Showing papers by "Davide Donadio published in 2008"

Canonical sampling through velocity rescaling

Abstract: The authors present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.

Canonical sampling through velocity-rescaling

Abstract: We present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. We illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent on the thermostat parameter also with regard to the dynamic properties.

Metadynamics Simulations of the High-Pressure Phases of Silicon Employing a High-Dimensional Neural Network Potential

Abstract: We study in a systematic way the complex sequence of the high-pressure phases of silicon obtained upon compression by combining an accurate high-dimensional neural network representation of the density-functional theory potential-energy surface with the metadynamics scheme. Starting from the thermodynamically stable diamond structure at ambient conditions we are able to identify all structural phase transitions up to the highest-pressure fcc phase at about 100 GPa. The results are in excellent agreement with experiment. The method developed promises to be of great value in the study of inorganic solids, including those having metallic phases.

Pressure‐induced phase transitions in silicon studied by neural network‐based metadynamics simulations

Abstract: We present a combination of the metadynamics method for the investigation of pressure-induced phase transitions in solids with a neural network representation of high-dimensional density-functional theory (DFT) potential-energy surfaces. In a recent illustration of the method for the complex high-pressure phase diagram of silicon [Behler et al., Phys. Rev. Lett. 100, 185501 (2008)] we have shown that the full sequence of phases can be reconstructed by a series of subsequent simulations. In the present paper we give a detailed account of the underlying methodology and discuss the scope and limitations of the approach, which promises to be a valuable tool for the investigation of a variety of inorganic materials. The method is several orders of magnitude faster than a direct coupling of metadynamics with electronic structure calculations, while the accuracy is essentially maintained, thus providing access to extended simulations of large systems. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

DFT research on the dehydroxylation reaction of pyrophyllite 1. First-principle molecular dynamics simulations.

Abstract: The dehydroxylation of pyrophyllite involves the reaction of OH groups and elimination of water molecules through two possible mechanisms, one involving the bridging hydroxyl groups of an octahedral Al (3+) pair and the other two hydroxyl groups reacting across the dioctahedral vacancy. First-principles molecular dynamics simulations at the density functional theory level are used together with the metadynamics algorithm to explore the free-energy surface (FES) of the initial step of the dehydroxylation. We observe that the two possible dehydroxylation mechanisms yield similar activation energies at 0 K, but at high temperatures, the cross mechanism has lower free energy than that of the on-site one. The dehydroxylation process produces different semidehydroxylated intermediates that should be taken into account. The role of the temperature in favoring a dehydroxylation nonconcerted chain mechanism over another is here elucidated, and a novel competitive mechanism, which is assisted by the structural apical oxygens in the high-temperature regime, is proposed.

Influence of Temperature and Anisotropic Pressure on the Phase Transitions in α-Cristobalite

Abstract: The role of temperature and anisotropy of the applied load in the pressure--induced transformations of $\ensuremath{\alpha}$-cristobalite is investigated by means of first principles molecular dynamics combined with the metadynamics algorithm for the study of solid-solid phase transitions. We reproduce the transition to $\ensuremath{\alpha}\mathrm{\text{\ensuremath{-}}}{\mathrm{PbO}}_{2}$ as found in experiments and we observe that the transition paths are qualitatively different and yield different products when a nonhydrostatic load is applied, giving rise to a new class of metastable structures with mixed tetrahedral and octahedral coordination.

DFT Research on the Dehydroxylation Reaction of Pyrophyllite 2. Characterization of Reactants, Intermediates, And Transition States along the Reaction Path

Abstract: We delineate the dehydroxylation reaction of pyrophyllite in detail by localizing the complete reaction path on the free energy surface obtained previously by Car-Parrinello molecular dynamics and the implemented metadynamics algorithm ( Molina-Montes et al. J. Phys. Chem. B 2008, 112, 7051 ). All intermediates were identified, and a transition state search was also undertaken with the PRFO algorithm. The characterization of this reaction and the atomic rearrangement in the intermediates and products at quantum mechanical level were performed for the two reaction paths found previously: (i) direct dehydroxylation through the octahedral hole (cross mechanism) or between contiguous hydroxyl groups (on-site mechanism) and (ii) two-step dehydroxylation assisted by apical oxygens for each of the two steps. New intermediates were found and determined structurally. The structural variations found for all intermediates and transition states are in agreement with experimental results. The formation of these structures indicates that the dehydroxylation process is much more complex than a first-order reaction and can explain the wide range of temperatures for completing the reaction, and these results can be extrapolated to the dehydroxylation of other dioctahedral 2:1 phyllosilicates.

Simulation of the grafting of organosilanes at the surface of dry amorphous silica

Abstract: We have performed first principles metadynamics simulations of the grafting process of tetraethoxysilane (TEOS) at two surface sites of dry amorphous silica: the two-membered silicon ring and the isolated silanol. The ab initio activation energies for the grafting reaction are 0.2 eV and 1.4 eV, at the 2M and SiOH sites, respectively. The simulations support the experimental evidence based on IR vibrational spectroscopy that the ring is more reactive than the surface SiOH group for the grating of organosilanes.