B. Quentrec and C. Brot, "New method for searching for neighbors in molecular dynamics computations," J. Comp. Phys., vol. 13, pp. 430--432, 1975. Home/Search Document Not in Database Summary Related Articles Check |
This paper is cited in the following contexts:
On The Implementation And Effectiveness Of Autoscheduling For.. - Moreira (1995) (16 citations) (Correct)
....another example of nonscalable functional parallelism. The functional parallelism is independent of the size of the problem and depends only on the structure of the code. 7.4.2. 7 Molecular dynamics (MDJ) This benchmark is extracted from an industrial molecular dynamics code from Asahi Chemical [120, 121]. The benchmark is a functional parallel section of the most heavily used subroutine in the code. This section consists of a loop that iterates over all the cells in the grid (total of 1000 cells) Each cell can be processed independently; therefore, the loop can be parallelized. Each iteration ....
B. Quentrec and C. Brot, "New method for searching for neighbors in molecular dynamics computations," J. Comp. Phys., vol. 13, pp. 430--432, 1975.
Enhancing the Performance of Autoscheduling in.. - Nikolopoulos.. (1998) (1 citation) (Correct)
....the performance implications of autoscheduling and the ability of our method to overcome them. The application benchmarks include the complex matrix multiplication kernel, the kernel of a Fourier Chebyschev spectral computational fluid dynamics code [7] and an industrial molecular dynamics code [16]. All benchmarks have two levels of exploitable parallelism, namely a constant degree of functional parallelism at the outer lelel and data parallelism at the inner level. The complex matrix multiplication and the cfd kernels use matrices of size 256 Theta256. The molecular dynamics kernel ....
B. Quentrec and C. Brot, New Method for Searching for Neighbors in Molecular Dynamics Computations, Journal of Computational Physics, Vol. 13, pp. 430--432, 1975. This article was processed using the L A T E X macro package with LLNCS style
Practical Parallelization of Molecular Dynamics on.. - Kuba, Brunet.. (1997) (1 citation) (Correct)
....Instead, a list is built containing all pairs of monomers within a certain distance of each other. Because monomers are moving in the system, this list needs to be updated. To avoid updating it every time step, we employ a mixed method of the Verlet neighbor list [24] and the cell index method [20], which are discussed in detail in the following subsections. As a result, the time required to compute the non bonding forces fF LJ i g is reduced to O(N ) We also discuss this in detail in the following subsections. The neighbor list is used for computing non bonding forces. For bonding ....
....in the next section. 3) In our experiments, we determined the value for this thickness by trial and error until we found an effective performance for each kind of polymer and hardware system. 1 2 3 4 5 6 Rc R1 0 Figure 3: Verlet Neighbor List 3.6. 2 The Cell Index Method The cell index method [20] is used to reduce the execution time for making a neighbor list. In this method, the original cell is divided into a lattice of M 2 M 2 M sub cells as shown in Figure 4. When the dotted monomer in this figure is of interest, we need to scan the monomers only in the shadowed sub cells as potential ....
B. Quentrec and C. Brot. New method for searching for neighbors in mole cular dynamics computations. J. Comp. Phys., 13:430--432, 1975.
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