A bridge between trust and control: computational workflows meet automated battery cycling.

Compliance with good research data management practices means trust in the integrity of the data, and it is achievable by full control of the data gathering process. In this work, we demonstrate tooling which bridges these two aspects, and illustrate its use in a case study of automated battery cycling. We successfully interface off-the-shelf battery cycling hardware with the computational workflow management software AiiDA, allowing us to control experiments, while ensuring trust in the data by tracking its provenance. We design user interfaces compatible with this tooling, which span the inventory, experiment design, and result analysis stages. Other features, including monitoring of workflows and import of externally generated and legacy data are also implemented. Finally, the full software stack required for this work is made available in a set of open-source packages.

AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance.

The ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of calculations and data to manage. Next-generation exascale supercomputers will harden these challenges, such that automated and scalable solutions become crucial. In recent years, we have been developing AiiDA (aiida.net), a robust open-source high-throughput infrastructure addressing the challenges arising from the needs of automated workflow management and data provenance recording. Here, we introduce developments and capabilities required to reach sustained performance, with AiiDA supporting throughputs of tens of thousands processes/hour, while automatically preserving and storing the full data provenance in a relational database making it queryable and traversable, thus enabling high-performance data analytics. AiiDA's workflow language provides advanced automation, error handling features and a flexible plugin model to allow interfacing with external simulation software. The associated plugin registry enables seamless sharing of extensions, empowering a vibrant user community dedicated to making simulations more robust, user-friendly and reproducible.

Transport and Spectroscopy in Conjugated Molecules: Two Properties and a Single Rationale.

In the context of electron dynamics simulations, when the charge density of a molecule is subject to a perturbation in the form of a short electric field pulse, density fluctuations develop in time. In the absence of dissipation, these oscillations continue indefinitely, reflecting the resonances of the electronic system; as a matter of fact, from the Fourier transform of the time dependent dipole arising from them, the absorption spectrum of the molecule can be calculated. Since these oscillations are the result of the electrons moving through the molecular structrure, it seems plausible that they carry information on the transport properties of the system. This is the idea explored in the present article for the case of conjugated polymers. Specifically, we depart from a nonequilibrium state with the charge concentrated on the ends of the molecule, and estimate the currents flowing back and forth during the evolution of electron dynamics simulations. These show that the charge oscillates between the sides of the polymer with the predominance of a frequency that is coincident with one of the main bands in the absorption spectrum, which can be ascribed to a charge transfer transition. Thus, from the charge transfer band frequency appearing in the absorption spectrum, the molecular conductance of a conjugated molecule can be calculated. Also interestingly, we find that, while a perturbation excites all resonances of an electronic system, the form in which this perturbation is applied can be manipulated to determine the relative manifestation of the response. The electric field pulse excites all resonances according to the transition dipole moment and is then appropriate to produce the absorption spectrum. A charge separated initial state, however, specifically stimulates the charge transfer mode and is then suitable to calculate transport properties. This allows us to propose a simple approach to obtain molecular conductances and tunneling decay constants in agreement with results from much more demanding electronic structure techniques.

Multiscale approach to electron transport dynamics.

Molecular simulations of transport dynamics in nanostructures usually require the implementation of open quantum boundary conditions. This can be instrumented in different frameworks including Green's functions, absorbing potentials, or the driven Liouville von Neumann equation, among others. In any case, the application of these approaches involves the use of large electrodes that introduce a high computational demand when dealing with first-principles calculations. Here, we propose a hybrid scheme where the electrodes are described at a semiempirical, tight binding level, coupled to a molecule or device represented with density functional theory (DFT). This strategy allows us to use massive electrodes at a negligible computational cost, preserving the accuracy of the DFT method in the modeling of the transport properties, provided that the electronic structure of every lead is properly defined to behave as a conducting fermionic reservoir. We study the nature of the multiscale coupling and validate the methodology through the computation of the tunneling decay constant in polyacetylene and of quantum interference effects in an aromatic ring. The present implementation is applied both in microcanonical and grand-canonical frameworks, in the last case using the Driven Liouville von Neumann equation, discussing the advantages of one or the other. Finally, this multiscale scheme is employed to investigate the role of an electric field applied normally to transport in the conductance of polyacetylene. It is shown that the magnitude and the incidence angle of the applied field have a considerable effect on the electron flow, hence constituting an interesting tool for current control in nanocircuits.

Electron transport in real time from first-principles.

While the vast majority of calculations reported on molecular conductance have been based on the static non-equilibrium Green's function formalism combined with density functional theory (DFT), in recent years a few time-dependent approaches to transport have started to emerge. Among these, the driven Liouville-von Neumann equation [C. G. Sánchez et al., J. Chem. Phys. 124, 214708 (2006)] is a simple and appealing route relying on a tunable rate parameter, which has been explored in the context of semi-empirical methods. In the present study, we adapt this formulation to a density functional theory framework and analyze its performance. In particular, it is implemented in an efficient all-electron DFT code with Gaussian basis functions, suitable for quantum-dynamics simulations of large molecular systems. At variance with the case of the tight-binding calculations reported in the literature, we find that now the initial perturbation to drive the system out of equilibrium plays a fundamental role in the stability of the electron dynamics. The equation of motion used in previous tight-binding implementations with massive electrodes has to be modified to produce a stable and unidirectional current during time propagation in time-dependent DFT simulations using much smaller leads. Moreover, we propose a procedure to get rid of the dependence of the current-voltage curves on the rate parameter. This method is employed to obtain the current-voltage characteristic of saturated and unsaturated hydrocarbons of different lengths, with very promising prospects.

Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework.

This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics Molecular-Mechanics (QM-MM) hamiltonian. The code delivers an all-electron description employing Gaussian basis functions, and incorporates the Amber force-field in the QM-MM treatment. The most expensive parts of the computation, comprising the commutators between the hamiltonian and the density matrix-required to propagate the electron dynamics-, and the evaluation of the exchange-correlation energy, were migrated to the CUDA platform to run on graphics processing units, which remarkably accelerates the performance of the code. The method was validated by reproducing linear-response TDDFT results for the absorption spectra of several molecular species. Two different schemes were tested to propagate the quantum dynamics: (i) a leap-frog Verlet algorithm, and (ii) the Magnus expansion to first-order. These two approaches were confronted, to find that the Magnus scheme is more efficient by a factor of six in small molecules. Interestingly, the presence of iron was found to seriously limitate the length of the integration time step, due to the high frequencies associated with the core-electrons. This highlights the importance of pseudopotentials to alleviate the cost of the propagation of the inner states when heavy nuclei are present. Finally, the methodology was applied to investigate the shifts induced by the chemical environment on the most intense UV absorption bands of two model systems of general relevance: the formamide molecule in water solution, and the carboxy-heme group in Flavohemoglobin. In both cases, shifts of several nanometers are observed, consistently with the available experimental data.