Simulations Tools that connect to the Rice cluster will be inoperable due to system upgrades from Tuesday, May 29th, 2018, 8:00am ET to Wednesday May 30, 2018, 5:00pm ET. We apologize for any inconvenience.
Find information on common issues.
Ask questions and find answers from other users.
Suggest a new site feature or improvement.
Check on status of your tickets.
Simulators can produce all sorts of numbers, but the numbers themselves aren't terribly meaningful until they are put into context by visualization techniques. For example, the coordinates of the various atoms in a molecule don't readily convey the shape of the molecule, but once those coordinates are loaded into VMD, the the resulting picture conveys not only the shape of the molecule, but other important properties as well.
Learn more about visualization techniques from the resources on this site, listed below.
AIDA: A tool for exhaustive enumeration of solutions to the quantized Frank-Bilby equation
08 Jan 2018 | | Contributor(s):: Ali Sangghaleh, Michael J. Demkowicz
We present a tool called Arrangement of Interface Dislocation Arrays (AIDA) for enumerating all dislocation networks that satisfy the quantized Frank-Bilby equation for any interface between cubic crystals with a single-atom basis, i.e. FCC/FCC, BCC/BCC, and FCC/BCC interfaces. The set of...
High-Resolution, High-Speed 3D Imaging and Applications
20 Jul 2017 | | Contributor(s):: Song Zhang
Introduction to Visualization
19 Oct 2016 | | Contributor(s):: Vetria L. Byrd
Exploring Materials Properties with Nanomaterial Mechanics Explorer Structure Files
24 Mar 2016 | | Contributor(s):: Tanya Faltens
This document describes how to generate and download simulation output files from the Nanomaterial Mechanics Explorer on nanoHUB and view them locally using OVITO.This can be particularly useful for more advanced manipulations of the trajectory files, and for sharing files with others, such...
[Illinois] Introduction to Cell Visualization
14 Jun 2013 | | Contributor(s):: Emad Tajkhorshid
Professor Emad Tajkhorshid speaks to University Laboratory High School students about his research in Computational Studies of Membranes and Membrane Associated PhenomenaMembrane proteins are of critical importance for all living cells. They are responsible for exchange of materials and...
Rappture Bootcamp 2.5: Advanced Visualization
16 Jul 2012 | | Contributor(s):: Michael McLennan
Computer Graphics Imagery for Motion Pictures and Commercial Advertising: The Achievement of Highly-Realistic Images
19 Aug 2011 | | Contributor(s):: Kenneth Torrance
The talk will review some of the underlying concepts from Radiation Heat Transfer that have now been implemented in synthetic images. In many cases, researchers in graphics have created algorithms that are many times faster and more detailed than the engineering algorithms from which they were...
Electron Density in a Nanowire
30 Jan 2011 | | Contributor(s):: Gerhard Klimeck, Saumitra Raj Mehrotra
Electron Density in a circular Silicon nanowire transistor.
Tunneling in an Nanometer-Scaled Transistor
25 Jan 2011 | | Contributor(s):: Gerhard Klimeck, Mathieu Luisier, Neerav Kharche, George A. Howlett, Insoo Woo, David Ebert
Electrons tunneling through the gate of an ultra-scaled transistor.
out of 5 stars
25 May 2008 | | Contributor(s):: Masahiko Suenaga
Facio is a 3D-graphics program for molecular modeling and visualization of quantum chemical calculations(GAMESS and Gaussian).It is a GUI for FMO (Fragment MO) calculation. Selected features include:(1) From a PDB file, create GAMESS/FMO input with 4 mouse clicks.(2) Manual fragmentation for the...
Northwestern University Initiative for Teaching Nanoscience
12 Aug 2008 | | Contributor(s):: Baudilio Tejerina
This package allows users to study and analyze of molecular properties using various electronic structure methods.
Theoretical Electron Density Visualizer
01 Jul 2008 | | Contributor(s):: Baudilio Tejerina
TEDVis calculates and displays 3D maps of molecular ED and its derivatives from the wave function.
UV/Vis Spectra simulator
04 Mar 2008 | | Contributor(s):: Baudilio Tejerina
This tool computes molecular electronic spectra.
Computational Nanoscience, Lecture 4: Geometry Optimization and Seeing What You're Doing
13 Feb 2008 | | Contributor(s):: Jeffrey C Grossman, Elif Ertekin
In this lecture, we discuss various methods for finding the ground state structure of a given system by minimizing its energy. Derivative and non-derivative methods are discussed, as well as the importance of the starting guess and how to find or generate good initial structures. We also briefly...
Molecular Structure Tracer
05 Feb 2008 | | Contributor(s):: Baudilio Tejerina
This tool provides a high quality display of molecular structures.
Electrons in Two Dimensions: Quantum Corrals and Semiconductor Microstructures
04 Dec 2007 | | Contributor(s):: Eric J. Heller
The images generated by a scanning tunneling microscope are iconic. Some of the most famous are Don Eigler’s quantum corrals, which reveal not only the guest atoms on a surface but especially the interference patterns of electrons shuttling back and forth along the surface. To understand the...
SPMW A fresh look to amplitude-modulation AFM: Force minimization, interaction measurement, and the quest for high resolution
05 Jan 2007 | | Contributor(s):: Udo D. Schwarz
Frequency modulation atomic force microscopy (FM-AFM) has been able to deliver high-resolution atomic-scale images in ultrahigh vacuum for over one decade. In addition, there have been recent reports where atomic resolution has been achieved in air and liquids using FM-AFM . Achieving...
From Research to Learning in Chemistry through Visualization and Computation
17 May 2007 | | Contributor(s):: Eric Jakobsson
Modern chemistry research and high school chemistry education are separated by institutional and geographical boundaries. As such, much of secondary chemistry education is still based on the periodic table instead of the computational methods that drive current chemistry research. In this talk,...
Is Seeing Believing? How to Think Visually and Analyze with Both Your Eyes and Brain
26 Mar 2007 |
This presentation will cover the basic techniques, and some of the available tools, for visualization, and will explain how to avoid miscommunicating information from visualizations.
What Can the TEM Tell You About Your Nanomaterial?
26 Feb 2007 | | Contributor(s):: Eric Stach
In this tutorial, I will present a brief overview of the ways that transmission electron microscopy can be used to characterize nanoscale materials. This tutorial will emphasize what TEM does well, as well where difficulties arise. In particular, I will discuss in an overview manner how...