Large scale simulation of pressure induced phase-field fracture propagation using Utopia.

Non-linear phase field models are increasingly used for the simulation of fracture propagation problems. The numerical simulation of fracture networks of realistic size requires the efficient parallel solution of large coupled non-linear systems. Although in principle efficient iterative multi-level methods for these types of problems are available, they are not widely used in practice due to the complexity of their parallel implementation.

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations.

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems.

Materials Cloud, a platform for open computational science.

Materials Cloud is a platform designed to enable open and seamless sharing of resources for computational science, driven by applications in materials modelling. It hosts (1) archival and dissemination services for raw and curated data, together with their provenance graph, (2) modelling services and virtual machines, (3) tools for data analytics, and pre-/post-processing, and (4) educational materials. Data is citable and archived persistently, providing a comprehensive embodiment of entire simulation pipelines (calculations performed, codes used, data generated) in the form of graphs that allow retracing and reproducing any computed result.

Dynamics of the Bulk Hydrated Electron from Many-Body Wave-Function Theory.

The structure of the hydrated electron is a matter of debate as it evades direct experimental observation owing to the short life time and low concentrations of the species. Herein, the first molecular dynamics simulation of the bulk hydrated electron based on correlated wave-function theory provides conclusive evidence in favor of a persistent tetrahedral cavity made up by four water molecules, and against the existence of stable non-cavity structures. Such a cavity is formed within less than a picosecond after the addition of an excess electron to neat liquid water, with less regular cavities appearing as intermediates.

Microcanonical RT-TDDFT simulations of realistically extended devices.

In this paper, real-time time-dependent density functional theory (RT-TDDFT) calculations of realistically sized nanodevices are presented. These microcanonical simulations rely on a closed boundary approach based on recent advances in the software package CP2K. The obtained results are compared to those derived from the open-boundary Non-equilibrium Green's Function (NEGF) formalism.

Decisive Role of Perimeter Sites in Silica-Supported Ag Nanoparticles in Selective Hydrogenation of CO to Methyl Formate in the Presence of Methanol.

Methyl formate synthesis by hydrogenation of carbon dioxide in the presence of methanol offers a promising path to valorize carbon dioxide. In this work, silica-supported silver nanoparticles are shown to be a significantly more active catalyst for the continuous methyl formate synthesis than the known gold and copper counterparts, and the origin of the unique reactivity of Ag is clarified. Transient in situ and operando vibrational spectroscopy and DFT calculations shed light on the reactive intermediates and reaction mechanisms: a key feature is the rapid formation of surface chemical species in equilibrium with adsorbed carbon dioxide.

Machine Learning Adaptive Basis Sets for Efficient Large Scale Density Functional Theory Simulation.

It is chemically intuitive that an optimal atom centered basis set must adapt to its atomic environment, for example by polarizing toward nearby atoms. Adaptive basis sets of small size can be significantly more accurate than traditional atom centered basis sets of the same size. The small size and well conditioned nature of these basis sets leads to large saving in computational cost, in particular in a linear scaling framework.

Efficient algorithms for large-scale quantum transport calculations.

Massively parallel algorithms are presented in this paper to reduce the computational burden associated with quantum transport simulations from first-principles. The power of modern hybrid computer architectures is harvested in order to determine the open boundary conditions that connect the simulation domain with its environment and to solve the resulting Schrödinger equation. While the former operation takes the form of an eigenvalue problem that is solved by a contour integration technique on the available central processing units (CPUs), the latter can be cast into a linear system of equations that is simultaneously processed by SplitSolve, a two-step algorithm, on general-purpose graphics processing units (GPUs).

Nuclear Quantum Effects on Aqueous Electron Attachment and Redox Properties.

Nuclear quantum effects (NQEs) on the reduction and oxidation properties of small aqueous species (CO, HO, and O) are quantified and rationalized by first-principles molecular dynamics and thermodynamic integration. Vertical electron attachment, or electron affinity, and detachment energies (VEA and VDE) are strongly affected by NQEs, decreasing in absolute value by 0.3 eV going from a classical to a quantum description of the nuclei.

Catalyst support effects on hydrogen spillover.

Hydrogen spillover is the surface migration of activated hydrogen atoms from a metal catalyst particle, on which they are generated, onto the catalyst support. The phenomenon has been much studied and its occurrence on reducible supports such as titanium oxide is established, yet questions remain about whether hydrogen spillover can take place on nonreducible supports such as aluminium oxide. Here we use the enhanced precision of top-down nanofabrication to prepare controlled and precisely tunable model systems that allow us to quantify the efficiency and spatial extent of hydrogen spillover on both reducible and nonreducible supports.

First-Principles Monte Carlo Simulations of Reaction Equilibria in Compressed Vapors.

Predictive modeling of reaction equilibria presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions arising from the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. Here we present a novel reactive first-principles Monte Carlo (RxFPMC) approach that allows for investigation of reaction equilibria without the need to prespecify a set of chemical reactions and their ideal-gas equilibrium constants.

Combining Linear-Scaling DFT with Subsystem DFT in Born-Oppenheimer and Ehrenfest Molecular Dynamics Simulations: From Molecules to a Virus in Solution.

In this work, methods for the efficient simulation of large systems embedded in a molecular environment are presented. These methods combine linear-scaling (LS) Kohn-Sham (KS) density functional theory (DFT) with subsystem (SS) DFT. LS DFT is efficient for large subsystems, while SS DFT is linear scaling with a smaller prefactor for large sets of small molecules.

Spin-Unrestricted Second-Order Møller-Plesset (MP2) Forces for the Condensed Phase: From Molecular Radicals to F-Centers in Solids.

To obtain consistent geometries for the computation of properties, nuclear gradients are essential. Here, we report a fully periodic Γ-point, massively parallel implementation of spin-unrestricted second-order Møller-Plesset (MP2) forces. It is based on the resolution-of-identity and Gaussian and plane waves approach to calculate electron repulsion integrals and is made available in the CP2K program.

Calculation of Electrochemical Energy Levels in Water Using the Random Phase Approximation and a Double Hybrid Functional.

Understanding charge transfer at electrochemical interfaces requires consistent treatment of electronic energy levels in solids and in water at the same level of the electronic structure theory. Using density-functional-theory-based molecular dynamics and thermodynamic integration, the free energy levels of six redox couples in water are calculated at the level of the random phase approximation and a double hybrid density functional. The redox levels, together with the water band positions, are aligned against a computational standard hydrogen electrode, allowing for critical analysis of errors compared to the experiment.

A generalized Poisson solver for first-principles device simulations.

Electronic structure calculations of atomistic systems based on density functional theory involve solving the Poisson equation. In this paper, we present a plane-wave based algorithm for solving the generalized Poisson equation subject to periodic or homogeneous Neumann conditions on the boundaries of the simulation cell and Dirichlet type conditions imposed at arbitrary subdomains. In this way, source, drain, and gate voltages can be imposed across atomistic models of electronic devices.

Forces and stress in second order Møller-Plesset perturbation theory for condensed phase systems within the resolution-of-identity Gaussian and plane waves approach.

The forces acting on the atoms as well as the stress tensor are crucial ingredients for calculating the structural and dynamical properties of systems in the condensed phase. Here, these derivatives of the total energy are evaluated for the second-order Møller-Plesset perturbation energy (MP2) in the framework of the resolution of identity Gaussian and plane waves method, in a way that is fully consistent with how the total energy is computed. This consistency is non-trivial, given the different ways employed to compute Coulomb, exchange, and canonical four center integrals, and allows, for example, for energy conserving dynamics in various ensembles.

Periodic MP2, RPA, and Boundary Condition Assessment of Hydrogen Ordering in Ice XV.

Ice XV is the hydrogen-ordered form of the ice VI phase whose structure was predicted to be Cc and ferroelectric using periodic DFT approaches. However, neutron diffraction and Raman spectroscopy data show the structure to have P1̅ symmetry and to be antiferroelectric. Recent work1 using fragment-based MP2 and CCSD(T) approaches predicts the experimental structure as the ground state.

Probing the structural and dynamical properties of liquid water with models including non-local electron correlation.

Water is a ubiquitous liquid that displays a wide range of anomalous properties and has a delicate structure that challenges experiment and simulation alike. The various intermolecular interactions that play an important role, such as repulsion, polarization, hydrogen bonding, and van der Waals interactions, are often difficult to reproduce faithfully in atomistic models. Here, electronic structure theories including all these interactions at equal footing, which requires the inclusion of non-local electron correlation, are used to describe structure and dynamics of bulk liquid water.

Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations.

We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence.

Redox potentials and acidity constants from density functional theory based molecular dynamics.

CONSPECTUS: All-atom methods treat solute and solvent at the same level of electronic structure theory and statistical mechanics. All-atom computation of acidity constants (pKa) and redox potentials is still a challenge. In this Account, we review such a method combining density functional theory based molecular dynamics (DFTMD) and free energy perturbation (FEP) methods.

The nature of excess electrons in anatase and rutile from hybrid DFT and RPA.

The behavior of excess electrons in undoped and defect free bulk anatase and rutile TiO2 has been investigated by state-of-the-art electronic structure methods including hybrid density functional theory (DFT) and the random phase approximation (RPA). Consistent with experiment, charge trapping and polaron formation is observed in both anatase and rutile. The difference in the anisotropic shape of the polarons is characterized, confirming for anatase the large polaron picture.

Aligning electronic and protonic energy levels of proton-coupled electron transfer in water oxidation on aqueous TiO₂.

The high overpotential in water oxidation on anodes is a limiting factor for the large-scale application of photoelectrochemical cells. To overcome this limitation, it is essential to understand the four proton-coupled electron transfer (PCET) steps in the reaction mechanism and their implications to the overpotential. Herein, a simple scheme to compute the energies of the PCET steps in water oxidation on the aqueous TiO2 surface using a hybrid density functional is described.

Synthesis of two-dimensional analogues of copolymers by site-to-site transmetalation of organometallic monolayer sheets.

Monolayer sheets have gained attention due to the unique properties derived from their two-dimensional structure. One of the key challenges in sheet modification/synthesis is to exchange integral parts while keeping them intact. We describe site-to-site transmetalation of Zn(2+) in the netpoints of cm(2)-sized, metal-organic sheets by Fe(2+), Co(2+), and Pb(2+).

Dielectric properties of water ice, the ice Ih/XI phase transition, and an assessment of density functional theory.

The dielectric properties of the hydrogen disordered hexagonal phase (Ih) of water ice have been computed using density functional theory (DFT) based Monte Carlo simulations in the isobaric-isothermal ensemble. Temperature dependent data yield a fit for the Curie-Weiss law of the system and hence a prediction of the temperature of the phase transition from the Ih phase to the hydrogen ordered ice XI phase. Direct simulations around the phase transition temperature confirm and refine the predicted phase transition temperatures and provide data for further properties, such as the linear thermal expansion coefficient.