对蒙特卡洛模拟的非添加高斯过程潜力的并行实现
Jack Broad1, Richard J Wheatley2, Richard S Graham3
1Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.
Journal of chemical theory and computation
|June 27, 2023
概括
本研究介绍了分子模拟中高斯过程潜力的并行编程策略,提高了三体相互作用的计算效率. 该方法显著加快了模拟速度,在120个过程中显示了30倍的改进.
科学领域:
- 计算化学计算化学
- 材料科学 材料科学 材料科学
- 统计力学 统计力学
背景情况:
- 高斯过程潜能为分子模拟提供了一种数据效率高的方法.
- 在大规模模拟中实现这些潜力需要有效的并行化策略.
- 准确模拟原子间相互作用,包括三体效应,对于可靠的模拟结果至关重要.
研究的目的:
- 在分子模拟中开发和实施高斯过程潜力的并行编程策略.
- 在这个框架内,专注于优化三体非增量能量的计算.
- 证明拟议方法的可扩展性和效率.
主要方法:
- 设计了一种并行编程方法,以在多个处理单元中分配分子模拟任务.
- 该策略专门针对一般潜力的对和三重相互作用的分布.
- 该实现在模拟盒中使用气进行了测试,执行了完整的盒子和原子位移计算.
主要成果:
- 平行策略有效地分配了对和三重相互作用,适用于附加和非附加能量.
- 观察到显著的加快速度:在5个过程中增加了4倍,在40个过程中达到20倍,在120个过程中达到30倍.
- 该方法在蒙特卡洛模拟中被证明是有效的,正如完整的盒子和原子位移计算所证明的那样.
结论:
- 提出的并行编程策略可以在分子模拟中有效地实现高斯过程潜力.
- 该方法展示了出色的可扩展性,并提供了大量的计算速度,使复杂的模拟更加可行.
- 这种方法广泛适用于各种潜力和模拟类型,推进了计算分子建模领域.
相关概念视频
Gauss's Law
7.4K
If a closed surface does not have any charge inside where an electric field line can terminate, then the electric field line entering the surface at one point must necessarily exit at some other point of the surface. Therefore, if a closed surface does not have any charges inside the enclosed volume, then the electric flux through the surface is zero. What happens to the electric flux if there are some charges inside the enclosed volume? Gauss's law gives a quantitative answer to this question.
7.4K
Poisson's And Laplace's Equation
3.1K
The electric potential of the system can be calculated by relating it to the electric charge densities that give rise to the electric potential. The differential form of Gauss's law expresses the electric field's divergence in terms of the electric charge density.
3.1K
Model Approaches for Pharmacokinetic Data: Distributed Parameter Models
99
Pharmacokinetic models are mathematical constructs that represent and predict the time course of drug concentrations in the body, providing meaningful pharmacokinetic parameters. These models are categorized into compartment, physiological, and distributed parameter models.
The distributed parameter models are specifically designed to account for variations and differences in some drug classes. This model is particularly useful for assessing regional concentrations of anticancer or...
The distributed parameter models are specifically designed to account for variations and differences in some drug classes. This model is particularly useful for assessing regional concentrations of anticancer or...
99
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
84
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
84
Propagation of Action Potentials
6.0K
The propagation of an action potential refers to the process by which a nerve impulse, or "action potential," travels along a neuron.
Neurons (nerve cells) have a resting membrane potential, with a slightly negative charge inside compared to outside. This is maintained by ion channels, such as sodium (Na+) and potassium (K+) channels, which control the flow of ions. When a stimulus, like a touch or a signal from another neuron, triggers the neuron, sodium channels open, allowing sodium ions to...
Neurons (nerve cells) have a resting membrane potential, with a slightly negative charge inside compared to outside. This is maintained by ion channels, such as sodium (Na+) and potassium (K+) channels, which control the flow of ions. When a stimulus, like a touch or a signal from another neuron, triggers the neuron, sodium channels open, allowing sodium ions to...
6.0K
Gauss's Law in Dielectrics
4.5K
Consider a polar dielectric placed in an external field. In such a dielectric, opposite charges on adjacent dipoles neutralize each other, such that the net charge within the dielectric is zero. When a polar dielectric is inserted in between the capacitor plates, an electric field is generated due to the presence of net charges near the edge of the dielectric and the metal plates interface. Since the external electrical field merely aligns the dipoles, the dielectric as a whole is neutral. An...
4.5K


