Multigranular Molecular Dynamics Simulations of Polymer Melts Using Multibody Algorithms

2005 ◽  
Author(s):  
Rudranarayan M. Mukherjee ◽  
Kurt S. Anderson ◽  
John Ziegler
Keyword(s):  
Molecular Dynamics ◽  
Polymer Melts ◽  
Parallel Implementation ◽  
Equations Of Motion ◽  
Low Frequency ◽  
Polymer Melt ◽  
Rigid Bodies ◽  
Computational Time ◽  
Integration Time ◽  
Test Case

In a multigranular approach for modeling molecular dynamics of polymer melts, different sections of the simulation box are modeled at different levels of detail viz. as particles, flexible bodies or rigid bodies. This approach eliminates high frequency localized motion while maintaining low frequency global conformational motion. This allows for longer integration time steps thus decreasing computational time. In this paper, we discuss our efforts to develop a consortium of dynamics algorithms capable of efficiently generating and solving the equations of motion at all three levels of modeling on a common software platform. A bead spring model of the polymer melt moving under the influence of truncated Lennard-Jones potential under periodic boundary conditions is pursued. Implementation issues and results from a test case consisting of 32 polymer chains of 16 beads each are presented. The paper also discusses the parallel implementation of this problem using MPI.

Investigation of GPU Use in Conjunction With DCA-Based Articulated Multibody Systems Simulation

2015 ◽  
Author(s):  
Jeremy J. Laflin ◽  
Kurt S. Anderson ◽  
Michael Hans
Keyword(s):  
Multibody Systems ◽  
Graphics Processing Units ◽  
Degrees Of Freedom ◽  
Equations Of Motion ◽  
Computational Time ◽  
Test Case ◽  
Time Step ◽  
Dynamic Simulations ◽  
Computational Performance ◽  
Compute Time

Since computational performance is critically important for simulations to be used as an effective tool to study and design dynamic systems, the computing performance gains offered by Graphics Processing Units (GPUs) cannot be ignored. Since the GPU is designed to execute a very large number of simultaneous tasks (nominally Single Instruction Multi-Data (SIMD)), recursive algorithms in general, such as the DCA, are not well suited to be executed on GPU-type architecture. This is because each level of recursion is dependent on the previous level. However, there are some ways that the GPU can be leveraged to increase computational performance when using the DCA to form and solve the equations of motion for articulated multibody systems with a very large number of degrees-of-freedom. Computational performance of dynamic simulations is highly dependent on the nature of the underlying formulation and the number of generalized coordinates used to characterize the system. Therefore, algorithms that scale in a more desirable (lower order) fashion with the number of degrees-of-freedom are generally preferred when dealing with large (N > 10) systems. However, the utility of using simulations as a scientific tool is directly related to actual compute time. The DCA, and other top performing methods, have demonstrated the desirable property of the required compute time scaling linearly with (O(n)) with the number of degrees-of-freedom (n) and sublinearly (O(logn) performance when implemented in parallel. However for the DCA, total compute time could be further reduced by exploiting the large number of independent operations involved in the first few levels of recursion. A simple chain-type pendulum example is used to explore the feasibility of using the GPU to execute the assembly and disassembly operations for the levels of recursion that contain enough bodies for this process to be computationally advantageous. A multi-core CPU is used to perform the operations in parallel using Open MP for the remaining levels. The number of levels of recursion that utilizes the GPU is varied from zero to all levels. The data corresponding to zero utilization of the GPU provides the reference compute-time in which the assembly and disassembly operations necessary at each level are performed in parallel using Open MP. The computational time required to simulate the system for one time-step where the GPU is utilized for various levels of recursion is compared to the reference compute time also varying the number of bodies in the system. A decrease in the compute-time when using the GPU is demonstrated relative to the reference compute-time even for systems of moderate size n < 1000 for arrangements using the GPU. This is a lower number of bodies than was expected for this test case and confirms that the GPU can bring significant increases in computational efficiency for large systems, while preserving the attractive sub-linear scalability (w.r.t. compute time) of the DCA.

Parallel Algorithm for Modeling Multi-Rigid Body System Dynamics With Nonholonomic Constraints

2013 ◽  
Author(s):  
Rudranarayan Mukherjee ◽  
Pawel Malczyk
Keyword(s):  
Rigid Body ◽  
Parallel Implementation ◽  
Equations Of Motion ◽  
Numerical Test ◽  
Nonholonomic Constraints ◽  
Test Case ◽  
Central Idea ◽  
Acceleration Level ◽  
Disassembly Process ◽  
Kinematic Joint

This paper presents a new algorithm for serial or parallel implementation of computer simulations of the dynamics of multi-rigid body systems subject to nonholonomic and holonomic constraints. The algorithm presents an elegant approach for eliminating the nonholonomic constraints explicitly from the equations of motion and implicitly expressing them in terms of nonlinear coupling in the operational inertias of the bodies subject to these constraints. The resulting equations are in the same form as those of a body subject to kinematic joint constraints. This enables the nonholohomic constraints to be seamlessly treated in either a (i) recursive or (ii) hierarchic assembly-disassembly process for solving the equations of motion of generalized multi-rigid body systems in serial or parallel implementations. The algorithm is non-iterative and although the nonholonomic constraints are imposed at the acceleration level, constraint satisfaction is excellent as demonstrated by the numerical test case implemented to verify the algorithm. The paper presents procedures for handling both cases where the nonholonomic constraints are imposed between terminal bodies of a system and the environment as well as when the constraints are imposed between bodies in the interior of the system topology. The algorithm uses a mixed set of coordinates and is built on the central idea of eliminating either constraint loads or relative accelerations from the equations of motion by projecting the equations of motion into the motion subspaces or their orthogonal complements.

Symmetric Multistep Methods Revisited: II. Numerical Experiments

1999 ◽  
Vol 173 ◽  
pp. 309-314 ◽  
Author(s):  
T. Fukushima
Keyword(s):  
Multistep Methods ◽  
Computational Time ◽  
Integration Time ◽  
Implicit Methods ◽  
Symmetric Methods ◽  
Celestial Bodies ◽  
The Stability ◽  
Predictor Corrector ◽  
Symmetric Multistep Methods ◽  
Integration Errors

AbstractBy using the stability condition and general formulas developed by Fukushima (1998 = Paper I) we discovered that, just as in the case of the explicit symmetric multistep methods (Quinlan and Tremaine, 1990), when integrating orbital motions of celestial bodies, the implicit symmetric multistep methods used in the predictor-corrector manner lead to integration errors in position which grow linearly with the integration time if the stepsizes adopted are sufficiently small and if the number of corrections is sufficiently large, say two or three. We confirmed also that the symmetric methods (explicit or implicit) would produce the stepsize-dependent instabilities/resonances, which was discovered by A. Toomre in 1991 and confirmed by G.D. Quinlan for some high order explicit methods. Although the implicit methods require twice or more computational time for the same stepsize than the explicit symmetric ones do, they seem to be preferable since they reduce these undesirable features significantly.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

2019 ◽  
Author(s):  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Étienne Derat ◽  
Jean-Philip Piquemal
Keyword(s):  
Molecular Dynamics ◽  
Parallel Implementation ◽  
Steered Molecular Dynamics ◽  
Massively Parallel

This paper is dedicated to the massively parallel implementation of Steered Molecular Dynamics in the Tinker-HP softwtare. It allows for direct comparisons of polarizable and non-polarizable simulations of realistic systems.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

2019 ◽  
Author(s):  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Étienne Derat ◽  
Jean-Philip Piquemal
Keyword(s):  
Molecular Dynamics ◽  
Parallel Implementation ◽  
Steered Molecular Dynamics ◽  
Massively Parallel

This paper is dedicated to the massively parallel implementation of Steered Molecular Dynamics in the Tinker-HP softwtare. It allows for direct comparisons of polarizable and non-polarizable simulations of realistic systems.

scholarly journals A Modified KNN Algorithm for High-Performance Computing on FPGA of Real-Time m-QAM Demodulators

Electronics ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 627
Author(s):  
David Marquez-Viloria ◽  
Luis Castano-Londono ◽  
Neil Guerrero-Gonzalez
Keyword(s):  
Real Time ◽  
High Performance ◽  
Interference Mitigation ◽  
Parallel Implementation ◽  
Computational Time ◽  
Successful Implementation ◽  
Interchannel Interference ◽  
The Difference ◽  
High Level ◽  
Performance Computing

A methodology for scalable and concurrent real-time implementation of highly recurrent algorithms is presented and experimentally validated using the AWS-FPGA. This paper presents a parallel implementation of a KNN algorithm focused on the m-QAM demodulators using high-level synthesis for fast prototyping, parameterization, and scalability of the design. The proposed design shows the successful implementation of the KNN algorithm for interchannel interference mitigation in a 3 × 16 Gbaud 16-QAM Nyquist WDM system. Additionally, we present a modified version of the KNN algorithm in which comparisons among data symbols are reduced by identifying the closest neighbor using the rule of the 8-connected clusters used for image processing. Real-time implementation of the modified KNN on a Xilinx Virtex UltraScale+ VU9P AWS-FPGA board was compared with the results obtained in previous work using the same data from the same experimental setup but offline DSP using Matlab. The results show that the difference is negligible below FEC limit. Additionally, the modified KNN shows a reduction of operations from 43 percent to 75 percent, depending on the symbol’s position in the constellation, achieving a reduction 47.25% reduction in total computational time for 100 K input symbols processed on 20 parallel cores compared to the KNN algorithm.

Analytical Solution for Rotational Rub-Impact Plate Under Thermal Shock

2016 ◽  
Vol 32 (3) ◽  
pp. 297-311
Author(s):  
T.-Y. Zhao ◽  
H.-Q. Yuan ◽  
B.-B. Li ◽  
Z.-J. Li ◽  
L.-M. Liu
Keyword(s):  
Thermal Shock ◽  
High Frequency ◽  
Equations Of Motion ◽  
Low Frequency ◽  
Cantilever Plate ◽  
Analysis Method ◽  
Multiple Frequency ◽  
Width Direction ◽  
Blade Tip ◽  
High Frequency Vibrations

AbstractThe analysis method is developed to obtain dynamic characteristics of the rotating cantilever plate with thermal shock and tip-rub. Based on the variational principle, equations of motion are derived considering the differences between rubbing forces in the width direction of the plate. The transverse deformation is decomposed into quasi-static deformation of the cantilever plate with thermal shock and dynamic deformation of the rubbing plate under thermal shock. Then deformations are obtained through the calculation of modal characteristics of rotating cantilever plate and temperature distribution function. Special attention is paid to the influence of tip-rub and thermal shock on the plate. The results show that tip-rub has the characteristics of multiple frequency vibrations, and high frequency vibrations are significant. On the contrary, thermal shock shows the low frequency vibrations. The thermal shock makes the rubbing plate gradually change into low frequency vibrations. Because rub-induced vibrations are more complicated than those caused by thermal shock, tip-rub is easier to result in the destruction of the blade. The increasing friction coefficient intensifies vibrations of the rubbing plate. Minimizing friction coefficients can be an effective way to reduce rub-induced damage through reducing the surface roughness between the blade tip and the inner surface of the casing.

A Convex Complementarity Approach for Simulating Large Granular Flows

2010 ◽  
Vol 5 (3) ◽  
Author(s):  
Alessandro Tasora ◽  
Mihai Anitescu
Keyword(s):  
Granular Flow ◽  
Complementarity Problems ◽  
Particle Interaction ◽  
Granular Flows ◽  
Rigid Bodies ◽  
Integration Time ◽  
Frictional Contacts ◽  
Physical Experiments ◽  
Dense Granular Flow ◽  
Number Of Particles

Aiming at the simulation of dense granular flows, we propose and test a numerical method based on successive convex complementarity problems. This approach originates from a multibody description of the granular flow: all the particles are simulated as rigid bodies with arbitrary shapes and frictional contacts. Unlike the discrete element method (DEM), the proposed approach does not require small integration time steps typical of stiff particle interaction; this fact, together with the development of optimized algorithms that can run also on parallel computing architectures, allows an efficient application of the proposed methodology to granular flows with a large number of particles. We present an application to the analysis of the refueling flow in pebble-bed nuclear reactors. Extensive validation of our method against both DEM and physical experiments results indicates that essential collective characteristics of dense granular flow are accurately predicted.

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