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.

Fast parallel algorithms for short-range molecular dynamics

SUNDIALS is a suite of advanced computational codes for solving large-scale problems that can be modeled as a system of nonlinear algebraic equations, or as initial-value problems in ordinary differential or differential-algebraic equations. The basic versions of these codes are called KINSOL, CVODE, and IDA, respectively. The codes are written in ANSI standard C and are suitable for either serial or parallel machine environments. Common and notable features of these codes include inexact Newton-Krylov methods for solving large-scale nonlinear systems; linear multistep methods for time-dependent problems; a highly modular structure to allow incorporation of different preconditioning and/or linear solver methods; and clear interfaces allowing for users to provide their own data structures underneath the solvers. We describe the current capabilities of the codes, along with some of the algorithms and heuristics used to achieve efficiency and robustness. We also describe how the codes stem from previous and widely used Fortran 77 solvers, and how the codes have been augmented with forward and adjoint methods for carrying out first-order sensitivity analysis with respect to model parameters or initial conditions.

SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers

We present CasADi, an open-source software framework for numerical optimization. CasADi is a general-purpose tool that can be used to model and solve optimization problems with a large degree of flexibility, larger than what is associated with popular algebraic modeling languages such as AMPL, GAMS, JuMP or Pyomo. Of special interest are problems constrained by differential equations, i.e. optimal control problems. CasADi is written in self-contained C++, but is most conveniently used via full-featured interfaces to Python, MATLAB or Octave. Since its inception in late 2009, it has been used successfully for academic teaching as well as in applications from multiple fields, including process control, robotics and aerospace. This article gives an up-to-date and accessible introduction to the CasADi framework, which has undergone numerous design improvements over the last 7 years.

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CasADi: a software framework for nonlinear optimization and optimal control

Initial-value ordinary differential equation solution via variable order Adams method (SIVA/DIVA) package is collection of subroutines for solution of nonstiff ordinary differential equations. There are versions for single-precision and double-precision arithmetic. Requires fewer evaluations of derivatives than other variable-order Adams predictor/ corrector methods. Option for direct integration of second-order equations makes integration of trajectory problems significantly more efficient. Written in FORTRAN 77.

Solving Ordinary Differential Equations

In recent years, the SUite of Nonlinear and DIfferential/ALgebraic equation Solvers (SUNDIALS) has been redesigned to better enable the use of application-specific and third-party algebraic solvers and data structures. Throughout this work, we have adhered to specific guiding principles that minimized the impact to current users while providing maximum flexibility for later evolution of solvers and data structures. The redesign was done through creation of new classes for linear and nonlinear solvers, enhancements to the vector class, and the creation of modern Fortran interfaces that leverage interoperability features of the Fortran 2003 standard. The vast majority of this work has been performed "behind-the-scenes," with minimal changes to the user interface and no reduction in solver capabilities or performance. However, these changes now allow advanced users to create highly customized solvers that exploit their problem structure, enabling SUNDIALS use on extreme-scale, heterogeneous computational architectures.

Enabling New Flexibility in the SUNDIALS Suite of Nonlinear and Differential/Algebraic Equation Solvers.

An adjoint sensitivity method is presented for parameter-dependent differential-algebraic equation systems (DAEs). The adjoint system is derived, along with conditions for its consistent initialization, for DAEs of index up to two (Hessenberg). For stable linear DAEs, stability of the adjoint system (for semi-explicit DAEs) or of an augmented adjoint system (for fully implicit DAEs) is shown. In addition, it is shown for these systems that numerical stability is maintained for the adjoint system or for the augmented adjoint system.

/pdf/adjoint-sensitivity-analysis-for-differential-algebraic-9h85fu0zuy.pdf

Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and Its Numerical Solution

CVODES, which is part of the SUNDIALS software suite, is a stiff and nonstiff ordinary differential equation initial value problem solver with sensitivity analysis capabilities. CVODES is written in a data-independent manner, with a highly modular structure to allow incorporation of different preconditioning and/or linear solver methods. It shares with the other SUNDIALS solvers several common modules, most notably the generic kernel of vector operations and a set of generic linear solvers and preconditioners. CVODES solves the IVP by one of two methods — backward differentiation formula or Adams-Moulton — both implemented in a variable-step, variable-order form. The forward sensitivity module in CVODES implements the simultaneous corrector method, as well as two flavors of staggered corrector methods. Its adjoint sensitivity module provides a combination of checkpointing and cubic Hermite interpolation for the efficient generation of the forward solution during the adjoint system integration. We describe the current capabilities of CVODES, its design principles, and its user interface, and provide an example problem to illustrate the performance of CVODES.Copyright © 2005 by ASME

CVODES: The Sensitivity-Enabled ODE Solver in SUNDIALS

We provide an overview of a multi-physics dynamics engine called Chrono. Its forte is the handling of complex and large dynamic systems containing millions of rigid bodies that interact through frictional contact. Chrono has been recently augmented to support the modeling of fluid-solid interaction (FSI) problems and linear and nonlinear finite element analysis (FEA). We discuss Chrono’s software layout/design and outline some of the modeling and numerical solution techniques at the cornerstone of this dynamics engine. We briefly report on some validation studies that gauge the predictive attribute of the software solution. Chrono is released as open source under a permissive BSD3 license and available for download on GitHub.

Chrono: An Open Source Multi-physics Dynamics Engine

https://isiarticles.com/bundles/Article/pre/pdf/25858.pdf

Radu Serban

Papers

SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers

Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and Its Numerical Solution

CVODES: The Sensitivity-Enabled ODE Solver in SUNDIALS

Chrono: An Open Source Multi-physics Dynamics Engine

Sensitivity analysis of differential-algebraic equations and partial differential equations