aiidalab_alc package¶

Subpackages¶

aiidalab_alc.common 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.process module¶

Module for handling AiiDA processes.

class aiidalab_alc.process.ChemShellProcess(model: MainAppModel)¶

Bases: object

Class to handle a ChemShell AiiDA process.

submit_process()¶: Submit the AiiDA process.

classmethod validate_model(model: MainAppModel) → bool¶

Validate the main application model.

Parameters:: model (MainAppModel) – The main application model to validate.
Returns:: True if the model is valid, False otherwise.
Return type:: bool

class aiidalab_alc.process.MainAppModel(*args: t.Any, **kwargs: t.Any)¶

Bases: HasTraits

The main AiiDAlab application MVC model.

block_results¶: A boolean (True, False) trait.

reset() → None¶: Reset the state of the model.

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 integer 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.results module¶

Module for defining widgets/models for viewing process progress and results.

class aiidalab_alc.results.ProcessModel(*args: t.Any, **kwargs: t.Any)¶

Bases: HasTraits

Model describing an AiiDA process.

property has_process: bool¶: Return true if a valid process node is associated with the uuid.

property inputs: NodeLinksManager | list¶: Return the inputs for the process.

property outputs: NodeLinksManager | list¶: Return the outputs for teh process.

property process: ProcessNode | None¶: Return the process node for the stored uuid.

process_uuid¶: A trait for unicode strings.

class aiidalab_alc.results.ResultsModel(*args: t.Any, **kwargs: t.Any)¶

Bases: ProcessModel

MVC results step model.

blocked¶: A boolean (True, False) trait.

class aiidalab_alc.results.ResultsWizardStep(*args: t.Any, **kwargs: t.Any)¶

Bases: VBox, WizardAppWidgetStep

Wizard for viewing process progress and results.

render() → None¶: Render the wizard’s uninitialised content.

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

aiidalab_alc.utils.open_link_in_new_tab(path: str, _=None) → None¶

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.