Atomistic Visualization Research Articles

Atomic Mechanisms of Crystallization in Nano-Sized Metallic Glasses

Understanding crystallization mechanisms in nano-sized metallic glasses (MGs) is important to the manufacturing and application of these new nanomaterials that possess a unique combination of structural and functional properties. Due to the two-dimensional projections and limited spatial and/or temporal resolutions in experiments, significant questions (e.g., whether nucleation takes place on the free surface or in a near-surface layer) regarding this subject remain under debate. Here, we address these outstanding questions using molecular dynamics simulations of crystallization in MG nanorods together with atomistic visualization and data analysis. We show that nucleation in the nano-sized MGs predominantly takes place on the surface by converting the high-energy liquid surface to a lower-energy crystal surface (the most close-packed atomic plane). This is true for all the nanorods with different diameters studied. On the other hand, the apparent growth mode (inward/radial, lateral or longitudinal) and the resulting grain structure are more dependent on the nanorod diameter. For a relatively big diameter of the nanorod, the overall growth rate does not differ much among the three directions and the resulting grains are approximately semispherical. For small diameters, grains appear to grow more in longitudinal direction and some grains may form relatively long single-crystal segments along the length of the nanorod. The reasons for the difference are discussed. The study provides direct atomistic insights into the crystallization mechanisms in nano-sized MGs, which can facilitate the manufacturing and application of these new advanced materials.

SPaMD studio: An integrated platform for atomistic modeling, simulation, analysis, and visualization

An integrated platform for custom and modular atomistic modeling, high-throughput implementation of various functional simulations, robust atomic topological analysis, and high-fidelity processing and visualization was developed in this study, called the Scalable Parallel Molecular Dynamics (SPaMD) studio. The modular modeling system provides a fast and direct means of constructing specific models such as those of nanostructures, dislocations, and cracks, as well as complex models such as those of bilayers, multilayers, and nanocomposites. Further, the custom modeling system enables consecutive nested processing of selections and operations with a comprehensive workflow to obtain arbitrary models with complicated geometry. Various high-throughput schemes were designed for functional simulations through the integration of automatic modeling tools, load-balanced task allocation systems, adaptive real-time data analysis, and visualization methods, as well as a robust logic feedback system. In addition, the atomistic analysis supports both on-the-fly and post-quantification for crystal structure, orientation, and dislocation by integrating AACSD and AADIS codes. To facilitate processing and simulation, a user-friendly graphical user interface was designed for SPaMD, which also supports highly efficient rendering for tens of millions of atoms. To demonstrate the efficiency and functionalities of this platform, it was critically validated by conducting several evaluations and tests, which provide guidance for and confidence in its potential applications in targeted atomistic simulations.

Graphene Confers Ultralow Friction on Nanogear Cogs.

Friction-induced energy dissipation impedes the performance of nanomechanical devices. Nevertheless, the application of graphene is known to modulate frictional dissipation by inducing local strain. This work reports on the nanomechanics of graphene conformed on different textured silicon surfaces that mimic the cogs of a nanoscale gear. The variation in the pitch lengths regulates the strain induced in capped graphene revealed by scanning probe techniques, Raman spectroscopy, and molecular dynamics simulation. The atomistic visualization elucidates asymmetric straining of CC bonds over the corrugated architecture resulting in distinct friction dissipation with respect to the groove axis. Experimental results are reported for strain-dependent solid lubrication which can be regulated by the corrugation and leads to ultralow frictional forces. The results are applicable for graphene covered corrugated structures with movable components such as nanoelectromechanical systems, nanoscale gears, and robotics.

Defect-driven selective metal oxidation at atomic scale

Nanoscale materials modified by crystal defects exhibit significantly different behaviours upon chemical reactions such as oxidation, catalysis, lithiation and epitaxial growth. However, unveiling the exact defect-controlled reaction dynamics (e.g. oxidation) at atomic scale remains a challenge for applications. Here, using in situ high-resolution transmission electron microscopy and first-principles calculations, we reveal the dynamics of a general site-selective oxidation behaviour in nanotwinned silver and palladium driven by individual stacking-faults and twin boundaries. The coherent planar defects crossing the surface exhibit the highest oxygen binding energies, leading to preferential nucleation of oxides at these intersections. Planar-fault mediated diffusion of oxygen atoms is shown to catalyse subsequent layer-by-layer inward oxide growth via atomic steps migrating on the oxide-metal interface. These findings provide an atomistic visualization of the complex reaction dynamics controlled by planar defects in metallic nanostructures, which could enable the modification of physiochemical performances in nanomaterials through defect engineering.

Atomistic modelling of carbon nanotube networks and analysis of inter filler distance

This paper provides a new approach to model the formation of networks by carbon nanotubes (CNTs) in three dimensions. Network formation by the CNTs plays a vital role in understanding the overall behaviour of the nanocomposites. It is often complicated to analyze the 3D distribution of the fillers inside a nanocomposite experimentally. This 3D atomistic visualization of CNTs through simulations will prove highly beneficial to understand the effect of filler concentration and other experimental parameters. The proposed approach is at the atomistic scale, i.e. each CNT will be built using the appropriate number of carbon atoms depending on its aspect ratio and dimensions. This method aims to be more realistic by eliminating 2D approximation techniques and the cylinder approximation method for the CNTs. Inter filler distances in uniformly distributed short-chopped CNTs are analyzed using this approach. Probable least resistive paths were estimated, and an extended analysis reveals that the minimum filler concentration for initiating electrical conductivity in such short fillers to be around 0.6 vol%.

Crossing interfacial conduction in nanometer-sized graphitic carbon layers.

Graphitic carbon layers (GCLs), exemplified by graphene, have been proposed for potential application in high-performance functional devices due to superior electrical properties, e.g., high electron mobility. In state-of-the-art electronics, it is required that GCLs are miniaturized to nanometer scales and incorporated into the integrated circuits to exhibit novel functions at nanometer scales. However, the implementation of nanometer-scale GCLs is suspended; the function in devices is deteriorated by increasing contact resistance in miniaturized GCL/electrode interfaces. In this study, nanometer-sized GCL/gold (Au) interfaces were fabricated via atomistic visualization of nanomanipulation, and simultaneously their contact resistance was measured. We showed that the contact resistivity of the interfaces was decreased to the order of 10-10Ω cm2, which was 104 times smaller than that of micrometer-sized or larger GCL/metal interfaces. In addition, it was revealed that peculiar electrical conduction at the nanometer-sized GCL/Au interfaces emerged; current flows throughout the entire area of the interfaces unlike micrometer-sized or larger GCL/metal interfaces. These results directly contribute to actual application of GCLs in advanced nanodevices.

A decade of particle-based scientific visualization

In this manuscript, we review the evolution of atomistic visualization over the last 12 years and put the development of the community in context with our own efforts within the DFG collaborative research center 716. The goal is to provide a comprehensive summary of all relevant work that has been conducted under the auspices of project D.3. In this project, we focused on the visualization and analysis of particle-based data sets, and on how to bring these visualizations onto the workstation of domain scientists without the need for a large rendering infrastructure. We discuss how our decisions and goals evolved over time and show the success stories and publications. Finally, we give an outlook on the challenges that still require additional research and to which extent the requirements and constraints of current research have changed the way visualization works after these 12 years.

Free-Space Nanometer Wiring via Nanotip Manipulation.

Relentless efforts in semiconductor technology have driven nanometer-scale miniaturization of transistors, diodes, and interconnections in electronic chips. Free-space writing enables interconnections of stacked modules separated by an arbitrary distance, leading to ultimate integration of electronics. We have developed a free-space method for nanometer-scale wiring on the basis of manipulating a metallic nanotip while applying a bias voltage without radiative heating, lithography, etching, or electrodeposition. The method is capable of fabricating wires with widths as low as 1–6 nm and lengths exceeding 200 nm with a breakdown current density of 8 TA/m2. Structural evolution and conduction during wire formation were analyzed by direct atomistic visualization using in situ high-resolution transmission electron microscopy.

View-dependent level-of-detail abstraction for interactive atomistic visualization of biological structures

The visualization of biological structures is a challenging task because it requires rendering millions to billions of atoms in real time. In this paper, we propose a view-dependent approach by which a large biological scene can be visualized interactively. In this scheme, we first extract several levels of building blocks of biological structures from a molecular abstraction based on hierarchical clustering. We then define a volume-based distance metric for the clustering process to reduce “inflation” error and propose a quantitative error metric for the object space error evaluation. Finally, we utilize an adaptive screen-space level-of-detail selection with the error metric at run time. Empirical results demonstrate that our molecular hierarchical abstraction method achieves high quality rendering results and performs better than other existing methods. Moreover, our result also shows that the view-dependent approach provides valid results in a large biological scene with more than 10 billion elements.

A “Rosetta Stone” for AViz

The Computational Physics group at the Technion has developed a visualization code, AViz, for atomistic visualization. AViz can visualize atoms, vector spins, quadrupoles, electronic densities, polymers and more. The required input of data files in the standard .xyz format can be prepared from a wide range of private and public domain simulation codes; and in the event that these are not the natural output of the code, conversion can be made. In order to extend its use, especially for industrial simulations, it is highly desirable to simplify the translation from simulation output to visualization input. We describe some steps towards the goal of providing a “Rosetta Stone” for such translation that can lead to better understanding. A recent simulation of liquid crystals is used as an example.

3d visualization of atomistic simulations on every desktop

Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given.

Molecular Dynamics Modeling of Nanoscale Machining of Silicon

In this study, the brittle-ductile transition in nanometric machining of mono-crystalline silicon with precise tool specifications and parameter choices is accessed. Due to its brittle nature, silicon material requires a ductile-mode machining for improved surface quality. Molecular dynamics (MD) methods are thus applied to investigate the atomistic reaction at the tool/workpiece surface to clearly expose the ductile transition response of this nanometric process. However, the need for experimental validations to determine the accuracy of these simulation models is essential. This research is particularly concerned with the application of the molecular dynamics simulation approach to the atomistic visualization of the plastic material flow at the tool/workpiece interface during orthogonal cutting. Simulated MD acting force and temperature outputs are evaluated to access the accuracy of the model. This evaluation substantiates the need for additional experimental validation of certain process conditions for verifiable MD results.

A cloud computing system in windows azure platform for data analysis of crystalline materials

SUMMARYCloud computing is attracting the attention of the scientific community. In this paper, we develop a new cloud‐based computing system in the Windows Azure platform that allows users to use the Zeolite Structure Predictor (ZSP) model through a Web browser. The ZSP is a novel machine learning approach for classifying zeolite crystals according to their framework type. The ZSP can categorize entries from the Inorganic Crystal Structure Database into 41 framework types. The novel automated system permits a user to calculate the vector of descriptors used by ZSP and to apply the model using the Random Forest™ algorithm for classifying the input zeolite entries. The workflow presented here integrates executables in Fortran and Python for number crunching with packages such as Weka for data analytics and Jmol for Web‐based atomistic visualization in an interactive compute system accessed through the Web. The compute system is robust and easy to use. Communities of scientists, engineers, and students knowledgeable in Windows‐based computing should find this new workflow attractive and easy to be implemented in scientific scenarios in which the developer needs to combine heterogeneous components. Copyright © 2012 John Wiley & Sons, Ltd.

Nanoscale View of Shock Wave Propagation in Single Crystal Fe, W, and Ta for Nuclear Fusion Technology

We report non-equilibrium Molecular Dynamics simulations providing a nanoscale view for the modeling of shock wave generation, propagation and melting in single crystalline materials Fe, Ta, W, of clear interest for Nuclear Fusion Technology. Our methodology successfully uses massive parallel molecular dynamics in an attempt to cover similar times and length scales as laser-shock experiments. Response of the materials are analyzed in terms of modern atomistic visualization and evolution of their structural properties. Preliminary results point that Wand Ta behave more efficiently in terms of uniformity under shock propagation than lighter materials like Fe. This kind of materials must attract our attention in the short term as possible designs in inertial confinement fusion (ICF) targets.

Atomistic visualization: Space–time multiresolution integration of data analysis and rendering

Time-varying three-dimensional scattered data representing snapshots of atomic configurations produced by molecular dynamics simulations are not illuminating by themselves; gaining insight into them poses a tremendous challenge. In order to take the advantage of maximal information offered by these simulations, we have proposed an efficient scheme, which integrates various analysis and rendering tasks together in order to support interactive visualization of the data at space–time multiresolution. Additional data produced by various analytical techniques on the fly represent the atomic system under consideration at diverse length- (e.g., nearest neighbor, next-nearest neighbor or beyond) and time- (e.g., instantaneous, finite intervals or overall averages) scales. In particular, the radial distribution functions, coordination environments, clusters and rings are computed and visualized to understand the structural behavior whereas a variety of displacement data and covariance matrices are explored to understand the dynamical behavior. While the spatial distributions of atoms need to be reproduced correctly during rendering, we take the advantage of high flexibility in rendering other attributes because of the lack of their direct physical relevance. A combination of different techniques including animation, color maps, pathlines, different types of glyphs, and graphics hardware accelerated approach is exploited to render the original and extracted data. First-principles molecular dynamics simulation data for liquid systems are used to justify the effectiveness and usefulness of the proposed scheme.

Visualization techniques for modelling carbon allotropes

Carbon takes many different forms, each with its own electronic structure and has a fantastic range of properties. As well as graphite/diamond, a hexagonal diamond called londsdaleite, and amorphous carbons of sp 2, sp 3 and mixed natures there are all the fullerenes, graphene, nanotubes, etc. Fortunately, their different electronic structures take distinct geometrical forms, so that deducing the geometry of a sample that has been simulated is a crucial step towards understanding its properties. Visualization is essential for understanding sample geometries. AViz [J. Adler, Computers in Science and Engineering 5 (2003) 61] is an Atomistic Visualization package developed at the Technion that can be freely downloaded and installed. Both still and animated AViz implementations for viewing data from our atomistic simulations of carbon allotropes enable understanding of the simulation results and when compared with laboratory experiments and theoretical models provide insight into nanodiamond growth, gas flow in nanotubes, nanotube vibrations and other topics of current research interest.

3D Simulation Software for Visualization of MEMS Microfabrication Processes

In this paper we present a software for 3D visualization and simulation of the microfabrications process utilized in micro-electro-mechanical systems (MEMS) development. The simulations are based on a geometric approach and, differently from other academic and free distributed tools, the software include modules for simulation of both, bulk and surface micromachining, and for atomistic visualization of etched crystalline structures. Sophisticated rendering tools for coloring, illumination and transparency, as well as, tools to create and edit arbitrary 2D geometries and 3D solids were implemented. Related to the simulation capabilities, the bulk micromachining module lead with the anisotropic etching of (100) oriented Si substrates in alkaline solutions (KOH). The surface micromachining module works with the deposition and etching of up to 6 levels of structural and sacrificial films, which can be deposited on surfaces with complex 3D topography, and simulate the etching of sacrificial layers through etch holes in a structural layer.

Space–time multiresolution atomistic visualization of MgO and MgSiO3 liquid data

First-principles molecular dynamics simulations of complex material systems such as geophysically relevant oxide and silicate liquids produce massive amounts of time-varying three-dimensional data for the atomic configurations. Given the high accuracy of these data, it is desirable to extract as much information hidden in the data as possible. In this paper, we elaborate on our recently proposed scheme to support interactive visualization at space–time multiresolution of the atomistic simulation data. Instead of just focusing on direct rendering of the given data, additional data (containing more quantitative and qualitative information) that usually have to be extracted by some other means are extracted and rendered on the fly. This allows us to gain better insight into the global as well as local spatio-temporal behavior of the data in the context of bonding, radial distribution, atomic coordination, clustering, structural stability and distortion, and diffusion. We illustrate such visualization for the simulation data on the liquid phases of MgO and MgSiO3—the two most abundant components of Earth’s mantle. Our analysis shows that the structure and dynamics of both liquids change substantially with compression, with no discernible effects of temperature in most cases.

AtomEye: an efficient atomistic configuration viewer

AtomEye is free atomistic visualization software for all major UNIX platforms. It is based on a newly developed graphics core library of higher quality than the X-window standard, with area-weighted anti-aliasing. An order-N neighbourlist algorithm is used to compute the bond connectivity. The functionalities of AtomEye include: parallel and perspective projections with full three-dimensional navigation; customizable bond and coordination number calculation; colour-encoding of arbitrary user-defined quantities; local atomic strain invariant; coloured atom tiling and tracing; up to 16 cutting planes; periodic boundary condition translations; high-quality JPEG, PNG and EPS screenshots; and animation scripting. The program is efficient compared to OpenGL hardware acceleration by employing special algorithms to treat spheres (atoms) and cylinders (bonds), in which they are rendered as primitive objects rather than as composites of polygons. AtomEye can handle more than one million atoms on a PC with 1 GB memory. It is a robust, low-cost tool for surveying nanostructures and following their evolutions.

結晶境界挙動の原子直視観察

Atomistic visualization of behavior of internal crystalline boundaries, such as grain boundaries and interfaces, was realized by time-resolved high-resolution transmission electron microscopy at a spatial resolution of 0.1 nm and a time resolution of 1/60 s. Various types of atomic processes in mechanical interaction including approach, contact, bonding deformation and fracture, grain boundary migration, and interface formation in gas-phase epitaxial growth, were demonstrated in this review.