panels Package

Contents

• panels Package

  • panels Package

  • core Module

  • ddb Module

  • fatbands Module

  • flows Module

  • gsr Module

  • hist Module

  • outputs Module

  • phonons Module

  • pipelines Module

  • sigeph Module

  • structure Module

  • tasks Module

  • works Module

panels Package

core Module

“Basic tools and mixin classes for AbiPy panels.

abipy.panels.core.get_abinit_template_cls_kwds()

abipy.panels.core.set_abinit_template(template_name)

abipy.panels.core.abipanel(panel_template='FastList')

Activate panel extensions used by AbiPy. Return panel module.

Parameters

panel_template – String with the name of the panel template to be used by default.

abipy.panels.core.gen_id(n=1, pre='uuid-')

Generate n universally unique identifiers prepended with pre string. Return string if n == 1 or list of strings if n > 1

abipy.panels.core.get_template_cls_from_name(name)

Return panel template from string. Support name in the form FastList as well as FastListTemplate.

abipy.panels.core.depends_on_btn_click(btn_name, show_exc=True)

This decorator is used for callbacks triggered by a button of name btn_name If show_exc is True, a Markdown pane with the backtrace is returned if an exception is raised.

abipy.panels.core.my_depends(*args, **kwargs)

abipy.panels.core.show_exception(func)

This decorator returns a Markdown pane with the backtrace if the function raises an exception.

class abipy.panels.core.HTMLwithClipboardBtn(object=None, btn_cls=None, **params)

Bases: panel.pane.markup.HTML

params(style=Dict, default_layout=ClassSelector, object=Parameter, loading=Boolean, align=ClassSelector, aspect_ratio=Parameter, background=Parameter, css_classes=List, height=Integer, height_policy=ObjectSelector, margin=Parameter, max_height=Integer, max_width=Integer, min_height=Integer, min_width=Integer, sizing_mode=ObjectSelector, width=Integer, width_policy=ObjectSelector, name=String)

Receives an HTML string and returns an HTML pane with a button that allows the user to copy the content to the system clipboard. Requires call to abipanel to load the JS extension.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

align ‘start’ ClassSelector V RW aspect_ratio None Parameter V RW AN background None Parameter V RW AN css_classes None List (0, None) V RW AN default_layout <class ‘panel.layout.base.Row’> ClassSelector V RW height None Integer (0, None) V RW AN height_policy ‘auto’ ObjectSelector V RW loading False Boolean (0, 1) V RW margin 5 Parameter V RW max_height None Integer (0, None) V RW AN max_width None Integer (0, None) V RW AN min_height None Integer (0, None) V RW AN min_width None Integer (0, None) V RW AN object None Parameter V RW AN sizing_mode None ObjectSelector V RW style None Dict V RW AN width None Integer (0, None) V RW AN width_policy ‘auto’ ObjectSelector V RW

Parameter docstrings: =====================

align: Whether the object should be aligned with the start, end or  center of its container. If set as a tuple it will declare  (vertical, horizontal) alignment. aspect_ratio: Describes the proportional relationship between component’s  width and height. This works if any of component’s dimensions  are flexible in size. If set to a number, width / height =                 aspect_ratio relationship will be maintained. Otherwise, if  set to "auto", component’s preferred width and height will  be used to determine the aspect (if not set, no aspect will be  preserved). background: Background color of the component. css_classes: CSS classes to apply to the layout. default_layout: Defines the layout the model(s) returned by the pane will  be placed in. height: The height of the component (in pixels). This can be either  fixed or preferred height, depending on height sizing policy. height_policy: Describes how the component should maintain its height.    "auto"``                     Use component's preferred sizing policy.                                  ``"fixed"``                     Use exactly ``height pixels. Component will overflow if  it can’t fit in the available vertical space.    "fit"``                     Use component's preferred height (if set) and allow to fit                     into the available vertical space within the minimum and                     maximum height bounds (if set). Component's height neither                     will be aggressively minimized nor maximized.                                  ``"min"``                     Use as little vertical space as possible, not less than                     the minimum height (if set).  The starting point is the                     preferred height (if set). The height of the component may                     shrink or grow depending on the parent layout, aspect                     management and other factors.                                  ``"max"``                     Use as much vertical space as possible, not more than the                     maximum height (if set).  The starting point is the                     preferred height (if set). The height of the component may                     shrink or grow depending on the parent layout, aspect                     management and other factors. loading:        Whether or not the Viewable is loading. If True a loading spinner                 is shown on top of the Viewable. margin:         Allows to create additional space around the component. May                 be specified as a two-tuple of the form (vertical, horizontal)                 or a four-tuple (top, right, bottom, left). max_height:     Minimal height of the component (in pixels) if height is adjustable. max_width:      Minimal width of the component (in pixels) if width is adjustable. min_height:     Minimal height of the component (in pixels) if height is adjustable. min_width:      Minimal width of the component (in pixels) if width is adjustable. object:         The object being wrapped, which will be converted to a                 Bokeh model. sizing_mode:    How the component should size itself.                                  This is a high-level setting for maintaining width and height                 of the component. To gain more fine grained control over                 sizing, use ``width_policy, height_policy and  aspect_ratio instead (those take precedence over  sizing_mode).    "fixed"``                     Component is not responsive. It will retain its original                     width and height regardless of any subsequent browser                     window resize events.                                  ``"stretch_width"``                     Component will responsively resize to stretch to the                     available width, without maintaining any aspect ratio. The                     height of the component depends on the type of the                     component and may be fixed or fit to component's contents.                                  ``"stretch_height"``                     Component will responsively resize to stretch to the                     available height, without maintaining any aspect                     ratio. The width of the component depends on the type of                     the component and may be fixed or fit to component's                     contents.                                  ``"stretch_both"``                     Component is completely responsive, independently in width                     and height, and will occupy all the available horizontal                     and vertical space, even if this changes the aspect ratio                     of the component.                                  ``"scale_width"``                     Component will responsively resize to stretch to the                     available width, while maintaining the original or                     provided aspect ratio.                                  ``"scale_height"``                     Component will responsively resize to stretch to the                     available height, while maintaining the original or                     provided aspect ratio.                                  ``"scale_both"``                     Component will responsively resize to both the available                     width and height, while maintaining the original or                     provided aspect ratio. style:          Dictionary of CSS property:value pairs to apply to this Div. width:          The width of the component (in pixels). This can be either                 fixed or preferred width, depending on width sizing policy. width_policy:   Describes how the component should maintain its width.                                  ``"auto"``                     Use component's preferred sizing policy.                                  ``"fixed"``                     Use exactly ``width pixels. Component will overflow if  it can’t fit in the available horizontal space.    ``”fit”``  Use component’s preferred width (if set) and allow it to  fit into the available horizontal space within the minimum  and maximum width bounds (if set). Component’s width  neither will be aggressively minimized nor maximized.    ``”min”``  Use as little horizontal space as possible, not less than  the minimum width (if set). The starting point is the  preferred width (if set). The width of the component may  shrink or grow depending on the parent layout, aspect  management and other factors.    ``”max”``  Use as much horizontal space as possible, not more than  the maximum width (if set). The starting point is the  preferred width (if set). The width of the component may  shrink or grow depending on the parent layout, aspect  management and other factors.

name = 'HTMLwithClipboardBtn'

abipy.panels.core.mpl(fig, sizing_mode='stretch_width', with_controls=False, with_divider=True, **kwargs)

Helper function returning a panel Column with a matplotly pane followed by a divider and (optionally) controls to customize the figure.

abipy.panels.core.ply(fig, sizing_mode='stretch_width', with_chart_studio=True, with_help=True, with_divider=True, with_controls=False)

Helper function returning a panel Column with a plotly pane, buttons to push the figure to plotly chart studio and, optionally, controls to customize the figure.

abipy.panels.core.dfc(df, wdg_type='dataframe', with_export_btn=True, with_controls=False, with_divider=True, transpose=False, **kwargs)

Helper function returning a panel Column with a DataFrame or Tabulator widget followed by a divider and (optionally) controls to customize the figure.

Note that not all the options work as exected. See comments below.

class abipy.panels.core.MyMarkdown(object=None, **params)

Bases: panel.pane.markup.Markdown

params(dedent=Boolean, extensions=List, style=Dict, default_layout=ClassSelector, object=Parameter, loading=Boolean, align=ClassSelector, aspect_ratio=Parameter, background=Parameter, css_classes=List, height=Integer, height_policy=ObjectSelector, margin=Parameter, max_height=Integer, max_width=Integer, min_height=Integer, min_width=Integer, sizing_mode=ObjectSelector, width=Integer, width_policy=ObjectSelector, name=String)

A Markdown pane renders the markdown markup language to HTML and displays it inside a bokeh Div model. It has no explicit priority since it cannot be easily be distinguished from a standard string, therefore it has to be invoked explicitly.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

align ‘start’ ClassSelector V RW aspect_ratio None Parameter V RW AN background None Parameter V RW AN css_classes None List (0, None) V RW AN dedent True Boolean (0, 1) V RW default_layout <class ‘panel.layout.base.Row’> ClassSelector V RW extensions [‘extra’, ‘smarty’, ‘codehilite’] List (0, None) V RW height None Integer (0, None) V RW AN height_policy ‘auto’ ObjectSelector V RW loading False Boolean (0, 1) V RW margin 5 Parameter V RW max_height None Integer (0, None) V RW AN max_width None Integer (0, None) V RW AN min_height None Integer (0, None) V RW AN min_width None Integer (0, None) V RW AN object None Parameter V RW AN sizing_mode None ObjectSelector V RW style None Dict V RW AN width None Integer (0, None) V RW AN width_policy ‘auto’ ObjectSelector V RW

Parameter docstrings: =====================

align: Whether the object should be aligned with the start, end or  center of its container. If set as a tuple it will declare  (vertical, horizontal) alignment. aspect_ratio: Describes the proportional relationship between component’s  width and height. This works if any of component’s dimensions  are flexible in size. If set to a number, width / height =                 aspect_ratio relationship will be maintained. Otherwise, if  set to "auto", component’s preferred width and height will  be used to determine the aspect (if not set, no aspect will be  preserved). background: Background color of the component. css_classes: CSS classes to apply to the layout. dedent: Whether to dedent common whitespace across all lines. default_layout: Defines the layout the model(s) returned by the pane will  be placed in. extensions: Markdown extension to apply when transforming markup. height: The height of the component (in pixels). This can be either  fixed or preferred height, depending on height sizing policy. height_policy: Describes how the component should maintain its height.    "auto"``                     Use component's preferred sizing policy.                                  ``"fixed"``                     Use exactly ``height pixels. Component will overflow if  it can’t fit in the available vertical space.    "fit"``                     Use component's preferred height (if set) and allow to fit                     into the available vertical space within the minimum and                     maximum height bounds (if set). Component's height neither                     will be aggressively minimized nor maximized.                                  ``"min"``                     Use as little vertical space as possible, not less than                     the minimum height (if set).  The starting point is the                     preferred height (if set). The height of the component may                     shrink or grow depending on the parent layout, aspect                     management and other factors.                                  ``"max"``                     Use as much vertical space as possible, not more than the                     maximum height (if set).  The starting point is the                     preferred height (if set). The height of the component may                     shrink or grow depending on the parent layout, aspect                     management and other factors. loading:        Whether or not the Viewable is loading. If True a loading spinner                 is shown on top of the Viewable. margin:         Allows to create additional space around the component. May                 be specified as a two-tuple of the form (vertical, horizontal)                 or a four-tuple (top, right, bottom, left). max_height:     Minimal height of the component (in pixels) if height is adjustable. max_width:      Minimal width of the component (in pixels) if width is adjustable. min_height:     Minimal height of the component (in pixels) if height is adjustable. min_width:      Minimal width of the component (in pixels) if width is adjustable. object:         The object being wrapped, which will be converted to a                 Bokeh model. sizing_mode:    How the component should size itself.                                  This is a high-level setting for maintaining width and height                 of the component. To gain more fine grained control over                 sizing, use ``width_policy, height_policy and  aspect_ratio instead (those take precedence over  sizing_mode).    "fixed"``                     Component is not responsive. It will retain its original                     width and height regardless of any subsequent browser                     window resize events.                                  ``"stretch_width"``                     Component will responsively resize to stretch to the                     available width, without maintaining any aspect ratio. The                     height of the component depends on the type of the                     component and may be fixed or fit to component's contents.                                  ``"stretch_height"``                     Component will responsively resize to stretch to the                     available height, without maintaining any aspect                     ratio. The width of the component depends on the type of                     the component and may be fixed or fit to component's                     contents.                                  ``"stretch_both"``                     Component is completely responsive, independently in width                     and height, and will occupy all the available horizontal                     and vertical space, even if this changes the aspect ratio                     of the component.                                  ``"scale_width"``                     Component will responsively resize to stretch to the                     available width, while maintaining the original or                     provided aspect ratio.                                  ``"scale_height"``                     Component will responsively resize to stretch to the                     available height, while maintaining the original or                     provided aspect ratio.                                  ``"scale_both"``                     Component will responsively resize to both the available                     width and height, while maintaining the original or                     provided aspect ratio. style:          Dictionary of CSS property:value pairs to apply to this Div. width:          The width of the component (in pixels). This can be either                 fixed or preferred width, depending on width sizing policy. width_policy:   Describes how the component should maintain its width.                                  ``"auto"``                     Use component's preferred sizing policy.                                  ``"fixed"``                     Use exactly ``width pixels. Component will overflow if  it can’t fit in the available horizontal space.    ``”fit”``  Use component’s preferred width (if set) and allow it to  fit into the available horizontal space within the minimum  and maximum width bounds (if set). Component’s width  neither will be aggressively minimized nor maximized.    ``”min”``  Use as little horizontal space as possible, not less than  the minimum width (if set). The starting point is the  preferred width (if set). The width of the component may  shrink or grow depending on the parent layout, aspect  management and other factors.    ``”max”``  Use as much horizontal space as possible, not more than  the maximum width (if set). The starting point is the  preferred width (if set). The width of the component may  shrink or grow depending on the parent layout, aspect  management and other factors.

extensions = ['extra', 'smarty', 'codehilite']

name = 'MyMarkdown'

class abipy.panels.core.ButtonContext(btn)

Bases: object

A context manager for buttons triggering computations on the server.

This manager disables the button when we __enter__ and changes the name of the button to “running”. It reverts to the initial state of the button ocne __exit__ is invoked, showing the Exception type in a “red” button if an exception is raised during the computation.

This a very important tool because we need to disable the button when we start the computation to prevent the user from triggering multiple callbacks while the server is still working. At the same time, whathever happens in the callback, the button should go back to “clickable” mode when the callback returns so that the user can try to change the parameters and rerun.

Note also that we want to provide some graphical feedback to the user if something goes wrong. At present we don’t expose the python traceback on the client. It would be nice but we need panel machinery to do that. Moreover this is not the recommended approach for security reasons so we just change the “color” of the button and use the string representation of the exception as button name.

class abipy.panels.core.Loading(panel_obj, err_wdg=None, width=70)

Bases: object

A context manager for setting the loading attribute of a panel object.

class abipy.panels.core.ActiveBar(progress, err_wdg=None, width=70)

Bases: object

A context manager that sets progress.active to True on entry and False when we exit.

class abipy.panels.core.AbipyParameterized(**params)

Bases: param.parameterized.Parameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Base class for AbiPy panels. Provides helper functions for typical operations needed for building dashboard and basic parameters supported by the subclasses.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

verbose = 0

mpi_procs = 1

has_remote_server = False

warning = Markdown(str, name='warning')

mpl_kwargs()

Default arguments passed to AbiPy matplotlib plot methods.

pws_col(keys)

pws(keys)

Helper function returning the list of parameters and widgets defined in self from a list of strings. Accepts also widget or parameter instances.

helpc(method_name, extra_items=None)

Add accordion with a brief description and a warning after the button. The description of the tool is taken from the docstring of the callback. Return Column.

wdg_exts_with_get_panel(name='File extensions supported:')

Return Select widget with the list of file extensions implementing a get_panel method.

static html_with_clipboard_btn(html_str, **kwargs)

static get_software_stack()

Return column with version of python packages in tabular format.

static get_fileinput_section(file_input)

static get_abifile_from_file_input(file_input, use_structure=False)

get_ebands_from_file_input(file_input, remove=True)

Read and return an abipy.electrons.ebands.ElectronBands object from a file_input widget. Return None if the file does not provide an ebands object. Remove the file if remove==True.

static get_alert_data_transfer()

static get_template_cls_from_name(template)

get_abinit_template_cls_kwds()

get_template_from_tabs(tabs, template, tabs_location='above', closable=False)

This method receives panel Tabs or a dictionary, include them in a template and return the template.

name = 'AbipyParameterized'

class abipy.panels.core.PanelWithStructure(structure, **params)

Bases: abipy.panels.core.AbipyParameterized

params(structure_viewer=ObjectSelector, has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Mixin class for panel objects providing a abipy.core.structure.Structure object.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW structure_viewer ‘jsmol’ ObjectSelector V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. structure_viewer: < No docstring available > verbose: Verbosity Level

structure_viewer = 'jsmol'

on_view_structure()

Visualize input structure.

get_struct_view_tab_entry()

Return tab entry to visualize the structure.

get_structure_info()

Return Column with lattice parameters, angles and atomic positions grouped by type.

name = 'PanelWithStructure'

abipy.panels.core.get_structure_info(structure)

Return Column with lattice parameters, angles and atomic positions grouped by type.

class abipy.panels.core.NcFileMixin(**params)

Bases: param.parameterized.Parameterized

params(name=String)

This mixin class allows the user to inspect the dimensions and the variables reported in a netcdf file. Subclasses should implement the ncfile property

 Object has no parameters.

property ncfile

abc does not play well with parametrized so we rely on this to enforce the protocol.

get_ncfile_panel()

name = 'NcFileMixin'

class abipy.panels.core.PanelWithElectronBands(ebands, **params)

Bases: abipy.panels.core.PanelWithStructure

params(ebands_kmesh_fileinput=FileSelector, ebands_kpath_fileinput=FileSelector, edos_method=ObjectSelector, edos_step_ev=Number, edos_width_ev=Number, set_fermie_to_vbm=Boolean, skw_line_density=Integer, skw_lpratio=Integer, with_gaps=Boolean, structure_viewer=ObjectSelector, has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Mixin class for panel object associated to AbiPy object providing an abipy.electrons.ebands.ElectronBands object.

Subclasses should implement the ebands property.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

ebands_kmesh_fileinput None FileSelector V RW ebands_kpath_fileinput None FileSelector V RW edos_method ‘gaussian’ ObjectSelector V RW edos_step_ev 0.1 Number (1e-06, None) V RW edos_width_ev 0.2 Number (1e-06, None) V RW has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW set_fermie_to_vbm False Boolean (0, 1) V RW skw_line_density 20 Integer V RW skw_lpratio 5 Integer (1, None) V RW structure_viewer ‘jsmol’ ObjectSelector V RW verbose 0 Integer (0, None) V RW with_gaps False Boolean (0, 1) V RW

Parameter docstrings: =====================

ebands_kmesh_fileinput: < No docstring available > ebands_kpath_fileinput: < No docstring available > edos_method: e-DOS method edos_step_ev: e-DOS step in eV edos_width_ev: e-DOS Gaussian broadening in eV has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. set_fermie_to_vbm: Set Fermie to VBM skw_line_density: < No docstring available > skw_lpratio: < No docstring available > structure_viewer: < No docstring available > verbose: Verbosity Level with_gaps: < No docstring available >

with_gaps = False

set_fermie_to_vbm = False

edos_method = 'gaussian'

edos_step_ev = 0.1

edos_width_ev = 0.2

skw_lpratio = 5

skw_line_density = 20

ebands_kpath = None

ebands_kpath_fileinput = None

ebands_kmesh = None

ebands_kmesh_fileinput = None

get_ebands_kpath()

Receives the netcdf file selected by the user as binary string.

get_plot_ebands_widgets()

Column with the widgets used to plot ebands.

on_plot_ebands_btn()

Button triggering ebands plot.

get_plot_edos_widgets()

Column with widgets associated to the e-DOS computation.

on_plot_edos_btn()

Button triggering edos plot.

on_plot_skw_btn()

get_plot_skw_widgets()

Widgets to compute e-DOS.

get_plot_fermi_surface_widgets()

Widgets to compute the Fermi surface.

on_plot_fermi_surface_btn()

name = 'PanelWithElectronBands'

class abipy.panels.core.BaseRobotPanel(robot, **params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Base class for panels with AbiPy robot.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

on_compare_params_btn()

get_compare_params_widgets()

name = 'BaseRobotPanel'

class abipy.panels.core.PanelWithEbandsRobot(robot, **params)

Bases: abipy.panels.core.BaseRobotPanel

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Mixin class for panels with a robot that owns a list of of abipy.electrons.ebands.ElectronBands.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

get_ebands_plotter_widgets()

on_ebands_plotter_btn()

get_edos_plotter_widgets()

on_edos_plotter_btn()

Plot the electronic density of states.

name = 'PanelWithEbandsRobot'

abipy.panels.core.jsmol_html(structure, width=700, height=700, color='black', spin='false')

ddb Module

“Panels for DDB files.

class abipy.panels.ddb.PanelWithAnaddbParams(**params)

Bases: param.parameterized.Parameterized

params(asr=ObjectSelector, chneut=ObjectSelector, dipdip=ObjectSelector, dos_method=ObjectSelector, gamma_ev=Number, lo_to_splitting=ObjectSelector, ndivsm=Integer, nqsmall=Integer, plot_ifc_yscale=ObjectSelector, temp_range=Range, units=ObjectSelector, w_range=Range, name=String)

Mixin for panel classes requiring widgets to invoke Anaddb via AbiPy. Used, for instance, by DdbFilePanel and DdbRobotPanel so that we don’t have to repeat the same parameters over and over again.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

asr 2 ObjectSelector V RW chneut 1 ObjectSelector V RW dipdip 1 ObjectSelector V RW dos_method ‘tetra’ ObjectSelector V RW gamma_ev 0.0001 Number (1e-20, None) V RW lo_to_splitting ‘automatic’ ObjectSelector V RW ndivsm 5 Integer V RW nqsmall 10 Integer (1, None) V RW plot_ifc_yscale ‘linear’ ObjectSelector V RW temp_range (0.0, 300.0) Range (0, 1000) V RW units ‘eV’ ObjectSelector V RW w_range (0.0, 0.1) Range (0.0, 1.0) V RW

Parameter docstrings: =====================

asr: Abinit variable chneut: Abinit variable dipdip: Abinit variable dos_method: Integration method for DOS gamma_ev: Phonon linewidth in eV lo_to_splitting: < No docstring available > ndivsm: Number of divisions for smallest vector to generate the q-path nqsmall: Number of divisions for smallest vector to generate the q-mesh plot_ifc_yscale: < No docstring available > temp_range: Temperature range in K. units: Energy units w_range: Frequency range (eV)

nqsmall = 10

ndivsm = 5

lo_to_splitting = 'automatic'

chneut = 1

dipdip = 1

asr = 2

units = 'eV'

dos_method = 'tetra'

temp_range = (0.0, 300.0)

gamma_ev = 0.0001

w_range = (0.0, 0.1)

plot_ifc_yscale = 'linear'

kwargs_for_anaget_phbst_and_phdos_files(**extra_kwargs)

Return the parameters require to invoke anaget_phbst_and_phdos_files Additional kwargs can be specified if needed.

name = 'PanelWithAnaddbParams'

class abipy.panels.ddb.DdbFilePanel(ddb, **params)

Bases: abipy.panels.core.PanelWithStructure, abipy.panels.ddb.PanelWithAnaddbParams

params(structure_viewer=ObjectSelector, has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, asr=ObjectSelector, chneut=ObjectSelector, dipdip=ObjectSelector, dos_method=ObjectSelector, gamma_ev=Number, lo_to_splitting=ObjectSelector, ndivsm=Integer, nqsmall=Integer, plot_ifc_yscale=ObjectSelector, temp_range=Range, units=ObjectSelector, w_range=Range, name=String)

A panel to analyze a abipy.dfpt.ddb.DdbFile. Provides widgets to invoke anaddb and visualize the results.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

asr 2 ObjectSelector V RW chneut 1 ObjectSelector V RW dipdip 1 ObjectSelector V RW dos_method ‘tetra’ ObjectSelector V RW gamma_ev 0.0001 Number (1e-20, None) V RW has_remote_server False Boolean (0, 1) V RW lo_to_splitting ‘automatic’ ObjectSelector V RW mpi_procs 1 Integer (1, None) V RW ndivsm 5 Integer V RW nqsmall 10 Integer (1, None) V RW plot_ifc_yscale ‘linear’ ObjectSelector V RW structure_viewer ‘jsmol’ ObjectSelector V RW temp_range (0.0, 300.0) Range (0, 1000) V RW units ‘eV’ ObjectSelector V RW verbose 0 Integer (0, None) V RW w_range (0.0, 0.1) Range (0.0, 1.0) V RW

Parameter docstrings: =====================

asr: Abinit variable chneut: Abinit variable dipdip: Abinit variable dos_method: Integration method for DOS gamma_ev: Phonon linewidth in eV has_remote_server: < No docstring available > lo_to_splitting: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. ndivsm: Number of divisions for smallest vector to generate the q-path nqsmall: Number of divisions for smallest vector to generate the q-mesh plot_ifc_yscale: < No docstring available > structure_viewer: < No docstring available > temp_range: Temperature range in K. units: Energy units verbose: Verbosity Level w_range: Frequency range (eV)

get_epsinf()

Compute eps_infinity and Born effective charges from DDB.

plot_eps0w()

Compute eps0(omega) from DDB and plot the results.

on_plot_phbands_and_phdos()

Compute phonon bands and DOS from DDB by invoking Anaddb then plot results.

plot_vsound()

Compute the speed of sound by fitting phonon frequencies along selected directions by linear least-squares fit.

plot_without_asr_dipdip()

Compare phonon bands and DOSes computed with/without the acoustic sum rule and the treatment of the dipole-dipole interaction in the dynamical matrix. Requires DDB file with eps_inf, BECS.

plot_dos_vs_qmesh()

Compare phonon DOSes computed with/without the inclusion of the dipole-quadrupole and quadrupole-quadrupole terms in the dynamical matrix. Requires DDB file with eps_inf, BECS and dynamical quadrupoles.

plot_phbands_quad()

Compare phonon bands and DOSes computed with/without the inclusion of the dipole-quadrupole and quadrupole-quadrupole terms in the dynamical matrix. Requires DDB file with eps_inf, BECS and dynamical quadrupoles.

on_plot_ifc()

get_panel(as_dict=False, **kwargs)

Return tabs with widgets to interact with the DDB file.

name = 'DdbFilePanel'

class abipy.panels.ddb.PanelWithFileInput(use_structure=False, **params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) Parameters of ‘PanelWithFileInput’ ==================================  Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

info_str = '\nPost-process the data stored in one of the ABINIT output files.\n'

on_file_input(event)

on_mpid_input(event)

get_panel()

name = 'PanelWithFileInput'

class abipy.panels.ddb.PanelWithStructureInput(**params)

Bases: abipy.panels.ddb.PanelWithFileInput

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) Parameters of ‘PanelWithStructureInput’ =======================================  Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

info_str = '\nThis application allows user to upload a file with structural info and operate on it.\n'

name = 'PanelWithStructureInput'

class abipy.panels.ddb.DdbPanelWithFileInput(**params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) Parameters of ‘DdbPanelWithFileInput’ =====================================  Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

info_str = '\nThis application allows users to post-process the data stored in one of the Abinit output files.\nThe main difference with respect to [Abinit Output File Analyzer](/outfile) is that\nit is also possible to fetch the DDB file from the Materials Project Database.\n'

on_file_input(event)

on_mpid_input(event)

get_panel()

name = 'DdbPanelWithFileInput'

class abipy.panels.ddb.CompareDdbWithMP(**params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) Parameters of ‘CompareDdbWithMP’ ================================  Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

info_str = '\nThis panel alllows users to upload a DDB file and compare it with the one available on the MP.\n'

on_file_input(event)

get_panel()

name = 'CompareDdbWithMP'

class abipy.panels.ddb.DdbRobotPanel(robot, **params)

Bases: abipy.panels.core.BaseRobotPanel, abipy.panels.ddb.PanelWithAnaddbParams

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, asr=ObjectSelector, chneut=ObjectSelector, dipdip=ObjectSelector, dos_method=ObjectSelector, gamma_ev=Number, lo_to_splitting=ObjectSelector, ndivsm=Integer, nqsmall=Integer, plot_ifc_yscale=ObjectSelector, temp_range=Range, units=ObjectSelector, w_range=Range, name=String)

A panel to analyze multiple DdbFiles via the low-level API provided by DdbRobot. Provides widgets to invoke anaddb and visualize the results.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

asr 2 ObjectSelector V RW chneut 1 ObjectSelector V RW dipdip 1 ObjectSelector V RW dos_method ‘tetra’ ObjectSelector V RW gamma_ev 0.0001 Number (1e-20, None) V RW has_remote_server False Boolean (0, 1) V RW lo_to_splitting ‘automatic’ ObjectSelector V RW mpi_procs 1 Integer (1, None) V RW ndivsm 5 Integer V RW nqsmall 10 Integer (1, None) V RW plot_ifc_yscale ‘linear’ ObjectSelector V RW temp_range (0.0, 300.0) Range (0, 1000) V RW units ‘eV’ ObjectSelector V RW verbose 0 Integer (0, None) V RW w_range (0.0, 0.1) Range (0.0, 1.0) V RW

Parameter docstrings: =====================

asr: Abinit variable chneut: Abinit variable dipdip: Abinit variable dos_method: Integration method for DOS gamma_ev: Phonon linewidth in eV has_remote_server: < No docstring available > lo_to_splitting: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. ndivsm: Number of divisions for smallest vector to generate the q-path nqsmall: Number of divisions for smallest vector to generate the q-mesh plot_ifc_yscale: < No docstring available > temp_range: Temperature range in K. units: Energy units verbose: Verbosity Level w_range: Frequency range (eV)

kwargs_for_anaget_phbst_and_phdos_files(**extra_kwargs)

Extend method of base class to handle lo_to_splitting

plot_combiplot(**kwargs)

Plot phonon band structures.

plot_without_asr_dipdip()

Compare phonon bands and DOSes computed with/without the acoustic sum rule and the treatment of the dipole-dipole interaction in the dynamical matrix. Requires DDB file with eps_inf, BECS.

get_panel(as_dict=False, **kwargs)

Return tabs with widgets to interact with the DDB file.

name = 'DdbRobotPanel'

class abipy.panels.ddb.RobotWithFileInput(**params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) Parameters of ‘RobotWithFileInput’ ==================================  Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

info_str = '\nThis application allows users to create an AbiPy robot to post-process\na set of ABINIT output files of the same type.\n '

on_load_files(event)

get_panel()

name = 'RobotWithFileInput'

fatbands Module

Panels for interacting with FATBANDS.nc files.

class abipy.panels.fatbands.FatBandsFilePanel(ncfile, **params)

Bases: abipy.panels.core.PanelWithElectronBands

params(ebands_kmesh_fileinput=FileSelector, ebands_kpath_fileinput=FileSelector, edos_method=ObjectSelector, edos_step_ev=Number, edos_width_ev=Number, set_fermie_to_vbm=Boolean, skw_line_density=Integer, skw_lpratio=Integer, with_gaps=Boolean, structure_viewer=ObjectSelector, has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Panel with widgets to interact with a abipy.electrons.fatbands.FatBandsFile.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

ebands_kmesh_fileinput None FileSelector V RW ebands_kpath_fileinput None FileSelector V RW edos_method ‘gaussian’ ObjectSelector V RW edos_step_ev 0.1 Number (1e-06, None) V RW edos_width_ev 0.2 Number (1e-06, None) V RW has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW set_fermie_to_vbm False Boolean (0, 1) V RW skw_line_density 20 Integer V RW skw_lpratio 5 Integer (1, None) V RW structure_viewer ‘jsmol’ ObjectSelector V RW verbose 0 Integer (0, None) V RW with_gaps False Boolean (0, 1) V RW

Parameter docstrings: =====================

ebands_kmesh_fileinput: < No docstring available > ebands_kpath_fileinput: < No docstring available > edos_method: e-DOS method edos_step_ev: e-DOS step in eV edos_width_ev: e-DOS Gaussian broadening in eV has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. set_fermie_to_vbm: Set Fermie to VBM skw_line_density: < No docstring available > skw_lpratio: < No docstring available > structure_viewer: < No docstring available > verbose: Verbosity Level with_gaps: < No docstring available >

property ncfile

on_plot_fatbands_btn()

on_plot_fatdos_btn()

get_panel(as_dict=False, **kwargs)

Return tabs with widgets to interact with the FATBANDS.nc file.

name = 'FatBandsFilePanel'

flows Module

“Panels to interact with AbiPy flows.

class abipy.panels.flows.FlowPanel(flow, **params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Panel to interact with an AbiPy Flow.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

on_status_btn()

on_task_btn()

on_history_btn()

on_graphviz_btn()

Visualize the flow with graphviz.

on_debug_btn()

on_events_btn()

on_corrections_btn()

on_handlers_btn()

on_vars_btn()

on_dims_btn()

on_structures_btn()

get_panel(as_dict=False, **kwargs)

Return tabs with widgets to interact with the flow.

name = 'FlowPanel'

gsr Module

Panels to interact with GSR files.

class abipy.panels.gsr.GsrFilePanel(gsr, **params)

Bases: abipy.panels.core.PanelWithElectronBands, abipy.panels.core.NcFileMixin

params(ebands_kmesh_fileinput=FileSelector, ebands_kpath_fileinput=FileSelector, edos_method=ObjectSelector, edos_step_ev=Number, edos_width_ev=Number, set_fermie_to_vbm=Boolean, skw_line_density=Integer, skw_lpratio=Integer, with_gaps=Boolean, structure_viewer=ObjectSelector, has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Panel with widgets to interact with a abipy.electrons.gsr.GsrFile.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

ebands_kmesh_fileinput None FileSelector V RW ebands_kpath_fileinput None FileSelector V RW edos_method ‘gaussian’ ObjectSelector V RW edos_step_ev 0.1 Number (1e-06, None) V RW edos_width_ev 0.2 Number (1e-06, None) V RW has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW set_fermie_to_vbm False Boolean (0, 1) V RW skw_line_density 20 Integer V RW skw_lpratio 5 Integer (1, None) V RW structure_viewer ‘jsmol’ ObjectSelector V RW verbose 0 Integer (0, None) V RW with_gaps False Boolean (0, 1) V RW

Parameter docstrings: =====================

ebands_kmesh_fileinput: < No docstring available > ebands_kpath_fileinput: < No docstring available > edos_method: e-DOS method edos_step_ev: e-DOS step in eV edos_width_ev: e-DOS Gaussian broadening in eV has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. set_fermie_to_vbm: Set Fermie to VBM skw_line_density: < No docstring available > skw_lpratio: < No docstring available > structure_viewer: < No docstring available > verbose: Verbosity Level with_gaps: < No docstring available >

property ncfile

This for for the NcFileMixin mixin

get_panel(as_dict=False, **kwargs)

Return tabs with widgets to interact with the GSR file.

name = 'GsrFilePanel'

class abipy.panels.gsr.GsrRobotPanel(robot, **params)

Bases: abipy.panels.core.PanelWithEbandsRobot

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

A Panel to interact with multiple GSR files.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

on_gsr_dataframe_btn()

get_panel(as_dict=False, **kwargs)

Return tabs with widgets to interact with the abipy.electrons.gsr.GsrRobot.

name = 'GsrRobotPanel'

hist Module

“Panels for HIST files.

class abipy.panels.hist.HistFilePanel(hist, **params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Panel with widgets to interact with a abipy.dynamics.hist.HistFile.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

on_plot_relax_btn()

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

on_view_relax_btn()

get_panel(as_dict=False, **kwargs)

Return tabs with widgets to interact with the HIST.nc file.

name = 'HistFilePanel'

outputs Module

Panels for interacting with output files in text format.

class abipy.panels.outputs.AbinitOutputFilePanel(outfile, **params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Panel with widgets to interact with the Abinit main output file.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

get_panel(as_dict=False, **kwargs)

Return tabs with widgets to interact with the Abinit output file.

name = 'AbinitOutputFilePanel'

class abipy.panels.outputs.AbinitOutputFilePanelWithFileInput(**params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) Parameters of ‘AbinitOutputFilePanelWithFileInput’ ==================================================  Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

info_str = '\nThis application allows users to analyze the Abinit main output file\n'

on_file_input(event)

get_panel()

name = 'AbinitOutputFilePanelWithFileInput'

phonons Module

“Panels for phonon-related objects.

class abipy.panels.phonons.PhononBandsPlotterPanel(plotter, **params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) Parameters of ‘PhononBandsPlotterPanel’ =======================================  Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

on_phbands_plot_btn()

get_panel(as_dict=False, **kwargs)

Return tabs with widgets to interact with the abipy.dfpt.phonons.PhononBandsPlotter.

name = 'PhononBandsPlotterPanel'

pipelines Module

sigeph Module

structure Module

“GUIs for structure.

class abipy.panels.structure.StructurePanel(structure, with_inputs=True, **params)

Bases: abipy.panels.core.PanelWithStructure

params(structure_viewer=ObjectSelector, has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Panel with widgets to interact with an AbiPy Structure

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW structure_viewer ‘jsmol’ ObjectSelector V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. structure_viewer: < No docstring available > verbose: Verbosity Level

convert()

Convert the input structure to one of the format selected by the user.

spglib_summary()

Call spglib to find space group symmetries and Wyckoff positions.

on_abisanitize_btn()

Returns a new structure in which:

• Structure is refined.

• Reduced to primitive settings.

• Lattice vectors are exchanged if the triple product is negative

symprec:

Symmetry precision used to refine the structure.

angle_tolerance:

Tolerance on angles.

primitive:

Returns most primitive structure found.

primitive_standard:

Whether to convert to a primitive cell using the standards defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: Challenges and tools. Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010

get_kpath()

Generate high-symmetry k-path from input structure in the ABINIT format.

get_gs_input()

Return an AbinitInput for GS calculation from the parameters selected via the widgets.

on_gs_input_btn()

Generate minimalistic input file from the structure.

on_ebands_input_btn()

Generate minimalistic input file from band structure calculation.

on_ph_input_btn()

Generate minimalistic input file from phonon calculations with DFPT.

on_mp_match_btn()

get_panel(as_dict=False, **kwargs)

Build panel with widgets to interact with the structure either in a notebook or in a bokeh app

name = 'StructurePanel'

class abipy.panels.structure.InputFileGenerator(**params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) Parameters of ‘InputFileGenerator’ ==================================  Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

info_str = '\nGenerate ABINIT input files for performing basic\n\n   - ground-state calculations\n   - band structure calculations\n   - DFPT phonon calculations\n\nstarting from a crystalline structure provided by the user either via an external file\nor through the Materials Project identifier (*mp-id*).\n'

on_file_input(event)

on_mpid_input(event)

update_main_area()

get_panel()

name = 'InputFileGenerator'

tasks Module

“Panels to interact with the AbiPy tasks.

class abipy.panels.tasks.AbinitTaskPanel(task, **params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Panel to interact with an AbiPy Flow.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

on_status_btn()

on_history_btn()

on_graphviz_btn()

Visualize the flow with graphviz.

on_debug_btn()

on_events_btn()

on_corrections_btn()

on_handlers_btn()

on_files_btn()

on_dims_btn()

on_structures_btn()

get_panel(as_dict=False, **kwargs)

Return tabs with widgets to interact with the flow.

name = 'AbinitTaskPanel'

works Module

“Panels to interact with the AbiPy tasks.

class abipy.panels.works.WorkPanel(work, **params)

Bases: abipy.panels.core.AbipyParameterized

params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)

Panel to interact with an AbiPy Flow.

 Parameters changed from their default values are marked in red. Soft bound values are marked in cyan. C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None

Name Value Type Bounds Mode 

has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW

Parameter docstrings: =====================

has_remote_server: < No docstring available > mpi_procs: Number of MPI processes used for running Fortran code. verbose: Verbosity Level

on_status_btn()

on_history_btn()

on_graphviz_btn()

Visualize the flow with graphviz.

on_debug_btn()

on_events_btn()

on_corrections_btn()

on_handlers_btn()

on_dims_btn()

on_structures_btn()

get_panel(as_dict=False, **kwargs)

Return tabs with widgets to interact with the flow.

name = 'WorkPanel'