arXiv subjects

Rodolphe Vuilleumier

Publications and source records attributed to Rodolphe Vuilleumier.

31 records · Page 2Linked to original sources

arXiv2018

Fully quantum description of the Zundel ion: combining variational quantum Monte Carlo with path integral Langevin dynamics

We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo (QMC) solution of the electronic part with the path integral (PI) formalism for the quantum nuclear dynamics. On the one hand, the PI molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. On the other hand, variational QMC can provide Born-Oppenheimer (BO) potential energy surfaces with a precision comparable to the most advanced post Hartree-Fock approaches, and with a favorable scaling with the system size. To deal with the intrinsic QMC noise, we generalize the PI molecular dynamics using a Langevin thermostat correlated according to the covariance matrix of QMC nuclear forces. The variational parameters of the QMC wave function are evolved during the nuclear dynamics, such that the BO potential energy surface is unbiased. Statistical errors on the wave function parameters are reduced by resorting to bead grouping average, which we show to be accurate and well controlled. Our general algorithm relies on a Trotter breakup between the dynamics driven by ionic forces and the one set by the harmonic interbead couplings. The latter is exactly integrated even in presence of the Langevin thermostat, thanks to the mapping onto an Ornstein-Uhlenbeck process. This framework turns out to be very efficient also in the case of deterministic ionic forces. The new implementation is validated on the Zundel ion by direct comparison with standard PI Langevin dynamics calculations made with a coupled cluster potential energy surface. Nuclear quantum effects are confirmed to be dominant over thermal effects well beyond room temperature giving the excess proton an increased mobility by quantum tunneling.

physics.chem-ph↗

arXiv2017

Transient hydrodynamic finite size effects in simulations under periodic boundary conditions

We use Lattice-Boltzmann and analytical calculations to investigate transient hydrodynamic finite size effects induced by the use of periodic boundary conditions in simulations at the molecular, mesoscopic or continuum levels of description. We analyze the transient response to a local perturbation in the fluid and obtain via linear response theory the local velocity correlation function. This new approach is validated by comparing the finite size effects on the steady-state velocity with the known results for the diffusion coefficient. We next investigate the full time-dependence of the local velocity auto-correlation function. We find at long times a cross-over between the expected $t^{-3/2}$ hydrodynamic tail and an oscillatory exponential decay, and study the scaling with the system size of the cross-over time, exponential rate and amplitude, and oscillation frequency. We interpret these results from the analytic solution of the compressible Navier-Stokes equation for the slowest modes, which are set by the system size. The present work not only provides a comprehensive analysis of hydrodynamic finite size effects in bulk fluids, but also establishes the Lattice-Boltzmann method as a suitable tool to investigate such effects in general.

physics.comp-ph↗

arXiv2016

On the mass of atoms in molecules: Beyond the Born-Oppenheimer approximation

Describing the dynamics of nuclei in molecules requires a potential energy surface, which is traditionally provided by the Born-Oppenheimer or adiabatic approximation. However, we also need to assign masses to the nuclei. There, the Born-Oppenheimer picture does not account for the inertia of the electrons and only bare nuclear masses are considered. Nowadays, experimental accuracy challenges the theoretical predictions of rotational and vibrational spectra and requires to include the participation of electrons in the internal motion of the molecule. More than 80 years after the original work of Born and Oppenheimer, this issue still is not solved in general. Here, we present a theoretical and numerical framework to address this problem in a general and rigorous way. Starting from the exact factorization of the electron-nuclear wave function, we include electronic effects beyond the Born-Oppenheimer regime in a perturbative way via position-dependent corrections to the bare nuclear masses. This maintains an adiabatic-like point of view: the nuclear degrees of freedom feel the presence of the electrons via a single potential energy surface, whereas the inertia of electrons is accounted for and the total mass of the system is recovered. This constitutes a general framework for describing the mass acquired by slow degrees of freedom due to the inertia of light, bounded particles. We illustrate it with a model of proton transfer, where the light particle is the proton, and with corrections to the vibrational spectra of molecules. Inclusion of the light particle inertia allows to gain orders of magnitude in accuracy.

physics.chem-ph↗

arXiv2016

Molecular hydrodynamics from memory kernels

The memory kernel for a tagged particle in a fluid, computed from molecular dynamics simulations, decays algebraically as $t^{-3/2}$. We show how the hydrodynamic Basset-Boussinesq force naturally emerges from this long-time tail and generalize the concept of hydrodynamic added mass. This mass term is negative in the present case of a molecular solute, at odds with incompressible hydrodynamics predictions. We finally discuss the various contributions to the friction, the associated time scales and the cross-over between the molecular and hydrodynamic regimes upon increasing the solute radius.

physics.comp-ph↗

arXiv2016

Insight into the Li$_2$CO$_3$-K$_2$CO$_3$ eutectic mixture from classical molecular dynamics: thermodynamics, structure and dynamics

In this work, we use molecular dynamics simulations to study the thermodynamics, structure and dynamics of the Li$_2$CO$_3$-K$_2$CO$_3$ (62:38 mol%) eutectic mixture. We present a new classical non-polarizable force field for this molten salt mixture, optimized using experimental and first principles molecular dynamics simulations as reference data. This simple force field allows efficient molecular simulations of phenomena at long timescales. We use this optimized force field to describe the behavior of the eutectic mixture in the 900-1100 K temperature range, at pressures between 0 and 5 GPa. After studying the equation of state in these thermodynamic conditions, we present molecular insight into the structure and dynamics of the melt. In particular, we present an analysis of the temperature and pressure dependence of the eutectic mixture's self diffusion coefficients, viscosity and ionic conductivity.

physics.chem-ph↗

arXiv2015

Nuclear velocity perturbation theory for vibrational circular dichroism: An approach based on the exact factorization of the electron-nuclear wave function

The nuclear velocity perturbation theory (NVPT) for vibrational circular dichroism (VCD) is derived from the exact factorization of the electron-nuclear wave function. This new formalism offers an exact starting point to include correction terms to the Born-Oppenheimer (BO) form of the molecular wave function, similarly to the complete-adiabatic approximation. The corrections depend on a small parameter that, in a classical treatment of the nuclei, is identified as the nuclear velocity. Apart from proposing a rigorous basis for the NVPT, we show that the rotational strengths, related to the intensity of the VCD signal, contain a new contribution beyond-BO that can be evaluated with the NVPT and that only arises when the exact factorization approach is employed. Numerical results are presented for chiral and non-chiral systems to test the validity of the approach.

physics.chem-ph↗

arXiv2015

Maximum probability domains for the analysis of the microscopic structure of liquids

We introduce the concept of maximum probability domains (MPDs), developed in the context of the analysis of electronic densities, in the study of the microscopic spatial structures of liquids. The idea of locating a particle in a three dimensional region, by determining the domain where the probability of finding that, and only that, particle is maximum, gives an interesting characterization of the local structure of the liquid. The optimization procedure, required for the search of the domain of maximum probability, is carried out by the implementation of the level set method. Results for a couple of case studies are presented, to illustrate the structure of liquid water at ambient conditions and upon increasing pressure from the point of view of MPDs and to compare the information encoded in the solvation shells of sodium in water with, once again, that extracted from the MPDs.

physics.chem-ph↗

arXiv2014

Challenges in first-principles NPT molecular dynamics of soft porous crystals: A case study on MIL-53(Ga)

Soft porous crystals present a challenge to molecular dynamics simulations with flexible size and shape of the simulation cell (i.e., in the NPT ensemble), since their framework responds very sensitively to small external stimuli. Hence, all interactions have to be described very accurately in order to obtain correct equilibrium structures. Here, we report a methodological study on the nanoporous metal-organic framework MIL-53(Ga), which undergoes a large-amplitude transition between a narrow- and a large-pore phase upon a change in temperature. Since this system has not been investigated by density functional theory (DFT)-based NPT simulations so far, we carefully check the convergence of the stress tensor with respect to computational parameters. Furthermore, we demonstrate the importance of dispersion interactions and test two different ways of incorporating them into the DFT framework. As a result, we propose two computational schemes which describe accurately the narrow- and the large-pore phase of the material, respectively. These schemes can be used in future work on the delicate interplay between adsorption in the nanopores and structural flexibility of the host material.

cond-mat.mtrl-sci↗

arXiv2013

Molecular Density Functional Theory of Water

Three dimensional implementations of liquid state theories offer an efficient alternative to computer simulations for the atomic-level description of aqueous solutions in complex environments. In this context, we present a (classical) molecular density functional theory (MDFT) of water that is derived from first principles and is based on two classical density fields, a scalar one, the particle density, and a vectorial one, the multipolar polarization density. Its implementation requires as input the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the k-dependent longitudinal and transverse dielectric constants. It has to be complemented by a solute-solvent three-body term that reinforces tetrahedral order at short range. The approach is shown to provide the correct three-dimensional microscopic solvation profile around various molecular solutes, possibly possessing H-bonding sites, at a computer cost two-three orders of magnitude lower than with explicit simulations.

physics.chem-ph↗

arXiv2012

Solvation of complex surfaces via molecular density functional theory

We show that classical molecular density functional theory (MDFT), here in the homogeneous reference fluid approximation in which the functional is inferred from the properties of the bulk solvent, is a powerful new tool to study, at a fully molecular level, the solvation of complex surfaces and interfaces by polar solvents. This implicit solvent method allows for the determination of structural, orientational and energetic solvation properties that are on a par with all-atom molecular simulations performed for the same system, while reducing the computer time by two orders of magnitude. This is illustrated by the study of an atomistically-resolved clay surface composed of over a thousand atoms wetted by a molecular dipolar solvent. The high numerical efficiency of the method is exploited to carry a systematic analysis of the electrostatic and non-electrostatic components of the surface-solvent interaction within the popular CLAYFF force field. Solvent energetics and structure are found to depend weakly upon the atomic charges distribution of the clay surface, even for a rather polar solvent. We conclude on the consequences of such findings for force-field development.

physics.chem-ph↗

arXiv2012

Scalar fundamental measure theory for hard spheres in three dimensions. Application to hydrophobic solvation

Hard-sphere mixtures provide one a solvable reference system that can be used to improve the density functional theory of realistic molecular fluids. We show how the Kierlik-Rosinberg's scalar version of the fundamental measure density functional theory of hard spheres [Phys. Rev. A, {\bf 42}, 3382 (1990)], which presents computational advantages with respect to the original Rosenfeld's vectorial formulation or its extensions, can be implemented and minimized in three dimensions to describe fluid mixtures in complex environments. This implementation is used as a basis for defining a molecular density functional theory of water around molecular hydrophobic solutes of arbitrary shape.

physics.chem-ph↗

arXiv2012

A transferable ab-initio based force field for aqueous ions

We present a new polarizable force field for aqueous ions (Li+, Na+, K+, Rb+, Cs+, Mg2+, Ca2+, Sr2+ and Cl-) derived from condensed phase ab-initio calculations. We use Maximally Localized Wannier Functions together with a generalized force and dipole-matching procedure to determine the whole set of parameters. Experimental data is then used only for validation purposes and a good agreement is obtained for structural, dynamic and thermodynamic properties. The same procedure applied to crystalline phases allows to parametrize the interaction between cations and the chloride anion. Finally, we illustrate the good transferability of the force field to other thermodynamic conditions by investigating concentrated solutions.

physics.chem-ph↗

arXiv2012

Including many-body effects in models for ionic liquids

Realistic modeling of ionic systems necessitates taking explicitly account of many-body effects. In molecular dynamics simulations, it is possible to introduce explicitly these effects through the use of additional degrees of freedom. Here we present two models: The first one only includes dipole polarization effect, while the second also accounts for quadrupole polarization as well as the effects of compression and deformation of an ion by its immediate coordination environment. All the parameters involved in these models are extracted from first-principles density functional theory calculations. This step is routinely done through an extended force-matching procedure, which has proven to be very succesfull for molten oxides and molten fluorides. Recent developments based on the use of localized orbitals can be used to complement the force-matching procedure by allowing for the direct calculations of several parameters such as the individual polarizabilities.

cond-mat.stat-mech↗