Steven G. Satterfield

The Visible Cement Data Set

With advances in x-ray microtomography, it is now possible to obtain three-dimensional representations of a material’s microstructure with a voxel size of less than one micrometer. The Visible Cement Data Set represents a collection of 3-D data sets obtained using the European Synchrotron Radiation Facility in Grenoble, France in September 2000. Most of the images obtained are for hydrating portland cement pastes, with a few data sets representing hydrating Plaster of Paris and a common building brick. All of these data sets are being made available on the Visible Cement Data Set website at http://visiblecement.nist.gov. The website includes the raw 3-D datafiles, a description of the material imaged for each data set, example two-dimensional images and visualizations for each data set, and a collection of C language computer programs that will be of use in processing and analyzing the 3-D microstructural images. This paper provides the details of the experiments performed at the ESRF, the analysis procedures utilized in obtaining the data set files, and a few representative example images for each of the three materials investigated.

DIVERSE: a framework for building extensible and reconfigurable device independent virtual environments

We present DIVERSE, a highly modular collection of complimentary software packages designed to facilitate the creation of device independent virtual environments. DIVERSE is free/open source software, containing both end-user programs and C++ APIs (Application Programming Interfaces). DgiPf is the DIVERSE graphics interface to OpenGL Performer/sup TM/. A program using DgiPf can run on platforms ranging from fully immersive systems such as CAVEs/sup TM/ to generic desktop workstations without modification. We describe DgiPfs design and present a specific example of how it is being used to aid researchers.

A parallel reaction-transport model applied to cement hydration and microstructure development

A recently described stochastic reaction-transport model on three-dimensional lattices is parallelized and is used to simulate the time-dependent structural and chemical evolution in multicomponent reactive systems. The model, called HydratiCA, uses probabilistic rules to simulate the kinetics of diffusion, homogeneous reactions and heterogeneous phenomena such as solid nucleation, growth and dissolution in complex three-dimensional systems. The algorithms require information only from each lattice site and its immediate neighbors, and this localization enables the parallelized model to exhibit near-linear scaling up to several hundred processors. Although applicable to a wide range of material systems, including sedimentary rock beds, reacting colloids and biochemical systems, validation is performed here on two minerals that are commonly found in Portland cement paste, calcium hydroxide and ettringite, by comparing their simulated dissolution or precipitation rates far from equilibrium to standard rate equations, and also by comparing simulated equilibrium states to thermodynamic calculations, as a function of temperature and pH. Finally, we demonstrate how HydratiCA can be used to investigate microstructure characteristics, such as spatial correlations between different condensed phases, in more complex microstructures.

DIVERSE: a framework for building extensible and reconfigurable device-independent virtual environments and distributed asynchronous simulations

We present DIVERSE, a highly modular collection of complimentary software packages designed to facilitate the creation of device-independent virtual environments and distributed asynchronous simulations. DIVERSE is free/open source software, containing both end-user programs and C++ application programming interfaces (APIs). DPF is the DIVERSE graphics interface to OpenGL Performer. A program using the DPF API can run without modification on platforms ranging from fully immersive systems such as CAVEs to generic desktop workstations. The DIVERSE toolkit (DTK) contains all the nongraphical components of DIVERSE, such as networking utilities, hardware device access, and navigational techniques. It introduces a software implementation of networks of replicated noncoherent shared memory. It also introduces a method that seamlessly extends hardware drivers into interprocess and Internet hardware services. We will describe the design of DIVERSE and present a specific example of how it is being used to aid researchers.

Accelerating Scientific Discovery Through Computation and Visualization II

The rate of scientific discovery can be accelerated through computation and visualization. This acceleration results from the synergy of expertise, computing tools, and hardware for enabling high-performance computation, information science, and visualization that is provided by a team of computation and visualization scientists collaborating in a peer-to-peer effort with the research scientists. In the context of this discussion, high performance refers to capabilities beyond the current state of the art in desktop computing. To be effective in this arena, a team comprising a critical mass of talent, parallel computing techniques, visualization algorithms, advanced visualization hardware, and a recurring investment is required to stay beyond the desktop capabilities. This article describes, through examples, how the Scientific Applications and Visualization Group (SAVG) at NIST has utilized high performance parallel computing and visualization to accelerate condensate modeling, (2) fluid flow in porous materials and in other complex geometries, (3) flows in suspensions, (4) x-ray absorption, (5) dielectric breakdown modeling, and (6) dendritic growth in alloys.

Measurement Tools for the Immersive Visualization Environment: Steps Toward the Virtual Laboratory

This paper describes a set of tools for performing measurements of objects in a virtual reality based immersive visualization environment. These tools enable the use of the immersive environment as an instrument for extracting quantitative information from data representations that hitherto had be used solely for qualitative examination. We provide, within the virtual environment, ways for the user to analyze and interact with the quantitative data generated. We describe results generated by these methods to obtain dimensional descriptors of tissue engineered medical products. We regard this toolbox as our first step in the implementation of a virtual measurement laboratory within an immersive visualization environment.

Science at the speed of thought

Scientific discoveries occur with iterations of theory, experiment, and analysis. But the methods that scientists use to go about their work are changing [1]. Experiment types are changing. Increasingly, experiment means computational experiment [2], as computers increase in speed, memory, and parallel processing capability. Laboratory experiments are becoming parallel as combinatorial experiments become more common. Acquired datasets are changing. Both computer and laboratory experiments can produce large quantities of data where the time to analyze data can exceed the time to generate it. Data from experiments can come in surges where the analysis of each set determines the direction of the next experiments. The data generated by experiments may also be non-intuitive. For example, nanoscience is the study of materials whose properties may change greatly as their size is reduced [3]. Thus analyses may benefit from new ways to examine and interact with data.

Extending Measurement Science to Interactive Visualisation Environments

We describe three classes of tools to turn visualizations into a visual laboratory to interactively measure and analyze scientific data. We move the nor- mal activities that scientists perform to understand their data into the visualization environment, which becomes our virtual laboratory, combining the qualitative with the quantitative. We use representation, interactive selection, quantification, and display to add quantitative measurement methods, input tools, and output tools. These allow us to obtain numerical information from each visualization. The exact form that the tools take within each of our three categories depends on features present in the data, hence each is manifested differently in different situations. We illustrate the three approaches with a variety of case studies from immersive to desktop environments that demonstrate the methods used to obtain quantitative knowledge interactively from visual objects.

Incorporating D3.js information visualization into immersive virtual environments

We have created an integrated interactive visualization and analysis environment that can be used immersively or on the desktop to study a simulation of microstructure development during hydration or degradation of cement pastes and concrete. Our environment combines traditional 3D scientific data visualization with 2D information visualization using D3.js running in a web browser. By incorporating D3.js, our visualization allowed the scientist to quickly diagnose and debug errors in the parallel implementation of the simulation.

Accelerating Scientific Discovery Through Computation and Visualization III. Tight-Binding Wave Functions for Quantum Dots.

This is the third in a series of articles that describe, through examples, how the Scientific Applications and Visualization Group (SAVG) at NIST has utilized high performance parallel computing, visualization, and machine learning to accelerate scientific discovery. In this article we focus on the use of high performance computing and visualization for simulations of nanotechnology.