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Lecture

Atomic scale structures: Representing atoms on a computer

In course

MSE-305: Introduction to atomic-scale modeling

This course provides an introduction to the modeling of matter at the atomic scale, using interactive Jupyter notebooks to see several of the core concepts of materials science in action. ...

Description

This lecture covers the representation of atomic structures on a computer, including atomic positions, atom types, and storage formats like .xyz files. It introduces exercises based on Jupyter notebooks and discusses periodic and non-periodic systems.

Instructor

Michele Ceriotti

Michele Ceriotti received his Ph.D. in Physics from ETH Zürich in 2010. He spent three years in Oxford as a Junior Research Fellow at Merton College. Since 2013 he leads the laboratory for Computational Science and Modeling in the Institute of Materials at EPFL. His research revolves around the atomic-scale modelling of materials, based on the sampling of quantum and thermal fluctuations and on the use of machine learning to predict and rationalize structure-property relations. He has been awarded the IBM Research Forschungspreis in 2010, the Volker Heine Young Investigator Award in 2013, an ERC Starting Grant in 2016, and the IUPAP C10 Young Scientist Prize in 2018.

Official source

Related concepts (32)

Periodic point

In mathematics, in the study of iterated functions and dynamical systems, a periodic point of a function is a point which the system returns to after a certain number of function iterations or a certain amount of time. Given a mapping f from a set X into itself, a point x in X is called periodic point if there exists an n so that where f_n is the nth iterate of f. The smallest positive integer n satisfying the above is called the prime period or least period of the point x.

File format

A file format is a standard way that information is encoded for storage in a . It specifies how bits are used to encode information in a digital storage medium. File formats may be either proprietary or free. Some file formats are designed for very particular types of data: PNG files, for example, store bitmapped using lossless data compression. Other file formats, however, are designed for storage of several different types of data: the Ogg format can act as a container for different types of multimedia including any combination of audio and video, with or without text (such as subtitles), and metadata.

Data storage

Data storage is the recording (storing) of information (data) in a storage medium. Handwriting, phonographic recording, magnetic tape, and optical discs are all examples of storage media. Biological molecules such as RNA and DNA are considered by some as data storage. Recording may be accomplished with virtually any form of energy. Electronic data storage requires electrical power to store and retrieve data. Data storage in a digital, machine-readable medium is sometimes called digital data.

Group (periodic table)

In chemistry, a group (also known as a family) is a column of elements in the periodic table of the chemical elements. There are 18 numbered groups in the periodic table; the 14 f-block columns, between groups 2 and 3, are not numbered. The elements in a group have similar physical or chemical characteristics of the outermost electron shells of their atoms (i.e., the same core charge), because most chemical properties are dominated by the orbital location of the outermost electron.

Computer

A computer is a machine that can be programmed to carry out sequences of arithmetic or logical operations (computation) automatically. Modern digital electronic computers can perform generic sets of operations known as programs. These programs enable computers to perform a wide range of tasks. A computer system is a nominally complete computer that includes the hardware, operating system (main software), and peripheral equipment needed and used for full operation.

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