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Andreas Pedersen

Publications and source records attributed to Andreas Pedersen.

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Reassignment of magic numbers for icosahedral Au clusters: 310, 564, 928 and 1426

Icosahedral Au clusters with three and four shells of atoms are found to deviate significantly from the commonly assumed Mackay structures. By introducing additional atoms in the surface shell and creating a vacancy in the center of the cluster, the calculated energy per atom can be lowered significantly, according to several different descriptions of the interatomic interaction. Analogous icosahedral structures with five and six shells of atoms are generated using the same structural motifs and are similarly found to be more stable than Mackay icosahedra. The lowest energy per atom is obtained with clusters containing 310, 564, 928 and 1426 atoms, as compared with the commonly assumed magic numbers of 309, 561, 923 and 1415. Some of the vertices in the optimized clusters have a hexagonal ring of atoms, rather than a pentagon, with the vertex atom missing. An inner shell atom in some cases moves outwards by more than an \AA{}ngstr\"om into the surface shell at the vertex site. This feature, as well as the wide distribution of nearest-neighbor distances in the surface layer, can strongly influence the catalytic properties of icosahedral clusters. The structural optimization is initially carried out using the GOUST method with atomic forces estimated with the EMT empirical potential function, but the atomic coordinates are then refined by minimization using electron density functional theory (DFT) or Gaussian approximation potential (GAP). A single energy barrier is found to separate the Mackay icosahedron from a lower energy structure where a string of atoms moves outwards in a concerted manner from the center so as to create a central vacancy while placing an additional atom in the surface shell.

physics.comp-ph

Atomic and electronic structures of a vacancy in amorphous silicon

Locally, the atomic structure in well annealed amorphous silicon appears similar to that of crystalline silicon. We address here the question whether a point defect, specifically a vacancy, in amorphous silicon also resembles that in the crystal. From density functional theory calculations of a large number of nearly defect free configurations, relaxed after an atom has been removed, we conclude that there is little similarity. The analysis is based on formation energy, relaxation energy, bond lengths, bond angles, Voronoï volume, coordination, atomic charge and electronic gap states. All these quantities span a large and continuous range in amorphous silicon and while the removal of an atom leads to the formation of one to two bond defects and to a lowering of the local atomic density, the relaxation of the bonding network is highly effective, and the signature of the vacancy generally unlike that of a vacancy in the crystal.

cond-mat.mtrl-sci

Pushing Back the Limit of Ab-initio Quantum Transport Simulations on Hybrid Supercomputers

The capabilities of CP2K, a density-functional theory package and OMEN, a nano-device simulator, are combined to study transport phenomena from first-principles in unprecedentedly large nanostructures. Based on the Hamiltonian and overlap matrices generated by CP2K for a given system, OMEN solves the Schroedinger equation with open boundary conditions (OBCs) for all possible electron momenta and energies. To accelerate this core operation a robust algorithm called SplitSolve has been developed. It allows to simultaneously treat the OBCs on CPUs and the Schroedinger equation on GPUs, taking advantage of hybrid nodes. Our key achievements on the Cray-XK7 Titan are (i) a reduction in time-to-solution by more than one order of magnitude as compared to standard methods, enabling the simulation of structures with more than 50000 atoms, (ii) a parallel efficiency of 97% when scaling from 756 up to 18564 nodes, and (iii) a sustained performance of 15 DP-PFlop/s.

physics.comp-ph

Electronic Properties of Lithiated SnO-based Anode Materials

In this paper we use an ab-initio quantum transport approach to study the electron current flowing through lithiated SnO anodes for potential applications in Li-ion batteries. By investigating a set of lithiated structures with varying lithium concentrations, it is revealed that LixSnO can be a good conductor, with values comparable to bulk $β$-Sn and Li. A deeper insight into the current distribution indicates that electrons preferably follow specific trajectories, which offer superior conducting properties than others. These channels have been identified and it is shown here how they can enhance or deteriorate the current flow in lithiated anode materials.

cond-mat.mtrl-sci

Diffusion Mechanisms in Li$_{0.5}$CoO$_2$ -- A Computational Study

An atomistic study of the order-effect occurring in Li$_{x}$CoO$_{2}$ at $x=0.5$ is presented and an explanation for the computationally and experimentally observed dip in the Li diffusivity is proposed. Configurations where a single half-filled Li layer arranged in either a linear or a zig-zag pattern are simulated. It is found that the lowest energy phase is the zig-zag pattern rather than the linear arrangement that currently is considered to be of lowest energy. Atomic interactions are modeled at the DFT level of accuracy and energy barriers for Li-ion diffusion are determined from searches for first order saddle points on the resulting potential energy surface. The determined saddle points reveal that the barriers for diffusion parallel and perpendicular to the zig-zag phase differ significantly and explain the observed dip in diffusivity.

cond-mat.mtrl-sci

Long-timescale simulations of H$_2$O admolecule diffusion on Ice Ih(0001) surfaces

Long-timescale simulations of the diffusion of a H$_2$O admolecule on the (0001) basal plane of ice Ih were carried out over a temperature range of 100 to 200 K using the adaptive kinetic Monte Carlo method and TIP4P/2005f interaction potential function. The arrangement of dangling H atoms was varied from the proton-disordered surface to the perfectly ordered Fletcher surface. A large variety of sites was found leading to a broad distribution in adsorption energy at both types of surfaces. Up to 4 % of the sites on the proton-disordered surface have an adsorption energy exceeding the cohesive energy of ice Ih. The mean squared displacement of a simulated trajectory at 175 K for the proton-disordered surface gave a diffusion constant of 6$\cdot$10$^{-10}$ cm$^2$/s, consistent with an upper bound previously reported from experimental measurements. During the simulation, dangling H atoms were found to rearrange so as to reduce clustering, thereby approaching a linear Fletcher type arrangement. Diffusion on the perfectly ordered Fletcher surface was estimated to be significantly faster, especially in the direction along the rows of dangling hydrogen atoms. From simulations over the range in temperature, an effective activation energy of diffusion was estimated to be 0.16 eV and 0.22 eV for diffusion parallel and perpendicular to the rows, respectively. Even a slight disruption of the rows of the Fletcher surface made the diffusion isotropic.

physics.comp-ph

The reversible lithiation of SnO: a three-phase process

A high reversible capacity is a key feature for any rechargeable battery. In the lithium-ion battery technology, tin-oxide anodes do fulfill this requirement, but a fast loss of capacity hinders a full commercialization. Using first-principles calculations, we propose a microscopic model that sheds light on the reversible lithiation/delithiation of SnO and reveals that a sintering of Sn causes a strong degradation of SnO-based anodes. When the initial irreversible transformation ends, active anode grains consist of Li-oxide layers separated by Sn bilayers. During the following reversible lithiation, the Li-oxide undergoes two phase transformations that give rise to a Li-enrichment of the oxide and the formation of a layered SnLi composite. We find that the model-predicted anode volume expansion and voltage profile agree well with experiment, and a layered anode grain is highly-conductive and has a theoretical reversible capacity of 4.5 Li atoms per a SnO host unit. The model suggests that the grain structure has to remain layered to sustain its reversible capacity and a thin-film design of battery anodes could be a remedy for the capacity loss.

cond-mat.mtrl-sci

Lithiation of Tin Oxide: A Computational Study

We suggest that the lithiation of pristine SnO forms a layered Li$_\text{X}$O structure while the expelled tin atoms agglomerate into 'surface' planes separating the Li$_\text{X}$O layers. The proposed lithiation model widely differs from the common assumption that tin segregates into nano-clusters embedded in the lithia matrix. With this model we are able to account for the various tin bonds that are seen experimentally and explain the three volume expansion phases that occur when SnO undergoes lithiation: (i) at low concentrations Li behaves as an intercalated species inducing small volume increases; (ii) for intermediate concentrations SnO transforms into lithia causing a large expansion; (iii) finally, as the Li concentration further increases a saturation of the lithia takes place until a layered Li$_2$O is formed. A moderate volume expansion results from this last process. We also report a 'zipper' nucleation mechanism that could provide the seed for the transformation from tin oxide to lithium oxide.

physics.comp-ph

Molecular reordering processes on ice (0001) surfaces from long timescale simulations

We report results of long timescale adaptive kinetic Monte Carlo simulations aimed at identifying possible molecular reordering processes on both proton-disordered and ordered (Fletcher) basal plane (0001) surfaces of hexagonal ice. The simulations are based on a force field for flexible molecules and span a time interval of up to 50 μs at a temperature of 100 K, which represents a lower bound to the temperature range of Earth's atmosphere. Additional calculations using both density functional theory and an ab initio based polarizable potential function are performed to test and refine the force field predictions. Several distinct processes are found to occur readily even at this low temperature, including concerted reorientation (flipping) of neighboring surface molecules, which changes the pattern of dangling H-atoms, and the formation of interstitial defects by the downwards motion of upper-bilayer molecules. On the proton-disordered surface, one major surface roughening process is observed that significantly disrupts the crystalline structure. Despite much longer simulation time, such roughening processes are not observed on the highly ordered Fletcher surface which is energetically more stable because of smaller repulsive interaction between neighboring dangling H-atoms. However, a more localized process takes place on the Fletcher surface involving a surface molecule transiently leaving its lattice site. The flipping process provides a facile pathway of increasing proton-order and stabilizing the surface, supporting a predominantly Fletcher-like ordering of low-temperature ice surfaces, but our simulations also show that proton- disordered patches on the surface may induce significant local reconstructions. Further, a subset of the molecules on the Fletcher surface are susceptible to forming interstitial defects.

physics.chem-ph

Bowl breakout, escaping the positive region when searching for saddle points

We present a scheme improving the minimum-mode following method for finding first order saddle points by confining the displacements of atoms to the subset of those subject to the largest force. By doing so it is ensured that the displacement remains of a local character within regions where all eigenvalues of the Hessian matrix are positive. However, as soon as a region is entered where an eigenvalue turns negative all atoms are released to maintain the ability of determining concerted moves. Applying the proposed scheme reduces the required number of force calls for the determination of connected saddle points by a factor two or more compared to a free search. Furthermore, a wider distribution of the relevant low barrier saddle points is obtained. Finally, the dependency on the initial distortion and the applied maximal step size is reduced making minimum-mode guided searches both more robust and applicable.

cond-mat.mtrl-sci

Improved initial guess for minimum energy path calculations

A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of the true minimum energy path using some method of choice for evaluating the energy and atomic forces, for example by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to the true minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50 % to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used.

cond-mat.mtrl-sci

Photoelectric charging of dust grains in the environment of Young Stellar Objects

The evolution of disks around Young Stellar Objects (YSOs) is deeply affected by the YSOs ultraviolet (UV) radiation field especially in the 500-1100 Å spectral range. The two dominant processes are; the photo-dissociation of H_2 molecules in the Werner and Lyman bands, and the emission of photo-electrons from dust grains when high energy photons are absorbed. Photo-electrons are an important source of gas heating. Dust grain charging when exposed to various possible UV fields in the YSOs environment is investigated. Numerical simulation of the evolution of photo-electrons in the electric field created by the charged dust grains are carried out to obtain a charging profile. From the simulations it appears that the different spectra produce significant quantitative and qualitative different charging processes. Both the UV background and the Ae-Herbig star radiation field produce a relatively slow charging of dust grains due to the low fraction of sufficiently energetic photons. The radiation field of T Tauri Stars (TTSs) is harder due to the release of magnetic energy in the dense magnetospheric environment. These numerical results have been used to propose a new simple analytical model for grain charging in the atmosphere of protostellar disks around TTSs susceptible to be used in any disk modeling. It has been found that the yield decreases exponentially with the dust charge and that two populations of photoelectrons are produced. The high energy population is susceptible of dissociating the H_2 and ionizing some low ionization potential species, such as the Mg. These results add an additional role to dust on the chemistry of the layers just below the H_2 photoionization front. This photoelectic yield has been applied to a simple evaluation of the dust charge in the atmospheres of accretion disks and a simple evaluation of the dust charge in the atmospheres of accretion disks.

astro-ph.SR

Space-charge modulation in vacuum microdiodes at THz frequencies

We investigate the dynamics of a space-charge limited, photoinjected, electron beam in a microscopic vacuum diode. Due to the small nature of the system it is possible to conduct high-resolution simulations where the number of simulated particles is equal to the number of electrons within the system. In a series of simulations of molecular dynamics type, where electrons are treated as point-charges, we address and analyze space-charge effects in a $μ$m-scale vacuum diode. We have been able to reproduce breakup of a single pulse injected with a current density beyond the Child-Langmuir limit, and we find that continuous injection of current into the diode gap results in a well defined train of electron bunches corresponding to THz frequency. A simple analytical explanation of this behavior is given.

physics.plasm-ph

Theoretical study of kinks on screw dislocation in silicon

Theoretical calculations of the structure, formation and migration of kinks on a non-dissociated screw dislocation in silicon have been carried out using density functional theory calculations as well as calculations based on interatomic potential functions. The results show that the structure of a single kink is characterized by a narrow core and highly stretched bonds between some of the atoms. The formation energy of a single kink ranges from 0.9 to 1.36 eV, and is of the same order as that for kinks on partial dislocations. However, the kinks migrate almost freely along the line of an undissociated dislocation unlike what is found for partial dislocations. The effect of stress has also been investigated in order to compare with previous silicon deformation experiments which have been carried out at low temperature and high stress. The energy barrier associated with the formation of a stable kink pair becomes as low as 0.65 eV for an applied stress on the order of 1 GPa, indicating that displacements of screw dislocations likely occur via thermally activated formation of kink pairs at room temperature.

cond-mat.mtrl-sci

Evolution dynamics in terraced NK landscapes

We study populations of agents evolving in fitness landscapes constructed according to the rules of a modified NK model with a tunable amount of neutral paths. In the `punctuated equilibrium' regime evolutionary events are identified as jumps in the mean population fitness, and the statistics of these jumps in an ensemble of independently evolving populations is analyzed. We show that, for a wide range of landscapes parameters, the number of events in time t is Poisson distributed, with the time parameter replaced by the logarithm of time. This simple log-Poisson statistics likewise describes the number n of records in any sequence of t independently generated random numbers. The implications of this behavior for evolution dynamics are discussed.

adap-org