i-PI: A Python interface for ab initio path integral molecular dynamics simulations

Recent developments in path integral methodology have signicantly reduced the computational expense of including quantum mechanical eects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming eort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the eort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to rst principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forceeld code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum eects in high pressure water.

[1]  Michele Parrinello,et al.  Nuclear quantum effects and hydrogen bond fluctuations in water , 2013, Proceedings of the National Academy of Sciences.

[2]  Joost VandeVondele,et al.  Auxiliary Density Matrix Methods for Hartree-Fock Exchange Calculations. , 2010, Journal of chemical theory and computation.

[3]  Mark E. Tuckerman,et al.  Reversible multiple time scale molecular dynamics , 1992 .

[4]  S. D. Hamann.  Electrolyte Solutions at High Pressure , 1974 .

[5]  S. Grimme,et al.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.

[6]  M. Parrinello,et al.  The nature of the hydrated excess proton in water , 1999, Nature.

[7]  Giovanni Bussi,et al.  Langevin equation with colored noise for constant-temperature molecular dynamics simulations. , 2008, Physical review letters.

[8]  Giovanni Bussi,et al.  Colored-Noise Thermostats à la Carte , 2010, 1204.0822.

[9]  Michele Ceriotti,et al.  Efficient first-principles calculation of the quantum kinetic energy and momentum distribution of nuclei. , 2012, Physical review letters.

[10]  D. Manolopoulos,et al.  An efficient ring polymer contraction scheme for imaginary time path integral simulations. , 2008, The Journal of chemical physics.

[11]  Thomas E. Markland,et al.  Competing quantum effects in the dynamics of a flexible water model. , 2009, The Journal of chemical physics.

[12]  E. Wang,et al.  Nature of proton transport in a water-filled carbon nanotube and in liquid water. , 2013, Physical chemistry chemical physics : PCCP.

[13]  Jianshu Cao,et al.  The formulation of quantum statistical mechanics based on the Feynman path centroid density. IV. Algorithms for centroid molecular dynamics , 1994 .

[14]  Michele Parrinello,et al.  The δ-thermostat: selective normal-modes excitation by colored-noise Langevin dynamics , 2010 .

[15]  Thomas F. Miller,et al.  Ring-polymer molecular dynamics: quantum effects in chemical dynamics from classical trajectories in an extended phase space. , 2013, Annual review of physical chemistry.

[16]  Joost VandeVondele,et al.  Isobaric-isothermal molecular dynamics simulations utilizing density functional theory: an assessment of the structure and density of water at near-ambient conditions. , 2009, The journal of physical chemistry. B.

[17]  M. Parrinello,et al.  AB INITIO PATH INTEGRAL MOLECULAR DYNAMICS : BASIC IDEAS , 1996 .

[18]  Michele Ceriotti,et al.  Efficient methods and practical guidelines for simulating isotope effects. , 2012, The Journal of chemical physics.

[19]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[20]  R. Feynman,et al.  Quantum Mechanics and Path Integrals , 1965 .

[21]  Michele Parrinello,et al.  Displaced path integral formulation for the momentum distribution of quantum particles. , 2010, Physical review letters.

[22]  David E. Manolopoulos,et al.  A refined ring polymer contraction scheme for systems with electrostatic interactions , 2008 .

[23]  D. Ceperley.  Path integrals in the theory of condensed helium , 1995 .

[24]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

[25]  M. Parrinello,et al.  Accurate sampling using Langevin dynamics. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[26]  Bambi Hu,et al.  Computation of the temperature dependence of the heat capacity of complex molecular systems using random color noise. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[27]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.

[28]  M. Parrinello,et al.  Study of an F center in molten KCl , 1984 .

[29]  William H. Miller,et al.  Quantum statistics and classical mechanics : Real time correlation functions from ring polymer molecular dynamics , 2002 .

[30]  Mark E Tuckerman,et al.  Proton transport in triflic acid hydrates studied via path integral car-parrinello molecular dynamics. , 2009, The journal of physical chemistry. B.

[31]  Michele Parrinello,et al.  Accelerating the convergence of path integral dynamics with a generalized Langevin equation. , 2011, The Journal of chemical physics.

[32]  William J. Nellis,et al.  Equation of state and electrical conductivity of water and ammonia shocked to the 100 GPa (1 Mbar) pressure range , 1982 .

[33]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[34]  Peter G. Wolynes,et al.  Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids , 1981 .

[35]  Giovanni Bussi,et al.  Nuclear quantum effects in solids using a colored-noise thermostat. , 2009, Physical review letters.

[36]  Mark E. Tuckerman,et al.  Molecular dynamics algorithms for path integrals at constant pressure , 1999 .

[37]  Michele Parrinello,et al.  Efficient stochastic thermostatting of path integral molecular dynamics. , 2010, The Journal of chemical physics.

[38]  Jean-Jacques Greffet,et al.  Quantum thermal bath for molecular dynamics simulation. , 2009, Physical review letters.

[39]  K. Burke.  Perspective on density functional theory. , 2012, The Journal of chemical physics.

[40]  M. Parrinello,et al.  Isothermal-isobaric molecular dynamics using stochastic velocity rescaling. , 2009, The Journal of chemical physics.

[41]  Takeshi Yamamoto,et al.  Path-integral virial estimator based on the scaling of fluctuation coordinates: application to quantum clusters with fourth-order propagators. , 2005, The Journal of chemical physics.

[42]  Gerbrand Ceder,et al.  Predicting crystal structure by merging data mining with quantum mechanics , 2006, Nature materials.

[43]  H. C. Andersen.  Molecular dynamics simulations at constant pressure and/or temperature , 1980 .

[44]  Joost VandeVondele,et al.  Robust Periodic Hartree-Fock Exchange for Large-Scale Simulations Using Gaussian Basis Sets. , 2009, Journal of chemical theory and computation.

[45]  Jianshu Cao,et al.  A new perspective on quantum time correlation functions , 1993 .

[46]  L. Fried,et al.  Dynamic ionization of water under extreme conditions. , 2005, Physical review letters.

[47]  Teter,et al.  Separable dual-space Gaussian pseudopotentials. , 1996, Physical review. B, Condensed matter.

[48]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[49]  F. Gygi,et al.  Dissociation of water under pressure. , 2001, Physical review letters.

[50]  Michele Parrinello,et al.  Efficient and general algorithms for path integral Car–Parrinello molecular dynamics , 1996 .