Integrated workflows and interfaces for data-driven semi-empirical electronic structure calculations.

Modern software engineering of electronic structure codes has seen a paradigm shift from monolithic workflows toward object-based modularity. Software objectivity allows for greater flexibility in the application of electronic structure calculations, with particular benefits when integrated with approaches for data-driven analysis. Here, we discuss different approaches to create deep modular interfaces that connect big-data workflows and electronic structure codes and explore the diversity of use cases that they can enable. We present two such interface approaches for the semi-empirical electronic structure package, DFTB+. In one case, DFTB+ is applied as a library and provides data to an external workflow; in another, DFTB+receives data via external bindings and processes the information subsequently within an internal workflow. We provide a general framework to enable data exchange workflows for embedding new machine-learning-based Hamiltonians within DFTB+ or enabling deep integration of DFTB+ in multiscale embedding workflows. These modular interfaces demonstrate opportunities in emergent software and workflows to accelerate scientific discovery by harnessing existing software capabilities.

Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials.

We report the development and testing of new integrated cyberinfrastructure for performing free energy simulations with generalized hybrid quantum mechanical/molecular mechanical (QM/MM) and machine learning potentials (MLPs) in Amber. The Sander molecular dynamics program has been extended to leverage fast, density-functional tight-binding models implemented in the DFTB+ and xTB packages, and an interface to the DeePMD-kit software enables the use of MLPs. The software is integrated through application program interfaces that circumvent the need to perform "system calls" and enable the incorporation of long-range Ewald electrostatics into the external software's self-consistent field procedure. The infrastructure provides access to QM/MM models that may serve as the foundation for QM/MM-ΔMLP potentials, which supplement the semiempirical QM/MM model with a MLP correction trained to reproduce ab initio QM/MM energies and forces. Efficient optimization of minimum free energy pathways is enabled through a new surface-accelerated finite-temperature string method implemented in the FE-ToolKit package. Furthermore, we interfaced Sander with the i-PI software by implementing the socket communication protocol used in the i-PI client-server model. The new interface with i-PI allows for the treatment of nuclear quantum effects with semiempirical QM/MM-ΔMLP models. The modular interoperable software is demonstrated on proton transfer reactions in guanine-thymine mispairs in a B-form deoxyribonucleic acid helix. The current work represents a considerable advance in the development of modular software for performing free energy simulations of chemical reactions that are important in a wide range of applications.

Mechanism of proton-coupled electron transfer described with QM/MM implementation of coupled-perturbed density-functional tight-binding.

Coupled-perturbed equations for degenerate orbitals were implemented for third order density-functional tight binding, which allowed the use of Mulliken charges as reaction coordinates. The method was applied to proton-coupled electron transfer (PCET) reactions in a model system and thoroughly tested for QM and QM/MM setups (i.e., coupled quantum and molecular mechanics). The performed enhanced sampling simulations were stable, and the obtained potentials of the mean force were able to address the thermodynamic and kinetic features of the reactions by showing the expected topography and energy barriers. Hence, this method has the potential to distinguish between concerted and sequential mechanisms and could next be applied to proton-coupled electron transfer reactions in more complex systems like proteins.

Accelerating the density-functional tight-binding method using graphical processing units.

Acceleration of the density-functional tight-binding (DFTB) method on single and multiple graphical processing units (GPUs) was accomplished using the MAGMA linear algebra library. Two major computational bottlenecks of DFTB ground-state calculations were addressed in our implementation: the Hamiltonian matrix diagonalization and the density matrix construction. The code was implemented and benchmarked on two different computer systems: (1) the SUMMIT IBM Power9 supercomputer at the Oak Ridge National Laboratory Leadership Computing Facility with 1-6 NVIDIA Volta V100 GPUs per computer node and (2) an in-house Intel Xeon computer with 1-2 NVIDIA Tesla P100 GPUs. The performance and parallel scalability were measured for three molecular models of 1-, 2-, and 3-dimensional chemical systems, represented by carbon nanotubes, covalent organic frameworks, and water clusters.

Imaging Threading Dislocations and Surface Steps in Nitride Thin Films Using Electron Backscatter Diffraction.

Extended defects, like threading dislocations, are detrimental to the performance of optoelectronic devices. In the scanning electron microscope, dislocations are traditionally imaged using diodes to monitor changes in backscattered electron intensity as the electron beam is scanned over the sample, with the sample positioned so the electron beam is at, or close to the Bragg angle for a crystal plane/planes. Here, we use a pixelated detector instead of single diodes, specifically an electron backscatter diffraction (EBSD) detector. We present postprocessing techniques to extract images of dislocations and surface steps, for a nitride thin film, from measurements of backscattered electron intensities and intensity distributions in unprocessed EBSD patterns. In virtual diode (VD) imaging, the backscattered electron intensity is monitored for a selected segment of the unprocessed EBSD patterns. In center of mass (COM) imaging, the position of the center of the backscattered electron intensity distribution is monitored. Additionally, both methods can be combined (VDCOM). Using both VD and VDCOM, images of only threading dislocations, or dislocations and surface steps can be produced, with VDCOM images exhibiting better signal-to-noise. The applicability of VDCOM imaging is demonstrated across a range of nitride semiconductor thin films, with varying surface step and dislocation densities.

Kikuchi pattern simulations of backscattered and transmitted electrons.

We discuss a refined simulation approach which treats Kikuchi diffraction patterns in electron backscatter diffraction (EBSD) and transmission Kikuchi diffraction (TKD). The model considers the result of two combined mechanisms: (a) the dynamical diffraction of electrons emitted coherently from point sources in a crystal and (b) diffraction effects on incoherent diffuse intensity distributions. Using suitable parameter settings, the refined simulation model allows to reproduce various thickness- and energy-dependent features which are observed in experimental Kikuchi diffraction patterns. Excess-deficiency features are treated by the effect of gradients in the incoherent background intensity. Based on the analytical two-beam approximation to dynamical electron diffraction, a phenomenological model of excess-deficiency features is derived, which can be used for pattern matching applications. The model allows to approximate the effect of the incident beam geometry as a correction signal for template patterns which can be reprojected from pre-calculated reference data. As an application, we find that the accuracy of fitted projection centre coordinates in EBSD and TKD can be affected by changes in the order of 10 - 3 - 10 - 2 if excess-deficiency features are not considered in the theoretical model underlying a best-fit pattern matching approach. Correspondingly, the absolute accuracy of simulation-based EBSD strain determination can suffer from biases of a similar order of magnitude if excess-deficiency effects are neglected in the simulation model.

Coincident electron channeling and cathodoluminescence studies of threading dislocations in GaN.

We combine two scanning electron microscopy techniques to investigate the influence of dislocations on the light emission from nitride semiconductors. Combining electron channeling contrast imaging and cathodoluminescence imaging enables both the structural and luminescence properties of a sample to be investigated without structural damage to the sample. The electron channeling contrast image is very sensitive to distortions of the crystal lattice, resulting in individual threading dislocations appearing as spots with black-white contrast. Dislocations giving rise to nonradiative recombination are observed as black spots in the cathodoluminescence image. Comparison of the images from exactly the same micron-scale region of a sample demonstrates a one-to-one correlation between the presence of single threading dislocations and resolved dark spots in the cathodoluminescence image. In addition, we have also obtained an atomic force microscopy image from the same region of the sample, which confirms that both pure edge dislocations and those with a screw component (i.e., screw and mixed dislocations) act as nonradiative recombination centers for the Si-doped c-plane GaN thin film investigated.

A Real-Time Time-Dependent Density Functional Tight-Binding Implementation for Semiclassical Excited State Electron-Nuclear Dynamics and Pump-Probe Spectroscopy Simulations.

The increasing need to simulate the dynamics of photoexcited molecular systems and nanosystems in the subpicosecond regime demands new efficient tools able to describe the quantum nature of matter at a low computational cost. By combining the power of the approximate DFTB method with the semiclassical Ehrenfest method for nuclear-electron dynamics, we have achieved a real-time time-dependent DFTB (TD-DFTB) implementation that fits such requirements. In addition to enabling the study of nuclear motion effects in photoinduced charge transfer processes, our code adds novel features to the realm of static and time-resolved computational spectroscopies. In particular, the optical properties of periodic materials such as graphene nanoribbons or the use of corrections such as the "LDA+U" and "pseudo SIC" methods to improve the optical properties in some systems can now be handled at the TD-DFTB level. Moreover, the simulation of fully atomistic time-resolved transient absorption spectra and impulsive vibrational spectra can now be achieved within reasonable computing time, owing to the good performance of the implementation and a parallel simulation protocol. Its application to the study of UV/visible light-induced vibrational coherences in molecules is demonstrated and opens a new door into the mechanisms of nonequilibrium ultrafast phenomena in countless materials with relevant applications.

Energy-weighted dynamical scattering simulations of electron diffraction modalities in the scanning electron microscope.

Transmission Kikuchi diffraction (TKD) has been gaining momentum as a high resolution alternative to electron back-scattered diffraction (EBSD), adding to the existing electron diffraction modalities in the scanning electron microscope (SEM). The image simulation of any of these measurement techniques requires an energy dependent diffraction model for which, in turn, knowledge of electron energies and diffraction distances distributions is required. We identify the sample-detector geometry and the effect of inelastic events on the diffracting electron beam as the important factors to be considered when predicting these distributions. However, tractable models taking into account inelastic scattering explicitly are lacking. In this study, we expand the Monte Carlo (MC) energy-weighting dynamical simulations models used for EBSD [1] and ECP [2] to the TKD case. We show that the foil thickness in TKD can be used as a means of energy filtering and compare band sharpness in the different modalities. The current model is shown to correctly predict TKD patterns and, through the dictionary indexing approach, to produce higher quality indexed TKD maps than conventional Hough transform approach, especially close to grain boundaries.

Dataset on coherent control of fields and induced currents in nonlinear multiphoton processes in a nanosphere.

We model a scheme for the coherent control of light waves and currents in metallic nanospheres which applies independently of the nonlinear multiphoton processes at the origin of waves and currents. Using exact mathematical formulae, we calculate numerically with a custom fortran code the effect of an external control field which enable us to change the radiation pattern and suppress radiative losses or to reduce absorption, enabling the particle to behave as a perfect scatterer or as a perfect absorber. Data are provided in tabular, comma delimited value format and illustrate narrow features in the response of the particles that result in high sensitivity to small variations in the local environment, including subwavelength spatial shifts.

Coherent control of radiation patterns of nonlinear multiphoton processes in nanoparticles.

We propose a scheme for the coherent control of light waves and currents in metallic nanospheres which applies independently of the nonlinear multiphoton processes at the origin of waves and currents. We derive conditions on the external control field which enable us to change the radiation pattern and suppress radiative losses or to reduce absorption, enabling the particle to behave as a perfect scatterer or as a perfect absorber. The control introduces narrow features in the response of the particles that result in high sensitivity to small variations in the local environment, including subwavelength spatial shifts.

Treatment of collinear and noncollinear electron spin within an approximate density functional based method.

We report benchmark calculations of the density functional based tight-binding method concerning the magnetic properties of small iron clusters (Fe2 to Fe5) and the Fe13 icosahedron. Energetics and stability with respect to changes of cluster geometry of collinear and noncollinear spin configurations are in good agreement with ab initio results. The inclusion of spin-orbit coupling has been tested for the iron dimer.