### Browsing by Author "Jónsson, Hannes"

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Item Calculations of Al dopant in alpha-quartz using a variational implementation of the Perdew-Zunger self-interaction correction(2015) Gudmundsdóttir, H.; Jónsson, E.Ö.; Jónsson, Hannes; Department of Applied Physics; Multiscale Statistical and Quantum PhysicsItem Charge localization in a diamine cation provides a test of energy functionals and self-interaction correction(2016-03-16) Cheng, Xinxin; Zhang, Yao; Jónsson, Elvar; Jónsson, Hannes; Weber, Peter M.; Brown University; Department of Applied PhysicsDensity functional theory (DFT) is widely applied in calculations of molecules and materials. Yet, it suffers from a well-known over-emphasis on charge delocalization arising from self-interaction error that destabilizes localized states. Here, using the symmetric diamine N,N′-dimethylpiperazine as a model, we have experimentally determined the relative energy of a state with positive charge localized on one of the two nitrogen atoms, and a state with positive charge delocalized over both nitrogen atoms. The charge-localized state was found to be 0.33 (0.04) eV higher in energy than the charge-delocalized state. This provides an important test of theoretical approaches to electronic structure calculations. Calculations with all DFT functionals commonly used today, including hybrid functionals with exact exchange, fail to predict a stable charge-localized state. However, the application of an explicit self-interaction correction to a semi-local functional identifies both states and gives relative energy in excellent agreement with both experiment and CCSD(T) calculations.Item Classical to quantum mechanical tunneling mechanism crossover in thermal transitions between magnetic states(ROYAL SOC CHEMISTRY, 2016) Vlasov, Sergei; Bessarab, Pavel F.; Uzdin, Valery M.; Jónsson, Hannes; St. Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO); St. Petersburg State University; Department of Applied PhysicsTransitions between states of a magnetic system can occur by jumps over an energy barrier or by quantum mechanical tunneling through the energy barrier. The rate of such transitions is an important consideration when the stability of magnetic states is assessed for example for nanoscale candidates for data storage devices. The shift in transition mechanism from jumps to tunneling as the temperature is lowered is analyzed and a general expression derived for the crossover temperature. The jump rate is evaluated using a harmonic approximation to transition state theory. First, the minimum energy path for the transition is found with the geodesic nudged elastic band method. The activation energy for the jumps is obtained from the maximum along the path, a saddle point on the energy surface, and the eigenvalues of the Hessian matrix at that point as well as at the initial state minimum used to estimate the entropic pre-exponential factor. The crossover temperature for quantum mechanical tunneling is evaluated from the second derivatives of the energy with respect to orientation of the spin vector at the saddle point. The resulting expression is applied to test problems where analytical results have previously been derived, namely uniaxial and biaxial spin systems with two-fold anisotropy. The effect of adding four-fold anisotropy on the crossover temperature is demonstrated. Calculations of the jump rate and crossover temperature for tunneling are also made for a molecular magnet containing an Mn4 group. The results are in excellent agreement with previously reported experimental measurements on this system.Item Computational study of electrochemical CO2 reduction at transition metal electrodes(2015) Hussain, Javed; Skúlason, Egill; Jónsson, Hannes; University of Iceland; Department of Applied PhysicsA detailed understanding of the mechanism of electrochemical reduction of CO2 to form hydrocarbons can help design improved catalysts for this important reaction. Density functional theory calculations were used here to model the various elementary steps in this reaction on transition metal surfaces, in particular Cu(111) and Pt(111). The minimum energy paths for sequential protonation by either Tafel or Heyrovsky mechanism were calculated using the nudged elastic band method for applied potentials comparable to those used in experimental studies, ranging from -0.7 V to -1.7 V. A detailed mechanism for CO2 reduction on Cu(111) has been identified where the highest activation energy is 0.5 eV at -1.3 V vs. RHE. On Pt(111), a different mechanism is found to be optimal but it involves a higher barrier, 0.7 eV at -1.0 V vs. RHE. Hydrogen production is then a faster reaction with activation energy of only 0.3 eV on Pt(111) at the same potential, while on Cu(111) hydrogen production has an activation energy of 0.9 eV at -1.3 V. These results are consistent with experimental findings where copper electrodes are found to lead to relatively high yield of CH4 while H2 forms almost exclusively at platinum electrodes.Item Determination of the structure and properties of an edge dislocation in rutile TiO2(2019-01-15) Maras, Emile; Saito, Mitsuhiro; Inoue, Kazutoshi; Jónsson, Hannes; Ikuhara, Yuichi; McKenna, Keith P.; Department of Applied Physics; Tohoku University; University of Tokyo; University of York; University of IcelandA global optimization procedure is used to predict the structure and electronic properties of the b = c[001] edge dislocation in rutile TiO2. Over 1000 different atomic configurations have been generated using both semi-empirical and density functional theory estimates of the energy of the system to identify the most stable structure. Both stoichiometric and oxygen deficient dislocation core structures are predicted to be stable depending on the oxygen chemical potential. The latter is associated with Ti3+ species in the dislocation core. The dislocation is predicted to act as a trap for electrons but not for holes suggesting they are not strong recombination centers. The predicted structures and properties are found to be consistent with experimental results obtained using scanning transmission electron microscopy and electron energy loss spectroscopy on samples produced using the bicrystal approach.Item Duplication, Collapse, and Escape of Magnetic Skyrmions Revealed Using a Systematic Saddle Point Search Method(2018-11-06) Müller, Gideon P.; Bessarab, Pavel F.; Vlasov, Sergei M.; Lux, Fabian; Kiselev, Nikolai S.; Blügel, Stefan; Uzdin, Valery M.; Jónsson, Hannes; University of Iceland; Forschungszentrum Jülich; St. Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO); Multiscale Statistical and Quantum Physics; Department of Applied PhysicsVarious transitions that a magnetic Skyrmion can undergo are found in calculations using a method for climbing up the energy surface and converging onto first order saddle points. In addition to collapse and escape through a boundary, the method identifies a transition where the Skyrmion divides and forms two Skyrmions. The activation energy for this duplication process can be similar to that of collapse and escape. A tilting of the external magnetic field for a certain time interval is found to induce the duplication process in a dynamical simulation. Such a process could turn out to be an important avenue for the creation of Skyrmions in future magnetic devices.Item The effect of temperature and external field on transitions in elements of kagome spin ice(2017-11-01) Liashko, Sergei Y.; Jónsson, Hannes; Uzdin, Valery M.; St. Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO); Department of Applied PhysicsTransitions between magnetic states of one and two ring kagome spin ice elements consisting of 6 and 11 prolate magnetic islands are calculated and the lifetime of the ground states evaluated using harmonic transition state theory and the stationary state approximation. The calculated values are in close agreement with experimental lifetime measurements made by Farhan and co-workers (Farhan et al 2013 Nat. Phys. 9 375) when values of the parameters in the Hamiltonian are chosen to be best estimates for a single island, obtained from measurements and micromagnetic modeling. The effective pre-exponential factor in the Arrhenius rate law for the elementary steps turns out to be quite small, on the order of 109 s-1, three orders of magnitude smaller than has been assumed in previous analysis of the experimental data, while the effective activation energy is correspondingly lower than the previous estimate. The application of an external magnetic field is found to strongly affect the energy landscape of the system. Even a field of can eliminate states that correspond to ground states in the absence of a field. The theoretical approach presented here and the close agreement found with experimental data demonstrates that the properties of spin ice systems can be calculated using the tools of rate theory and a Hamiltonian parametrized only from the properties of a single island.Item Efficient dynamical correction of the transition state theory rate estimate for a flat energy barrier(2016-09-07) Mökkönen, Harri; Ala-Nissilä, Tapio; Jónsson, Hannes; Department of Applied PhysicsThe recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch between the initial and final state energy wells while the polymer beads undergo diffusive motion back and forth over the barrier. We present an efficient method for evaluating the correction factor by constructing a sequence of hyperplanes starting at the transition state and calculating the probability that the system advances from one hyperplane to another towards the product. This is analogous to what is done in forward flux sampling except that there the hyperplane sequence starts at the initial state. The method is applied to the escape of polymers with up to 64 beads from a potential well. For high temperature, the results are compared with direct Langevin dynamics simulations as well as forward flux sampling and excellent agreement between the three rate estimates is found. The use of a sequence of hyperplanes in the evaluation of the recrossing correction speeds up the calculation by an order of magnitude as compared with the traditional approach. As the temperature is lowered, the direct Langevin dynamics simulations as well as the forward flux simulations become computationally too demanding, while the harmonic transition state theory estimate corrected for recrossings can be calculated without significant increase in the computational effort.Item First-principles Green's-function method for surface calculations: A pseudopotential localized basis set approach(2017-11-30) Smidstrup, Søren; Stradi, Daniele; Wellendorff, Jess; Khomyakov, Petr A.; Vej-Hansen, Ulrik G.; Lee, Maeng Eun; Ghosh, Tushar; Jónsson, Elvar; Jónsson, Hannes; Stokbro, Kurt; Department of Applied Physics; QuantumWise A/SWe present an efficient implementation of a surface Green's-function method for atomistic modeling of surfaces within the framework of density functional theory using a pseudopotential localized basis set approach. In this method, the system is described as a truly semi-infinite solid with a surface region coupled to an electron reservoir, thereby overcoming several fundamental drawbacks of the traditional slab approach. The versatility of the method is demonstrated with several applications to surface physics and chemistry problems that are inherently difficult to address properly with the slab method, including metal work function calculations, band alignment in thin-film semiconductor heterostructures, surface states in metals and topological insulators, and surfaces in external electrical fields. Results obtained with the surface Green's-function method are compared to experimental measurements and slab calculations to demonstrate the accuracy of the approach.Item A general-purpose machine learning Pt interatomic potential for an accurate description of bulk, surfaces, and nanoparticles(American Institute of Physics, 2023-04-07) Kloppenburg, Jan; Pártay, Livia B.; Jónsson, Hannes; Caro, Miguel A.; DAS Group; University of Warwick; Department of Applied Physics; Department of Chemistry and Materials Science; Department of Electrical Engineering and Automation; Department of Applied PhysicsA Gaussian approximation machine learning interatomic potential for platinum is presented. It has been trained on density-functional theory (DFT) data computed for bulk, surfaces, and nanostructured platinum, in particular nanoparticles. Across the range of tested properties, which include bulk elasticity, surface energetics, and nanoparticle stability, this potential shows excellent transferability and agreement with DFT, providing state-of-the-art accuracy at a low computational cost. We showcase the possibilities for modeling of Pt systems enabled by this potential with two examples: the pressure-temperature phase diagram of Pt calculated using nested sampling and a study of the spontaneous crystallization of a large Pt nanoparticle based on classical dynamics simulations over several nanoseconds.Item GPAW : An open Python package for electronic structure calculations(American Institute of Physics, 2024-03-07) Mortensen, Jens Jørgen; Larsen, Ask Hjorth; Kuisma, Mikael; Ivanov, Aleksei V.; Taghizadeh, Alireza; Peterson, Andrew; Haldar, Anubhab; Dohn, Asmus Ougaard; Schäfer, Christian; Jónsson, Elvar Örn; Hermes, Eric D.; Nilsson, Fredrik Andreas; Kastlunger, Georg; Levi, Gianluca; Jónsson, Hannes; Häkkinen, Hannu; Fojt, Jakub; Kangsabanik, Jiban; Sødequist, Joachim; Lehtomäki, Jouko; Heske, Julian; Enkovaara, Jussi; Winther, Kirsten Trøstrup; Dulak, Marcin; Melander, Marko M.; Ovesen, Martin; Louhivuori, Martti; Walter, Michael; Gjerding, Morten; Lopez-Acevedo, Olga; Erhart, Paul; Warmbier, Robert; Würdemann, Rolf; Kaappa, Sami; Latini, Simone; Boland, Tara Maria; Bligaard, Thomas; Skovhus, Thorbjørn; Susi, Toma; Maxson, Tristan; Rossi, Tuomas; Chen, Xi; Schmerwitz, Yorick Leonard A.; Schiøtz, Jakob; Olsen, Thomas; Jacobsen, Karsten Wedel; Thygesen, Kristian Sommer; Department of Applied Physics; Technical University of Denmark; Riverlane Ltd; Brown University; Boston University College of Engineering; Chalmers University of Technology; University of Iceland; Quantum-Si; University of Jyväskylä; CSC - IT Center for Science Ltd.; SLAC National Accelerator Laboratory; University of Freiburg; Universidad de Antioquia; University of the Witwatersrand, Johannesburg; Tampere University; University of Alabama at Tuscaloosa; Lanzhou University; University of ViennaWe review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for the implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE), providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe-Salpeter Equation, variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn-Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support for graphics processing unit (GPU) acceleration has been achieved with minor modifications to the GPAW code thanks to the CuPy library. We end the review with an outlook, describing some future plans for GPAW.Item Indirect mechanism of Au adatom diffusion on the Si(100) surface(American Physical Society, 2022-05-15) Peña-Torres, Alejandro; Ali, Abid; Stamatakis, Michail; Jónsson, Hannes; University of Iceland; University College London; Department of Applied Physics; Department of Applied PhysicsCalculations of the diffusion of a Au adatom on the dimer reconstructed Si(100)-2×1 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 is the temperature. 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 to 900 K. While the activation energy for the direct diffusion mechanism, both parallel and perpendicular to the dimer rows, is calculated to be 0.84 eV, the effective activation energy for the indirect mechanism parallel to the rows is on average 0.56 eV.Item Is the doped MoS2 basal plane an efficient hydrogen evolution catalyst? Calculations of voltage-dependent activation energy(Royal Society of Chemistry, 2023) Hanslin, Sander I.; Jónsson, Hannes; Akola, Jaakko; Norwegian University of Science and Technology; Multiscale Statistical and Quantum Physics; Department of Applied PhysicsTransition 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 the preparation method. In order to gain information about the mechanism and active sites for the 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.Item Lifetime of racetrack skyrmions(2018-12-01) Bessarab, Pavel F.; Müller, Gideon P.; Lobanov, Igor S.; Rybakov, Filipp N.; Kiselev, Nikolai S.; Jónsson, Hannes; Uzdin, Valery M.; Blügel, Stefan; Bergqvist, Lars; Delin, Anna; Department of Applied Physics; Multiscale Statistical and Quantum Physics; University of Iceland; St. Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO); KTH Royal Institute of Technology; Jülich Research CentreThe skyrmion racetrack is a promising concept for future information technology. There, binary bits are carried by nanoscale spin swirls-skyrmions-driven along magnetic strips. Stability of the skyrmions is a critical issue for realising this technology. Here we demonstrate that the racetrack skyrmion lifetime can be calculated from first principles as a function of temperature, magnetic field and track width. Our method combines harmonic transition state theory extended to include Goldstone modes, with an atomistic spin Hamiltonian parametrized from density functional theory calculations. We demonstrate that two annihilation mechanisms contribute to the skyrmion stability: At low external magnetic field, escape through the track boundary prevails, but a crossover field exists, above which the collapse in the interior becomes dominant. Considering a Pd/Fe bilayer on an Ir(111) substrate as a well-established model system, the calculated skyrmion lifetime is found to be consistent with reported experimental measurements. Our simulations also show that the Arrhenius pre-exponential factor of escape depends only weakly on the external magnetic field, whereas the pre-exponential factor for collapse is strongly field dependent. Our results open the door for predictive simulations, free from empirical parameters, to aid the design of skyrmion-based information technology.Item Magnetic exchange force microscopy(ROYAL SOC CHEMISTRY, 2017-09-21) Ivanov, Aleksei; Bessarab, Pavel F.; Uzdin, Valery M.; Jónsson, Hannes; University of Iceland; St. Petersburg State University; Department of Applied PhysicsIn magnetic exchange force microscopy a magnetic tip is scanned over the surface of a solid and an image representing the exchange interaction recorded. Sudden changes in the image corresponding to magnetization switching can be monitored as a function of the tip-surface distance thereby giving important information about the lifetime of metastable magnetic states and how it is affected by the exchange interaction. Here, theoretical calculations are carried out to study the tip-surface interaction and determine the mechanism and rate of transitions in a magnetic exchange force microscopy experiment, and comparison made with reported experimental data on an Fe cluster interacting with an antiferromagnetic Fe overlayer on a W(001) surface. The activation energy was determined from calculations of minimum energy paths and the pre-exponential factor in the Arrhenius rate expression evaluated from harmonic transition state theory, extended to account for zero modes. A noncollinear extension of the Alexander-Anderson model was used to describe the magnetic properties of an atomic scale representation of the system. The calculations reveal how the tip size, tip-surface distance and magnetic field affect the lifetime of the magnetic states.Item Qualitative insight and quantitative analysis of the effect of temperature on the coercivity of a magnetic system(2016-02-01) Moskalenko, Mariia; Bessarab, Pavel F.; Uzdin, Valery M.; Jónsson, Hannes; St. Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO); St. Petersburg State University; Department of Applied PhysicsThe temperature dependence of the response of a magnetic system to an applied field can be understood qualitatively by considering variations in the energy surface characterizing the system and estimated quantitatively with rate theory. In the system analysed here, Fe/Sm-Co spring magnet, the width of the hysteresis loop is reduced to a half when temperature is raised from 25 K to 300 K. This narrowing can be explained and reproduced quantitatively without invoking temperature dependence of model parameters as has typically been done in previous data analysis. The applied magnetic field lowers the energy barrier for reorientation of the magnetization but thermal activation brings the system over the barrier. A 2-dimensional representation of the energy surface is developed and used to gain insight into the transition mechanism and to demonstrate how the applied field alters the transition path. Our results show the importance of explicitly including the effect of thermal activation when interpreting experiments involving the manipulation of magnetic systems at finite temperature.Item Towards an optimal gradient-dependent energy functional of the PZ-SIC form(2015) Jónsson, E.; Lehtola, S.; Jónsson, Hannes; Department of Applied PhysicsResults of Perdew–Zunger self-interaction corrected (PZ-SIC) density functional theory calculations of the atomization energy of 35 molecules are compared to those of high-level quantum chemistry calculations. While the PBE functional, which is commonly used in calculations of condensed matter, is known to predict on average too high atomization energy (overbinding of the molecules), the application of PZ-SIC gives a large overcorrection and leads to significant underestimation of the atomization energy. The exchange enhancement factor that is optimal for the generalized gradient approximation within the Kohn-Sham (KS) approach may not be optimal for the self-interaction corrected functional. The PBEsol functional, where the exchange enhancement factor was optimized for solids, gives poor results for molecules in KS but turns out to work better than PBE in PZ-SIC calculations. The exchange enhancement is weaker in PBEsol and the functional is closer to the local density approximation. Furthermore, the drop inthe exchange enhancement factor for increasing reduced gradient in the PW91 functional gives more accurate results than the plateaued enhancement in the PBE functional. A step towards an optimal exchange enhancement factor for a gradient dependent functional of the PZ-SIC form is taken by constructing an exchange enhancement factor that mimics PBEsol for small values of the reduced gradient, and PW91 for large values. The average atomization energy is then in closer agreement with the high-level quantum chemistry calculations, but the variance is still large, the F2 molecule being a notable outlier.Item Variational Density Functional Calculations of Excited States: Conical Intersection and Avoided Crossing in Ethylene Bond Twisting(AMERICAN CHEMICAL SOCIETY, 2022-05-12) Schmerwitz, Yorick L.A.; Ivanov, Aleksei V.; Jónsson, Elvar; Jónsson, Hannes; Levi, Gianluca; Department of Applied Physics; Multiscale Statistical and Quantum Physics; University of IcelandTheoretical 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.