The atomic simulation environment-a Python library for working with atoms.

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks.

Reproducibility in density functional theory calculations of solids.

The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals.

Equilibrium Geometries of Noncovalently Bound Intermolecular Complexes Derived from Subsystem Formulation of Density Functional Theory.

The subsystem formulation of density functional theory is used to obtain equilibrium geometries and interaction energies for a representative set of noncovalently bound intermolecular complexes. The results are compared with literature benchmark data. The range of applicability of two considered approximations to the exchange-correlation- and nonadditive kinetic energy components of the total energy is determined.

Interaction energies in non-covalently bound intermolecular complexes derived using the subsystem formulation of density functional theory.

Interaction energies for a representative sample of 39 intermolecular complexes are calculated using two computational approaches based on the subsystem formulation of density functional theory introduced by Cortona (Phys. Rev. B 44:8454, 1991), adopted for studies of intermolecular complexes (Wesolowski and Weber in Chem.

Nonlinearity of the Bifunctional of the Nonadditive Kinetic Energy: Numerical Consequences in Orbital-Free Embedding Calculations.

The bifunctional of the nonadditive kinetic energy in the reference system of noninteracting electrons ([Formula: see text] [ρA, ρB] = Ts[ρA + ρB] - Ts[ρA] - Ts[ρB]) is the key quantity in orbital-free embedding calculations because they hinge on approximations to[Formula: see text] [ρA,ρB]. Since[Formula: see text] [ρA,ρB] is not linear in ρA, the associated potential (functional derivative)[Formula: see text] [ρ,ρB]/δρ|ρ=ρA(r⃗) changes if ρA varies. In this work, for two approximations to[Formula: see text] [ρA,ρB], which are nonlinear in ρA (gradient-free and gradient-dependent), their linearized versions are constructed, and the resulting changes (linearization errors) in various properties of embedded systems (orbital energies, dipole moments, interaction energies, and electron densities) are analyzed.

On the electron leak problem in orbital-free embedding calculations.

Computer simulation methods using orbital level of description only for a selected part of the larger systems are prone to the artificial charge leak to the parts which are described without orbitals. The absence of orbitals in one of the subsystems makes it impossible to impose explicitly the orthogonality condition. Using the subsystem formulation of density functional theory, it is shown that the absence of explicit condition of orthogonality between orbitals belonging to different subsystems, does not cause any breakdown of this type of description for the chosen intermolecular complexes (F(-)H(2)O and Li(+)H(2)O), for which a significant charge-leak problem could be a priori expected.

Mechanism of nitrate reduction by Desulfovibrio desulfuricans nitrate reductase--a theoretical investigation.

The oxidative half-reaction of oxygen atom transfer from nitrate to an Mo(IV) complex has been investigated at various levels of theory. Two models have been used to simulate the enzyme active site. In the second, more advanced model, additional amino acid residues capable of significantly affecting the catalytic efficiency of the enzyme were included.

Water trapped in dibenzo-18-crown-6: theoretical and spectroscopic (IR, Raman) studies.

Experimental (IR and Raman) and theoretical (Kohn-Sham calculations) methods are used in a combined analysis aimed at refining the available structural data concerning the molecular guests in channels formed by stacked dibenzo-18-crown-6 (DB18C6) crown ether. The calculations are performed for a simplified model comprising isolated DB18C6 unit and its complexes with either H2O or H3O+ guests, which are the simplest model ingredients of a one-dimensional diluted acid chain, to get structural and energetic data concerning the formation of the complex and to assign the characteristic spectroscopic bands. The oxygen centers in the previously reported crystallographic structure are assigned to either H2O or protonated species.