Andri Arnaldsson

Bio: Andri Arnaldsson is an academic researcher from University of Iceland. The author has contributed to research in topics: Saddle point & Global optimization. The author has an hindex of 10, co-authored 14 publications receiving 6695 citations. Previous affiliations of Andri Arnaldsson include University of Gothenburg & University of Washington.

Comparison of methods for finding saddle points without knowledge of the final states

Abstract: Within the harmonic approximation to transition state theory, the biggest challenge involved in finding the mechanism or rate of transitions is the location of the relevant saddle points on the multidimensional potential energy surface. The saddle point search is particularly challenging when the final state of the transition is not specified. In this article we report on a comparison of several methods for locating saddle points under these conditions and compare, in particular, the well-established rational function optimization (RFO) methods using either exact or approximate Hessians with the more recently proposed minimum mode following methods where only the minimum eigenvalue mode is found, either by the dimer or the Lanczos method. A test problem involving transitions in a seven-atom Pt island on a Pt(111) surface using a simple Morse pairwise potential function is used and the number of degrees of freedom varied by varying the number of movable atoms. In the full system, 175 atoms can move so 525 degrees of freedom need to be optimized to find the saddle points. For testing purposes, we have also restricted the number of movable atoms to 7 and 1. Our results indicate that if attempting to make a map of all relevant saddle points for a large system (as would be necessary when simulating the long time scale evolution of a thermal system) the minimum mode following methods are preferred. The minimum mode following methods are also more efficient when searching for the lowest saddle points in a large system, and if the force can be obtained cheaply. However, if only the lowest saddle points are sought and the calculation of the force is expensive but a good approximation for the Hessian at the starting position of the search can be obtained at low cost, then the RFO approaches employing an approximate Hessian represent the preferred choice. For small and medium sized systems where the force is expensive to calculate, the RFO approaches employing an approximate Hessian is also the more efficient, but when the force and Hessian can be obtained cheaply and only the lowest saddle points are sought the RFO approach using an exact Hessian is the better choice. These conclusions have been reached based on a comparison of the total computational effort needed to find the saddle points and the number of saddle points found for each of the methods. The RFO methods do not perform very well with respect to the latter aspect, but starting the searches further away from the initial minimum or using the hybrid RFO version presented here improves this behavior considerably in most cases.

Comparison of quantum dynamics and quantum transition state theory estimates of the H + CH4 reaction rate.

Abstract: Thermal rate constants are calculated for the H + CH(4) --> CH(3) + H(2) reaction employing the potential energy surface of Espinosa-Garcia (Espinosa-Garcia, J. J. Chem. Phys. 2002, 116, 10664). Two theoretical approaches are used. First, we employ the multiconfigurational time-dependent Hartree method combined with flux correlation functions. In this way rate constants in the range 225-400 K are obtained and compared with previous results using the same theoretical method but the potential energy surface of Wu et al. (Wu, T.; Werner, H.-J.; Manthe, U. Science 2004, 306, 2227). It is found that the Espinosa-Garcia surface results in larger rate constants. Second, a harmonic quantum transition state theory (HQTST) implementation of instanton theory is used to obtain rate constants in a temperature interval from 20 K up to the crossover temperature at 296 K. The HQTST estimates are larger than MCTDH ones by a factor of about three in the common temperature range. Comparison is also made with various tunneling corrections to transition state theory and quantum instanton theory.

Theoretical calculations of CH4 and H2 associative desorption from Ni(111): could subsurface hydrogen play an important role?

Abstract: The results of theoretical calculations of associative desorption of CH(4) and H(2) from the Ni(111) surface are presented. Both minimum-energy paths and classical dynamics trajectories were generated using density-functional theory to estimate the energy and atomic forces. In particular, the recombination of a subsurface H atom with adsorbed CH(3) (methyl) or H at the surface was studied. The calculations do not show any evidence for enhanced CH(4) formation as the H atom emerges from the subsurface site. In fact, there is no minimum-energy path for such a concerted process on the energy surface. Dynamical trajectories started at the transition state for the H-atom hop from subsurface to surface site also did not lead to direct formation of a methane molecule but rather led to the formation of a thermally excited H atom and CH(3) group bound to the surface. The formation (as well as rupture) of the H-H and C-H bonds only occurs on the exposed side of a surface Ni atom. The transition states are quite similar for the two molecules, except that in the case of the C-H bond, the underlying Ni atom rises out of the surface plane by 0.25 A. Classical dynamics trajectories started at the transition state for desorption of CH(4) show that 15% of the barrier energy, 0.8 eV, is taken up by Ni atom vibrations, while about 60% goes into translation and 20% into vibration of a desorbing CH(4) molecule. The most important vibrational modes, accounting for 90% of the vibrational energy, are the four high-frequency CH(4) stretches. By time reversibility of the classical trajectories, this means that translational energy is most effective for dissociative adsorption at low-energy characteristic of thermal excitations but energy in stretching modes is also important. Quantum-mechanical tunneling in CH(4) dissociative adsorption and associative desorption is estimated to be important below 200 K and is, therefore, not expected to play an important role under typical conditions. An unexpected mechanism for the rotation of the adsorbed methyl group was discovered and illustrated a strong three-center C-H-Ni contribution to the methyl-surface bonding.

Phd by thesis

Abstract: Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

A grid-based Bader analysis algorithm without lattice bias

Abstract: A computational method for partitioning a charge density grid into Bader volumes is presented which is efficient, robust, and scales linearly with the number of grid points. The partitioning algorithm follows the steepest ascent paths along the charge density gradient from grid point to grid point until a charge density maximum is reached. In this paper, we describe how accurate off-lattice ascent paths can be represented with respect to the grid points. This improvement maintains the efficient linear scaling of an earlier version of the algorithm, and eliminates a tendency for the Bader surfaces to be aligned along the grid directions. As the algorithm assigns grid points to charge density maxima, subsequent paths are terminated when they reach previously assigned grid points. It is this grid-based approach which gives the algorithm its efficiency, and allows for the analysis of the large grids generated from plane-wave-based density functional theory calculations.

Improved grid-based algorithm for Bader charge allocation.

Abstract: An improvement to the grid-based algorithm of Henkelman et al. for the calculation of Bader volumes is suggested, which more accurately calculates atomic properties as predicted by the theory of Atoms in Molecules. The CPU time required by the improved algorithm to perform the Bader analysis scales linearly with the number of interatomic surfaces in the system. The new algorithm corrects systematic deviations from the true Bader surface, calculated by the original method and also does not require explicit representation of the interatomic surfaces, resulting in a more robust method of partitioning charge density among atoms in the system. Applications of the method to some small systems are given and it is further demonstrated how the method can be used to define an energy per atom in ab initio calculations.

Monolayer honeycomb structures of group-IV elements and III-V binary compounds: First-principles calculations

Abstract: Using first-principles plane wave calculations, we investigate two dimensional honeycomb structure of Group IV elements and their binary compounds, as well as the compounds of Group III-V elements. Based on structure optimization and phonon mode calculations, we determine that 22 different honeycomb materials are stable and correspond to local minima on the Born-Oppenheimer surface. We also find that all the binary compounds containing one of the first row elements, B, C or N have planar stable structures. On the other hand, in the honeycomb structures of Si, Ge and other binary compounds the alternating atoms of hexagons are buckled, since the stability is maintained by puckering. For those honeycomb materials which were found stable, we calculated optimized structures, cohesive energies, phonon modes, electronic band structures, effective cation and anion charges, and some elastic constants. The band gaps calculated within Density Functional Theory using Local Density Approximation are corrected by GW0 method. Si and Ge in honeycomb structure are semimetal and have linear band crossing at the Fermi level which attributes massless Fermion character to charge carriers as in graphene. However, all binary compounds are found to be semiconductor with band gaps depending on the constituent atoms. We present a method to reveal elastic constants of 2D honeycomb structures from the strain energy and calculate the Poisson’s ratio as well as in-plane stiffness values. Preliminary results show that the nearly lattice matched heterostructures of these compounds can offer new alternatives for nanoscale electronic devices. Similar to those of the three-dimensional Group IV and Group III-V compound semiconductors, one deduces interesting correlations among the calculated properties of present honeycomb structures. PACS numbers: 73.22.-f, 61.48.De, 63.22.-m, 62.23.Kn

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg