Development of molecular dynamics simulation and its visualization using parallel computing

我们打算利用并行计算系统将可视化工具整合到分子动力学模拟中。我们的目标是如何为第一原理MD软件包FHI98MD开发一个可视化编程工具，以找到优化的计算过程。我们的目标是计算氢从GaAs界面到气相的脱附过程的过渡能或在Ga原子上的吸收能。该软件包能够在我们的可视化系统的并行计算机上运行。建立了有效的表面生长动力学过程的计算系统。我们还提出了以下两个额外的结果：1)我们计算了三维物体的时间演化，例如生长中的晶体。物体界面的增长速度只取决于它的三维曲率。仿真过程包括基于OpenGL的三维计算机图形系统。由于在计算过程中对可视化数据进行了校核，因此可以有效地避免非物理形状，并得到适当的渐近模式。该模型适用于积雪的烧结过程。2)利用OpenGL系统进行了热扩散的分子动力学模拟。二元Lennard-Jones流体是在系统温度梯度恒定的条件下使用的。我们观察到公平的Soret效应，在我们的系统中，重分子和小分子倾向于在冷区聚集，而其他分子倾向于在热区移动。此外，我们还研究了轻分子流体中一个较重分子或一个较小分子的行为。我们观察到，重分子倾向于在冷区运动，小分子倾向于在冷区运动。我们应该在恒定温度梯度下的布朗运动点研究这种特殊情况。

We intended to incorporate a visualization tool into a molecular dynamics simulation using parallel computing system. Our goal was how to develop a visualization programming tool for the First-Principles MD Package, FHI98MD in order to find the optimized calculation processes. Our target was to calculate the transition energy for desorption process of hydrogen from GaAs interface to vapor phase or the energy for absorption on a Ga atom. The package is able to be run on our parallel computer with our visualization system. We can establish the effective computing system for the kinetic processes for growing surface.We also present the following two additional results :1)We calculated the time evolution of a three dimensional object, such as a growing crystal. The growth speed of the object interface depends only on its three-dimensional curvature. The simulation process includes a three dimensional computer graphic system based on OpenGL. Since we check the visualized data during calculation, we can avoid the nonphysical shape and reach the appropriate asymptotic pattern effectively. This model can apply to sintering processes for accumulated snow.2)We demonstrated the molecular dynamics simulation of thermal diffusion by OpenGL system. The binary Lennard-Jones fluids is used under the condition of a constant temperature gradient in system. We observed that the fair Soret effect, the heavier molecule and smaller molecule tend to accumulate in the cold region, while the other ones tend to move the hot region in our system. Furthermore, we investigated the behavior of only one heavier molecule or that of only one smaller molecule in lighter molecule fluid. We observed that the heavier molecule tend to move in the cold region and smaller molecule in the cold region. We should study this special case in the point of the Brownian motion under a constant temperature gradient.