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Article Dans Une Revue Journal of Computational Chemistry Année : 2021

CHAMPION: Chalmers hierarchical atomic, molecular, polymeric and ionic analysis toolkit

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Résumé

We present CHAMPION (Chalmers hierarchical atomic, molecular, polymeric, and ionic analysis toolkit): a software developed to automatically detect time-dependent bonds between atoms based on their dynamics, classify the local graph topology around them, and analyze the physicochemical properties of these topologies by statistical physics. In stark contrast to methodologies where bonds are detected based on static conditions such as cut-off distances, CHAMPION considers pairs of atoms to be bound only if they move together and act as a bound pair over time. Furthermore, the time-dependent global bond graph is possible to split into dynamically shifting connected components or subgraphs around a certain chemical motif and thereby allow the physicochemical properties of each such topology to be analyzed by statistical physics. Applicable to condensed matter and liquids in general, and electrolytes in particular, this allows both quantitative and qualitative descriptions of local structure, as well as dynamical processes such as speciation and diffusion. We present here a detailed overview of CHAMPION, including its underlying methodology, implementation, and capabilities.

Domaines

Chimie Matériaux

Dates et versions

hal-03610983 , version 1 (16-03-2022)

Identifiants

Citer

Rasmus Andersson, Fabian Aren, Alejandro A. Franco, Patrik Johansson. CHAMPION: Chalmers hierarchical atomic, molecular, polymeric and ionic analysis toolkit. Journal of Computational Chemistry, 2021, 42 (23), pp.1632-1642. ⟨10.1002/jcc.26699⟩. ⟨hal-03610983⟩
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