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On the energy conservation during the active deformation in molecular dynamics simulations

机译：分子动力学模拟中主动变形过程中的能量守恒

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摘要

In this paper, we examined the energy conservation for the current schemes of applying active deformation in molecular dynamics (MD) simulations. Specifically, two methods are examined. One is scaling the dimension of the simulation box and the atom positions via an affine transformation, suitable for the periodic system. The other is moving the rigid walls that interact with the atoms in the system, suitable for the non-periodic system. Based on the calculation of the external work and the internal energy change, we present that the atom velocities also need to be updated in the first deformation method; otherwise the energy conservation cannot be satisfied. The classic updating scheme is examined, in which any atom crossing the periodic boundary experiences a velocity delta that is equal to the velocity difference between the opposite boundaries. In addition, a new scheme which scales the velocities of all the atoms according to the strain increment is proposed, which is more efficient and realistic than the classic scheme. It is also demonstrated that the Virial stress instead of its interaction part is the correct stress definition that corresponds to Cauchy stress in the continuum mechanics.
机译：在本文中，我们研究了在分子动力学（MD）模拟中应用主动变形的当前方案的能量守恒。具体来说，研究了两种方法。一种是通过仿射变换来缩放模拟框的尺寸和原子位置，适用于周期系统。另一种方法是移动与系统中原子相互作用的刚性壁，适用于非周期性系统。在计算外部功和内部能量变化的基础上，我们提出在第一种变形方法中还需要更新原子速度。否则不能满足节能要求。研究了经典的更新方案，其中任何穿过周期边界的原子都会经历一个速度增量，该速度增量等于相对边界之间的速度差。此外，提出了一种根据应变增量缩放所有原子速度的新方案，该方案比经典方案更有效，更现实。还证明了，维里应力而不是其相互作用部分是与连续力学中柯西应力相对应的正确应力定义。

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