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A new computer program for topological, visual analysis of 3D particle configurations based on visual representation of radial distribution function peaks as bonds
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).ORCID iD: 0000-0003-0237-7250
(English)In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944Article in journal (Refereed) Submitted
Abstract [en]

We present a new program able to perform unique visual analysis on generic particle systems: PASYVAT (PArticle SYstem Visual Analysis Tool). More specifically, it can perform a selection of multiple interparticle distance ranges from a radial distribution function (RDF) plot and display them in 3D as bonds. This software can be used with any data set representing a system of particles in 3D. In this manuscript the reader will find a description of the program and its internal structure, with emphasis on its applicability in the study of certain particle configurations, obtained from classical molecular dynamics simulation in condensed matter physics.

Keyword [en]
radial distribution function, molecular dynamics, visual analysis, bonding, topology
National Category
Condensed Matter Physics Software Engineering
Research subject
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-115845OAI: oai:DiVA.org:su-115845DiVA: diva2:800392
Available from: 2015-04-03 Created: 2015-04-03 Last updated: 2017-12-04
In thesis
1. On the nature of self-assembly in low-density condensed matter: A classical molecular dynamics approach
Open this publication in new window or tab >>On the nature of self-assembly in low-density condensed matter: A classical molecular dynamics approach
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The study of the physics of self-assembly in low-density condensed matter is an extremely interesting, mostly unexplored field of scientific research. The contribution reported in this thesis explains how this problem can be addressed using molecular dynamics simulation of 3D systems composed by simple, identical particles, interacting via a spherically symmetric pair potential, which belongs to the class of Dzugutov potentials. Such approach resulted in four, self-assembled archetypal structures, which are reported in the included papers I, II, III, IV. In order to produce the reported results, a major effort of software development has been done by the author, both in the simulation and the analysis programs used. This thesis will start with a brief introduction to the field, highlighting the important aspects needed to have a more complete, general understanding of the reported scientific results. Some conclusions will be drawn, together with some possible future endeavors.

Place, publisher, year, edition, pages
Stockholm: Department of Materials and Environmental Chemistry (MMK), Stockholm University, 2015. 96 p.
National Category
Condensed Matter Physics Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-115849 (URN)978-91-7649-149-2 (ISBN)
Public defence
2015-05-12, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted. Paper 4: Submitted. Paper 5: Submitted.

Available from: 2015-04-20 Created: 2015-04-03 Last updated: 2015-04-23Bibliographically approved

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arXiv:1503.04449

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