arXiv subjects

Venkat Kapil

Publications and source records attributed to Venkat Kapil.

46 records · Page 3Linked to original sources

arXiv2021

Uncertainty estimation for molecular dynamics and sampling

Machine learning models have emerged as a very effective strategy to sidestep time-consuming electronic-structure calculations, enabling accurate simulations of greater size, time scale and complexity. Given the interpolative nature of these models, the reliability of predictions depends on the position in phase space, and it is crucial to obtain an estimate of the error that derives from the finite number of reference structures included during the training of the model. When using a machine-learning potential to sample a finite-temperature ensemble, the uncertainty on individual configurations translates into an error on thermodynamic averages, and provides an indication for the loss of accuracy when the simulation enters a previously unexplored region. Here we discuss how uncertainty quantification can be used, together with a baseline energy model, or a more robust although less accurate interatomic potential, to obtain more resilient simulations and to support active-learning strategies. Furthermore, we introduce an on-the-fly reweighing scheme that makes it possible to estimate the uncertainty in the thermodynamic averages extracted from long trajectories. We present examples covering different types of structural and thermodynamic properties, and systems as diverse as water and liquid gallium.

physics.chem-ph↗

arXiv2019

Inexpensive modelling of quantum dynamics using path integral generalized Langevin equation thermostats

The properties of molecules and materials containing light nuclei are affected by their quantum mechanical nature. Modelling these quantum nuclear effects accurately requires computationally demanding path integral techniques. Considerable success has been achieved in reducing the cost of such simulations by using generalized Langevin dynamics to induce frequency-dependent fluctuations. Path integral generalized Langevin equation methods, however, have this far been limited to the study of static, thermodynamic properties due to the large perturbation to the system's dynamics induced by the aggressive thermostatting. Here we introduce a post-processing scheme, based on analytical estimates of the dynamical perturbation induced by the generalized Langevin dynamics, that makes it possible to recover meaningful time correlation properties from a thermostatted trajectory. We show that this approach yields spectroscopic observables for model and realistic systems which have an accuracy comparable to much more demanding approximate quantum dynamics techniques based on full path integral simulations.

physics.chem-ph↗

arXiv2019

An Assessment of Approximate Methods for Anharmonic Free Energies

Quantitative evaluations of the free energy of materials must take into account thermal and zero-point energy fluctuations. While these effects can easily be estimated within a harmonic approximation, corrections arising from the anharmonic nature of the interatomic potential are often crucial and require computationally costly path integral simulations. Consequently, different approximate frameworks for computing affordable estimates of the anharmonic free energies have been developed over the years. Understanding which of the approximations involved are justified for a given system is complicated by the lack of comparative benchmarks. To facilitate this choice we assess the accuracy and efficiency of some of the commonly used approximate methods -- the vibrational self-consistent field and self-consistent phonons -- by comparing the anharmonic correction to the Helmholtz free energy against reference path integral calculations. These benchmarks are performed for a diverse set of systems, ranging from simple quasi-harmonic solids to flexible molecular crystals with freely-rotating units. Our results suggest that for simple solids such as allotropes of carbon these methods yield results that are in excellent agreement with the reference calculations, at a considerably lower computational cost. For more complex molecular systems such as polymorphs of ice and paracetamol the methods do not consistently provide a reliable approximation of the anharmonic correction. Despite substantial cancellation of errors when comparing the stability of different phases, we do not observe a systematic improvement over the harmonic approximation even for relative free-energies. Our results suggest that efforts towards obtaining computationally-feasible anharmonic free-energies for flexible molecular solids should therefore be directed towards reducing the expense of path integral methods

cond-mat.mtrl-sci↗

arXiv2019

Modeling the structural and thermal properties of loaded metal-organic frameworks. An interplay of quantum and anharmonic fluctuations

Metal-organic frameworks show both fundamental interest and great promise for applications in adsorption-based technologies, such as the separation and storage of gases. The flexibility and complexity of the molecular scaffold poses a considerable challenge to atomistic modeling, especially when also considering the presence of guest molecules. We investigate the role played by quantum and anharmonic fluctuations in the archetypical case of MOF-5, comparing the material at various levels of methane loading. Accurate path integral simulations of such effects are made affordable by the introduction of an accelerated simulation scheme and the use of an optimized force field based on first-principles reference calculations. We find that the level of statistical treatment that is required for predictive modeling depends significantly on the property of interest. The thermal properties of the lattice are generally well described by a quantum harmonic treatment, with the adsorbate behaving in a classical but strongly anharmonic manner. The heat capacity of the loaded framework - which plays an important role in the characterization of the framework and in determining its stability to thermal fluctuations during adsorption/desorption cycles - requires, however, a full quantum and anharmonic treatment, either by path integral methods or by a simple but approximate scheme. We also present molecular-level insight into the nanoscopic interactions contributing to the material's properties and suggest design principles to optimize them

cond-mat.mtrl-sci↗

arXiv2018

i-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations

Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born-Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives.

physics.chem-ph↗

arXiv2018

The Anisotropy of the Proton Momentum Distribution in Water

One of the many peculiar properties of water is the pronounced deviation of the proton momentum distribution from Maxwell-Boltzmann behaviour. This deviation from the classical limit is a manifestation of the quantum mechanical nature of protons. Its extent, which can be probed directly by Deep Inelastic Neutron Scattering (DINS) experiments, gives important insight on the potential of mean force felt by H atoms. The determination of the full distribution of particle momenta, however, is a real tour de force for both experiments and theory, which has led to unresolved discrepancies between the two. In this Letter we present comprehensive, fully-converged momentum distributions for water at several thermodynamic state points, focusing on the components that cannot be described in terms of a scalar contribution to the quantum kinetic energy, and providing a benchmark that can serve as a reference for future simulations and experiments. In doing so, we also introduce a number of technical developments that simplify and accelerate greatly the calculation of momentum distributions by means of atomistic simulations.

physics.chem-ph↗

arXiv2017

Fine Tuning Classical and Quantum Molecular Dynamics using a Generalized Langevin Equation

Generalized Langevin Equation (GLE) thermostats have been used very effectively as a tool to manipulate and optimize the sampling of thermodynamic ensembles and the associated static properties. Here we show that a similar, exquisite level of control can be achieved for the dynamical properties computed from thermostatted trajectories. By developing quantitative measures of the disturbance induced by the GLE to the Hamiltonian dynamics of a harmonic oscillator, we show that these analytical results accurately predict the behavior of strongly anharmonic systems. We also show that it is possible to correct, to a significant extent, the effects of the GLE term onto the corresponding microcanonical dynamics, which puts on more solid grounds the use of non-equilibrium Langevin dynamics to approximate quantum nuclear effects and could help improve the prediction of dynamical quantities from techniques that use a Langevin term to stabilize dynamics. Finally we address the use of thermostats in the context of approximate path-integral-based models of quantum nuclear dynamics. We demonstrate that a custom-tailored GLE can alleviate some of the artifacts associated with these techniques, improving the quality of results for the modelling of vibrational dynamics of molecules, liquids and solids.

physics.chem-ph↗

arXiv2016

High Order Path Integrals Made Easy

The precise description of quantum nuclear fluctuations in atomistic modelling is possible by employing path integral techniques, which involve a considerable computational overhead due to the need of simulating multiple replicas of the system. Many approaches have been suggested to reduce the required number of replicas. Among these, high-order factorizations of the Boltzmann operator are particularly attractive for high-precision and low-temperature scenarios. Unfortunately, to date several technical challenges have prevented a widespread use of these approaches to study nuclear quantum effects in condensed-phase systems. Here we introduce an inexpensive molecular dynamics scheme that overcomes these limitations, thus making it possible to exploit the improved convergence of high-order path integrals without having to sacrifice the stability, convenience and flexibility of conventional second-order techniques. The capabilities of the method are demonstrated by simulations of liquid water and ice, as described by a neural-network potential fitted to dispersion-corrected hybrid density functional theory calculations.

physics.chem-ph↗

arXiv2016

Sampling Free Energy Surfaces as Slices by Combining Umbrella Sampling and Metadynamics

Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad and unbound free energy wells, the computational time to sample them becomes very large. To alleviate this problem, we combine the standard Umbrella Sampling (US) technique with MTD to sample orthogonal collective variables (CVs) in a simultaneous way. Within this scheme, we construct the equilibrium distribution of CVs from biased distributions obtained from independent MTD simulations with umbrella potentials. Reweighting is carried out by a procedure that combines US reweighting and Tiwary-Parrinello MTD reweighting within the Weighted Histogram Analysis Method (WHAM). The approach is ideal for a controlled sampling of a CV in a MTD simulation, making it computationally efficient in sampling flat, broad and unbound free energy surfaces. This technique also allows for a distributed sampling of a high-dimensional free energy surface, further increasing the computational efficiency in sampling. We demonstrate the application of this technique in sampling high-dimensional surface for various chemical reactions using ab initio and QM/MM hybrid molecular dynamics simulations. Further, in order to carry out MTD bias reweighting for computing forward reaction barriers in ab initio or QM/MM simulations, we propose a computationally affordable approach that does not require recrossing trajectories.

physics.comp-ph↗

arXiv2015

Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: using density functional theory to accelerate wavefunction methods

The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modelling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator, or generalized Langevin equation thermostats.

cond-mat.mtrl-sci↗