
Homework assignment: learning about elastic constants via molecular dynamics simulations
11 Mar 2015   Contributor(s):: Alejandro Strachan, David Ray Johnson
In this homework assignment students will use molecular dynamics to compute the elastic constants of metals using an embedded atom model to describe atomic interactions. They will deform a single crystal along different directions and obtain c11, c12 and c44 elastic constants from the...

Melting via molecular dynamics simulations
10 Mar 2015   Contributor(s):: Alejandro Strachan
In this assignment you will use MD simulations to study melting in metals using the nanoMATERIALS simulation tool in nanoHUB. You will build a supercell and heat it up to study its melting. You can visualize the atomic configuration as the temperature is increased and after melting. From the...

Atomic Picture of Plastic Deformation in Metals: Lab Assignment Handout
19 Jan 2010   Contributor(s):: Alejandro Strachan
In this lab students will perform online molecular dynamics (MD) simulations of metallic nanowires deformed uniaxially and analyze the results...

Computational Nanoscience, Homework Assignment 3: Molecular Dynamics Simulation of Carbon Nanotubes
14 Feb 2008   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 completed following lectures 5 and 6 using the "LAMMPS" program in the Berkeley Computational Nanoscience...

Computational Nanoscience, Homework Assignment 2: Molecular Dynamics Simulation of a LennardJones Liquid
14 Feb 2008   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 classical particles interacting via the LennardJones potential.This assignment is to be...

Computational Nanoscience, Lecture 6: Pair Distribution Function and More on Potentials
13 Feb 2008   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 examples of typical functional forms, relative energy scales, and what to keep in mind when...

Computational Nanoscience, Lecture 5: A Day of InClass Simulation: MD of Carbon Nanostructures
13 Feb 2008   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 the energy per atom of different fullerenes and nantubes, computing the Young's modulus of a...

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 nonderivative methods are discussed, as well as the importance of the starting guess and how to find or generate good initial structures. We also briefly...

Computational Nanoscience, Lecture 2: Introduction to Molecular Dynamics
30 Jan 2008   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 such as choice of timestep. A brief discussion of interatomic potentials (the pair potential and...

REBO Nanofluidics Exercise
10 May 2006   Contributor(s):: Susan Sinnott, Hetal Patel
Nanofluidics exercise showing the variation of energy and positionof methane and butane molecules flowing through an opened carbonnanotube as the system temperature and the length of the nanotubeare varied.