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How to prepare an input file for surface calculations
Abstract and Figures
This how-to is intended to guide the reader during the preparation of the input le for an intended surface calculation study. Mainly VESTA software is used to manipulate and transform initial structure le along with some home brewed scripts to do simple operations such as translations.
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Dans l’industrie du pneumatique, l’ajout de nanoparticules de silice dans la gomme est un procédé couramment utilisé en raison des propriétés mécaniques remarquables du matériau composite résultant de ce mélange. Cependant, l’origine physico-chimique du comportement de ce matériau demeure inexpliquée. Le but de cette thèse est de sonder ce système par simulation moléculaire. Afin de couvrir de larges étendues spatiales et temporelles, inhérentes à ce type de matériau, nous avons adopté une stratégie de simulation multi-échelle. À partir de trajectoires atomistiques de référence de haute résolution obtenues par dynamique moléculaire, nous construisons des potentiels gros grain réalistes en utilisant la méthode d’optimisation bayésienne. Nos modèles rendent compte quantitativement du comportement caractéristique de chaînes enchevêtrées. La démarche multi-échelle, étendue à l’interaction polymère-silice, nous permet de modéliser convenablement les propriétés thermodynamiques, structurales et dynamiques d’un système composé d’une nanoparticule de silice, greffée ou non, plongée dans une matrice de polymère amorphe. Ce travail ouvre la voie à la prédiction quantitative des propriétés viscoélastiques des caoutchoucs renforcés sur des échelles temporelles de l’ordre de la microseconde. Ces dernières, inatteignables à l’aide d’une description atomistique, sont désormais accessibles à l’aide de nos jeux de potentiels gros grain.
The Bilbao Crystallographic Server is a web site with crystallographic databases and programs available on-line at www.cryst.ehu.es. It has been operating for about six years and new applications are being added regularly. The programs available on the server do not need a local installation and can be used free of charge. The only requirement is an Internet connection and a web browser.
The server is built on a core of databases, and contains different shells. The innermost one is formed by simple retrieval tools which serve as an interface to the databases and permit to obtain the stored symmetry information for space groups and layer groups. The k -vector database includes the Brillouin zones and the wave-vector types for all space groups. As a part of the server one can find also the database of incommensurate structures. The second shell contains applications which are essential for prob lems involving group-subgroup relations between space groups ( e.g. subgroups and supergroups of space groups, splittings of Wyckoff positions), while the third shell contains more sophisticated programs for the computation of space-group representations and their correlations for group-subgroup related space groups. There are also programs for calculations focused on specific problems of solid-state physics. The aim of the article is to report on the current state of the server and to provide a brief description of the accessible databases and crystallographic computing programs. The use of the programs is demonstrated by illustrative examples.
The Bilbao Crystallographic Server is a web site with crystallographic databases and programs available online (www.cryst.ehu.es). It has been operating for more than ten years and new applications are being added regularly. The programs available on the server do not need a local installation and can be used free of charge. The server gives access to general information related to crystallographic symmetry groups (generators, general and special positions, maximal subgroups, Brillouin zones, etc.). Apart from the simple tools for retrieving the stored data, there are programs for the analysis of group-subgroup relations between space groups. There are also software package studying specific problems of solid-state physics, structural chemistry and crystallography.
We present an efficient scheme for calculating the Kohn-Sham ground state of metallic systems using pseudopotentials and a plane-wave basis set. In the first part the application of Pulay's DIIS method (direct inversion in the iterative subspace) to the iterative diagonalization of large matrices will be discussed. Our approach is stable, reliable, and minimizes the number of order N-atoms(3) operations. In the second part, we will discuss an efficient mixing scheme also based on Pulay's scheme. A special ''metric'' and a special ''preconditioning'' optimized for a plane-wave basis set will be introduced. Scaling of the method will be discussed in detail for non-self-consistent calculations. It will be shown that the number of iterations required to obtain a specific precision is almost independent of the system size. Altogether an order N-atoms(2) scaling is found for systems up to 100 electrons. If we take into account that the number of k points can be implemented these algorithms within a powerful package called VASP (Vienna ab initio simulation package). The program and the techniques have been used successfully for a large number of different systems (liquid and amorphous semiconductors, liquid simple and transition metals, metallic and semiconducting surfaces, phonons in simple metals, transition metals, and semiconductors) and turned out to be very reliable.
Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely
on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility
to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed
website provides capabilities for all registered users to deposit published and so far unpublished structures as personal
communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously.
This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based
collaborative platform dedicated to the collection and curation of structural knowledge.
VESTA
is a three-dimensional visualization system for crystallographic studies and electronic state calculations. It has been upgraded to the latest version,
VESTA 3
, implementing new features including drawing the external morphology of crystals; superimposing multiple structural models, volumetric data and crystal faces; calculation of electron and nuclear densities from structure parameters; calculation of Patterson functions from structure parameters or volumetric data; integration of electron and nuclear densities by Voronoi tessellation; visualization of isosurfaces with multiple levels; determination of the best plane for selected atoms; an extended bond-search algorithm to enable more sophisticated searches in complex molecules and cage-like structures; undo and redo in graphical user interface operations; and significant performance improvements in rendering isosurfaces and calculating slices.
Using the density-functional linear response method, we study the dynamical properties of ground state zinc-blende and high pressure NaCl phases of platinum carbide (PtC). The calculated phonon dispersion curve does not show any soft modes for all wave vectors, indicating the dynamic stability of the ground state zinc-blende phase. The high pressure rock-salt phase exhibits imaginary frequencies, practically along all directions of the Brillouin zone, which means that PtC cannot exist in the NaCl phase at least up to a high pressure of 100 GPa.
The specification of a new standard Crystallographic Information File (CIF) is described. Its development is based on the Self-Defining Text Archive and Retrieval (STAR) procedure [Hall (1991). J. Chem. Inf. Comput. Sci. 31, 326-333]. The CIF is a general, flexible and easily extensible free-format archive file; it is human and machine readable and can be edited by a simple text editor. The CIF is designed for the electronic transmission of crystallographic data between individual laboratories, journals and databases: it has been adopted by the International Union of Crystallography as the recommended medium for this purpose. The file consists of data names and data items, together with a loop facility for repeated items. The data names, constructed hierarchically so as to form data categories, are self-descriptive within a 32-character limit. The sorted list of data names, together with their precise definitions, constitutes the CIF Dictionary (Core Version 1991). The CIF Core Dictionary is presented in full and covers the fundamental and most commonly used data items relevant to crystal structure analysis. The Dictionary is also available as an electronic file suitable for CIF computer applications. Future extensions to the Dictionary will include data items used in more specialized areas of crystallography.
The materials community in both science and industry use crystallographic data models on a daily basis to visualize, explain and predict the behavior of chemicals and materials. Access to reliable information on the structure of crystalline materials helps researchers concentrate experimental work in directions that optimize the discovery process. The Inorganic Crystal Structure Database (ICSD) is a comprehensive collection of more than 60,000 crystal structure entries for inorganic materials and is produced cooperatively by Fachinformationszentrum Karlsruhe (FIZ), Germany, and the US National Institute of Standards and Technology (NIST). The ICSD is disseminated in computerized formats with scientific software tools to exploit the content of the database. Features of a new Windows-based graphical user interface for the ICSD are outlined, together with directions for future development in support of materials research and design.
The Bilbao Crystallographic Server is a web site with crystallographic programs and databases freely available on-line (http://www.cryst.ehu.es). The server gives access to general information related to crystallographic symmetry groups (generators, general and special positions, maximal subgroups, Brillouin zones etc.). Apart from the simple tools for retrieving the stored data, there are programs for the analysis of group-subgroup relations between space groups (subgroups and supergroups, Wyckoff-position splitting schemes etc.). There are also software packages studying specific problems of solid-state physics, structural chemistry and crystallography. This article reports on the programs treating representations of point and space groups. There are tools for the construction of irreducible representations, for the study of the correlations between representations of group-subgroup pairs of space groups and for the decompositions of Kronecker products of representations.
Using a first-principles parameterized lattice-gas Hamiltonian we study the adsorbate ordering behavior at atomic steps of a Pd(100) surface exposed to an oxygen environment. We identify a wide range of gas-phase conditions comprising near atmospheric pressures and elevated temperatures around 900 K, in which the step is decorated by a characteristic O zigzag arrangement. For catalytic processes like the high-temperature combustion of methane that operate under these conditions our approach thus provides first insight into the structure and composition at a prominent defect on the working surface. Comment: 5 pages including 3 figures; related publications can be found at http://www.fhi-berlin.mpg.de/th/th.html