arXiv subjects

Hannes Jónsson

Publications and source records attributed to Hannes Jónsson.

At least 55 records · Page 3Linked to original sources

arXiv2023

Variational Density Functional Calculations of Excited States: Conical Intersection and Avoided Crossing in Ethylene Bond Twisting

Theoretical studies of photochemical processes require a description of the energy surfaces of excited electronic states, especially near degeneracies, where transitions between states are most likely. Systems relevant to photochemical applications are typically too large for high-level multireference methods, and while time-dependent density functional theory (TDDFT) is efficient, it can fail to provide the required accuracy. A variational, time-independent density functional approach is applied to the twisting of the double bond and pyramidal distortion in ethylene, the quintessential model for photochemical studies. By allowing for symmetry breaking, the calculated energy surfaces exhibit the correct topology around the twisted-pyramidalized conical intersection even when using a semilocal functional approximation, and by including explicit self-interaction correction, the torsional energy curves are in close agreement with published multireference results. The findings of the present work point to the possibility of using a single determinant time-independent density functional approach to simulate nonadiabatic dynamics, even for large systems where multireference methods are impractical and TDDFT is often not accurate enough.

physics.chem-ph↗

arXiv2023

Is the doped MoS2 basal plane an efficient hydrogen evolution catalyst? Calculations of voltage-dependent activation energy

Transition metal dichalcogenides are cheap and earth-abundant candidates for the replacement of precious metals as catalyst materials. Experimental measurements of the hydrogen evolution reaction (HER), for example, have demonstrated significant electrocatalytic activity of MoS2 but there is large variation depending on preparation method. In order to gain information about the mechanism and active sites for HER, we have carried out calculations of the reaction and activation energy for HER at the transition metal doped basal plane of MoS2 under electrochemical conditions, i.e. including applied electrode potential and solvent effects. The calculations are based on identifying the relevant saddle points on the energy surface obtained from density functional theory within the generalized gradient approximation, and the information on energetics is used to construct voltage-dependent volcano plots. Doping with 3d-metal atoms as well as Pt is found to enhance hydrogen adsorption onto the basal plane by introducing electronic states within the band gap, and in some cases (Co, Ni, Cu, Pt) significant local symmetry breaking. The Volmer-Heyrovsky mechanism is found to be most likely and the associated energetics show considerable dopant and voltage-dependence. While the binding free energy of hydrogen can be tuned to be seemingly favorable for HER, the calculated activation energy turns out to be significant, at least 0.7 eV at a voltage of -0.5 V vs. SHE, indicating low catalytic activity of the doped basal plane. This suggests that other sites are responsible for the experimental activity, possibly edges or basal plane defects.

cond-mat.mtrl-sci↗

arXiv2022

Stability of Hopfions in Bulk Magnets with Competing Exchange Interactions

Magnetic hopfions are string-like three-dimensional topological solitons, characterised by the Hopf invariant. They serve as a fundamental prototype for three-dimensional magnetic quasi-particles and are an inspiration for novel device concepts in the field of spintronics. Based on a micromagnetic model and without considering temperature, the existence of such hopfions has been predicted in certain magnets with competing exchange interactions. However, physical realisation of freely moving hopfions in bulk magnets have so far been elusive. Here, we consider an effective Heisenberg model with competing exchange interactions and study the stability of small toroidal hopfions with Hopf number $Q_\text{H}=1$ by finding first-order saddle points on the energy surface representing the transition state for the decay of hopfions via the formation of two coupled Bloch points. We combine the geodesic nudged elastic band method and an adapted implementation of the dimer method to resolve the sharp energy profile of the reaction path near the saddle point. Our analysis reveals that the energy barrier can reach substantial height and is largely determined by the size of the hopfion relative to the lattice constant.

cond-mat.mes-hall↗

arXiv2022

Transferable Potential Function for Flexible H$_2$O Molecules Based on the Single Center Multipole Expansion

A potential function is presented for describing a system of flexible H$_2$O molecules based on the single center multipole expansion (SCME) of the electrostatic interaction. The model, referred to as SCME/f, includes the variation of the molecular quadrupole moment as well as the dipole moment with changes in bond length and angle so as to reproduce results of high level electronic structure calculations. The multipole expansion also includes fixed octupole and hexadecapole moments, as well as anisotropic dipole-dipole, dipole-quadrupole and quadrupole-quadrupole polarizability tensors. The model contains five adjustable parameters related to the repulsive interaction and damping functions in the electrostatic and dispersion interactions. Their values are adjusted to reproduce the lowest energy isomers of small clusters, (H$_2$O)$_n$ with $n=2-6$, as well as measured properties of the ice Ih crystal. Subsequent calculations of the energy difference between the various isomer configurations of the clusters show that SCME/f gives good agreement with results of electronic structure calculations and represents a significant improvement over the previously presented rigid SCME potential function. Analysis of the vibrational frequencies of the clusters and structural properties of ice Ih crystal show the importance of accurately describing the variation of the quadrupole moment with molecular structure.

physics.comp-ph↗

arXiv2022

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 Ångström 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↗

arXiv2022

Simulations of the Electrochemical Oxidation of Pt Nanoparticles of Various Shapes

The activity and stability of a platinum nanoparticle (NP) is not only affected by its size but additionally depends on its shape. To this end, simulations can identify structure-property relationships to make a priori decisions on the most promising structures. While activity is routinely probed by electronic structure calculations on simplified surface models, modeling the stability of NP model systems in electrochemical reactions is challenging due to the long timescale of relevant processes such as oxidation beyond the point of reversibility. In this work, a routine for simulating electrocatalyst stability is presented. The procedure is referred to as GREG after its main ingredients - a grand-canonical simulation approach using reactive force fields to model electrochemical reactions as a function of the galvanic cell potential. The GREG routine is applied to study the oxidation of 3 nm octahedral, cubic, dodecahedral, cuboctahedral, spherical, and tetrahexahedral platinum NPs. The oxidation process is analyzed using adsorption isobars as well as interaction energy heat maps that provide the basis for constructing electrochemical phase diagrams. Onset potentials for surface oxidation increase in the sequence cube ~= dodecahedron <= octahedron <= tetrahexahdron < sphere < cuboctahedron, establishing a relationship between oxidation behavior and surface facet structure. The electrochemical results are rationalized using structural and electronic analysis.

physics.chem-ph↗

arXiv2022

Indirect Mechanism of Au adatom Diffusion on the Si(100) Surface

Calculations of the diffusion of a Au adatom on the dimer reconstructed Si(100)-2x1 surface reveal an interesting mechanism that differs significantly from a direct path between optimal binding sites, which are located in between dimer rows. Instead, the active diffusion mechanism involves promotion of the adatom to higher energy sites on top of a dimer row and then fast migration along the row, visiting ca. a hundred sites at room temperature, before falling back down into an optimal binding site. This top-of-row mechanism becomes more important the lower the temperature is. The calculations are carried out by finding minimum energy paths on the energy surface obtained from density functional theory within the PBEsol functional approximation followed by kinetic Monte Carlo simulations of the diffusion over a range of temperature from 200 K to 900 K. While the activation energy for the direct diffusion mechanism is calculated to be 0.84 eV, the effective activation energy for the indirect mechanism is on average 0.56 eV.

cond-mat.mtrl-sci↗

arXiv2021

Assessment of the Accuracy of Density Functionals for Calculating Oxygen Reduction Reaction on Nitrogen Doped Graphene

Experimental studies of the oxygen reduction reaction (ORR) at nitrogen doped graphene electrodes have reported a remarkably low overpotential, on the order of 0.5 V, similar to Pt based electrodes. Theoretical calculations using density functional theory have lent support for this claim. However, other measurements have indicated that transition metal impurities are actually responsible for the ORR activity, thereby raising questions about the reliability of both the experiments and the calculations. In order to assess the accuracy of the theoretical calculations, various generalized gradient approximation (GGA), meta-GGA and hybrid functionals are employed here and calibrated against high-level wave function based coupled cluster calculations (CCSD(T)) of the overpotential as well as self-interaction corrected density functional calculations and published quantum Monte Carlo calculations of O adatom binding to graphene. The PBE0 and HSE06 hybrid functionals are found to give more accurate results than the GGA and meta-GGA functionals, as would be expected, and for low dopant concentration, 3.1%, the overpotential is calculated to be 1.0 V. The GGA and meta-GGA functionals give a lower estimate by as much as 0.4 V. When the dopant concentration is doubled, the overpotential calculated with hybrid functionals drops, while it increases in GGA functional calculations. The opposite trends result from different potential determining steps, the *OOH species being of central importance in the hybrid functional calculations while the reduction of *O determines the overpotential obtained in GGA and meta-GGA calculations. The results presented here are mainly based on calculations of periodic representations of the system, but a comparison is also made with molecular flake models which are found to give erratic results.

cond-mat.mtrl-sci↗

arXiv2021

Direct Energy Minimization Based on Exponential Transformation in Density Functional Calculations of Finite and Extended Systems

The energy minimization involved in density functional calculations of electronic systems can be carried out using an exponential transformation that preserves the orthonormality of the orbitals. The energy of the system is then represented as a function of the elements of a skew-Hermitian matrix that can be optimized directly using unconstrained minimization methods. An implementation based on the limited memory Broyden-Fletcher-Goldfarb-Shanno approach with inexact line search and a preconditioner is presented and the performance compared with that of the commonly used self-consistent field approach. Results are presented for the G2 set of 148 molecules, liquid water configurations with up to 576 molecules and some insulating crystals. A general preconditioner is presented that is applicable to systems with fractional orbital occupation as is, for example, needed in the k-point sampling for periodic systems. This exponential transformation direct minimization approach is found to outperform the standard implementation of the self-consistent field approach in that all the calculations converge with the same set of parameter values and it requires less computational effort on average. The formulation of the exponential transformation and the gradients of the energy presented here are quite general and can be applied to energy functionals that are not unitary invariant such as self-interaction corrected functionals.

physics.comp-ph↗

arXiv2021

Method for Calculating Excited Electronic States Using Density Functionals and Direct Orbital Optimization with Real Space Grid or Plane Wave Basis Set

A direct orbital optimization method is presented for density functional calculations of excited electronic states using either a real space grid or a plane wave basis set. The method is variational, provides atomic forces in the excited states, and can be applied to Kohn-Sham (KS) functionals as well as orbital-density dependent functionals (ODD) including explicit self-interaction correction. The implementation for KS functionals involves two nested loops: (1) An inner loop for finding a stationary point in a subspace spanned by the occupied and a few virtual orbitals corresponding to the excited state; (2) an outer loop for minimizing the energy in a tangential direction in the space of the orbitals. For ODD functionals, a third loop is used to find the unitary transformation that minimizes the energy functional among occupied orbitals only. Combined with the maximum overlap method, the algorithm converges in challenging cases where conventional self-consistent field algorithms tend to fail. The benchmark tests presented include two charge-transfer excitations in nitrobenzene and an excitation of CO to degenerate $π^\ast$ orbitals where the importance of complex orbitals is illustrated. An application of the method to several metal-to-ligand charge-transfer and metal-centred excited states of an Fe$^{\rm II}$ photosensitizer complex is described and the results compared to reported experimental estimates. The method is also used to study the effect of Perdew-Zunger self-interaction correction on valence and Rydberg excited states of several molecules, both singlet and triplet states, and the performance compared to semilocal and hybrid functionals.

physics.comp-ph↗

arXiv2021

Mn Dimer can be Described Accurately with Density Functional Calculations when Self-interaction Correction is Applied

Qualitatively incorrect results are obtained for the Mn dimer in density functional theory calculations using the generalized gradient approximation (GGA) and similar results are obtained from local density and meta-GGA functionals. The coupling is predicted to be ferromagnetic rather than antiferromagnetic and the bond between the atoms is predicted to be an order of magnitude too strong and about an Ångstrøm too short. Explicit, self-interaction correction (SIC) applied to a commonly used GGA energy functional, however, provides close agreement with both experimental data and high-level, multi-reference wave function calculations. These results show that the failure is not due to strong correlation but rather the single electron self-interaction that is necessarily introduced in estimates of the classical Coulomb and exchange-correlation energy when only the total electron density is used as input. The corrected functional depends explicitly on the orbital densities and can, therefore, avoid the introduction of self-Coulomb interaction. The error arises because of over-stabilization of bonding $d$-states in the minority spin channel resulting from an overestimate of the $d$-electron self-interaction in the semi-local exchange-correlation functionals. Since the computational effort in the self-interaction corrected calculations scales with system size in the same way as for regular semi-local functional calculations, this approach provides a way to calculate properties of Mn nanoclusters as well as biomolecules and extended solids where Mn dimers and larger cluster are present, while multi-reference wave function calculations can only be applied to small systems.

physics.chem-ph↗

arXiv2021

From AC-STEM Image to 3D Structure: A Systematic Analysis of Au55 nanocluster

Aberration-corrected scanning electron microscopy (AC-STEM) can provide valuable information on the atomic structure of nanoclusters, an essential input for gaining an understanding of their physical and chemical properties. A systematic method is presented here for the extraction of atom coordinates from an AC-STEM image in a way that is general enough to be applicable to irregular structures. The two-dimensional information from the image is complemented with an approximate description of the atomic interactions so as to construct a three-dimensional structure and, at a final stage, the structure is refined using electron density functional theory (DFT) calculations. The method is applied to an AC-STEM image of Au55. Analysis of the local structure shows that the cluster is a combination of a part with icosahedral structure elements and a part with local atomic arrangement characteristic of crystal packing, including a segment of a flat surface facet. The energy landscape of the cluster is explored in calculations of minimum energy paths between the optimal fit structure and other candidates generated in the analysis. This reveals low energy barriers for conformational changes, showing that such transitions can occur on laboratory timescale even at room temperature and lead to large changes in the AC-STEM image. The paths furthermore reveal additional cluster configurations, some with lower DFT energy and providing nearly as good fit to the experimental image.

cond-mat.mtrl-sci↗

arXiv2021

Elastic Collision Based Dynamic Partitioning Scheme for Hybrid Simulations

The scattering-adapted flexible inner region ensemble separator (SAFIRES) is a partitioning scheme designed to divide a simulation cell into two regions to be treated with different computational methodologies. SAFIRES prevents particles from crossing between regions and resolves boundary events through elastic collisions of the particles mediated by the boundary, conserving energy and momenta. A multiple-time-step propagation algorithm is introduced where the time step is scaled automatically to identify the moment a collision occurs. If the length of the time step is kept constant, the new propagator reduces to a regular algorithm for Langevin dynamics, and to the velocity Verlet algorithm for classical dynamics if the friction coefficient is set to zero. SAFIRES constitutes the exact limit of the premise behind boundary-based methods such as FIRES, BEST, and BCC which take advantage of the indistinguishability of molecules on opposite sides of the separator. It gives correct average ensemble statistics despite the introduction of an ensemble separator. SAFIRES is tested in simulations where the molecules on the two sides are treated in the same way, for a Lennard-Jones (LJ) liquid and a LJ liquid in contact with a surface, as well as for liquid modelling simulations using the TIP4P force field. Simulations using SAFIRES are shown to reproduce the unconstrained reference simulations without significant deviations.

physics.chem-ph↗

arXiv2020

Fast and Robust Algorithm for the Energy Minimization of Spin Systems Applied in an Analysis of High Temperature Spin Configurations in Terms of Skyrmion Density

An algorithm for the minimization of the energy of magnetic systems is presented and applied to the analysis of thermal configurations of a ferromagnet to identify inherent structures, i.e. the nearest local energy minima, as a function of temperature. Over a rather narrow temperature interval, skyrmions appear and reach a high temperature limit for the skyrmion density. In addition, the performance of the algorithm is further demonstrated in a self-consistent field calculation of a skyrmion in an itinerant magnet. The algorithm is based on a geometric approach in which the curvature of the spherical domain is taken into account and as a result the length of the magnetic moments is preserved in every iteration. In the limit of infinitesimal rotations, the minimization path coincides with that obtained using damped spin dynamics while the use of limited-memory quasi-newton minimization algorithms, such as the limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) algorithm, significantly accelerates the convergence.

physics.comp-ph↗

arXiv2020

Efficient Optimization Method for Finding Minimum Energy Paths of Magnetic Transitions

Efficient algorithms for the calculation of minimum energy paths of magnetic transitions are implemented within the geodesic nudged elastic band (GNEB) approach. While an objective function is not available for GNEB and a traditional line search can, therefore, not be performed, the use of limited memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) and conjugate gradient algorithms in conjunction with orthogonal spin optimization (OSO) approach is shown to greatly outperform the previously used velocity projection and dissipative Landau-Lifschitz dynamics optimization methods. The implementation makes use of energy weighted springs for the distribution of the discretization points along the path and this is found to improve performance significantly. The various methods are applied to several test problems using a Heisenberg-type Hamiltonian, extended in some cases to include Dzyaloshinskii-Moriya and exchange interactions beyond nearest neighbours. Minimum energy paths are found for magnetization reversals in a nano-island, collapse of skyrmions in two-dimensional layers and annihilation of a chiral bobber near the surface of a three-dimensional magnet. The LBFGS-OSO method is found to outperform the dynamics based approaches by up to a factor of 8 in some cases.

physics.comp-ph↗

arXiv2020

Variational density functional calculations of excited states via direct optimization

The development of variational density functional theory approaches to excited electronic states is impeded by limitations of the commonly used self-consistent field (SCF) procedure. A method based on a direct optimization approach as well as the maximum overlap method is presented and the performance compared with previously proposed SCF strategies. Excited-state solutions correspond to saddle points of the energy as a function of the electronic degrees of freedom. The approach presented here makes use of a preconditioner determined with the help of the maximum overlap method to guide the convergence on a target nth-order saddle point. The method is found to be more robust and to converge faster than previously proposed SCF approaches for a set of 89 excited states of molecules. A limited-memory formulation of the symmetric rank-one method for updating the inverse Hessian is found to give the best performance. A conical intersection for the carbon monoxide molecule is calculated without resorting to fractional occupation numbers. Calculations on excited states of the hydrogen atom and a doubly excited state of the dihydrogen molecule using a self-interaction corrected functional are presented. For these systems, the self-interaction correction is found to improve the accuracy of density functional calculations of excited states.

physics.chem-ph↗

arXiv2020

Skyrmions in antiferromagnets: thermal stability and the effect of external field and impurities

Calculations of skyrmions in antiferromagnets (AFMs) are presented, and their properties compared with skyrmions in corresponding ferromagnets (FMs). The rates of skyrmion collapse and escape through the boundary of a track, as well as the binding to and collapse at a non-magnetic impurity, are calculated as a function of applied magnetic field. The activation energy for skyrmion annihilation is the same in AFMs and corresponding FMs in the absence of an applied magnetic field. The pre-exponential factor in the Arrhenius rate law is, however, different because skyrmion dynamics is different in the two systems. An applied magnetic field has opposite effects on skyrmions in the two types of materials. In AFMs the rate of collapse of skyrmions as well as the rate of escape through the edge of a magnetic strip decreases slightly with increasing field, while these rates increase strongly for a skyrmion in the corresponding FMs when the field is directed antiparallel to the magnetization in the center of the skyrmion. A non-magnetic impurity is less likely to trap a skyrmion in AFMs especially in the presence of a magnetic field. This, together with the established fact that a spin polarized current moves skyrmions in AFMs in the direction of the current, while in FMs skyrmions move at an angle to the current, demonstrates that skyrmions in AFMs have several advantageous properties over skyrmions in FMs for memory and spintronic devices.

cond-mat.mtrl-sci↗

arXiv2020

Magnetic Skyrmion Annihilation by Quantum Mechanical Tunneling

Magnetic skyrmions are nano-scale magnetic states that could be used in various spintronics devices. A central issue is the mechanism and rate of various possible annihilation processes and the lifetime of metastable skyrmions. While most studies have focused on classical over-the-barrier mechanism for annihilation, it is also possible that quantum mechanical tunneling through the energy barrier takes place. Calculations of the lifetime of magnetic skyrmions in a two-dimensional lattice are presented and the rate of tunneling compared with the classical annihilation rate. A remarkably strong variation in the crossover temperature and the lifetime of the skyrmion is found as a function of the values of parameters in the extended Heisenberg Hamiltonian, i.e. the out-of-plane anisotropy, Dzyaloshinskii-Moriya interaction (DMI) and applied magnetic field. Materials parameters and conditions are identified where the onset of tunneling could be observed on a laboratory time scale. In particular, it is predicted that skyrmion tunneling could be observed in the PdFe/Ir(111) system when an external magnetic field on the order of 6 T is applied.

cond-mat.mes-hall↗