
Computational Nanoscience, Lecture 10: Brief Review, Kinetic Monte Carlo, and Random Numbers
25 Feb 2008  Teaching Materials  Contributor(s): Elif Ertekin, Jeffrey C Grossman
We conclude our discussion of Monte Carlo methods with a brief review of the concepts covered in the three previous lectures. Then, the Kinetic Monte Carlo method is introduced, including …
http://nanohub.org/resources/4090

Computational Nanoscience, Lecture 11: Phase Transitions and the Ising Model
27 Feb 2008  Teaching Materials  Contributor(s): Elif Ertekin, Jeffrey C Grossman
In this lecture, we present an introduction to simulations of phase transitions in materials. The use of Monte Carlo methods to model phase transitions is described, and the Ising Model is given as …
http://nanohub.org/resources/4122

Computational Nanoscience, Lecture 9: HardSphere Monte Carlo InClass Simulation
19 Feb 2008  Teaching Materials  Contributor(s): Elif Ertekin, Jeffrey C Grossman
In this lecture we carry out simulations inclass, with guidance from the instructors. We use the HSMC tool (within the nanoHUB simulation toolkit for this course). The hard sphere system is one of …
http://nanohub.org/resources/4067

Computational Nanoscience, Lecture 8: Monte Carlo Simulation Part II
14 Feb 2008  Teaching Materials  Contributor(s): Elif Ertekin, Jeffrey C Grossman
In this lecture, we continue our discussion of Monte Carlo simulation. Examples from Hard Sphere Monte Carlo simulations based on the Metropolis algorithm and from Grand Canonical Monte Carlo …
http://nanohub.org/resources/4056

Computational Nanoscience, Homework Assignment 3: Molecular Dynamics Simulation of Carbon Nanotubes
14 Feb 2008  Teaching Materials  Contributor(s): Elif Ertekin, Jeffrey C Grossman
The purpose of this assignment is to perform molecular dynamics simulations to calculate various properties of carbon nanotubes using LAMMPS and Tersoff potentials. This assignment is to be …
http://nanohub.org/resources/4054

Computational Nanoscience, Homework Assignment 2: Molecular Dynamics Simulation of a LennardJones Liquid
14 Feb 2008  Teaching Materials  Contributor(s): Elif Ertekin, Jeffrey C Grossman
The purpose of this assignment is to perform a full molecular dynamics simulation based on the Verlet algorithm to calculate various properties of a simple liquid, modeled as an ensemble of identical …
http://nanohub.org/resources/4052

Computational Nanoscience, Lecture 1: Introduction to Computational Nanoscience
13 Feb 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
In this lecture, we present a historical overview of computational science. We describe modeling and simulation as forms of "theoretical experiments" and "experimental theory". We also discuss …
http://nanohub.org/resources/4045

Computational Nanoscience, Lecture 6: Pair Distribution Function and More on Potentials
13 Feb 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
In this lecture we remind ourselves what a pair distribution function is, how to compute it, and why it is so important in simulations. Then, we revisit potentials and go into more detail including …
http://nanohub.org/resources/4039

Computational Nanoscience, Lecture 5: A Day of InClass Simulation: MD of Carbon Nanostructures
13 Feb 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
In this lecture we carry out simulations inclass, with guidance from the instructors. We use the LAMMPS tool (within the nanoHUB simulation toolkit for this course). Examples include calculating …
http://nanohub.org/resources/4037

Computational Nanoscience, Lecture 4: Geometry Optimization and Seeing What You're Doing
13 Feb 2008  Teaching Materials  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 nonderivative methods are discussed, as well as the …
http://nanohub.org/resources/4035

Computational Nanoscience, Lecture 3: Computing Physical Properties
11 Feb 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
In this lecture, we'll cover how to choose initial conditions, and how to compute a number of important physical observables from the MD simulation. For example, temperature, pressure, diffusion …
http://nanohub.org/resources/4028

Computational Nanoscience, Lecture 2: Introduction to Molecular Dynamics
30 Jan 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
In this lecture, we present and introduction to classical molecular dynamics. Approaches to integrating the equations of motion (Verlet and other) are discussed, along with practical considerations …
http://nanohub.org/resources/3940

Computational Nanoscience, Homework Assignment 1: Averages and Statistical Uncertainty
30 Jan 2008  Teaching Materials  Contributor(s): Jeffrey C Grossman, Elif Ertekin
The purpose of this assignment is to explore statistical errors and data correlation. This assignment is to be completed following lectures 1 and 2 using the "Average" program in the Berkeley …
http://nanohub.org/resources/3935