aiidalab_dlpoly package

Application

Defines the main AiiDAlab application page.

class aiidalab_dlpoly.main.MainApp

Bases: object

The main AiiDAlab application class.

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

Bases: VBox

The main app view.

Module for handling the top-level application model and AiiDA processes.

class aiidalab_dlpoly.process.DLPOLYProcess(model: MainAppModel)

Bases: object

Class to handle a DL_POLY AiiDA process.

submit_process() → None

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_dlpoly.process.MainAppModel(*args: Any, **kwargs: Any)

Bases: HasTraits

The main AiiDAlab application MVC model.

Aggregates the per-step models used across the configuration wizard and handles submission of the resulting DL_POLY process to AiiDA.

block_results = True
reset() → None

Reset the state of the model.

Contains utility functions used throughout the python package.

Open a given link in a new browser tab.

Parameters:

path (str) – The link to be opened.

aiidalab_dlpoly.utils.test_aiida_dlpoly_import() → bool

Test if the aiida-dlpoly plugin is installed.

Returns:

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

Return type:

bool

Models

The structure input model for DL_POLY input configuration.

class aiidalab_dlpoly.models.structure.StructureInputModel(*args: Any, **kwargs: 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.

The workflow input model for DL_POLY input configuration.

class aiidalab_dlpoly.models.workflow.WorkflowInputModel(*args: Any, **kwargs: Any)

Bases: HasTraits

Model for the DL_POLY workflow configuration step.

Stores the force field definition and the simulation control input. The control input can be supplied either as a pre-formatted DL_POLY CONTROL file or, when use_detailed_control is set, as a set of key control parameters that are assembled into a control dictionary for the aiida-dlpoly plugin.

CONTROL_UNITS = {'cutoff': 'ang', 'ensemble_thermostat_coupling': 'ps', 'padding': 'ang', 'stats_frequency': 'steps', 'temperature': 'K', 'time_equilibration': 'steps', 'time_run': 'steps', 'timestep': 'ps'}
DPD_ORDERS = (0, 1, 2)
ENSEMBLES = ('NVE', 'NVT', 'NPT', 'NST', 'PMF')
ENSEMBLE_METHODS = {'NPT': ('Langevin', 'Berendsen', 'Hoover', 'MTK'), 'NST': ('Langevin', 'Berendsen', 'Hoover', 'MTK'), 'NVT': ('Evans', 'Langevin', 'Anderson', 'Berendsen', 'Hoover', 'gentle', 'ttm', 'dpd')}
property available_ensemble_methods: tuple

The ensemble methods valid for the currently selected ensemble.

Returns an empty tuple for ensembles (NVE, PMF) that do not take a method.

property control_parameters: dict

Return the detailed control parameters as a control dictionary.

The format matches the control dictionary consumed by the aiida-dlpoly plugin, where every numeric input is a (value, unit) pair. The ensemble parameters are added as plain values, with ensemble_method only included when the ensemble requires one and ensemble_dpd_order only when the method is dpd.

property has_control_file: bool

True if a control file has been attached to the model.

property has_force_field: bool

True if a force field file has been attached to the model.

property has_valid_ensemble: bool

True if the ensemble configuration is complete and self-consistent.

The ensemble must be a recognised type; when it requires a method the method must be one of the valid options for that ensemble; and when the method is dpd a valid DPD order must be selected.

property is_valid: bool

True if the model holds a complete, submittable configuration.

A force field is always required. When detailed control is disabled a control file must be supplied; when enabled a valid ensemble configuration is required.

property requires_dpd_order: bool

True if the selected ensemble method requires a DPD order.

property requires_ensemble_method: bool

True if the selected ensemble requires an ensemble method.

property requires_thermostat_coupling: bool

True if the ensemble requires a thermostat coupling time.

Applies to the NVT/NPT/NST ensembles, except when the DPD method is selected (which uses the DPD order instead).

Defines the MVC model for computational resource configuration for AiiDA.

class aiidalab_dlpoly.models.resources.ComputationalResourcesModel(*args: Any, **kwargs: Any)

Bases: HasTraits

Model for the resource setup stage.

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

Validate the model’s inputs.

Returns:

True if all inputs are valid, False otherwise.

Return type:

bool

Defines the MVC model for a full DL_POLY process.

class aiidalab_dlpoly.models.process.ProcessModel(*args: Any, **kwargs: 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 the process.

property process: ProcessNode | None

Return the process node for the stored uuid.

process_uuid = None

Defines the MVC model for holding DL_POLY results information.

class aiidalab_dlpoly.models.results.ResultsModel(*args: Any, **kwargs: Any)

Bases: ProcessModel

MVC results step model.

blocked = True

Wizard steps

Defines the wizard widget for the main AiiDAlab DL_POLY application.

class aiidalab_dlpoly.wizards.main_app.MainAppWizardWidget(*args: Any, **kwargs: Any)

Bases: VBox

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

on_step_change(change)

Switch between wizard steps when selected by the user.

property steps

Alias to the wizard’s steps list.

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

class aiidalab_dlpoly.wizards.structure.StructureWizardStep(*args: Any, **kwargs: 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.

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

class aiidalab_dlpoly.wizards.workflow.WorkflowWizardStep(*args: Any, **kwargs: Any)

Bases: VBox, WizardAppWidgetStep

Wizard step for configuring the DL_POLY workflow.

Provides a required force field file upload and a control input which can either be a pre-formatted DL_POLY CONTROL file or, when the detailed control checkbox is ticked, a set of key control parameters.

CONTROL_FIELDS = (('temperature', 'Temperature', 'K', False), ('timestep', 'Timestep', 'ps', False), ('time_run', 'Run time', 'steps', True), ('time_equilibration', 'Equilibration time', 'steps', True), ('cutoff', 'Cutoff', 'ang', False), ('padding', 'Padding', 'ang', False), ('stats_frequency', 'Stats frequency', 'steps', True))
render()

Render the wizard’s contents if not already rendered.

submit_workflow(_)

Submit the workflow step.

Defines the model and view for the resource setup stage.

class aiidalab_dlpoly.wizards.resources.ComputationalResourcesWizardStep(*args: Any, **kwargs: Any)

Bases: VBox, WizardAppWidgetStep

Main view for the resource setup stage.

render()

Render the wizard’s contents if not already rendered.

class aiidalab_dlpoly.wizards.resources.ResourceSetupBox(*args: Any, **kwargs: Any)

Bases: VBox

A box widget for defining computational resources.

update_codes(_=None) → None

Update the list of available codes.

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

class aiidalab_dlpoly.wizards.results.ResultsWizardStep(*args: Any, **kwargs: Any)

Bases: VBox, WizardAppWidgetStep

Wizard for viewing process progress and results.

render() → None

Render the wizard’s uninitialised content.

Common widgets

Module handling navigation controls within the app.

class aiidalab_dlpoly.common.navigation.QuickAccessButtons(*args: Any, **kwargs: Any)

Bases: HBox

Quick access buttons present in the app’s header and start banner.

Defines a custom AiiDA node visualiser.

class aiidalab_dlpoly.common.node_viewers.CustomAiidaNodeViewWidget(*args: Any, **kwargs: Any)

Bases: VBox

Custom viewer based on a specific AiiDA node type.

An extension of the aiidalab_widgets_base.viewers.AiidaNodeViewWidget which prioritises the ALC-developed node viewers (which handle the DL_POLY output node types such as trajectories, statistics arrays and structure files) before falling back to the default AiiDAlab viewers.

Widget for selecting an input structure from various sources.

class aiidalab_dlpoly.common.structure_uploader.StructureSelectionWidget(*args: Any, **kwargs: Any)

Bases: VBox, HasTraits

Widget for selecting an input structure from various sources.

disable(val: bool = True) → None

Disable the widget and all children.