the same run.
describes how the data can be read. Keywords can be:
archive: name of the archive from which retrieve the logfiles.
- member: name of the logfile within the archive. If absent, all the
files of the archive will be considered as args.
label: the label of the logfile instance
- dictionary: parsed logfile given as a dictionary,
serialization of the yaml logfile
>>> l = Logfile('one.yaml','two.yaml') >>> l = Logfile(archive='calc.tgz') >>> l = Logfile(archive='calc.tgz',member='one.yaml') >>> l = Logfile(dictionary=dict1) >>> l = Logfile(dictionary=[dict1, dict2])
Document the automatically generated attributes, perhaps via an inner function in futile python module
For a set of logfiles construct the convergence plot if available. Plot the Maximum value of the forces against the difference between the minimum value of the energy and the energy of the iteration. Also an errorbar is given indicating the noise on the forces for a given point. Show the plot as per plt.show() with matplotlib.pyplots as plt
>>> tt=Logfile('log-with-geometry-optimization.yaml') >>> tt.geopt_plot()
Return an instance of the BrillouinZone class, useful for band structure. :returns: Brillouin Zone of the logfile :rtype:
Get the density of states from the logfile.
Fill a py:class:~BigDFT.DoS.DoS class object with the information which is stored in this logfile.
**kwargs – Keyword Arguments of the py:class:~BigDFT.DoS.DoS class.
- class instance. Filled with bandarrays and
- Return type
Label of the Logfile instance
Absolute path of the directory of logfile
Plot the wavefunction convergence. :Example:
>>> tt=Logfile('log-with-wfn-optimization.yaml',label='a label') >>> tt.wfn_plot()
Identify the different block of the iterations of the wavefunctions optimization.
Should be generalized and checked for mixing calculation and O(N) logfiles
log (dictionary) – logfile load
wavefunction residue per iterations, per each subspace diagonalization
- Return type
numpy array of rank two
Return a list of loaded logfiles from files, which is a list of paths leading to logfiles.
files – List of filenames indicating the logfiles
List of Logfile instances associated to filename
- plot_wfn_convergence(wfn_it, gnrm_cv, label=None)¶
Plot the convergence of the wavefunction coming from the find_iterations function. Cumulates the plot in matplotlib.pyplot module
wfn_it – list coming from
gnrm_cv – convergence criterion for the residue of the wfn_it list
label – label for the given plot