Table of Contents
CE 530 Molecular Simulation
Review and Preview
Classical Equations of Motion
Newtonian Formulation
Generalized Coordinates
Lagrangian Formulation
Hamiltonian Formulation 1. Motivation
Hamiltonian Formulation 2. Preparation
Hamiltonian Formulation 3. Defintion
Hamiltonian Formulation 4. Dynamics
Hamiltonian Formulation 5. Example
Phase Space (again)
Integration Algorithms
Verlet Algorithm 1. Equations
Verlet Algorithm 2. Flow diagram
Verlet Algorithm 2. Flow Diagram
Verlet Algorithm 2. Flow Diagram
Verlet Algorithm 2. Flow Diagram
Verlet Algorithm 2. Flow Diagram
Verlet Algorithm 3. Java Code
Verlet Algorithm 3. Relevant Methods in Java Code
Verlet Algorithm 3. Relevant Methods in Java Code
Forces 1. Formalism
Forces 2. LJ Model
Forces 3. Java Code
Forces 3. Relevant Methods from Java Code
Verlet Algorithm. 4. Loose Ends
Verlet Algorithm 5. Performance Issues
Initial Velocities (from Lecture 3)
Leapfrog Algorithm
Leapfrog Algorithm
Leapfrog Algorithm
Leapfrog Algorithm
Leapfrog Algorithm
Leapfrog Algorithm 2. Flow Diagram
Leapfrog Algorithm 2. Flow Diagram
Leapfrog Algorithm 2. Flow Diagram
Leapfrog Algorithm 2. Flow Diagram
Leapfrog Algorithm 2. Flow Diagram
Leapfrog Algorithm. 3. Loose Ends
Velocity Verlet Algorithm
Velocity Verlet Algorithm 2. Flow Diagram
Velocity Verlet Algorithm 2. Flow Diagram
Velocity Verlet Algorithm 2. Flow Diagram
Velocity Verlet Algorithm 2. Flow Diagram
Velocity Verlet Algorithm 2. Flow Diagram
Velocity Verlet Algorithm 2. Flow Diagram
Other Algorithms
Summary
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