i-PI 2.0: A universal force engine for advanced molecular simulations

Kapil, Venkat; Rossi, Mariana; Maršálek, Ondřej; Petraglia, Riccardo; Litman, Yair; Spura, Thomas; Cheng, Bingqing; Cuzzocrea, Alice; Meißner, Robert H.; Wilkins, David M.; Helfrecht, Benjamin A.; Juda, Przemysław; Bienvenue, Sébastien P.; Fang, Wei; Keßler, Jan Henning; Poltavsky, Igor; Vandenbrande, Steven; Wieme, Jelle; Corminbœuf, Clémence; Kühne, Thomas D.; Manolopoulos, David E.; Markland, Thomas E.; Richardson, Jeremy O.; Tkatchenko, Alexandre; Tribello, Gareth A.; Speybroeck, Véronique Van; Ceriotti, Michele

doi:10.1016/j.cpc.2018.09.020

Cited by 314 publications

(263 citation statements)

References 71 publications

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“…The simple, robust post-processing approach we discussed here allows one to extract dynamical properties from trajectories thermostatted using PIGLET, and dramatically reduces the cost of obtaining quantum spectroscopic quantities. The implementation of the method is made available as a post-processing tool of the opensource simulation code i-PI [56]. The accuracy of this approach is comparable with that of other, more demanding approximate methods based on path integral simulations, as we demonstrate for a harmonic oscillator (for which the method is exact), a Morse oscillator and an empirical force field for codensed phases of water.…”

Section: ( )mentioning

confidence: 78%

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

Kapil

Wilkins

Lan

et al. 2020

The Journal of Chemical Physics

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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.Vibrational spectroscopic techniques -from conventional infrared (IR) and Raman to advanced femtosecond pump-probe [1, 2], sum-frequency generation, second harmonic scattering [3, 4], and multi-dimensional vibrational spectroscopy [5] -are a cornerstone of chemistry [6]. These techniques have a multitude of applications such as the characterization of functional groups in chemical systems [7], the determination of the atomistic mechanisms of phase transitions through insight into chemical environments [8], and identification of unique structural fingerprints of molecular crystals [9]. The use of atomistic simulations for the computation of spectroscopic properties facilitates the interpretation of these experiments and provides support to the characterization of novel materials.Even neglecting effects that go beyond the Born-Oppenheimer (BO) decoupling of electronic and nuclear degrees of freedom, accurate calculations of the vibrational spectra of materials require an explicit treatment of the quantum dynamics of the nuclear degrees of freedom [10] on the electronic ground state potential energy surface. Quantum dynamics is in principle exactly obtained from the solution of the time dependent Schrödinger equation for the nuclei, but this is only practical for systems containing a handful of degrees of freedom [11,12]. Condensed phase systems can be studied [13] either by an exact treatment of the quantum dynamics of a subset of the nuclear degrees of freedom [14], or through classical dynamics on the quantum free energy surface of the nuclei [15,16]. Among the methods in the latter class, several of the most popular ones are based on the imaginary time path integral framework -such as (thermostatted) ring polymer molecular dynamics [17,18] ((T)RPMD), centroid molec- * venkat.kapil@epfl.ch ular dynamics [19,20] (CMD) and the recently developed quasi-centroid molecular dynamics [21] (QCMD). These methods ignore real time cohe...

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Section: ( )mentioning

confidence: 78%

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

Kapil

Wilkins

Lan

et al. 2020

The Journal of Chemical Physics

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“…36 (along with the other simulation parameters in this reference), we propagated eight independent 100 ps TRPMD+GLE(C) trajectories at 300 and 150 K, using the i-PI package. 77 The resulting spectra in the stretch-region are shown in Fig. 8; (the lower-frequency parts of the spectrum, which are corrupted by the thermostat, are shown in Appendix D).…”

Section: Stretch Region Of the Qcmd Infrared Spectrummentioning

confidence: 99%

Path-integral dynamics of water using curvilinear centroids

Trenins

Willatt

Althorpe

2019

The Journal of Chemical Physics

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We develop a path-integral dynamics method for water that resembles centroid molecular dynamics (CMD), except that the centroids are averages of curvilinear, rather than cartesian, bead coordinates. The curvilinear coordinates are used explicitly only when computing the potential of mean force, the components of which are re-expressed in terms of cartesian 'quasi-centroids' (so-called because they are close to the cartesian centroids). Cartesian equations of motion are obtained by making small approximations to the quantum Boltzmann distribution. Simulations of the infrared spectra of various water models over 150-600 K show these approximations to be justified: for a two-dimensional OH-bond model, the quasi-centroid molecular dynamics (QCMD) spectra lie close to the exact quantum spectra, and almost on top of the Matsubara dynamics spectra; for gas-phase water, the QCMD spectra are close to the exact quantum spectra; for liquid water and ice (using the q-TIP4P/F surface), the QCMD spectra are close to the CMD spectra at 600 K, and line up with the results of thermostatted ring-polymer molecular dynamics and approximate quantum calculations at 300 and 150 K. The QCMD spectra show no sign of the CMD 'curvature problem' (of erroneous red shifts and broadening). In the liquid and ice simulations, the potential of mean force was evaluated onthe-fly by generalising an adiabatic CMD algorithm to curvilinear coordinates; the full limit of adiabatic separation needed to be taken, which made the QCMD calculations 8 times more expensive than partially adiabatic CMD at 300 K, and 32 times at 150 K (and the intensities may still not be converged at this temperature). The QCMD method is probably generalisable to many other systems, provided collective bead-coordinates can be identified that yield compact mean-field ring-polymer distributions.

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“…MD simulations are carried out using a combination of the i-Pi and LAMMPS software packages [42][43][44][45]. At each time step LAMMPS is used to evaluate the forces on the nuclei using an empirical potential and i-PI performs the time integration and thermostatting.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

Efficient and Versatile Model for Vibrational STEM-EELS

Zeiger

Rusz

2020

Phys. Rev. Lett.

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We introduce a novel method for the simulation of the impact scattering in vibrational scanning transmission electron microscopy electron energy loss spectroscopy (STEM-EELS) simulations. The phonon-loss process is modeled by a combination of molecular dynamics and elastic multislice calculations within a modified frozen phonon approximation. The key idea is thereby to use a so-called δ-thermostat in the classical molecular dynamics simulation to generate frequency dependent configurations of the vibrating specimen's atomic structure. The method includes correlated motion of atoms and provides vibrational spectrum images at the cost comparable to standard frozen phonon calculations. We demonstrate good agreement of our method with simulations and experiments for a 15 nm flake of hexagonal boron-nitride (hBN).Excellent spatial resolution is the highlight of the transmission electron microscope [1-6], allowing atomically resolved elemental mapping and chemistry. Recent instrumental developments have improved the energy resolution of electron energy loss spectroscopy down to 4.2 meV [7,8]. This unique combination of high spatial and energy resolution opened doors to unprecedented experiments such as temperature measurement at the nanoscale [9, 10], identification and mapping of isotopically labeled molecules [11], position-and momentum-resolved mapping of phonon modes [12,13], mapping of bulk and surface modes of nanocubes [14], or investigations of the nature of polariton modes in van der Waals crystals [15].Inelastic electron scattering on atomic vibrations in a polar material consists of two major contributions, namely, impact scattering and dipolar scattering [16,17]. The latter stems from a long ranged interaction between the beam electron and an oscillating dipole moment generated by the atomic vibrations. It can be used to perform damage-free vibrational spectroscopy in an aloof beam geometry [18,19]. High-angle impact scattering on the other hand is quite localized scattering on the atomic potential and allows for high resolution imaging and spectroscopy [17,[20][21][22].From a theoretical point of view, there is a limited number of approaches one can follow to simulate vibrational spectroscopy and imaging. Dwyer presents a treatment of both single impact and single dipolar scattering including a detailed phonon dispersion from a density functional theory calculation in a multislice scheme [23]. Forbes et al. introduced a quantum excitation of phonons model, which allows for the inclusion of thermal diffuse scattering into multislice image simulations [24]. The thermal vibrations are modeled within the Einstein model for quick image calculations, neglecting correlations in atomic movements and dispersion effects. Such an approach is not able to simulate vibrational spectra but in principle one could use different models of atomic vibrations to generate the necessary configurations. In a more recent work, Forbes et al. described a method to model the vibrational sector of the electron energy loss spectrum [25...

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i-PI 2.0: A universal force engine for advanced molecular simulations

Cited by 314 publications

References 71 publications

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

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

Path-integral dynamics of water using curvilinear centroids

Efficient and Versatile Model for Vibrational STEM-EELS

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