Browsing by Author "Fernández-Pendás, M."
Now showing items 1-7 of 7
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Adapting Hybrid Monte Carlo methods for solving complex problems in life and materials sciences
(2018-05-11)Efficient sampling is the key to success of molecular simulation of complex physical systems. Still, a unique recipe for achieving this goal is unavailable. Hybrid Monte Carlo (HMC) is a promising sampling tool offering a ... -
Adaptive multi-stage integrators for optimal energy conservation in molecular simulations
Fernández-Pendás, M.; Akhmatskaya, E.
; Sanz-Serna, J.M. (2016-10-01)
We introduce a new Adaptive Integration Approach (AIA) to be used in a wide range of molecular simulations. Given a simulation problem and a step size, the method automatically chooses the optimal scheme out of an available ... -
Adaptive Splitting Integrators for Enhancing Sampling Efficiency of Modified Hamiltonian Monte Carlo Methods in Molecular Simulation
Akhmatskaya, E.; Fernández-Pendás, M.; Radivojevic, T.; Sanz-Serna, J.M. (2017-10-24)
The modified Hamiltonian Monte Carlo (MHMC) methods, i.e., importance sampling methods that use modified Hamiltonians within a Hybrid Monte Carlo (HMC) framework, often outperform in sampling efficiency standard techniques ... -
Constant pressure hybrid Monte Carlo simulations in GROMACS
Fernández-Pendás, M.; Escribano, B.; Radivojevic, T.; Akhmatskaya, E. (2014-12-31)
Adaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPT-GSHMC, combines ... -
Enhancing sampling in atomistic simulations of solid state materials for batteries: a focus on olivine NaFePO$_4$
Escribano, B.; Lozano, A.; Radivojevic, T.; Fernández-Pendás, M.; Carrasco, J.; Akhmatskaya, E. (2017-03-07)
The study of ion transport in electrochemically active materials for energy storage systems requires simulations on quantum-, atomistic- and meso-scales. The methods accessing these scales not only have to be effective but ... -
Multi-stage splitting integrators for sampling with modified Hamiltonian Monte Carlo methods
Radivojevic, T.; Fernández-Pendás, M.; Sanz-Serna, J.M.; Akhmatskaya, E. (2018-07-17)
Modified Hamiltonian Monte Carlo (MHMC) methods combine the ideas behind two popular sampling approaches: Hamiltonian Monte Carlo (HMC) and importance sampling. As in the HMC case, the bulk of the computational cost of ... -
Synthesis of Monodisperse Spherical Nanocrystals
Cregan, V.; Bacsa, R.; Calvo Schwarzwälder, M.; Fernández-Pendás, M.; Florio, B.; Marquina, A.; Moyles, I.; Myers, T.; Ribera Ponsa, H.; Rusconi, S.; Serna, S. (2016-01-29)
Nanoparticles, small units of matter with dimensions in the range 1-100 nm, exhibit many advantageous size-dependent magnetic, electrical, chemical and optical prop- erties, which are not observed at the microscale or ...