Materials Chemistry

Connecting lab experiments with computer experiments: Making "routine" simulations routine

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Abstract

Nowadays, computer simulations and experiments are closely interlocked. However, the data and analysis workflows are often barred into "silos" of knowledge — even for routine simulations. Here, we show how a typical electronic laboratory notebook (ELN) environment can be seamlessly integrated with a computational modelling infrastructure. We developed a protocol to initiate advanced molecular or atomic simulations directly from an ELN. Such integration ensures that all the relevant sample and experimental data are transferred from the ELN to the modelling infrastructure, and — once the calculations have completed — back to the ELN. The presented protocol works similar to sending out a sample for external characterisation and enables experimentalists to routinely perform "routine" simulations to compare with their experiments while keeping track of the full experiment and simulation provenance. We illustrate our protocol with some examples of geometry optimisation followed by the calculation of adsorption isotherms, but the implementation can be readily generalised to other techniques such as optical absorption or X-ray photoelectron spectroscopy.

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Supplementary material

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Supplementary Material
Further implementation details on the ELN connector, cheminfopy, and the PXRD case study.

Supplementary weblinks

AiiDAlab
Materials Cloud work section on AiiDAlab, the simulation platform used in our work.
The public deployment of the cheminfo ELN
We implemented the deployment with the cheminfo ELN. This link directs to the public deployment.
Further information about the cheminfo ecosystem
This link provides more details about the cheminfo ecosystem, which provides FAIR building blocks for chemistry. The cheminfo ELN is an assembly of many of such FAIR building blocks.
cheminfopy package
This package implements a Python interface for the REST-API of the cheminfo ELN
aiidalab-eln
This package implements the abstract as well as the concrete connection between AiiDAlab and the ELN
mofchecker
The mofchecker library provides pre-simulation sanity checks that we use in this work.
aiidalab-widgets-base
Implements, among others, the importer and exporter widgets for the ELN
aiidalab-epfl-lsmo
Implements AiiDAlab applications discussed in the paper
rest-on-couch
The rest-on-couch library implements an interface for CouchDB and the REST-API of the cheminfo ELN.