Search for: All records

Abstract SPPARKS is an open-source parallel simulation code for developing and running various kinds of on-lattice Monte Carlo models at the atomic or meso scales. It can be used to study the properties of solid-state materials as well as model their dynamic evolution during processing. The modular nature of the code allows new models and diagnostic computations to be added without modification to its core functionality, including its parallel algorithms. A variety of models for microstructural evolution (grain growth), solid-state diffusion, thin film deposition, and additive manufacturing (AM) processes are included in the code. SPPARKS can also be used to implement grid-based algorithms such as phase field or cellular automata models, to run either in tandem with a Monte Carlo method or independently. For very large systems such as AM applications, the Stitch I/O library is included, which enables only a small portion of a huge system to be resident in memory. In this paper we describe SPPARKS and its parallel algorithms and performance, explain how new Monte Carlo models can be added, and highlight a variety of applications which have been developed within the code. 

Abstract AimBiodiversity on Earth is threatened by climate change. Despite the vulnerability of freshwater habitats to human impacts, most climate change projections have focused on terrestrial systems. Here, we examined how the current distributions and biodiversity of stream taxa might change under mitigated, stabilizing and increasing greenhouse gas emissions. LocationConterminous USA. Time periodPresent day to 2070. Major taxa studiedStream diatoms, insects and fish. MethodsWe developed species distribution models for 336 freshwater taxa from 1,227 distinct stream localities using water chemistry, watershed and climatic variables. Models based only on climate were used to project changes in the distributions and biodiversity of cold‐ versus warm‐water taxa under representative concentration pathways (RCPs) ranging from 2.6 to 8.5 W/m². ResultsIn all three organismal groups, climate emerged as the strongest predictor of species distributions, providing comparable explanatory power to water chemistry and watershed variables combined. The RCP‐based projections suggested a widespread expansion of warm‐water taxa, outpacing the decline of cold‐water taxa. Consequently, overall species richness would increase, but beta diversity would decrease drastically with the severity of climate change. A closer look at individual taxa and functional guilds revealed that vulnerable cold‐water taxa included: (a) diatom guilds forming the base and bulk of the biofilm; (b) environmentally sensitive insects, characteristic of unimpacted streams; and (c) ecologically and recreationally important salmonids, which were forecast to diminish dramatically in source habitats. Warm‐water fish projected to increase their distributions include bait bucket release minnows and dominant predators. Main conclusionsOur results suggest potentially devastating impacts of climate change on stream ecosystems, with the restructuring of diatom, insect and fish communities, diminished distributions of functionally important taxa and widespread expansion of warm‐water taxa, giving rise to biotic homogenization. Given that the magnitude of these biotic shifts depends on the severity of climate change, appropriate current policy decisions are necessary to preserve freshwater ecosystems.