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. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

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. The combination of SS and LS, which is an embedding approach, can result in a 10-fold speedup over a pure LS simulation for large systems in aqueous solution. In addition to a ground-state Born-Oppenheimer SS+LS implementation, a time-dependent density functional theory-based Ehrenfest molecular dynamics (EMD) using density matrix propagation is presented that allows for performing nonadiabatic dynamics. Density matrix-based EMD in the SS framework is naturally linear scaling and appears suitable to study the electronic dynamics of molecules in solution. In the LS framework, linear scaling results as long as the density matrix remains sparse during time propagation. However, we generally find a less than exponential decay of the density matrix after a sufficiently long EMD run, preventing LS EMD simulations with arbitrary accuracy. The methods are tested on various systems, including spectroscopy on dyes, the electronic structure of TiO2 nanoparticles, electronic transport in carbon nanotubes, and the satellite tobacco mosaic virus in explicit solution.

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. In addition, a modified form of Hotelling's iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

Effect of methylprednisolone on mammalian neuronal networks in vitro.

Glucocorticosteroids (GCS) are widely used for the treatment of neurological diseases, e.g. multiple sclerosis. High levels of GCS are toxic to the central nervous system and can produce adverse effects. The effect of methylprednisolone (MP) on mammalian neuronal networks was studied in vitro. We demonstrate a dose-dependent excitatory effect of MP on cultured neuronal networks, followed by a shut-down of electrical activity using the microelectrode array technique.

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+). This novel transformation was done both randomly and at predetermined patterns defined by photolithography to create monolayer sheets composed of different netpoints. All transmetalated sheets are mechanically strong enough to be spanned over 20 × 20 µm(2) sized holes. Density functional theory calculations provide both a model for the molecular structure of an Fe(2+)-based sheet and first insights into how transmetalation proceeds. Such transmetalated sheets with random and patterned netpoints can be considered as two-dimensional analogues of linear copolymers. Their nanoscale synthesis presents an advance in monolayer/polymer chemistry with applications in fields such as surface coating, molecular electronics, device fabrication, imaging, and sensing.

Synthesis of a covalent monolayer sheet by photochemical anthracene dimerization at the air/water interface and its mechanical characterization by AFM indentation.

Covalent monolayer sheets in 2 hours: spreading of threefold anthracene-equipped shape-persistent and amphiphilic monomers at the air/water interface followed by a short photochemical treatment provides access to infinitely sized, strictly monolayered, covalent sheets with in-plane elastic modulus in the range of 19 N/m.

A polar corundum oxide displaying weak ferromagnetism at room temperature.

Combining long-range magnetic order with polarity in the same structure is a prerequisite for the design of (magnetoelectric) multiferroic materials. There are now several demonstrated strategies to achieve this goal, but retaining magnetic order above room temperature remains a difficult target. Iron oxides in the +3 oxidation state have high magnetic ordering temperatures due to the size of the coupled moments. Here we prepare and characterize ScFeO(3) (SFO), which under pressure and in strain-stabilized thin films adopts a polar variant of the corundum structure, one of the archetypal binary oxide structures. Polar corundum ScFeO(3) has a weak ferromagnetic ground state below 356 K-this is in contrast to the purely antiferromagnetic ground state adopted by the well-studied ferroelectric BiFeO(3).

Conformer interconversion in a switchable porous organic cage.

Porous organic cage crystals can show unique properties, such as switching from being porous to non-porous in the solid state. Conformer interconversion plays a crucial role in this for the imine cage molecule, CC1. The barriers to interconversion were calculated and found to match experimentally determined values. Calculations suggest that solvent interactions reduce these activation barriers.

An atomistic picture of the regeneration process in dye sensitized solar cells.

A highly efficient mechanism for the regeneration of the cis-bis(isothiocyanato)bis(2,2'-bipyridyl-4,4'-dicarboxylato)-ruthenium(II) sensitizing dye (N3) by I(-) in acetonitrile has been identified by using molecular dynamics simulation based on density functional theory. Barrier-free complex formation of the oxidized dye with both I(-) and , and facile dissociation of and from the reduced dye are key steps in this process. In situ vibrational spectroscopy confirms the reversible binding of I(2) to the thiocyanate group. Additionally, simulations of the electrolyte near the interface suggest that acetonitrile is able to cover the (101) surface of anatase with a passivating layer that inhibits direct contact of the redox mediator with the oxide, and that the solvent structure specifically enhances the concentration of I(-) at a distance which further favors rapid dye regeneration.

Ab initio molecular dynamics using hybrid density functionals.

Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

Atomistic simulations of a solid/liquid interface: a combined force field and first principles approach to the structure and dynamics of acetonitrile near an anatase surface.

The acetonitrile/anatase(101) interface can be considered a prototypical interface between an oxide and a polar aprotic liquid, and is common in dye sensitized solar cells. Using first principles molecular dynamics simulations of a slab of TiO(2) in contact with neat acetonitrile (MeCN), the liquid structure near this interface has been characterized. Furthermore, in order to investigate properties that require extensive sampling, a classical force field to describe the MeCN/TiO(2) interaction has been optimized, and we show that this force field accurately describes the structure near the interface. We find a surprisingly strong interaction of MeCN with TiO(2), which leads to an ordered first MeCN layer displaying a significantly enhanced molecular dipole. The strong dipolar interactions between solvent molecules lead to pronounced layering further away from the interface, each successive layer having an alternate orientation of the molecular dipoles. At least seven distinct solvent layers (approximately 12 Å) can be discerned in the orientational distribution function. The observed structure also strongly suppresses diffusion parallel to the interface in the first nanometer of the liquid. These results show that the properties of the liquid near the interface differ from those in the bulk, which suggests that solvation near the interface will be distinctly different from solvation in the bulk.