arXiv subjects

Hannes Jónsson

Publications and source records attributed to Hannes Jónsson.

At least 37 records · Page 2Linked to original sources

arXiv2025

Efficient Implementation of Gaussian Process Regression Accelerated Saddle Point Searches with Application to Molecular Reactions

The task of locating first order saddle points on high-dimensional surfaces describing the variation of energy as a function of atomic coordinates is an essential step for identifying the mechanism and estimating the rate of thermally activated events within the harmonic approximation of transition state theory. When combined directly with electronic structure calculations, the number of energy and atomic force evaluations needed for convergence is a primary issue. Here, we describe an efficient implementation of Gaussian process regression (GPR) acceleration of the minimum mode following method where a dimer is used to estimate the lowest eigenmode of the Hessian. A surrogate energy surface is constructed and updated after each electronic structure calculation. The method is applied to a test set of 500 molecular reactions previously generated by Hermez and coworkers [J. Chem. Theory Comput. 18, 6974 (2022)]. An order of magnitude reduction in the number of electronic structure calculations needed to reach the saddle point configurations is obtained by using the GPR compared to the dimer method. Despite the wide range in stiffness of the molecular degrees of freedom, the calculations are carried out using Cartesian coordinates and are found to require similar number of electronic structure calculations as an elaborate internal coordinate method implemented in the Sella software package. The present implementation of the GPR surrogate model in C++ is efficient enough for the wall time of the saddle point searches to be reduced in 3 out of 4 cases even though the calculations are carried out at a low Hartree-Fock level.

physics.chem-ph↗

arXiv2025

Dimerization of Ag adatoms on Si(100) at surprisingly low temperature due to adatom migration on top of Si-dimer rows

The puzzling experimental observations of Ag addimer formation on the Si(100) surface upon vapor deposition at low temperature, even as low as 140 K, reported by Huang et al. [Phys. Chem. Chem. Phys. 2021, 23, 4161], is explained by facile thermal migration on top of the Si dimer rows, while diffusion is inactive once an Ag adatom lands in one of the optimal binding sites in between dimer rows. The previously hypothesized transient mobility due to the hot spot formed as an Ag atom lands on the Si surface is found not to contribute significantly to mobility and dimer formation. The experimental conditions are simulated by a combination of classical dynamics calculations of the deposition events, systematic searches of saddle points representing transition states for thermally activated events and kinetic Monte Carlo simulations of long timescale evolution of the system over a temperature range from 100 K to 300 K. While the calculated energy barriers for diffusion parallel and perpendicular to the Si dimer rows are found to be nearly equal, indicating isotropic diffusion, the simulations show highly anisotropic diffusion, as the optimal migration mechanism involves multiple hops of Ag adatoms on top of Si dimer rows. Impinging Ag atoms are found to have a 90% chance of landing on top of a dimer row and while the hot spot created cools down too fast for transient mobility to play an important role, the energy barrier for thermally activated hops along the dimer row is low enough for migration to be active even at 100 K. A migrating Ag adatom can dimerise with another Ag adatom sitting at a stable binding site in between rows or another adatom on top of the same row. The simulations for deposition at 140 K show that most of the deposited Ag atoms end up forming dimers.

cond-mat.mtrl-sci↗

arXiv2025

Localised and Delocalised Charge Distribution in a Diamine Cation and Rydberg Excited State: A Challenging Test for Density Functionals

The balance between localised and delocalised electron distribution in the N,N'-dimethylpiperazine (DMP) molecule in the 3s Rydberg excited state and in the fully ionised DMP$^+$ provides a valuable test of density functionals, in particular the weight of Fock exchange (FE) in hybrid functionals and the scaling of explicit orbital-based self-interaction correction (SIC) applied to less elaborate functionals. We present results of calculations using density functionals of all rungs of Jacob's ladder, ranging from LDA to the DM21 machine learned local hybrid as well as double hybrids. For DMP$^+$, the commonly used hybrid functionals, such as PBE0(.25) with FE weight of 0.25, as well as PBE0(.32) with a weight of 0.32 only produce the more delocalised charge. The latter mimics the DM21 energy surface well. However, hybrid functionals with stronger FE, such as BHLYP and PBE0(.50) as well as some double hybrid functionals, also produce local energy minima corresponding to localised charge. When full SIC is applied to the PBE functional, an energy surface analogous to hybrid functionals with FE weight of 0.50 is obtained, while the scaling of SIC by 0.50, which has previously been shown to give improved atomisation energy and band gap of solids, only produces the more delocalised charge. For the 3s Rydberg excited state of DMP, two types of configurations with a localised hole are obtained in calculations using the PBE0(.32) functional, in addition to the delocalised hole, but only the latter is found with the PBE functional, showing that a significant reduction of the self-interaction error is needed in order to obtain agreement between density functional calculations and experimental measurements of the Rydberg state

physics.chem-ph↗

arXiv2025

Single Atom Substituents in Copper Surfaces May Adsorb Multiple CO Molecules

Copper is a good CO2 electroreduction catalyst as products beyond CO form, but efficiency and selectivity is low. Experiments have shown that admixture of other elements can help, and computational screening studies have pointed out various promising candidates based on the adsorption of a single CO molecule as a descriptor. Our calculations of CO adsorption on surfaces where a first row transition metal atom replaces a Cu atom show that multiple CO molecules, not just one, bind to the substitutional atom. For Fe, Co, and Ni atoms, a decrease in binding energy is found, but the reverse trend, namely increasing bond strength, is found for V, Cr, and Mn and the first three CO molecules. Magnetic moment, charge, and position of the substitutional atom are also strongly affected by the CO adsorption in most cases. Magnetic moment is stepwise reduced to zero, and the outward displacement of the substitutional atom increased.

cond-mat.mtrl-sci↗

arXiv2025

Co-existing magnetization reversal mechanisms in shakti spin ice systems

The switching mechanisms in artificial spin ice systems are investigated with focus on shakti and modified shakti lattices. Minimum energy paths are calculated using the geodesic nudged elastic band (GNEB) method implemented with a micromagnetic description of the system, including the internal magnetic structure of the islands and edge modulations. Two switching mechanisms, uniform magnetization rotation and domain wall formation, are found to have comparable activation energy. The preference for one over the other depends strongly on the saturation magnetization and the magnetic ordering of neighboring islands. Surprisingly, these mechanisms can coexist, leading to an enhanced probability of magnetization reversal. These results provide valuable insight that can help control internal magnetization switching processes in spin ice systems and help predict their thermodynamic properties.

cond-mat.mes-hall↗

arXiv2025

Decoherence and vibrational energy relaxation of the electronically excited PtPOP complex in solution

Understanding the ultrafast vibrational relaxation following photoexcitation of molecules in a condensed phase is essential to predict the outcome and improve the efficiency of photoinduced molecular processes. Here, the vibrational decoherence and energy relaxation of a binuclear complex, [Pt$_2$(P$_2$O$_5$H$_2$)$_4$]$^{4-}$ (PtPOP), upon electronic excitation in liquid water and acetonitrile are investigated through direct adiabatic dynamics simulations. A quantum mechanics/molecular mechanics (QM/MM) scheme is used where the excited state of the complex is modelled with orbital-optimized density functional calculations while solvent molecules are described using potential energy functions. The decoherence time of the Pt-Pt vibration dominating the photoinduced dynamics is found to be $\sim$1.6 ps in both solvents. This is in excellent agreement with experimental measurements in water, where intersystem crossing is slow ($>10$ ps). Pathways for the flow of excess energy are identified by monitoring the power of the solvent on vibrational modes. The latter are obtained as generalized normal modes from the velocity covariances, and the power is computed using QM/MM embedding forces. Excess vibrational energy is found to be predominantly released through short-range repulsive and attractive interactions between the ligand atoms and surrounding solvent molecules, whereas solute-solvent interactions involving the Pt atoms are less important. Since photoexcitation deposits most of the excess energy into Pt-Pt vibrations, energy dissipation to the solvent is inefficient. This study reveals the mechanism behind the exceptionally long vibrational coherence of the photoexcited PtPOP complex in solution and underscores the importance of short-range interactions for accurate simulations of vibrational energy relaxation of solvated molecules.

physics.chem-ph↗

arXiv2025

A Neural-Network-Based Selective Configuration Interaction Approach to Molecular Electronic Structure

By combining Hartree-Fock with a neural-network-supported quantum-cluster solver proposed recently in the context of solid-state lattice models, we formulate a scheme for selective neural-network configuration interaction (NNCI) calculations and implement it with various options for the type of basis set and boundary conditions. The method's performance is evaluated in studies of several small molecules as a step toward calculations of larger systems. In particular, the correlation energy in the N$_2$ molecule is compared with published full CI calculations that included nearly $10^{10}$ Slater determinants, and the results are reproduced with only $4\cdot10^{5}$ determinants using NNCI. A clear advantage is seen from increasing the set of orbitals included rather than approaching full CI for a smaller set. The method's high efficiency and implementation in a condensed matter simulation software expands the applicability of CI calculations to a wider range of problems, even extended systems through an embedding approach.

physics.chem-ph↗

arXiv2025

Identification of mechanisms of magnetic transitions using an efficient method for converging on first order saddle points

A method for locating first order saddle points on the energy surface of a magnetic system is described and several applications presented where the mechanism of various magnetic transitions is identified. The starting point for the iterative search algorithm can be anywhere, even close to a local energy minimum representing an initial state of the system, and the final state need not be specified. Convergence on a saddle point is obtained by inverting the component of the gradient along the minimum mode, thereby effectively transforming the neighbourhood of the saddle point to that of a local minimum. The method requires only the lowest two eigenvalues and corresponding eigenvectors of the Hessian of the system's energy and they are found using a quasi-Newton limited-memory Broyden-Fletcher-Goldfarb-Shanno solver for the minimization of the Rayleigh quotient without explicit evaluation of the Hessian. The method is applicable to large systems as the computational effort scales linearly with system size. Applications are presented to transitions in systems that reveal significant complexity of co-existing magnetic states, such as skyrmions, skyrmion bags, skyrmion tubes, chiral bobbers, and globules. When combined with rate theory within the harmonic approximation, the method can be used for simulations of the long timescale dynamics of complex magnetic systems characterized by multiple metastable states.

physics.comp-ph↗

arXiv2024

Doping-Induced Enhancement of Hydrogen Evolution at MoS2 Electrodes

Rate theory and DFT calculations of hydrogen evolution reaction (HER) on MoS2 with Co, Ni and Pt impurities show the significance of dihydrogen (H2*) complex where both hydrogen atoms are interacting with the surface. Stabilization of such a complex affects the competing Volmer-Heyrovsky (direct H2 release) and Volmer-Tafel (H2* intermediate) pathways. The resulting evolution proceeds with a very small overpotential for all dopants ($η$ = 0.1 to 0.2 V) at 25% edge substitution, significantly reduced from the already low $η$ = 0.27 V for the undoped edge. At full edge substitution, Co-MoS2 remains highly active ($η$ = 0.18 V) while Ni- and Pt-MoS2 are deactivated ($η$ = 0.4 to 0.5 V) due to unfavorable interaction with H2*. Instead of the single S-vacancy, the site of intrinsic activity in the basal plane was found to be the undercoordinated central Mo-atom in threefold S-vacancy configurations, enabling hydrogen evolution with $η$ = 0.52 V via a H2* intermediate. The impurity atoms interact favorably with the intrinsic sulfur vacancies on the basal plane, stabilizing but simultaneously deactivating the triple vacancy configuration. The calculated shifts in overpotential are consistent with reported measurements, and the dependence on doping level may explain variations in experimental observations.

cond-mat.mtrl-sci↗

arXiv2024

GPAW: An open Python package for electronic-structure calculations

We 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 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 (BSE), 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 of GPU acceleration has been achieved with minor modifications of the GPAW code thanks to the CuPy library. We end the review with an outlook describing some future plans for GPAW.

cond-mat.mtrl-sci↗

arXiv2024

Evidence of sharp transitions between octahedral and capped trigonal prism states of the solvation shell of Fe$^{+3}$(aq)

The structure of the solvation shell of aqueous Fe$^{+3}$ ion has been a subject of controversy due to discrepancies between experiments and different levels of theory. We address this issue by performing simulations for a wide range of ion concentrations, using various empirical potential energy functions, as well as density functional theory calculations of selected configurations. The solvation shell undergoes abrupt transitions between two states: an octahedral (OH) state with 6-fold coordination, and a capped trigonal prism (CTP) state with 7-fold coordination. The lifetime of these states is concentration dependent. In dilute $\mathrm{FeCl_3}$ solutions, the lifetime of the two states is similar ($\approx 1$ ns). However, the lifetime of the OH state increases with ion concentration, while that of the CTP state decreases slightly. When a uniform negative background charge is used instead of explicit counterions, the lifetime of the OH state is greatly overestimated. These findings underscore the need for further experimental measurements as well as high-level simulations over sufficiently long timescales and low concentration.

physics.chem-ph↗

arXiv2024

Saddle Point Search Algorithms for Variational Density Functional Calculations of Excited Electronic States with Self-Interaction Correction

Excited electronic states of molecules and solids play a fundamental role in fields such as catalysis and electronics. In electronic structure calculations, excited states typically correspond to saddle points on the surface described by the variation of the energy as a function of the electronic degrees of freedom. A direct optimization algorithm based on generalized mode following is presented for density functional calculations of excited states. While conventional direct optimization methods based on quasi-Newton algorithms usually converge to the stationary point closest to the initial guess, even minima, the generalized mode following approach systematically targets a saddle point of a specific order l by following the l lowest eigenvectors of the electronic Hessian up in energy. This approach thereby recasts the challenging saddle point search as a minimization, enabling the use of efficient and robust minimization algorithms. The initial guess orbitals and the saddle point order of the target excited state solution are evaluated by performing an initial step of constrained optimization freezing the electronic degrees of freedom involved in the excitation. In the context of Kohn-Sham density functional calculations, typical approximations to the exchange-and-correlation functional suffer from a self-interaction error. The Perdew and Zunger self-interaction correction can alleviate this problem, but makes the energy variant to unitary transformations in the occupied orbital space, introducing a large amount of unphysical solutions that do not fully minimize the self-interaction error. An extension of the generalized mode following method is proposed that ensures convergence to the solution minimizing the self-interaction error.

physics.chem-ph↗

arXiv2023

Orbital-optimized Density Functional Calculations of Molecular Rydberg Excited States with Real Space Grid Representation and Self-Interaction Correction

Density functional calculations of Rydberg excited states up to high energy are carried out for several molecules using an approach where the orbitals are variationally optimized by converging on saddle points on the electronic energy surface within a real space grid representation. Remarkably good agreement with experimental estimates of the excitation energy is obtained using the generalized gradient approximation (GGA) functional of Perdew, Burke and Ernzerhof (PBE) when Perdew-Zunger self-interaction correction is applied in combination with complex-valued orbitals. Even without the correction, the PBE functional gives quite good results despite the fact that corresponding Rydberg virtual orbitals have positive energy in the ground state calculation. Results obtained using the TPSS and r2SCAN meta-GGA functionals are also presented, but they do not provide a systematic improvement over the results from the uncorrected PBE functional. The grid representation combined with the projector augmented-wave approach gives a simpler and better representation of the diffuse Rydberg orbitals than a linear combination of atomic orbitals with commonly used basis sets, the latter leading to an overestimation of the excitation energy due to confinement of the excited states.

physics.chem-ph↗

arXiv2023

Improved Initialization of Optimal Path Calculations Using Sequential Traversal over the Image Dependent Pair Potential Surface

In reaction path optimization, such as the calculation of a minimum energy path (MEP) between given reactant and product configurations of atoms, it is advantageous to start with an initial guess where close proximity of atoms is avoided and bonds are not unnecessarily broken only to be reformed later. When the configurations of the atoms are described with Cartesian coordinates, a linear interpolation between the endpoints can be problematic, and a better option is provided by the so-called image dependent pair potential (IDPP) approach where interpolated pairwise distances are generated to form an objective function that can be used to generate an improved initial path. When started with a linear interpolation, this method can, however, still lead to unnecessary bond breaking in, for example, reactions where a molecular subgroup undergoes significant rotation. In the method presented here, this problem is addressed by constructing the path gradually, introducing images sequentially starting from the vicinity of the endpoints while the distance between images in the central region is larger. The distribution of images is controlled by systematically scaling the tightness of springs acting between the images until the desired number of images is obtained and they are evenly spaced. This procedure generates an initial path on the IDPP surface, a task that requires insignificant computational effort, as no evaluation of the energy of the system is needed. The calculation of the MEP, typically using electronic structure calculations, is then subsequently carried out in a way that makes efficient use of parallel computing with the nudged elastic band method. Several examples of reactions are given where the linear interpolation IDPP (LI-IDPP) method yields problematic paths with unnecessary bond breaking in some of the intermediate images, while the sequential IDPP (S-IDPP) method yields pat

physics.chem-ph↗

arXiv2023

Electronic excitations of the charged nitrogen-vacancy center in diamond obtained using time-independent variational density functional calculations

Elucidation of the mechanism for optical spin initialization of point defects in solids in the context of quantum applications requires an accurate description of the excited electronic states involved. While variational density functional calculations have been successful in describing the ground state of a great variety of systems, doubts have been expressed in the literature regarding the ability of such calculations to describe electronic excitations of point defects. A direct orbital optimization method is used here to perform time-independent, variational density functional calculations of a prototypical defect, the negatively charged nitrogen-vacancy center in diamond. The calculations include up to 511 atoms subject to periodic boundary conditions and the excited state calculations require similar computational effort as ground state calculations. Contrary to some previous reports, the use of local and semilocal density functionals gives the correct ordering of the low-lying triplet and singlet states, namely ${}^{3}A_2 < {}^{1}E < {}^{1}A_1 < {}^{3}E$. Furthermore, the more advanced meta generalized gradient approximation functionals give results that are in remarkably good agreement with high-level, many-body calculations as well as available experimental estimates, even for the excited singlet state which is often referred to as having multireference character. The lowering of the energy in the triplet excited state as the atom coordinates are optimized in accordance with analytical forces is also close to the experimental estimate and the resulting zero-phonon line triplet excitation energy is underestimated by only 0.15 eV. The approach used here is found to be a promising tool for studying electronic excitations of point defects in, for example, systems relevant for quantum technologies.

cond-mat.mtrl-sci↗

arXiv2023

A general-purpose machine learning Pt interatomic potential for an accurate description of bulk, surfaces and nanoparticles

A Gaussian approximation machine learning interatomic potential for platinum is presented. It has been trained on 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 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.

cond-mat.mtrl-sci↗

arXiv2023

On the challenge of obtaining an accurate solvation energy estimate in simulations of electrocatalysis

The effect of solvent on the free energy of reaction intermediates adsorbed on electrocatalyst surfaces can significantly change the thermochemical overpotential, but accurate calculations of this are challenging. Here, we present computational estimates of the solvation energy for reaction intermediates in oxygen reduction reaction (ORR) on a B-doped graphene (BG) model system where the overpotential is found to reduce by up to 0.6 V due to solvation. BG is experimentally reported to be an active ORR catalyst but recent computational estimates using state-of-the-art hybrid density functionals in the absence of solvation effects have indicated low activity. To test whether the inclusion of explicit solvation can bring the calculated activity estimates closer to the experimental reports, up to 4 layers of water molecules are included in the simulations reported here. The calculations are based on classical molecular dynamics and local minimization of energy using atomic forces evaluated from electron density functional theory. Data sets are obtained from regular and coarse-grained dynamics, as well as local minimization of structures resampled from dynamics simulations. The results differ greatly depending on the method used and the solvation energy estimates and are deemed untrustworthy. It is concluded that a significantly larger number of water molecules is required to obtain converged results for the solvation energy. As the present system includes up to 139 atoms, it already strains the limits of computational feasibility, so this points to the need for a hybrid simulation approach where efficient simulations of much larger number of solvent molecules is carried out using a lower level of theory while retaining the higher level of theory for the reacting molecules as well as their near neighbors and the catalyst.

physics.chem-ph↗

arXiv2023

Calculations of Excited Electronic States by Converging on Saddle Points Using Generalized Mode Following

Variational calculations of excited electronic states are carried out by finding saddle points on the surface that describes how the energy of the system varies as a function of the electronic degrees of freedom. This approach has several advantages over commonly used methods especially in the context of density functional calculations, as collapse to the ground state is avoided and yet, the orbitals are variationally optimized for the excited state. This optimization makes it possible to describe excitations with large charge transfer where calculations based on ground state orbitals are problematic, as in linear response time-dependent density functional theory. A generalized mode following method is presented where an $n^{\text{th}}$-order saddle point is found by inverting the components of the gradient in the direction of the eigenvectors of the $n$ lowest eigenvalues of the electronic Hessian matrix. This approach has the distinct advantage of following a chosen excited state through atomic configurations where the symmetry of the single determinant wave function is broken, as demonstrated in calculations of potential energy curves for nuclear motion in the ethylene and dihydrogen molecules. The method is implemented using a generalized Davidson algorithm and an exponential transformation for updating the orbitals within a generalized gradient approximation of the energy functional. Convergence is found to be more robust than for a direct optimization approach previously shown to outperform standard self-consistent field approaches, as illustrated here for charge transfer excitations in nitrobenzene and N-phenylpyrrole, involving calculations of $4^{\text{th}}$- and $6^{\text{th}}$-order saddle points, respectively. Finally, calculations of a diplatinum and silver complex are presented, illustrating the applicability of the method to excited state energy curves of large molecules.

physics.chem-ph↗