dynamics Package

Contents

• dynamics Package

  • dynamics Package

  • hist Module

dynamics Package

hist Module

History file with structural relaxation results.

class abipy.dynamics.hist.HistFile(filepath)

Bases: abipy.core.mixins.AbinitNcFile, abipy.core.mixins.NotebookWriter

File with the history of a structural relaxation or molecular dynamics calculation.

Usage example:

with HistFile("foo_HIST") as hist:
    hist.plot()

Inheritance Diagram

classmethod from_file(filepath)

Initialize the object from a netcdf file

close()

Close the file.

params()

OrderedDict with parameters that might be subject to convergence studies.

final_energy()

Total energy in eV of the last iteration.

final_pressure()

Final pressure in Gpa.

get_fstats_dict(step)

Return monty.collections.AttrDict with stats on the forces at the given step.

to_string(verbose=0, title=None)

String representation.

property num_steps

Number of iterations performed.

steps()

Step indices.

property initial_structure

The initial abipy.core.structure.Structure.

property final_structure

The abipy.core.structure.Structure of the last iteration.

structures()

List of abipy.core.structure.Structure objects at the different steps.

etotals()

numpy.ndarray with total energies in eV at the different steps.

get_relaxation_analyzer()

Return a pymatgen RelaxationAnalyzer object to analyze the relaxation in a calculation.

to_xdatcar(filepath=None, groupby_type=True, to_unit_cell=False, **kwargs)

Return Xdatcar pymatgen object. See write_xdatcar for the meaning of arguments.

Parameters

• to_unit_cell (bool) – Whether to translate sites into the unit cell.

• kwargs – keywords arguments passed to Xdatcar constructor.

write_xdatcar(filepath='XDATCAR', groupby_type=True, overwrite=False, to_unit_cell=False)

Write Xdatcar file with unit cell and atomic positions to file filepath.

Parameters

• filepath – Xdatcar filename. If None, a temporary file is created.

• groupby_type – If True, atoms are grouped by type. Note that this option may change the order of the atoms. This option is needed because there are post-processing tools (e.g. ovito) that do not work as expected if the atoms in the structure are not grouped by type.

• overwrite – raise RuntimeError, if False and filepath exists.

• to_unit_cell (bool) – Whether to translate sites into the unit cell.

Returns

path to Xdatcar file.

visualize(appname='ovito', to_unit_cell=False)

Visualize the crystalline structure with visualizer. See Visualizer for the list of applications and formats supported.

Parameters

to_unit_cell (bool) – Whether to translate sites into the unit cell.

plot_ax(ax, what, fontsize=8, **kwargs)

Helper function to plot quantity what on axis ax with matplotlib.

Parameters

• fontsize – fontsize for legend.

• are passed to matplotlib plot method. (kwargs) –

plotly_traces(fig, what, rcd=None, fontsize=8, showlegend=False, **kwargs)

Helper function to plot quantity what on figure fig with plotly.

Parameters

• rcd – If fig has subplots, rcd is used to add traces on these subplots.

• fontsize – fontsize for legend.

• are passed to fig.add_scatter method. (kwargs) –

plot(what_list=None, ax_list=None, fontsize=8, **kwargs)

Plot the evolution of structural parameters (lattice lengths, angles and volume) as well as pressure, info on forces and total energy with matplotlib.

Parameters

• what_list –

• ax_list – List of matplotlib.axes.Axes. If None, a new figure is created.

• fontsize – fontsize for legend

Returns: matplotlib.figure.Figure

Keyword arguments controlling the display of the figure:

kwargs	Meaning
title	Title of the plot (Default: None).
show	True to show the figure (default: True).
savefig	“abc.png” or “abc.eps” to save the figure to a file.
size_kwargs	Dictionary with options passed to fig.set_size_inches e.g. size_kwargs=dict(w=3, h=4)
tight_layout	True to call fig.tight_layout (default: False)
ax_grid	True (False) to add (remove) grid from all axes in fig. Default: None i.e. fig is left unchanged.
ax_annotate	Add labels to subplots e.g. (a), (b). Default: False
fig_close	Close figure. Default: False.

plotly(what_list=None, fig=None, fontsize=12, **kwargs)

Plot the evolution of structural parameters (lattice lengths, angles and volume) as well as pressure, info on forces and total energy with plotly.

Parameters

• what_list –

• fig – The fig for plot and the DOS plot. If None, a new figure is created.

• fontsize – fontsize for legend

Returns: plotly.graph_objects.Figure

Keyword arguments controlling the display of the figure: ================ ==================================================================== kwargs Meaning ================ ==================================================================== title Title of the plot (Default: None). show True to show the figure (default: True). hovormode True to show the hover info (default: False) savefig “abc.png” , “abc.jpeg” or “abc.webp” to save the figure to a file. write_json Write plotly figure to write_json JSON file.

Inside jupyter-lab, one can right-click the write_json file from the file menu and open with “Plotly Editor”. Make some changes to the figure, then use the file menu to save the customized plotly plot. Requires jupyter labextension install jupyterlab-chart-editor. See https://github.com/plotly/jupyterlab-chart-editor

renderer (str or None (default None)) –

A string containing the names of one or more registered renderers (separated by ‘+’ characters) or None. If None, then the default renderers specified in plotly.io.renderers.default are used. See https://plotly.com/python-api-reference/generated/plotly.graph_objects.Figure.html

config (dict) A dict of parameters to configure the figure. The defaults are set in plotly.js. chart_studio True to push figure to chart_studio server. Requires authenticatios.

Default: False.

plot_energies(ax=None, fontsize=8, **kwargs)

Plot the total energies as function of the iteration step.

Parameters

• ax – matplotlib.axes.Axes or None if a new figure should be created.

• fontsize – Legend and title fontsize.

Returns: matplotlib.figure.Figure

Keyword arguments controlling the display of the figure:

kwargs	Meaning
title	Title of the plot (Default: None).
show	True to show the figure (default: True).
savefig	“abc.png” or “abc.eps” to save the figure to a file.
size_kwargs	Dictionary with options passed to fig.set_size_inches e.g. size_kwargs=dict(w=3, h=4)
tight_layout	True to call fig.tight_layout (default: False)
ax_grid	True (False) to add (remove) grid from all axes in fig. Default: None i.e. fig is left unchanged.
ax_annotate	Add labels to subplots e.g. (a), (b). Default: False
fig_close	Close figure. Default: False.

yield_figs(**kwargs)

This function generates a predefined list of matplotlib figures with minimal input from the user.

yield_plotly_figs(**kwargs)

This function generates a predefined list of matplotlib figures with minimal input from the user.

mvplot_trajectories(colormap='hot', sampling=1, figure=None, show=True, with_forces=True, **kwargs)

Call mayavi to plot atomic trajectories and the variation of the unit cell.

mvanimate(delay=500)

get_panel(**kwargs)

Build panel with widgets to interact with the abipy.dynamics.hist.HistFile either in a notebook or in panel app.

write_notebook(nbpath=None)

Write a jupyter notebook to nbpath. If nbpath is None, a temporay file in the current working directory is created. Return path to the notebook.

class abipy.dynamics.hist.HistRobot(*args)

Bases: abipy.abio.robots.Robot

This robot analyzes the results contained in multiple HIST.nc files.

Inheritance Diagram

EXT = 'HIST'

to_string(verbose=0)

String representation with verbosity level verbose.

get_dataframe(with_geo=True, index=None, abspath=False, with_spglib=True, funcs=None, **kwargs)

Return a pandas.DataFrame with the most important final results and the filenames as index.

Parameters

• with_geo – True if structure info should be added to the dataframe

• abspath – True if paths in index should be absolute. Default: Relative to getcwd().

• index – Index of the dataframe, if None, robot labels are used

• with_spglib – If True, spglib is invoked to get the space group symbol and number

kwargs:

attrs:

List of additional attributes of the abipy.electrons.gsr.GsrFile to add to the pandas.DataFrame.

funcs: Function or list of functions to execute to add more data to the DataFrame.

Each function receives a abipy.electrons.gsr.GsrFile object and returns a tuple (key, value) where key is a string with the name of column and value is the value to be inserted.

property what_list

List with all quantities that can be plotted (what_list).

gridplot(what_list=None, sharex='row', sharey='row', fontsize=8, **kwargs)

Plot the what value extracted from multiple HIST.nc files on a grid.

Parameters

• what_list – List of quantities to plot. Must be in [“energy”, “abc”, “angles”, “volume”, “pressure”, “forces”]

• sharex – True if xaxis should be shared.

• sharey – True if yaxis should be shared.

• fontsize – fontsize for legend.

Returns: matplotlib.figure.Figure

Keyword arguments controlling the display of the figure:

kwargs	Meaning
title	Title of the plot (Default: None).
show	True to show the figure (default: True).
savefig	“abc.png” or “abc.eps” to save the figure to a file.
size_kwargs	Dictionary with options passed to fig.set_size_inches e.g. size_kwargs=dict(w=3, h=4)
tight_layout	True to call fig.tight_layout (default: False)
ax_grid	True (False) to add (remove) grid from all axes in fig. Default: None i.e. fig is left unchanged.
ax_annotate	Add labels to subplots e.g. (a), (b). Default: False
fig_close	Close figure. Default: False.

combiplot(what_list=None, colormap='jet', fontsize=6, **kwargs)

Plot multiple HIST.nc files on a grid. One plot for each what value.

Parameters

• what_list – List of strings with the quantities to plot. If None, all quanties are plotted.

• colormap – matplotlib color map.

• fontsize – fontisize for legend.

Returns: matplotlib.figure.Figure.

Keyword arguments controlling the display of the figure:

kwargs	Meaning
title	Title of the plot (Default: None).
show	True to show the figure (default: True).
savefig	“abc.png” or “abc.eps” to save the figure to a file.
size_kwargs	Dictionary with options passed to fig.set_size_inches e.g. size_kwargs=dict(w=3, h=4)
tight_layout	True to call fig.tight_layout (default: False)
ax_grid	True (False) to add (remove) grid from all axes in fig. Default: None i.e. fig is left unchanged.
ax_annotate	Add labels to subplots e.g. (a), (b). Default: False
fig_close	Close figure. Default: False.

yield_figs(**kwargs)

This function generates a predefined list of matplotlib figures with minimal input from the user.

write_notebook(nbpath=None)

Write a jupyter notebook to nbpath. If nbpath is None, a temporay file in the current working directory is created. Return path to the notebook.

class abipy.dynamics.hist.HistReader(path)

Bases: abipy.iotools.ETSF_Reader

This object reads data from the HIST file.

Inheritance Diagram

num_steps()

Number of iterations present in the HIST.nc file.

natom()

Number of atoms un the unit cell.

read_all_structures()

Return the list of structures at the different iteration steps.

read_eterms(unit='eV')

monty.collections.AttrDict with the decomposition of the total energy in units unit

read_cart_forces(unit='eV ang^-1')

Read and return a numpy.ndarray with the cartesian forces in unit unit. Shape (num_steps, natom, 3)

read_reduced_forces()

Read and return a numpy.ndarray with the forces in reduced coordinates Shape (num_steps, natom, 3)

read_cart_stress_tensors()

Return the stress tensors (nstep x 3 x 3) in cartesian coordinates (GPa) and the list of pressures in GPa unit.