Nonadiabatic Ehrenfest molecular dynamics within the projector augmented-wave method

We have derived equations for nonadiabatic Ehrenfest molecular dynamics which conserve the total energy in the case of time-dependent discretization for electrons. A discretization is time-dependent in all cases where it or part of it depends on the positions of the nuclei, for example, in atomic orbital basis sets, and in the projector augmented-wave (PAW) method, where the augmentation functions depend on the nuclear positions. We have derived, implemented, and analyzed the energy conserving equations and their most common approximations for a 1D test system where we can achieve numerical results converged to a high accuracy. Based on the observations in 1D, we implement and analyze the Ehrenfest molecular dynamics in 3D using the PAW method and the time-dependent density functional formalism. We demonstrate the applicability of our method by carrying out calculations for small and medium sized molecules in both the adiabatic and the nonadiabatic regime.Comment: 12 pages, 10 figure

All-electron density functional theory and time-dependent density functional theory with high-order finite elements

We present for static density functional theory and time-dependent density functional theory calculations an all-electron method which employs high-order hierarchical finite element bases. Our mesh generation scheme, in which structured atomic meshes are merged to an unstructured molecular mesh, allows a highly nonuniform discretization of the space. Thus it is possible to represent the core and valence states using the same discretization scheme, i.e., no pseudopotentials or similar treatments are required. The nonuniform discretization also allows the use of large simulation cells, and therefore avoids any boundary effects.Comment: 11 pages, 9 figures; final (=published) versio

All-electron time-dependent density functional theory with finite elements: Time-propagation approach

We present an all-electron method for time-dependent density functional theory which employs hierarchical nonuniform finite-element bases and the time-propagation approach. The method is capable of treating linear and nonlinear response of valence and core electrons to an external field. We also introduce (i) a preconditioner for the propagation equation, (ii) a stable way to implement absorbing boundary conditions, and (iii) a new kind of absorbing boundary condition inspired by perfectly matched layers.Peer reviewe

Response functions in TDDFT: Concepts and implementation

Many physical properties of interest about solids and molecules can be considered as the reaction of the system to an external perturbation, and can be expressed in terms of response functions, in time or frequency and in real or reciprocal space. Response functions in time-dependent densityfunctional theory (TDDFT) can be calculated by a variety of methods. Timepropagation is a non-perturbative approach in the time domain, whose static analogue is the method of finite differences. Other approaches are perturbative and are formulated in the frequency domain. The Sternheimer equation solves for the variation of the wavefunctions, the Dyson equation is used to solve directly for response functions, and the Casida equation solves for the excited states via an expansion in an electron-hole basis. These techniques can be used to study a range of different response functions, including electric, magnetic, structural, and k·p perturbations. In this chapter, we give an overview of the basic concepts behind response functions and the methods that can be employed to efficiently compute the response properties within TDDFT and the physical quantities that can be studied.DAS acknowledges support from the US National Science Foundation, Grant No. DMR10-1006184 and a graduate fellowship. LL and MALM acknowledges support from the French ANR (ANR-08-EXC8-008-01). AR acknowledges funding by the European Research Council Advanced Grant DYNamo (ERC-2010-AdG -Proposal No. 267374) Spanish MICINN (FIS2010-21282-C02-01), ACI-promociona project (ACI2009-1036), “Grupos Consolidados UPV/EHU del Gobierno Vasco” (IT-319-07), and the European Community through e-I3 ETSF project (Contract No. 211956). SGL was supported by the Director, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, U.S. Department of Energy under Contract No. DEAC02-05CH11231.Peer reviewe

Responses of zooplankton to long-term environmental changes in a small boreal lake

Peer reviewe

Time-dependent density-functional theory in the projector augmented-wave method

We present the implementation of the time-dependent density-functional theory both in linear-response and in time-propagation formalisms using the projector augmented-wave method in real-space grids. The two technically very different methods are compared in the linear-response regime where we found perfect agreement in the calculated photoabsorption spectra. We discuss the strengths and weaknesses of the two methods as well as their convergence properties. We demonstrate different applications of the methods by calculating excitation energies and excited state Born–Oppenheimer potential surfaces for a set of atoms and molecules with the linear-response method and by calculating nonlinear emission spectra using the time-propagation method.Peer reviewe

Food Web Responses to Artificial Mixing in a Small Boreal Lake

In order to simulate food web responses of small boreal lakes to changes in thermal stratification due to global warming, a 4 year whole-lake manipulation experiment was performed. Within that time, period lake mixing was intensified artificially during two successive summers. Complementary data from a nearby lake of similar size and basic water chemistry were used as a reference. Phytoplankton biomass and chlorophyll a did not respond to the greater mixing depth but an increase was observed in the proportional abundance of diatoms, and the proportional abundance of cryptophytes also increased immediately after the onset of mixing. Obligate anoxic green sulphur bacteria vanished at the onset of mixing but gradually recovered after re-establishment of hypolimnetic anoxic conditions. No major effect on crustacean zooplankton was found, but their diversity increased in the metalimnion. During the mixing, the density of rotifers declined but protozoan density increased in the hypolimnion. Littoral benthic invertebrate density increased during the mixing due to Ephemeroptera, Asellus aquaticus and Chironomidae, whereas the density of Chaoborus larvae declined during mixing and lower densities were still recorded one year after the treatment. No structural changes in fish community were found although gillnet catches increased after the onset of the study. The early growth of perch (Perca fluviatilis) increased compared to the years before the mixing and in comparison to the reference lake, suggesting improved food availability in the experimental lake. Although several food web responses to the greater mixing depth were found, their persistence and ecological significance were strongly dependent on the extent of the disturbance. To better understand the impacts of wind stress on small lakes, long term whole-lake experiments are needed.Peer reviewe

The crystal structure of cold compressed graphite

Through a systematic structural search we found an allotrope of carbon with Cmmm symmetry which we predict to be more stable than graphite for pressures above 10 GPa. This material, which we refer to as Z-carbon, is formed by pure sp3 bonds and is the only carbon allotrope which provides an excellent match to unexplained features in experimental X-ray diffraction and Raman spectra of graphite under pressure. The transition from graphite to Z-carbon can occur through simple sliding and buckling of graphene sheets. Our calculations predict that Z-carbon is a transparent wide band gap semiconductor with a hardness comparable to diamond.Comment: 4 pages, 5 figure

All-thiol-stabilized Ag44 and Au12Ag32 nanoparticles with single-crystal structures

该研究工作是在厦门大学郑南峰教授课题组和芬兰于韦斯屈莱大学Hannu Häkkinen课题组共同合作完成的。工作中的合成、结构表征和性能测试是在郑南峰教授指导下由博士生杨华艳（第一作者）和硕士生王羽、黄华奇完成的；Hannu Häkkinen课题组通过理论计算分析了Ag44的电子结构和吸收光谱。Noble metal nanoparticles stabilized by organic ligands are important for applications in assembly, site-specific bioconjugate labelling and sensing, drug delivery and medical therapy, molecular recognition and molecular electronics, and catalysis. Here we report crystal structures and theoretical analysis of three Ag44(SR)30 and three Au12Ag32(SR)30 intermetallic nanoclusters stabilized with fluorinated arylthiols (SR=SPhF, SPhF2 or SPhCF3). The nanocluster forms a Keplerate solid of concentric icosahedral and dodecahedral atom shells, protected by six Ag2(SR)5 units. Positive counterions in the crystal indicate a high negative charge of 4− per nanoparticle, and density functional theory calculations explain the stability as an 18-electron superatom shell closure in the metal core. Highly featured optical absorption spectra in the ultraviolet–visible region are analysed using time-dependent density functional perturbation theory. This work forms a basis for further understanding, engineering and controlling of stability as well as electronic and optical properties of these novel nanomaterials.国家自然科学基金（项目批准号：21131005, 21021061, 20925103）、科技部（项目批准号：2011CB932403, 2009CB930703）和芬兰科学院基