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Jean-philip Piquemal - One of the best experts on this subject based on the ideXlab platform.
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Polarizable molecular dynamics in a polarizable continuum solvent.
Journal of Chemical Theory and Computation, 2015Co-Authors: Filippo Lipparini, Louis Lagardère, Christophe Raynaud, Benjamin Stamm, Eric Cancès, Benedetta Mennucci, Michael J. Schnieders, Pengyu Ren, Yvon Maday, Jean-philip PiquemalAbstract:We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-Term Energy Conservation can be achieved. This paper is focused on ...
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Polarizable Molecular Dynamics in a Polarizable Continuum Solvent
Journal of Chemical Theory and Computation, 2015Co-Authors: Filippo Lipparini, Louis Lagardère, Christophe Raynaud, Benjamin Stamm, Eric Cancès, Benedetta Mennucci, Michael J. Schnieders, Yvon Maday, Pengju Ren, Jean-philip PiquemalAbstract:We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-Term Energy Conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique.
Filippo Lipparini - One of the best experts on this subject based on the ideXlab platform.
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Polarizable molecular dynamics in a polarizable continuum solvent.
Journal of Chemical Theory and Computation, 2015Co-Authors: Filippo Lipparini, Louis Lagardère, Christophe Raynaud, Benjamin Stamm, Eric Cancès, Benedetta Mennucci, Michael J. Schnieders, Pengyu Ren, Yvon Maday, Jean-philip PiquemalAbstract:We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-Term Energy Conservation can be achieved. This paper is focused on ...
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Polarizable Molecular Dynamics in a Polarizable Continuum Solvent
Journal of Chemical Theory and Computation, 2015Co-Authors: Filippo Lipparini, Louis Lagardère, Christophe Raynaud, Benjamin Stamm, Eric Cancès, Benedetta Mennucci, Michael J. Schnieders, Yvon Maday, Pengju Ren, Jean-philip PiquemalAbstract:We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-Term Energy Conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique.
Jean-pierre Vilotte - One of the best experts on this subject based on the ideXlab platform.
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The spectral element method for elastic wave equations—application to 2-D and 3-D seismic problems
International Journal for Numerical Methods in Engineering, 1999Co-Authors: Dimitri Komatitsch, Jean-pierre Vilotte, Rossana Vai, José Manuel Castillo-covarrubias, Francisco J. Sánchez-sesmaAbstract:A spectral element method for the approximate solution of linear elastodynamic equations, set in a weak form, is shown to provide an efficient tool for simulating elastic wave propagation in realistic geological structures in two- and three-dimensional geometries. The computational domain is discretized into quadrangles, or hexahedra, defined with respect to a reference unit domain by an invertible local mapping. Inside each reference element, the numerical integration is based on the tensor-product of a Gauss–Lobatto–Legendre 1-D quadrature and the solution is expanded onto a discrete polynomial basis using Lagrange interpolants. As a result, the mass matrix is always diagonal, which drastically reduces the computational cost and allows an efficient parallel implementation. Absorbing boundary conditions are introduced in variational form to simulate unbounded physical domains. The time discretization is based on an Energy-momentum conserving scheme that can be put into a classical explicit-implicit predictor/multicorrector format. Long Term Energy Conservation and stability properties are illustrated as well as the efficiency of the absorbing conditions. The accuracy of the method is shown by comparing the spectral element results to numerical solutions of some classical two-dimensional problems obtained by other methods. The potentiality of the method is then illustrated by studying a simple three-dimensional model. Very accurate modelling of Rayleigh wave propagation and surface diffraction is obtained at a low computational cost. The method is shown to provide an efficient tool to study the diffraction of elastic waves and the large amplification of ground motion caused by three-dimensional surface topographies. Copyright © 1999 John Wiley & Sons, Ltd.
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the spectral element method an efficient tool to simulate the seismic response of 2d and 3d geological structures
Bulletin of the Seismological Society of America, 1998Co-Authors: Dimitri Komatitsch, Jean-pierre VilotteAbstract:We present the spectral element method to simulate elastic-wave propagation in realistic geological structures involving complieated free-surface topography and material interfaces for two- and three-dimensional geometries. The spectral element method introduced here is a high-order variational method for the spatial approximation of elastic-wave equations. The mass matrix is diagonal by construction in this method, which drastically reduces the computational cost and allows an efficient parallel implementation. Absorbing boundary conditions are introduced in variational form to simulate unbounded physical domains. The time discretization is based on an Energy-momentum conserving scheme that can be put into a classical explicit-implicit predictor/multi-corrector format. Long-Term Energy Conservation and stability properties are illustrated as well as the efficiency of the absorbing conditions. The associated Courant condition behaves as Δ tC < O ( nel−1/nd N −2), with nel the number of elements, nd the spatial dimension, and N the polynomial order. In practice, a spatial sampling of approximately 5 points per wavelength is found to be very accurate when working with a polynomial degree of N = 8. The accuracy of the method is shown by comparing the spectral element solution to analytical solutions of the classical two-dimensional (2D) problems of Lamb and Garvin. The flexibility of the method is then illustrated by studying more realistic 2D models involving realistic geometries and complex free-boundary conditions. Very accurate modeling of Rayleigh-wave propagation, surface diffraction, and Rayleigh-to-body-wave mode conversion associated with the free-surface curvature are obtained at low computational cost. The method is shown to provide an efficient tool to study the diffraction of elastic waves by three-dimensional (3D) surface topographies and the associated local effects on strong ground motion. Complex amplification patterns, both in space and time, are shown to occur even for a gentle hill topography. Extension to a heterogeneous hill structure is considered. The efficient implementation on parallel distributed memory architectures will allow to perform real-time visualization and interactive physical investigations of 3D amplification phenomena for seismic risk assessment.
Louis Lagardère - One of the best experts on this subject based on the ideXlab platform.
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Polarizable molecular dynamics in a polarizable continuum solvent.
Journal of Chemical Theory and Computation, 2015Co-Authors: Filippo Lipparini, Louis Lagardère, Christophe Raynaud, Benjamin Stamm, Eric Cancès, Benedetta Mennucci, Michael J. Schnieders, Pengyu Ren, Yvon Maday, Jean-philip PiquemalAbstract:We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-Term Energy Conservation can be achieved. This paper is focused on ...
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Polarizable Molecular Dynamics in a Polarizable Continuum Solvent
Journal of Chemical Theory and Computation, 2015Co-Authors: Filippo Lipparini, Louis Lagardère, Christophe Raynaud, Benjamin Stamm, Eric Cancès, Benedetta Mennucci, Michael J. Schnieders, Yvon Maday, Pengju Ren, Jean-philip PiquemalAbstract:We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-Term Energy Conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique.
Christophe Raynaud - One of the best experts on this subject based on the ideXlab platform.
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Polarizable molecular dynamics in a polarizable continuum solvent.
Journal of Chemical Theory and Computation, 2015Co-Authors: Filippo Lipparini, Louis Lagardère, Christophe Raynaud, Benjamin Stamm, Eric Cancès, Benedetta Mennucci, Michael J. Schnieders, Pengyu Ren, Yvon Maday, Jean-philip PiquemalAbstract:We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-Term Energy Conservation can be achieved. This paper is focused on ...
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Polarizable Molecular Dynamics in a Polarizable Continuum Solvent
Journal of Chemical Theory and Computation, 2015Co-Authors: Filippo Lipparini, Louis Lagardère, Christophe Raynaud, Benjamin Stamm, Eric Cancès, Benedetta Mennucci, Michael J. Schnieders, Yvon Maday, Pengju Ren, Jean-philip PiquemalAbstract:We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (ddCOSMO), which involves a rigorous coupling of the continuum with the polarizable force field achieved through a robust variational formulation and an effective strategy to solve the coupled equations. The coupling of ddCOSMO with nonvariational force fields, including AMOEBA, is also addressed. The MD simulations are feasible, for real-life systems, on standard cluster nodes; a scalable parallel implementation allows for further acceleration in the context of a newly developed module in Tinker, named Tinker-HP. NVE simulations are stable, and long-Term Energy Conservation can be achieved. This paper is focused on the methodological developments, the analysis of the algorithm, and the stability of the simulations; a proof-of-concept application is also presented to attest to the possibilities of this newly developed technique.