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HPC II – Spring 2002

Lectures

Various Topics and Review

May 3: Lecture in PDF format may3.pdf.
References:

Direct Simulation Monte Carlo applet by Gregory Khanlarov
Molecular Monte Carlo home page
Random Walk Quantum Monte Carlo Java Applet
Path Integral Quantum Monte Carlo Java Applet

May 1: Lecture in PDF format may1.pdf.
References:

The Genetic Algorithms Archive
Genetic Algorithm Optimizer a Java applet
Genetic Algorithms and the Traveling Salesman Problem a senior thesis
Genetic Operators, the Fitness Landscape and the Traveling Salesman Problem
Character Recognition by Neural Nets from "Parallel Computing Works"
Neural Network and Associative Memory a Java applet

April 29: Lecture in PDF format apr29.pdf.
References:

Traveling Salesman Problem - Home Page at Princeton University
New Method of Solving the Traveling Salesman Problem Based on Real Space Renormalization Theory by Usami Yoshiyuki and Kano Yoshiki.
A compendium of NP optimization problems

April 26: Lecture in PDF format apr26.pdf.
References:

anneal.f - Code for "Animated Simulated Annealing", A. Silverman and J. Adler Computers in Physics 6, 277 (1992)
Two projects from University of Illinois course on Atomic Scale Simulation:
- Conformational Optimization of Silicon Cluster Using Simulated Annealing Techniques
- Silicon Cluster optimization using competent genetic algorithms
Crystallization on a Sphere

April 24: Colloquium by Dr. Walter Ermler
References:

actinides.pdf - summary of the main results presented in his colloquium

Topic 6: Cellular Automaton Methods

General References:

April 22: Lecture in PDF format apr22.pdf.
References:

The Nobel Prize in Chemistry 1998
Introduction to Molecular Approaches of Density Functional Theory by Jan K. Labanowski
Computational Techniques by Matthew D. Segall
Density Functional Theory by Wilfried G. Aulbur

April 19: Lecture in PDF format apr19.pdf.

April 17: Lecture in PDF format apr17.pdf.
References:

Dr. Sauro Succi, has written a new book The Lattice Boltzmann Equation - For Fluid Dynamics and Beyond. He has a simple warm-up LBGK code at the following FTP site:
```
     ftp.iac.rm.cnr.it
     cd incoming
     mget lbe.f, lbe.inp, lbe.par
```

April 15: Lecture in PDF format apr15.pdf.
References:

Conway's Game of Life
XToys cellular automata simulators by Michael Creutz.

Topic 5: Computational Fluid Dynamics: Particle Suspension

General References:

CFD Online
Notes on IBT-Navier-Stokes Computations by Dr. Pitman from HPC II 2000
Simulation and Modeling of Mono- and Bidisperse Suspensions Doctoral Thesis of Kai Höfler

April 12: Lecture in PDF format apr12.pdf.
References:

Lattice Gas Java Applet

April 10: Lecture in PDF format apr10.pdf.

April 8: Lecture in PDF format apr8.pdf.
References:

Charles S. Peskin's page has some of his papers on the Immersed Boundary Method.
IBIS Software from Aaron L. Fogelson.

April 5: Lecture in PDF format apr5.pdf.

April 1: Lecture in PDF format apr1.pdf.
References:

ss9607.ps.gz: project report by a student from EPCC. This is a nice a example of what your semester project report should look like!

Topic 4: Multigrid Methods

General References:

MGNet
Chapter 19.6 Multigrid Methods for Boundary Value Problems from Numerical Recipes.
Solving the Discrete Poisson Equation using Multigrid - lecture notes by Dr. Demmel.

March 22:

Intermediate MPI example programs on the MPI web site.

March 20:

Dr. Demmel's Notes: Parallelizing the FFT of a single vector.
MPI FFTW from the FFTW Home Page.

March 18: Lecture in PDF format mar18.pdf.

March 13: Lecture in PDF format mar13.pdf.

March 11: Lecture in PDF format mar11.pdf.
References:

An Introduction to Multigrid Methods by Pieter Wesseling. Good discussions of cell and vertex discretization, transfer operators, and multigrid algorithms.
Parallel.ps.gz Parallel Multigrid Tutorial by Jim Jones.

March 8: Lecture in PDF format mar8.pdf.

March 6: Lecture in PDF format mar6.pdf.

March 4: Lecture in PDF format mar4.pdf.
References:

Discrete Poisson Equation - Dr. Demmel's notes.

Topic 3: Monte Carlo Simulation of Magnetic Materials

General References:

March 1: Lecture in PDF format mar1.pdf.

February 27: Lecture in PDF format feb27.pdf.
References:

Percolation Java Applet. Uses the Hoshen-Kopelman algorithm to identify cluster in a 2-D site percolation model.

February 25: Lecture in PDF format feb25.pdf.

February 22: Lecture in PDF format feb22.pdf.

February 20: Lecture in PDF format feb20.pdf.

February 18: Lecture in PDF format feb18.pdf.
References:

Uniform deviates from "Numerical Recipes", discusses "Quick and Dirty" generator used to construct a parallel version qadrng.h using the Leapfrog method.
Generating the Gaussian Distribution

February 15: Lecture in PDF format feb15.pdf.
References:

2-D Ising Model Java Applet

Topic 2: Molecular Dynamics of Lennard-Jones System

February 13: Lecture in PDF format feb13.pdf.

February 11: Lecture in PDF format feb11.pdf.

February 8: Lecture in PDF format feb08.pdf.

February 6: Lecture in PDF format feb06.pdf.
References:

Parallel Molecular Dynamics: Notes and program pmd.c by Dr. Nakano.
Rubik's Cube: How many neighbors does the sub-cube in the center have?

February 4: Lecture in PDF format feb04.pdf.
References:

January 30: Lecture in PDF format jan30.pdf.
References:

Pair correlation function
Dr. Nakano's HPC Course
Has MD programs and discussion of OpenGL.

January 28: Lecture in PDF format jan28.pdf.
References:

Topic 1: Introduction

January 25: Lecture in PDF format jan25.pdf.
References:

January 23: Lecture in PDF format jan23.pdf.
References:

Questions or comments: phygons@buffalo.edu
Last updated: Thursday, 02 May 2002, 18:06:52