Other affiliations: University of the Sciences, University of Milan, University of Florence ...read more
Bio: Michele Parrinello is an academic researcher from Istituto Italiano di Tecnologia. The author has contributed to research in topics: Metadynamics & Ab initio. The author has an hindex of 133, co-authored 637 publications receiving 94674 citations. Previous affiliations of Michele Parrinello include University of the Sciences & University of Milan.
Papers published on a yearly basis
TL;DR: In this paper, a new Lagrangian formulation is introduced to make molecular dynamics (MD) calculations on systems under the most general externally applied, conditions of stress, which is well suited to the study of structural transformations in solids under external stress and at finite temperature.
Abstract: A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in solids under external stress and at finite temperature. As an example of the use of this technique we show how a single crystal of Ni behaves under uniform uniaxial compressive and tensile loads. This work confirms some of the results of static (i.e., zero temperature) calculations reported in the literature. We also show that some results regarding the stress‐strain relation obtained by static calculations are invalid at finite temperature. We find that, under compressive loading, our model of Ni shows a bifurcation in its stress‐strain relation; this bifurcation provides a link in configuration space between cubic and hexagonal close packing. It is suggested that such a transformation could perhaps be observed experimentally under extreme conditions of shock.
TL;DR: In this paper, the authors present a new molecular dynamics algorithm for sampling the canonical distribution, where the velocities of all the particles are rescaled by a properly chosen random factor.
Abstract: The authors present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.
TL;DR: In this article, a unified scheme combining molecular dynamics and density-functional theory is presented, which makes possible the simulation of both covalently bonded and metallic systems and permits the application of density functional theory to much larger systems than previously feasible.
Abstract: We present a unified scheme that, by combining molecular dynamics and density-functional theory, profoundly extends the range of both concepts. Our approach extends molecular dynamics beyond the usual pair-potential approximation, thereby making possible the simulation of both covalently bonded and metallic systems. In addition it permits the application of density-functional theory to much larger systems than previously feasible. The new technique is demonstrated by the calculation of some static and dynamic properties of crystalline silicon within a self-consistent pseudopotential framework.
TL;DR: A powerful method for exploring the properties of the multidimensional free energy surfaces of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates is introduced.
Abstract: We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the minima in the FES, allowing the efficient exploration and accurate determination of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissociation of a NaCl molecule in water and in the study of the conformational changes of a dialanine in solution.
TL;DR: It is shown how derivatives of the GPW energy functional, namely ionic forces and the Kohn–Sham matrix, can be computed in a consistent way and the computational cost is scaling linearly with the system size, even for condensed phase systems of just a few tens of atoms.
Abstract: We present the Gaussian and plane waves (GPW) method and its implementation in Quickstep which is part of the freely available program package CP2K. The GPW method allows for accurate density functional calculations in gas and condensed phases and can be effectively used for molecular dynamics simulations. We show how derivatives of the GPW energy functional, namely ionic forces and the Kohn–Sham matrix, can be computed in a consistent way. The computational cost of computing the total energy and the Kohn–Sham matrix is scaling linearly with the system size, even for condensed phase systems of just a few tens of atoms. The efficiency of the method allows for the use of large Gaussian basis sets for systems up to 3000 atoms, and we illustrate the accuracy of the method for various basis sets in gas and condensed phases. Agreement with basis set free calculations for single molecules and plane wave based calculations in the condensed phase is excellent. Wave function optimisation with the orbital transformation technique leads to good parallel performance, and outperforms traditional diagonalisation methods. Energy conserving Born–Oppenheimer dynamics can be performed, and a highly efficient scheme is obtained using an extrapolation of the density matrix. We illustrate these findings with calculations using commodity PCs as well as supercomputers.
TL;DR: A detailed description and comparison of algorithms for performing ab-initio quantum-mechanical calculations using pseudopotentials and a plane-wave basis set is presented in this article. But this is not a comparison of our algorithm with the one presented in this paper.
Abstract: We present a detailed description and comparison of algorithms for performing ab-initio quantum-mechanical calculations using pseudopotentials and a plane-wave basis set. We will discuss: (a) partial occupancies within the framework of the linear tetrahedron method and the finite temperature density-functional theory, (b) iterative methods for the diagonalization of the Kohn-Sham Hamiltonian and a discussion of an efficient iterative method based on the ideas of Pulay's residual minimization, which is close to an order Natoms2 scaling even for relatively large systems, (c) efficient Broyden-like and Pulay-like mixing methods for the charge density including a new special ‘preconditioning’ optimized for a plane-wave basis set, (d) conjugate gradient methods for minimizing the electronic free energy with respect to all degrees of freedom simultaneously. We have implemented these algorithms within a powerful package called VAMP (Vienna ab-initio molecular-dynamics package). The program and the techniques have been used successfully for a large number of different systems (liquid and amorphous semiconductors, liquid simple and transition metals, metallic and semi-conducting surfaces, phonons in simple metals, transition metals and semiconductors) and turned out to be very reliable.
TL;DR: The revised DFT-D method is proposed as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.
Abstract: The method of dispersion correction as an add-on to standard Kohn-Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15%-40% compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C(6) coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10%) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.
01 May 1993
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.
TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Abstract: In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints The influence of coupling time constants on dynamical variables is evaluated A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath
TL;DR: A new density functional of the generalized gradient approximation (GGA) type for general chemistry applications termed B97‐D is proposed, based on Becke's power‐series ansatz from 1997, and is explicitly parameterized by including damped atom‐pairwise dispersion corrections of the form C6 · R−6.
Abstract: A new density functional (DF) of the generalized gradient approximation (GGA) type for general chemistry applications termed B97-D is proposed. It is based on Becke's power-series ansatz from 1997 and is explicitly parameterized by including damped atom-pairwise dispersion corrections of the form C(6) x R(-6). A general computational scheme for the parameters used in this correction has been established and parameters for elements up to xenon and a scaling factor for the dispersion part for several common density functionals (BLYP, PBE, TPSS, B3LYP) are reported. The new functional is tested in comparison with other GGAs and the B3LYP hybrid functional on standard thermochemical benchmark sets, for 40 noncovalently bound complexes, including large stacked aromatic molecules and group II element clusters, and for the computation of molecular geometries. Further cross-validation tests were performed for organometallic reactions and other difficult problems for standard functionals. In summary, it is found that B97-D belongs to one of the most accurate general purpose GGAs, reaching, for example for the G97/2 set of heat of formations, a mean absolute deviation of only 3.8 kcal mol(-1). The performance for noncovalently bound systems including many pure van der Waals complexes is exceptionally good, reaching on the average CCSD(T) accuracy. The basic strategy in the development to restrict the density functional description to shorter electron correlation lengths scales and to describe situations with medium to large interatomic distances by damped C(6) x R(-6) terms seems to be very successful, as demonstrated for some notoriously difficult reactions. As an example, for the isomerization of larger branched to linear alkanes, B97-D is the only DF available that yields the right sign for the energy difference. From a practical point of view, the new functional seems to be quite robust and it is thus suggested as an efficient and accurate quantum chemical method for large systems where dispersion forces are of general importance.