A Hybrid Parallelizable Algorithm for Computer Simulation of Rigid Body Molecular Dynamics

2007 ◽  
Author(s):  
Shanzhong Duan
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Parallel Computing ◽  
Rigid Body ◽  
Computing System ◽  
Rigid Body Dynamics ◽  
Constraint Forces ◽  
Explicit Determination ◽  
Motion Behavior

Molecular dynamics is effective for a nano-scale phenomenon analysis. This paper presents a hybrid parallelizable algorithm for the computer simulation of the motion behavior of molecular chain and open-tree structure on parallel computing system. The algorithm is developed from an approach of rigid body dynamics, in which interbody constraints are exposed so that a system of largely independent multibody subchains is formed. The increased parallelism is obtainable through bringing interbody constraints to evidence and the explicit determination of the associated constraint forces combined with a sequential O(n) procedure. Each subchain then is assigned to a processor for parallel computing. The algorithm offers a sequential O(n) performance if there is only one processor available. The algorithm has O(log2n) computational efficiency if there are as many processors available as number for molecular bodies. For most common scenario, the algorithm will give a computational complexity between O(n) and O(log2n) if number of available processor is less than number of molecular bodies.

A Hybrid Highly Parallelizable Algorithm for the Dynamics of Rigid Body Chain Systems

1999 ◽  
Author(s):  
Shanzhong Duan ◽  
Kurt S. Anderson
Keyword(s):  
Rigid Body ◽  
Degrees Of Freedom ◽  
High Efficiency ◽  
Equations Of Motion ◽  
Constraint Forces ◽  
Dynamics Of Rigid Body ◽  
A Chain ◽  
Explicit Determination ◽  
Order Algorithm

Abstract The paper presents a new hybrid parallelizable low order algorithm for modeling the dynamic behavior of multi-rigid-body chain systems. The method is based on cutting certain system interbody joints so that largely independent multibody subchain systems are formed. These subchains interact with one another through associated unknown constraint forces f¯c at the cut joints. The increased parallelism is obtainable through cutting the joints and the explicit determination of associated constraint loads combined with a sequential O(n) procedure. In other words, sequential O(n) procedures are performed to form and solve equations of motion within subchains and parallel strategies are used to form and solve constraint equations between subchains in parallel. The algorithm can easily accommodate the available number of processors while maintaining high efficiency. An O[(n+m)Np+m(1+γ)Np+mγlog2Np](0<γ<1) performance will be achieved with Np processors for a chain system with n degrees of freedom and m constraints due to cutting of interbody joints.

scholarly journals A variational approach to nucleation simulation

2016 ◽  
Vol 195 ◽  
pp. 557-568 ◽  
Author(s):  
Pablo M. Piaggi ◽  
Omar Valsson ◽  
Michele Parrinello
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Free Energy ◽  
Variational Approach ◽  
Sampling Method ◽  
Enhanced Sampling ◽  
Technical Problems ◽  
Lennard Jones ◽  
Dynamics Simulations

We study by computer simulation the nucleation of a supersaturated Lennard-Jones vapor into the liquid phase. The large free energy barriers to transition make the time scale of this process impossible to study by ordinary molecular dynamics simulations. Therefore we use a recently developed enhanced sampling method [Valsson and Parrinello, Phys. Rev. Lett.113, 090601 (2014)] based on the variational determination of a bias potential. We differ from previous applications of this method in that the bias is constructed on the basis of the physical model provided by the classical theory of nucleation. We examine the technical problems associated with this approach. Our results are very satisfactory and will pave the way for calculating the nucleation rates in many systems.

On the topological compatibility of parallel tasks and computing systems

2021 ◽  
Author(s):  
A. F. Zadorozhny ◽  
V. A. Melent’ev
Keyword(s):  
Parallel Computing ◽  
Comparative Analysis ◽  
Computing System ◽  
Topological Model ◽  
Present Contribution ◽  
Computing Systems ◽  
Parallel Tasks ◽  
Different Types ◽  
Types Of Information

The aspects of topological compatibility of parallel computing systems and tasks are investigated in the present contribution. Based on the original topological model of parallel computations and on the unconventional graph description by its projections, the introduction of appropriate indexes is proposed and elucidated. On the example of hypercubic computing system (CS) and tasks with ring and star information topologies, we demonstrate the determination of indexes and their use in a comparative analysis of the applicability of interconnect with a given topology to solve the tasks with the same and different types of information topologies.

Rigid Body Dynamics, Constraints, and Inverses

2005 ◽  
Vol 74 (1) ◽  
pp. 47-56 ◽  
Author(s):  
Hooshang Hemami ◽  
Bostwick F. Wyman
Keyword(s):  
Rigid Body ◽  
State Space ◽  
Tracking Error ◽  
Feedback System ◽  
Rigid Body Dynamics ◽  
The Body ◽  
Contact Forces ◽  
Constraint Forces ◽  
Inverse Systems ◽  
Body Dynamics

Rigid body dynamics are traditionally formulated by Lagrangian or Newton-Euler methods. A particular state space form using Euler angles and angular velocities expressed in the body coordinate system is employed here to address constrained rigid body dynamics. We study gliding and rolling, and we develop inverse systems for estimation of internal and contact forces of constraint. A primitive approximation of biped locomotion serves as a motivation for this work. A class of constraints is formulated in this state space. Rolling and gliding are common in contact sports, in interaction of humans and robots with their environment where one surface makes contact with another surface, and at skeletal joints in living systems. This formulation of constraints is important for control purposes. The estimation of applied and constraint forces and torques at the joints of natural and robotic systems is a challenge. Direct and indirect measurement methods involving a combination of kinematic data and computation are discussed. The basic methodology is developed for one single rigid body for simplicity, brevity, and precision. Computer simulations are presented to demonstrate the feasibility and effectiveness of the approaches presented. The methodology can be applied to a multilink model of bipedal systems where natural and/or artificial connectors and actuators are modeled. Estimation of the forces is accomplished by the inverse of the nonlinear plant designed by using a robust high gain feedback system. The inverse is shown to be stable, and bounds on the tracking error are developed. Lyapunov stability methods are used to establish global stability of the inverse system.

scholarly journals Rotation of Lipids in Membranes: Molecular Dynamics Simulation, 31P Spin-Lattice Relaxation, and Rigid-Body Dynamics

2008 ◽  
Vol 94 (8) ◽  
pp. 3074-3083 ◽  
Author(s):  
Jeffery B. Klauda ◽  
Mary F. Roberts ◽  
Alfred G. Redfield ◽  
Bernard R. Brooks ◽  
Richard W. Pastor
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Rigid Body ◽  
Lattice Relaxation ◽  
Rigid Body Dynamics ◽  
Dynamics Simulation ◽  
Spin Lattice Relaxation ◽  
Spin Lattice ◽  
Body Dynamics

PARALLEL COMPUTING AT CRS4

1993 ◽  
Vol 04 (06) ◽  
pp. 1315-1321
Author(s):  
ALAN LOUIS SCHEININE
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Parallel Computing ◽  
Distributed Processing ◽  
High Energy ◽  
Seismic Migration ◽  
Distributed Processes ◽  
Real Time Visualization ◽  
Parallel Molecular Dynamics ◽  
High Energy Particles

An overview is given of parallel computing work being done at CRS4 (Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna). Parallel computation projects include: parallelization of a simulation of the interaction of high energy particles with matter (GEANT), domain decomposition for numerical solution of partial differential equations, seismic migration for oil prospecting, finite-element structural analysis, parallel molecular dynamics, a C++ library for distributed processing of specific functions, and real-time visualization of a computer simulation that runs as distributed processes.

scholarly journals A Simple Treatment of Constraint Forces and Constraint Moments in the Dynamics of Rigid Bodies

2014 ◽  
Vol 67 (1) ◽  
Author(s):  
Oliver M. O'Reilly ◽  
Arun R. Srinivasa
Keyword(s):  
Rigid Body ◽  
Classical Mechanics ◽  
Rigid Bodies ◽  
Rigid Body Dynamics ◽  
Constraint Forces ◽  
Simple Treatment ◽  
Body Dynamics ◽  
Expository Article

In this expository article, a simple concise treatment of Lagrange's prescription for constraint forces and constraint moments in the dynamics of rigid bodies is presented. The treatment is suited to both Newton–Euler and Lagrangian treatments of rigid body dynamics and is illuminated with a range of examples from classical mechanics and orthopedic biomechanics.

Determination of Interphase Thickness and Mechanical Properties of Effective Nanofillers in Polymer Nanocomposites by Molecular Dynamic Simulation

2010 ◽  
Vol 654-656 ◽  
pp. 1654-1657 ◽  
Author(s):  
Wen Xu ◽  
Qing Hua Zeng ◽  
Ai Bing Yu ◽  
Donald R. Paul
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Computer Simulation ◽  
Polymer Nanocomposites ◽  
Polymer Materials ◽  
Reinforced Composites ◽  
Physical Size ◽  
And Performance ◽  
Dynamics Simulations

The properties of interphase in polymer composites are often different from those of bulk polymer matrix, which may include chemical, physical, microstructural, and mechanical properties. The nature of interphase is critical to the overall properties and performance of polymer materials, in particular in nanofiller reinforced composites. Experimental efforts have been made to determine the effective interphase thickness and its properties, for example, by nanoindentation and nanoscratch techniques. Yet, it is very difficult to quantify the interphase and its properties because of its nanoscale nature and the unclear boundary. In this regard, computer simulation, e.g., molecular dynamics, provides an effective tool to characterize such interphase and the properties. In this work, molecular dynamics simulations are applied to quantify the interphase thickness in clay-based polymer nanocomposites. Then, the mechanical properties of the so-called effective nanofiller (i.e., the physical size of nanofiller plus the thickness of interphase) will be determined by a series of simulations.

A Hybrid Parallelizable Algorithm for Computer Simulation of the Motion Behaviors of a Branched Multibody System

2006 ◽  
Author(s):  
Shanzhong (Shawn) Duan ◽  
Yogesh Patel
Keyword(s):  
Computational Efficiency ◽  
Heterogeneous Computing ◽  
High Efficiency ◽  
Distributed Simulation ◽  
Equations Of Motion ◽  
Deep Understanding ◽  
Constraint Forces ◽  
The Relationship ◽  
Explicit Determination

This paper presents a hybrid parallelizable algorithm for the computer-aided modeling of the dynamic behavior of multibody open tree systems. The method is based on cutting certain system interbody joints at branched bodies so that a system of largely independent multibody subchains is formed. These subchains interact with one another through associated unknown constraint forces fc at the cut joints. The increased parallelism is obtainable through cutting joints and the explicit determination of associated constraint forces combined with a sequential O(n) procedure. Consequently, the sequential O(n) procedure is carried out within each subchain to form and solve the equations of motion, while parallel strategies are performed between the subchains to form and solve constraint equations concurrently. Two extreme cutting procedures are further discussed to conduct a comparison of computational efficiency. One case is to cut the joints at branched bodies so that the longest lengths of subchains are obtained and the other is to cut the joints at branched bodies so that the shortest lengths of subchains are formed. The algorithm can easily accommodate the available number of processors while maintaining high efficiency. The algorithm will also be implemented on both parallel homogeneous computing (PHC) systems and network-distributed heterogeneous computing (DHC) environment. The implementation of the algorithm in a DHC environment will permit engineers and researchers to conduct distributed simulation of dynamic behaviors of large and complex multibody systems on ubiquitous network-distributed PC workstations in their workplace. In short, the exploration of the parallelizable algorithm for a multibody tree system will provide a deep understanding of the relationship between computational load balancing and optimal joint locations to be cut. The computational efficiency of the algorithm can be increased further.

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