Batch Processing

Alongside the main New Calculation page, the AiiDAlab ChemShell plugin provides a dedicated Batch Processing page for running the same calculation across a whole collection of structures at once. It is accessed via the Batch Calculation button found in the start banner and in the navigation header shared across the plugin’s pages.

The batch page is built on the same wizard style interface as the main calculation page, so much of its operation will already be familiar. The key difference is that, rather than configuring a single structure and a choice of workflow, it takes a set of structures and runs each one through an identical single point energy calculation. This makes it well suited to tasks such as evaluating the energies of every frame of a trajectory or a library of candidate structures under a common set of parameters.

Configuration Wizard

As with the main page, the batch page is broken down into a series of wizard steps, each with a submit button that locks in the user’s choices before proceeding.

Select Structures Input

This step replaces the single structure input of the main page with a batch input. The supported inputs are:

• A multi-frame .xyz file, where each frame is treated as a separate structure.

• An AiiDA TrajectoryData object, for example one produced by a previous calculation or made available through the AiiDA command line interface (CLI).

Each frame of the supplied input is run as an individual single point energy calculation. Aside from accepting these multi-structure inputs, the step behaves the same as the standard Structure Input step.

Note

At present the visualisation of trajectories supplied via a multi-frame .xyz file is not fully supported and thus just the first frame will be shown in the viewer window.

Configure Workflow

The workflow step reuses the same configuration options as the Single Point Energy workflow on the main calculation page. Unlike the main page there is no choice of workflow type here; every structure in the batch is run with a single point energy calculation using the configuration defined in this step.

The single point options (including the QM/QM/MM settings, energy derivatives and vibrational frequency options) are configured once and then applied identically to every structure in the batch.

Configure Computational Resources

This step is identical to the resource setup step of the main calculation page, allowing the user to select the AiiDA code instance and the computational resources used to run the calculations. See Resource Management for more details on configuring the underlying computer and code instances.

Results

The final step provides the combined job monitor and results viewer, in the same manner as the main calculation page. Here the progress of the individual calculations making up the batch can be monitored and their results inspected once complete. As with the main page, results objects appear under each finished process and can be visualised directly within the interface.

Note

For a description of the underlying single point energy configuration options, and of the shared structure, resource and results steps, see the main ChemShell Workflow Configuration page.