并行回火模拟中副本在处理机上的最优分配

Extension of the constant exchange probability method to multi-dimensional replica exchange Monte Carlo applied to the tri-critical spin-1 Blume-Capel model

In replica exchange Monte Carlo (REM), tuning of the temperature set and the exchange scheduling are crucial in improving the accuracy and reducing calculation time. In multi-dimensional simulated tempering, the first order phase transition is accessible. Therefore it is important to study the tuning of parameter set and the scheduling of exchanges in the parallel counterpart, the multi-dimensional REM. We extend Hukushima's constant exchange probability method to multi-dimensional REM for the parameter set. We further propose a combined method to use this set and the Bittner-Nussbaumer-Janke'…

基于GPU的聚合物复制交换大规模并行模拟

Massively parallelized replica-exchange simulations of polymers on GPUs

我们讨论了并行化的优势，多线程的图形处理单元（GPU）的并行回火Monte Carlo计算机模拟的一个例子珠弹簧模型的均聚物。由于大量构象系综的采样是精确估计统计量的先决条件，例如构象转变的典型指标，如比热的峰结构，蒙特卡罗模拟性能大幅提高的优势不能被高估。采用多线程并利用GPU上大量内核的强大功能，在现代但标准的图形卡中可用，我们发现将部分代码从中央处理器（CPU）移植到GPU时，效率迅速提高。

Jeffreys 流：通过并行退火蒸馏实现鲁棒的玻尔兹曼生成器用于稀有事件采样

Jeffreys Flow: Robust Boltzmann Generators for Rare Event Sampling via Parallel Tempering Distillation

本文提出Jeffreys流，通过并行退火轨迹蒸馏数据，利用对称Jeffreys散度缓解玻尔兹曼生成器的模式崩溃问题，提升多模分布的采样精度与全局模式覆盖。

Massively parallel simulations for disordered systems

Simulations of systems with quenched disorder are extremely demanding, suffering from the combined effect of slow relaxation and the need of performing the disorder average. As a consequence, new algorithms, improved implementations, and alternative and even purpose-built hardware are often instrumental for conducting meaningful studies of such systems. The ensuing demands regarding hardware availability and code complexity are substantial and sometimes prohibitive. We demonstrate how with a moderate coding effort leaving the overall structure of the simulation code unaltered as compared to a …

Accelerating molecular dynamics simulations with population annealing

Population annealing is a powerful tool for large-scale Monte Carlo simulations. We adapt this method to molecular dynamics simulations and demonstrate its excellent accelerating effect by simulating the folding of a short peptide commonly used to gauge the performance of algorithms. The method is compared to the well established parallel tempering approach and is found to yield similar performance for the same computational resources. In contrast to other methods, however, population annealing scales to a nearly arbitrary number of parallel processors and it is thus a unique tool that enables…

Exchanging replicas with unequal cost, infinitely and permanently

We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably different, for instance, because the replicas run on different type of processor units or because of the algorithmic complexity. To prove detailed-balance, we make a paradigm shift from the common conceptual viewpoint in which the set of parallel replicas represents a high-dimensional superstate, to an ensemble based criterion in which the other ensembles represent an environment that might or might not participate in the Mo…

A Unified Approach to Enhanced Sampling

The sampling problem lies at the heart of atomistic simulations and over the years many different enhanced sampling methods have been suggested towards its solution. These methods are often grouped into two broad families. On the one hand methods such as umbrella sampling and metadynamics that build a bias potential based on few order parameters or collective variables. On the other hand, tempering methods such as replica exchange that combine different thermodynamic ensembles in one single expanded ensemble. We instead adopt a unifying perspective, focusing on the target probability distribut…