panels Package¶
Contents
core
Module¶
“Basic tools and mixin classes for AbiPy panels.
-
abipy.panels.core.
abipanel
(panel_template='FastList')[source]¶ 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-')[source]¶ Generate
n
universally unique identifiers prepended withpre
string. Return string if n == 1 or list of strings if n > 1
-
abipy.panels.core.
get_template_cls_from_name
(name)[source]¶ 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)[source]¶ 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.
show_exception
(func)[source]¶ 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)[source]¶ 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.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
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
[1;32mParameter docstrings: =====================[0m
[1;34malign: Whether the object should be aligned with the start, end or[0m [1;34m center of its container. If set as a tuple it will declare[0m [1;34m (vertical, horizontal) alignment.[0m [1;31maspect_ratio: Describes the proportional relationship between component’s[0m [1;31m width and height. This works if any of component’s dimensions[0m [1;31m are flexible in size. If set to a number,
width / height =[0m [1;31m aspect_ratio
relationship will be maintained. Otherwise, if[0m [1;31m set to"auto"
, component’s preferred width and height will[0m [1;31m be used to determine the aspect (if not set, no aspect will be[0m [1;31m preserved).[0m [1;34mbackground: Background color of the component.[0m [1;31mcss_classes: CSS classes to apply to the layout.[0m [1;34mdefault_layout: Defines the layout the model(s) returned by the pane will[0m [1;34m be placed in.[0m [1;31mheight: The height of the component (in pixels). This can be either[0m [1;31m fixed or preferred height, depending on height sizing policy.[0m [1;34mheight_policy: Describes how the component should maintain its height.[0m [1;34m [0m [1;34m"auto"``[0m [1;34m Use component's preferred sizing policy.[0m [1;34m [0m [1;34m ``"fixed"``[0m [1;34m Use exactly ``height
pixels. Component will overflow if[0m [1;34m it can’t fit in the available vertical space.[0m [1;34m [0m [1;34m"fit"``[0m [1;34m Use component's preferred height (if set) and allow to fit[0m [1;34m into the available vertical space within the minimum and[0m [1;34m maximum height bounds (if set). Component's height neither[0m [1;34m will be aggressively minimized nor maximized.[0m [1;34m [0m [1;34m ``"min"``[0m [1;34m Use as little vertical space as possible, not less than[0m [1;34m the minimum height (if set). The starting point is the[0m [1;34m preferred height (if set). The height of the component may[0m [1;34m shrink or grow depending on the parent layout, aspect[0m [1;34m management and other factors.[0m [1;34m [0m [1;34m ``"max"``[0m [1;34m Use as much vertical space as possible, not more than the[0m [1;34m maximum height (if set). The starting point is the[0m [1;34m preferred height (if set). The height of the component may[0m [1;34m shrink or grow depending on the parent layout, aspect[0m [1;34m management and other factors.[0m [1;31mloading: Whether or not the Viewable is loading. If True a loading spinner[0m [1;31m is shown on top of the Viewable.[0m [1;34mmargin: Allows to create additional space around the component. May[0m [1;34m be specified as a two-tuple of the form (vertical, horizontal)[0m [1;34m or a four-tuple (top, right, bottom, left).[0m [1;31mmax_height: Minimal height of the component (in pixels) if height is adjustable.[0m [1;34mmax_width: Minimal width of the component (in pixels) if width is adjustable.[0m [1;31mmin_height: Minimal height of the component (in pixels) if height is adjustable.[0m [1;34mmin_width: Minimal width of the component (in pixels) if width is adjustable.[0m [1;31mobject: The object being wrapped, which will be converted to a[0m [1;31m Bokeh model.[0m [1;34msizing_mode: How the component should size itself.[0m [1;34m [0m [1;34m This is a high-level setting for maintaining width and height[0m [1;34m of the component. To gain more fine grained control over[0m [1;34m sizing, use ``width_policy
,height_policy
and[0m [1;34maspect_ratio
instead (those take precedence over[0m [1;34msizing_mode
).[0m [1;34m [0m [1;34m"fixed"``[0m [1;34m Component is not responsive. It will retain its original[0m [1;34m width and height regardless of any subsequent browser[0m [1;34m window resize events.[0m [1;34m [0m [1;34m ``"stretch_width"``[0m [1;34m Component will responsively resize to stretch to the[0m [1;34m available width, without maintaining any aspect ratio. The[0m [1;34m height of the component depends on the type of the[0m [1;34m component and may be fixed or fit to component's contents.[0m [1;34m [0m [1;34m ``"stretch_height"``[0m [1;34m Component will responsively resize to stretch to the[0m [1;34m available height, without maintaining any aspect[0m [1;34m ratio. The width of the component depends on the type of[0m [1;34m the component and may be fixed or fit to component's[0m [1;34m contents.[0m [1;34m [0m [1;34m ``"stretch_both"``[0m [1;34m Component is completely responsive, independently in width[0m [1;34m and height, and will occupy all the available horizontal[0m [1;34m and vertical space, even if this changes the aspect ratio[0m [1;34m of the component.[0m [1;34m [0m [1;34m ``"scale_width"``[0m [1;34m Component will responsively resize to stretch to the[0m [1;34m available width, while maintaining the original or[0m [1;34m provided aspect ratio.[0m [1;34m [0m [1;34m ``"scale_height"``[0m [1;34m Component will responsively resize to stretch to the[0m [1;34m available height, while maintaining the original or[0m [1;34m provided aspect ratio.[0m [1;34m [0m [1;34m ``"scale_both"``[0m [1;34m Component will responsively resize to both the available[0m [1;34m width and height, while maintaining the original or[0m [1;34m provided aspect ratio.[0m [1;31mstyle: Dictionary of CSS property:value pairs to apply to this Div.[0m [1;34mwidth: The width of the component (in pixels). This can be either[0m [1;34m fixed or preferred width, depending on width sizing policy.[0m [1;31mwidth_policy: Describes how the component should maintain its width.[0m [1;31m [0m [1;31m ``"auto"``[0m [1;31m Use component's preferred sizing policy.[0m [1;31m [0m [1;31m ``"fixed"``[0m [1;31m Use exactly ``width
pixels. Component will overflow if[0m [1;31m it can’t fit in the available horizontal space.[0m [1;31m [0m [1;31m ``”fit”``[0m [1;31m Use component’s preferred width (if set) and allow it to[0m [1;31m fit into the available horizontal space within the minimum[0m [1;31m and maximum width bounds (if set). Component’s width[0m [1;31m neither will be aggressively minimized nor maximized.[0m [1;31m [0m [1;31m ``”min”``[0m [1;31m Use as little horizontal space as possible, not less than[0m [1;31m the minimum width (if set). The starting point is the[0m [1;31m preferred width (if set). The width of the component may[0m [1;31m shrink or grow depending on the parent layout, aspect[0m [1;31m management and other factors.[0m [1;31m [0m [1;31m ``”max”``[0m [1;31m Use as much horizontal space as possible, not more than[0m [1;31m the maximum width (if set). The starting point is the[0m [1;31m preferred width (if set). The width of the component may[0m [1;31m shrink or grow depending on the parent layout, aspect[0m [1;31m management and other factors.[0m-
name
= 'HTMLwithClipboardBtn'¶
-
-
abipy.panels.core.
mpl
(fig, sizing_mode='stretch_width', with_controls=False, with_divider=True, **kwargs)[source]¶ Helper function returning a panel Column with a matplotly pane followed by a divider and (optionally) controls to customize the figure.
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abipy.panels.core.
ply
(fig, sizing_mode='stretch_width', with_chart_studio=True, with_help=True, with_divider=True, with_controls=False)[source]¶ 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.
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abipy.panels.core.
dfc
(df, wdg_type='dataframe', with_export_btn=True, with_controls=False, with_divider=True, transpose=False, **kwargs)[source]¶ 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)[source]¶ 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.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
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
[1;32mParameter docstrings: =====================[0m
[1;34malign: Whether the object should be aligned with the start, end or[0m [1;34m center of its container. If set as a tuple it will declare[0m [1;34m (vertical, horizontal) alignment.[0m [1;31maspect_ratio: Describes the proportional relationship between component’s[0m [1;31m width and height. This works if any of component’s dimensions[0m [1;31m are flexible in size. If set to a number,
width / height =[0m [1;31m aspect_ratio
relationship will be maintained. Otherwise, if[0m [1;31m set to"auto"
, component’s preferred width and height will[0m [1;31m be used to determine the aspect (if not set, no aspect will be[0m [1;31m preserved).[0m [1;34mbackground: Background color of the component.[0m [1;31mcss_classes: CSS classes to apply to the layout.[0m [1;34mdedent: Whether to dedent common whitespace across all lines.[0m [1;31mdefault_layout: Defines the layout the model(s) returned by the pane will[0m [1;31m be placed in.[0m [1;34mextensions: Markdown extension to apply when transforming markup.[0m [1;31mheight: The height of the component (in pixels). This can be either[0m [1;31m fixed or preferred height, depending on height sizing policy.[0m [1;34mheight_policy: Describes how the component should maintain its height.[0m [1;34m [0m [1;34m"auto"``[0m [1;34m Use component's preferred sizing policy.[0m [1;34m [0m [1;34m ``"fixed"``[0m [1;34m Use exactly ``height
pixels. Component will overflow if[0m [1;34m it can’t fit in the available vertical space.[0m [1;34m [0m [1;34m"fit"``[0m [1;34m Use component's preferred height (if set) and allow to fit[0m [1;34m into the available vertical space within the minimum and[0m [1;34m maximum height bounds (if set). Component's height neither[0m [1;34m will be aggressively minimized nor maximized.[0m [1;34m [0m [1;34m ``"min"``[0m [1;34m Use as little vertical space as possible, not less than[0m [1;34m the minimum height (if set). The starting point is the[0m [1;34m preferred height (if set). The height of the component may[0m [1;34m shrink or grow depending on the parent layout, aspect[0m [1;34m management and other factors.[0m [1;34m [0m [1;34m ``"max"``[0m [1;34m Use as much vertical space as possible, not more than the[0m [1;34m maximum height (if set). The starting point is the[0m [1;34m preferred height (if set). The height of the component may[0m [1;34m shrink or grow depending on the parent layout, aspect[0m [1;34m management and other factors.[0m [1;31mloading: Whether or not the Viewable is loading. If True a loading spinner[0m [1;31m is shown on top of the Viewable.[0m [1;34mmargin: Allows to create additional space around the component. May[0m [1;34m be specified as a two-tuple of the form (vertical, horizontal)[0m [1;34m or a four-tuple (top, right, bottom, left).[0m [1;31mmax_height: Minimal height of the component (in pixels) if height is adjustable.[0m [1;34mmax_width: Minimal width of the component (in pixels) if width is adjustable.[0m [1;31mmin_height: Minimal height of the component (in pixels) if height is adjustable.[0m [1;34mmin_width: Minimal width of the component (in pixels) if width is adjustable.[0m [1;31mobject: The object being wrapped, which will be converted to a[0m [1;31m Bokeh model.[0m [1;34msizing_mode: How the component should size itself.[0m [1;34m [0m [1;34m This is a high-level setting for maintaining width and height[0m [1;34m of the component. To gain more fine grained control over[0m [1;34m sizing, use ``width_policy
,height_policy
and[0m [1;34maspect_ratio
instead (those take precedence over[0m [1;34msizing_mode
).[0m [1;34m [0m [1;34m"fixed"``[0m [1;34m Component is not responsive. It will retain its original[0m [1;34m width and height regardless of any subsequent browser[0m [1;34m window resize events.[0m [1;34m [0m [1;34m ``"stretch_width"``[0m [1;34m Component will responsively resize to stretch to the[0m [1;34m available width, without maintaining any aspect ratio. The[0m [1;34m height of the component depends on the type of the[0m [1;34m component and may be fixed or fit to component's contents.[0m [1;34m [0m [1;34m ``"stretch_height"``[0m [1;34m Component will responsively resize to stretch to the[0m [1;34m available height, without maintaining any aspect[0m [1;34m ratio. The width of the component depends on the type of[0m [1;34m the component and may be fixed or fit to component's[0m [1;34m contents.[0m [1;34m [0m [1;34m ``"stretch_both"``[0m [1;34m Component is completely responsive, independently in width[0m [1;34m and height, and will occupy all the available horizontal[0m [1;34m and vertical space, even if this changes the aspect ratio[0m [1;34m of the component.[0m [1;34m [0m [1;34m ``"scale_width"``[0m [1;34m Component will responsively resize to stretch to the[0m [1;34m available width, while maintaining the original or[0m [1;34m provided aspect ratio.[0m [1;34m [0m [1;34m ``"scale_height"``[0m [1;34m Component will responsively resize to stretch to the[0m [1;34m available height, while maintaining the original or[0m [1;34m provided aspect ratio.[0m [1;34m [0m [1;34m ``"scale_both"``[0m [1;34m Component will responsively resize to both the available[0m [1;34m width and height, while maintaining the original or[0m [1;34m provided aspect ratio.[0m [1;31mstyle: Dictionary of CSS property:value pairs to apply to this Div.[0m [1;34mwidth: The width of the component (in pixels). This can be either[0m [1;34m fixed or preferred width, depending on width sizing policy.[0m [1;31mwidth_policy: Describes how the component should maintain its width.[0m [1;31m [0m [1;31m ``"auto"``[0m [1;31m Use component's preferred sizing policy.[0m [1;31m [0m [1;31m ``"fixed"``[0m [1;31m Use exactly ``width
pixels. Component will overflow if[0m [1;31m it can’t fit in the available horizontal space.[0m [1;31m [0m [1;31m ``”fit”``[0m [1;31m Use component’s preferred width (if set) and allow it to[0m [1;31m fit into the available horizontal space within the minimum[0m [1;31m and maximum width bounds (if set). Component’s width[0m [1;31m neither will be aggressively minimized nor maximized.[0m [1;31m [0m [1;31m ``”min”``[0m [1;31m Use as little horizontal space as possible, not less than[0m [1;31m the minimum width (if set). The starting point is the[0m [1;31m preferred width (if set). The width of the component may[0m [1;31m shrink or grow depending on the parent layout, aspect[0m [1;31m management and other factors.[0m [1;31m [0m [1;31m ``”max”``[0m [1;31m Use as much horizontal space as possible, not more than[0m [1;31m the maximum width (if set). The starting point is the[0m [1;31m preferred width (if set). The width of the component may[0m [1;31m shrink or grow depending on the parent layout, aspect[0m [1;31m management and other factors.[0m-
extensions
= ['extra', 'smarty', 'codehilite']¶
-
name
= 'MyMarkdown'¶
-
-
class
abipy.panels.core.
ButtonContext
(btn)[source]¶ 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)[source]¶ 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)[source]¶ Bases:
object
A context manager that sets progress.active to True on entry and False when we exit.
-
class
abipy.panels.core.
AbipyParameterized
(**params)[source]¶ 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.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
verbose
= 0¶
-
mpi_procs
= 1¶
-
has_remote_server
= False¶
-
warning
= Markdown(str, name='warning')¶
-
pws
(keys)[source]¶ 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)[source]¶ 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:')[source]¶ Return Select widget with the list of file extensions implementing a get_panel method.
-
static
get_software_stack
()[source]¶ Return column with version of python packages in tabular format.
-
get_ebands_from_file_input
(file_input, remove=True)[source]¶ 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.
-
get_template_from_tabs
(tabs, template, tabs_location='above', closable=False)[source]¶ 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)[source]¶ 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.[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
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
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mstructure_viewer: < No docstring available >[0m [1;31mverbose: Verbosity Level[0m
-
structure_viewer
= 'jsmol'¶
-
get_structure_info
()[source]¶ Return Column with lattice parameters, angles and atomic positions grouped by type.
-
name
= 'PanelWithStructure'¶
-
-
abipy.panels.core.
get_structure_info
(structure)[source]¶ Return Column with lattice parameters, angles and atomic positions grouped by type.
-
class
abipy.panels.core.
NcFileMixin
(**params)[source]¶ 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
[0m Object has no parameters.
-
property
ncfile
¶ abc does not play well with parametrized so we rely on this to enforce the protocol.
-
name
= 'NcFileMixin'¶
-
property
-
class
abipy.panels.core.
PanelWithElectronBands
(ebands, **params)[source]¶ 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.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
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
[1;32mParameter docstrings: =====================[0m
[1;34mebands_kmesh_fileinput: < No docstring available >[0m [1;31mebands_kpath_fileinput: < No docstring available >[0m [1;34medos_method: e-DOS method[0m [1;31medos_step_ev: e-DOS step in eV[0m [1;34medos_width_ev: e-DOS Gaussian broadening in eV[0m [1;31mhas_remote_server: < No docstring available >[0m [1;34mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;31mset_fermie_to_vbm: Set Fermie to VBM[0m [1;34mskw_line_density: < No docstring available >[0m [1;31mskw_lpratio: < No docstring available >[0m [1;34mstructure_viewer: < No docstring available >[0m [1;31mverbose: Verbosity Level[0m [1;34mwith_gaps: < No docstring available >[0m
-
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¶
-
name
= 'PanelWithElectronBands'¶
-
-
class
abipy.panels.core.
BaseRobotPanel
(robot, **params)[source]¶ Bases:
abipy.panels.core.AbipyParameterized
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)
Base class for panels with AbiPy robot.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
name
= 'BaseRobotPanel'¶
-
-
class
abipy.panels.core.
PanelWithEbandsRobot
(robot, **params)[source]¶ 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
.[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
name
= 'PanelWithEbandsRobot'¶
-
ddb
Module¶
“Panels for DDB files.
-
class
abipy.panels.ddb.
PanelWithAnaddbParams
(**params)[source]¶ 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.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
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
[1;32mParameter docstrings: =====================[0m
[1;34masr: Abinit variable[0m [1;31mchneut: Abinit variable[0m [1;34mdipdip: Abinit variable[0m [1;31mdos_method: Integration method for DOS[0m [1;34mgamma_ev: Phonon linewidth in eV[0m [1;31mlo_to_splitting: < No docstring available >[0m [1;34mndivsm: Number of divisions for smallest vector to generate the q-path[0m [1;31mnqsmall: Number of divisions for smallest vector to generate the q-mesh[0m [1;34mplot_ifc_yscale: < No docstring available >[0m [1;31mtemp_range: Temperature range in K.[0m [1;34munits: Energy units[0m [1;31mw_range: Frequency range (eV)[0m
-
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)[source]¶ 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)[source]¶ 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.[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
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
[1;32mParameter docstrings: =====================[0m
[1;34masr: Abinit variable[0m [1;31mchneut: Abinit variable[0m [1;34mdipdip: Abinit variable[0m [1;31mdos_method: Integration method for DOS[0m [1;34mgamma_ev: Phonon linewidth in eV[0m [1;31mhas_remote_server: < No docstring available >[0m [1;34mlo_to_splitting: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mndivsm: Number of divisions for smallest vector to generate the q-path[0m [1;31mnqsmall: Number of divisions for smallest vector to generate the q-mesh[0m [1;34mplot_ifc_yscale: < No docstring available >[0m [1;31mstructure_viewer: < No docstring available >[0m [1;34mtemp_range: Temperature range in K.[0m [1;31munits: Energy units[0m [1;34mverbose: Verbosity Level[0m [1;31mw_range: Frequency range (eV)[0m
-
on_plot_phbands_and_phdos
()[source]¶ Compute phonon bands and DOS from DDB by invoking Anaddb then plot results.
-
plot_vsound
()[source]¶ Compute the speed of sound by fitting phonon frequencies along selected directions by linear least-squares fit.
-
plot_without_asr_dipdip
()[source]¶ 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
()[source]¶ 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
()[source]¶ 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.
-
name
= 'DdbFilePanel'¶
-
-
class
abipy.panels.ddb.
PanelWithFileInput
(use_structure=False, **params)[source]¶ Bases:
abipy.panels.core.AbipyParameterized
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) [1;32mParameters of ‘PanelWithFileInput’ ================================== [0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
info_str
= '\nPost-process the data stored in one of the ABINIT output files.\n'¶
-
name
= 'PanelWithFileInput'¶
-
-
class
abipy.panels.ddb.
PanelWithStructureInput
(**params)[source]¶ Bases:
abipy.panels.ddb.PanelWithFileInput
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) [1;32mParameters of ‘PanelWithStructureInput’ ======================================= [0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
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)[source]¶ Bases:
abipy.panels.core.AbipyParameterized
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) [1;32mParameters of ‘DdbPanelWithFileInput’ ===================================== [0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
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'¶
-
name
= 'DdbPanelWithFileInput'¶
-
-
class
abipy.panels.ddb.
CompareDdbWithMP
(**params)[source]¶ Bases:
abipy.panels.core.AbipyParameterized
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) [1;32mParameters of ‘CompareDdbWithMP’ ================================ [0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
info_str
= '\nThis panel alllows users to upload a DDB file and compare it with the one available on the MP.\n'¶
-
name
= 'CompareDdbWithMP'¶
-
-
class
abipy.panels.ddb.
DdbRobotPanel
(robot, **params)[source]¶ 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.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
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
[1;32mParameter docstrings: =====================[0m
[1;34masr: Abinit variable[0m [1;31mchneut: Abinit variable[0m [1;34mdipdip: Abinit variable[0m [1;31mdos_method: Integration method for DOS[0m [1;34mgamma_ev: Phonon linewidth in eV[0m [1;31mhas_remote_server: < No docstring available >[0m [1;34mlo_to_splitting: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mndivsm: Number of divisions for smallest vector to generate the q-path[0m [1;31mnqsmall: Number of divisions for smallest vector to generate the q-mesh[0m [1;34mplot_ifc_yscale: < No docstring available >[0m [1;31mtemp_range: Temperature range in K.[0m [1;34munits: Energy units[0m [1;31mverbose: Verbosity Level[0m [1;34mw_range: Frequency range (eV)[0m
-
kwargs_for_anaget_phbst_and_phdos_files
(**extra_kwargs)[source]¶ Extend method of base class to handle lo_to_splitting
-
plot_without_asr_dipdip
()[source]¶ 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.
-
name
= 'DdbRobotPanel'¶
-
-
class
abipy.panels.ddb.
RobotWithFileInput
(**params)[source]¶ Bases:
abipy.panels.core.AbipyParameterized
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) [1;32mParameters of ‘RobotWithFileInput’ ================================== [0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
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 '¶
-
name
= 'RobotWithFileInput'¶
-
fatbands
Module¶
Panels for interacting with FATBANDS.nc files.
-
class
abipy.panels.fatbands.
FatBandsFilePanel
(ncfile, **params)[source]¶ 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
.[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
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
[1;32mParameter docstrings: =====================[0m
[1;34mebands_kmesh_fileinput: < No docstring available >[0m [1;31mebands_kpath_fileinput: < No docstring available >[0m [1;34medos_method: e-DOS method[0m [1;31medos_step_ev: e-DOS step in eV[0m [1;34medos_width_ev: e-DOS Gaussian broadening in eV[0m [1;31mhas_remote_server: < No docstring available >[0m [1;34mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;31mset_fermie_to_vbm: Set Fermie to VBM[0m [1;34mskw_line_density: < No docstring available >[0m [1;31mskw_lpratio: < No docstring available >[0m [1;34mstructure_viewer: < No docstring available >[0m [1;31mverbose: Verbosity Level[0m [1;34mwith_gaps: < No docstring available >[0m
-
property
ncfile
¶
-
get_panel
(as_dict=False, **kwargs)[source]¶ Return tabs with widgets to interact with the FATBANDS.nc file.
-
name
= 'FatBandsFilePanel'¶
-
property
flows
Module¶
“Panels to interact with AbiPy flows.
-
class
abipy.panels.flows.
FlowPanel
(flow, **params)[source]¶ Bases:
abipy.panels.core.AbipyParameterized
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)
Panel to interact with an AbiPy Flow.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
name
= 'FlowPanel'¶
-
gsr
Module¶
Panels to interact with GSR files.
-
class
abipy.panels.gsr.
GsrFilePanel
(gsr, **params)[source]¶ 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
.[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
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
[1;32mParameter docstrings: =====================[0m
[1;34mebands_kmesh_fileinput: < No docstring available >[0m [1;31mebands_kpath_fileinput: < No docstring available >[0m [1;34medos_method: e-DOS method[0m [1;31medos_step_ev: e-DOS step in eV[0m [1;34medos_width_ev: e-DOS Gaussian broadening in eV[0m [1;31mhas_remote_server: < No docstring available >[0m [1;34mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;31mset_fermie_to_vbm: Set Fermie to VBM[0m [1;34mskw_line_density: < No docstring available >[0m [1;31mskw_lpratio: < No docstring available >[0m [1;34mstructure_viewer: < No docstring available >[0m [1;31mverbose: Verbosity Level[0m [1;34mwith_gaps: < No docstring available >[0m
-
property
ncfile
¶ This for for the NcFileMixin mixin
-
name
= 'GsrFilePanel'¶
-
property
-
class
abipy.panels.gsr.
GsrRobotPanel
(robot, **params)[source]¶ 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.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
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get_panel
(as_dict=False, **kwargs)[source]¶ Return tabs with widgets to interact with the
abipy.electrons.gsr.GsrRobot
.
-
name
= 'GsrRobotPanel'¶
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hist
Module¶
“Panels for HIST files.
-
class
abipy.panels.hist.
HistFilePanel
(hist, **params)[source]¶ 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
.[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
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on_plot_relax_btn
()[source]¶ Plot the evolution of structural parameters (lattice lengths, angles and volume) as well as pressure, info on forces and total energy.
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get_panel
(as_dict=False, **kwargs)[source]¶ Return tabs with widgets to interact with the HIST.nc file.
-
name
= 'HistFilePanel'¶
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outputs
Module¶
Panels for interacting with output files in text format.
-
class
abipy.panels.outputs.
AbinitOutputFilePanel
(outfile, **params)[source]¶ 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.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
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get_panel
(as_dict=False, **kwargs)[source]¶ Return tabs with widgets to interact with the Abinit output file.
-
name
= 'AbinitOutputFilePanel'¶
-
-
class
abipy.panels.outputs.
AbinitOutputFilePanelWithFileInput
(**params)[source]¶ Bases:
abipy.panels.core.AbipyParameterized
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) [1;32mParameters of ‘AbinitOutputFilePanelWithFileInput’ ================================================== [0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
info_str
= '\nThis application allows users to analyze the Abinit main output file\n'¶
-
name
= 'AbinitOutputFilePanelWithFileInput'¶
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phonons
Module¶
“Panels for phonon-related objects.
-
class
abipy.panels.phonons.
PhononBandsPlotterPanel
(plotter, **params)[source]¶ Bases:
abipy.panels.core.AbipyParameterized
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) [1;32mParameters of ‘PhononBandsPlotterPanel’ ======================================= [0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
get_panel
(as_dict=False, **kwargs)[source]¶ Return tabs with widgets to interact with the
abipy.dfpt.phonons.PhononBandsPlotter
.
-
name
= 'PhononBandsPlotterPanel'¶
-
structure
Module¶
“GUIs for structure.
-
class
abipy.panels.structure.
StructurePanel
(structure, with_inputs=True, **params)[source]¶ 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
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
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
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mstructure_viewer: < No docstring available >[0m [1;31mverbose: Verbosity Level[0m
-
on_abisanitize_btn
()[source]¶ 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_gs_input
()[source]¶ Return an AbinitInput for GS calculation from the parameters selected via the widgets.
-
get_panel
(as_dict=False, **kwargs)[source]¶ 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)[source]¶ Bases:
abipy.panels.core.AbipyParameterized
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String) [1;32mParameters of ‘InputFileGenerator’ ================================== [0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
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'¶
-
name
= 'InputFileGenerator'¶
-
tasks
Module¶
“Panels to interact with the AbiPy tasks.
-
class
abipy.panels.tasks.
AbinitTaskPanel
(task, **params)[source]¶ Bases:
abipy.panels.core.AbipyParameterized
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)
Panel to interact with an AbiPy Flow.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
name
= 'AbinitTaskPanel'¶
-
works
Module¶
“Panels to interact with the AbiPy tasks.
-
class
abipy.panels.works.
WorkPanel
(work, **params)[source]¶ Bases:
abipy.panels.core.AbipyParameterized
params(has_remote_server=Boolean, mpi_procs=Integer, verbose=Integer, name=String)
Panel to interact with an AbiPy Flow.
[0m [1;31mParameters changed from their default values are marked in red.[0m [1;36mSoft bound values are marked in cyan.[0m C/V= Constant/Variable, RO/RW = ReadOnly/ReadWrite, AN=Allow None
[1;34mName Value Type Bounds Mode [0m
has_remote_server False Boolean (0, 1) V RW mpi_procs 1 Integer (1, None) V RW verbose 0 Integer (0, None) V RW
[1;32mParameter docstrings: =====================[0m
[1;34mhas_remote_server: < No docstring available >[0m [1;31mmpi_procs: Number of MPI processes used for running Fortran code.[0m [1;34mverbose: Verbosity Level[0m
-
name
= 'WorkPanel'¶
-