aiidalab_alc package

Submodules

aiidalab_alc.main module

Defines the main AiiDAlab application page.

class aiidalab_alc.main.MainApp

Bases: object

The main AiiDAlab application class.

class aiidalab_alc.main.MainAppView(*args: t.Any, **kwargs: t.Any)

Bases: VBox

The main app view.

class aiidalab_alc.main.WizardWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

An ipywidgets based widget to hold the main application construct wizard.

on_step_change(change)

Switch between wizard steps when selected by the user.

property steps

Alias to the wizard’s steps list.

aiidalab_alc.resources module

Defines the model and view for the resource setup stage.

class aiidalab_alc.resources.ComputationalResourcesModel(*args: t.Any, **kwargs: t.Any)

Bases: HasTraits

Model for the resource setup stage.

code_label

A trait for unicode strings.

default_guide = '\n        <p>\n            Configure the computational resources required to run the ChemShell\n            calculation. Additionally, you can provide a label and description for\n            the AiiDA process that will be created.\n        </p>\n    '
ncpus

An int trait.

process_description

A trait for unicode strings.

process_label

A trait for unicode strings.

submitted

A boolean (True, False) trait.

validate() → bool

Validate the model’s inputs.

Returns:

True if all inputs are valid, False otherwise.

Return type:

bool

class aiidalab_alc.resources.ComputationalResourcesWizardStep(*args: t.Any, **kwargs: t.Any)

Bases: VBox, WizardAppWidgetStep

Main view for the resource setup stage.

render()

Render the wizard’s contents if not already rendered.

class aiidalab_alc.resources.ResourceSetupBox(*args: t.Any, **kwargs: t.Any)

Bases: VBox

A box widget for defining computational resources.

update_codes(_=None) → None

Update the list of available codes.

aiidalab_alc.structure module

Defines the model and view components for the structure setup stage.

class aiidalab_alc.structure.StructureStepModel(*args: t.Any, **kwargs: t.Any)

Bases: HasTraits

Model for structure selection and manipulation.

A model to define and store required information from the structure step in the app’s configuration wizard.

property has_file: bool

True if a raw structure file object has been attached to the model.

property has_structure: bool

True if a StructureData object has been attached to the model.

property is_periodic: bool

True if the attached StructureData object is a periodic structure.

structure

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

structure_file

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

submitted

A boolean (True, False) trait.

class aiidalab_alc.structure.StructureWizardStep(*args: t.Any, **kwargs: t.Any)

Bases: VBox, WizardAppWidgetStep

Wizard for structure selection and manipulation.

A step in a wizard based process widget which allows a user to configure a chemical structure to be used in their workflow.

render()

Render the wizard’s contents if not already rendered.

submit_structure(_)

Submit the structure step.

aiidalab_alc.utils module

Contains utility functions used throughout the python package.

aiidalab_alc.utils.get_app_dir() → Path

Return the absolute path for the root directory of this project.

Return the path to the root of the AiiDAlab application where the jupyter notebooks are contained to enable navigation between notebooks. This assumes that the environment variable AIIDALAB_APPS has been configured to point at the directory containing the app source code.

Returns:

The path to the root AiiDAlab application directory.

Return type:

pathlib.Path

aiidalab_alc.utils.get_chem_shell_params(key: str) → tuple

Return the ChemShell input dictionary keys defined by the aiida-chemshell plugin.

Parameters:

key (str) – The input field to be queried (“sp”: “Single Point”, “op”: “Geometry Optimisation”, “qm”: “Quantum Mechanics”, “mm”: “Molecular Mechanics”)

Returns:

A list of the input dictionary keys for the requested input field as defined by the aiida-chemshell plugin.

Return type:

tuple

aiidalab_alc.utils.get_py_app_dir() → Path

Return the absolute path for the AiiDAlab ALC app python package.

Returns:

The path to the root python package directory.

Return type:

pathlib.Path

Open a given link in a new browser tab.

Parameters:

path (str) – The link to be opened.

aiidalab_alc.utils.test_aiida_chemsh_import() → bool

Test if the aiida-chemshell plugin is installed.

Returns:

True if the aiida-chemshell plugin is installed, False otherwise.

Return type:

bool

aiidalab_alc.workflow module

Module defining the MVC for ChemShell workflow configuration.

class aiidalab_alc.workflow.ChemShellOptionsWidget(*args: t.Any, **kwargs: t.Any)

Bases: VBox

Widget for selecting the ChemShell input options.

disable(val: bool) → None

Disable the input fields.

render()

Render the options widget contents if not already rendered.

class aiidalab_alc.workflow.ChemShellWorkflowModel(*args: t.Any, **kwargs: t.Any)

Bases: HasTraits

The model for setting up a ChemShell workflow.

basis_quality

A boolean (True, False) trait.

default_guide = ''
force_field

A trait whose value must be an instance of a specified class.

The value can also be an instance of a subclass of the specified class.

Subclasses can declare default classes by overriding the klass attribute

mm_theory

A trait for unicode strings.

qm_region

An instance of a Python list.

qm_theory

A trait for unicode strings.

submitted

A boolean (True, False) trait.

use_mm

A boolean (True, False) trait.

class aiidalab_alc.workflow.MethodWizardStep(*args: t.Any, **kwargs: t.Any)

Bases: VBox, WizardAppWidgetStep

Wizard setup for the calculation workflow.

render()

Render the wizard contents if not already rendered.

Module contents

The main AiiDAlab ALC application python package.