Результаты поиска по 'molecular dynamics':
Найдено статей: 43
  1. Minkin A.S., Knizhnik A.A., Potapkin B.V.
    OpenCL realization of some many-body potentials
    Computer Research and Modeling, 2015, v. 7, no. 3, pp. 549-558

    Modeling of carbon nanostructures by means of classical molecular dynamics requires a lot of computations. One of the ways to improve the performance of basic algorithms is to transform them for running on SIMD-type computing systems such as systems with dedicated GPU. In this work we describe the development of algorithms for computation of many-body interaction based on Tersoff and embedded-atom potentials by means of OpenCL technology. OpenCL standard provides universality and portability of the algorithms and can be successfully used for development of the software for heterogeneous computing systems. The performance of algorithms is evaluated on CPU and GPU hardware platforms. It is shown that concurrent memory writes is effective for Tersoff bond order potential. The same approach for embedded-atom potential is shown to be slower than algorithm without concurrent memory access. Performance evaluation shows a significant GPU acceleration of energy-force evaluation algorithms for many-body potentials in comparison to the corresponding serial implementations.

    Keywords: GPGPU, OpenCL, many-body potentials, Tersoff potential, embedded-atom potential, atomic operations.
    Views (last year): 4. Citations: 1 (RSCI).
  2. Podryga V.O., Polyakov S.V.
    3D molecular dynamic simulation of thermodynamic equilibrium problem for heated nickel
    Computer Research and Modeling, 2015, v. 7, no. 3, pp. 573-579

    This work is devoted to molecular dynamic modeling of the thermal impact processes on the metal sample consisting of nickel atoms. For the solution of this problem, a continuous mathematical model on the basis of the classical Newton mechanics equations has been used; a numerical method based on the Verlet scheme has been chosen; a parallel algorithm has been offered, and its realization within the MPI and OpenMP technologies has been executed. By means of the developed parallel program, the investigation of thermodynamic equilibrium of nickel atoms’ system under the conditions of heating a sample to desired temperature has been executed. In numerical experiments both optimum parameters of calculation procedure and physical parameters of analyzed process have been defined. The obtained numerical results are well corresponding to known theoretical and experimental data.

    Keywords: molecular dynamic simulation, nickel, EAM, temperature, thermostat, Newton mechanics equations, parallel algorithm and program, MPI and OpenMP technologies.
    Views (last year): 2.
  3. Shefov K.S., Stepanova M.M.
    An implementation of a parallel global minimum search algorithm with an application to the ReaxFF molecular dynamic force field parameters optimization
    Computer Research and Modeling, 2015, v. 7, no. 3, pp. 745-752

    Molecular dynamic methods that use ReaxFF force field allow one to obtain sufficiently good results in simulating large multicomponent chemically reactive systems. Here is represented an algorithm of searching optimal parameters of molecular-dynamic force field ReaxFF for arbitrary chemical systems and its implementation. The method is based on the multidimensional technique of global minimum search suggested by R.G. Strongin. It has good scalability useful for running on distributed parallel computers.

    Keywords: numerical simulation, molecular dynamics, reactive force field, chemically reactive systems, parameter optimization, parallel algorithm, absolute extremum search.
    Views (last year): 1. Citations: 1 (RSCI).
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