Stochastic Parameter Optimization for Empirical Molecular Potentials function optimization simulated annealing tight binding parameters.

Slides:



Advertisements
Similar presentations
Vegetation Science Lecture 4 Non-Linear Inversion Lewis, Disney & Saich UCL.
Advertisements

Reactive and Potential Field Planners
13-Optimization Assoc.Prof.Dr. Ahmet Zafer Şenalp Mechanical Engineering Department Gebze Technical.
Neural and Evolutionary Computing - Lecture 4 1 Random Search Algorithms. Simulated Annealing Motivation Simple Random Search Algorithms Simulated Annealing.
Simulated Annealing Premchand Akella. Agenda Motivation The algorithm Its applications Examples Conclusion.
Acoustic design by simulated annealing algorithm
Simulated Annealing Methods Matthew Kelly April 12, 2011.
CHAPTER 8 A NNEALING- T YPE A LGORITHMS Organization of chapter in ISSO –Introduction to simulated annealing –Simulated annealing algorithm Basic algorithm.
Random numbers and optimization techniques Jorge Andre Swieca School Campos do Jordão, January,2003 second lecture.
Simulated Annealing Student (PhD): Umut R. ERTÜRK Lecturer : Nazlı İkizler Cinbiş
Spie98-1 Evolutionary Algorithms, Simulated Annealing, and Tabu Search: A Comparative Study H. Youssef, S. M. Sait, H. Adiche
Tabu Search for Model Selection in Multiple Regression Zvi Drezner California State University Fullerton.
Optimization via Search CPSC 315 – Programming Studio Spring 2009 Project 2, Lecture 4 Adapted from slides of Yoonsuck Choe.
MAE 552 – Heuristic Optimization Lecture 6 February 6, 2002.
1 Approximate Solution to an Exam Timetabling Problem Adam White Dept of Computing Science University of Alberta Adam White Dept of Computing Science University.
MAE 552 – Heuristic Optimization Lecture 3 January 28, 2002.
1 Simulated Annealing Terrance O ’ Regan. 2 Outline Motivation The algorithm Its applications Examples Conclusion.
Simulated Annealing Van Laarhoven, Aarts Version 1, October 2000.
4. Modeling 3D-periodic systems Cut-off radii, charges groups Ewald summation Growth units, bonds, attachment energy Predicting crystal structures.
D Nagesh Kumar, IIScOptimization Methods: M1L4 1 Introduction and Basic Concepts Classical and Advanced Techniques for Optimization.
Stochastic Relaxation, Simulating Annealing, Global Minimizers.
Joo Chul Yoon with Prof. Scott T. Dunham Electrical Engineering University of Washington Molecular Dynamics Simulations.
Optimization via Search CPSC 315 – Programming Studio Spring 2008 Project 2, Lecture 4 Adapted from slides of Yoonsuck Choe.
Molecular Modeling: Geometry Optimization C372 Introduction to Cheminformatics II Kelsey Forsythe.
Simulated Annealing G.Anuradha. What is it? Simulated Annealing is a stochastic optimization method that derives its name from the annealing process used.
By Rohit Ray ESE 251.  Most minimization (maximization) strategies work to find the nearest local minimum  Trapped at local minimums (maxima)  Standard.
Elements of the Heuristic Approach
Molecular Modeling: Geometry Optimization C372 Introduction to Cheminformatics II Kelsey Forsythe.
Bioinf. Data Analysis & Tools Molecular Simulations & Sampling Techniques117 Jan 2006 Bioinformatics Data Analysis & Tools Molecular simulations & sampling.
JM - 1 Introduction to Bioinformatics: Lecture XVI Global Optimization and Monte Carlo Jarek Meller Jarek Meller Division of Biomedical.
1 IE 607 Heuristic Optimization Simulated Annealing.
Free energies and phase transitions. Condition for phase coexistence in a one-component system:
MonteCarlo Optimization (Simulated Annealing) Mathematical Biology Lecture 6 James A. Glazier.
Optimization in Engineering Design Georgia Institute of Technology Systems Realization Laboratory Mixed Integer Problems Most optimization algorithms deal.
Boltzmann Machine (BM) (§6.4) Hopfield model + hidden nodes + simulated annealing BM Architecture –a set of visible nodes: nodes can be accessed from outside.
Simulated Annealing.
Doshisha Univ., Kyoto, Japan CEC2003 Adaptive Temperature Schedule Determined by Genetic Algorithm for Parallel Simulated Annealing Doshisha University,
Thursday, May 9 Heuristic Search: methods for solving difficult optimization problems Handouts: Lecture Notes See the introduction to the paper.
Solving the Maximum Cardinality Bin Packing Problem with a Weight Annealing-Based Algorithm Kok-Hua Loh University of Maryland Bruce Golden University.
Simulated Annealing G.Anuradha.
Introduction to Simulated Annealing Study Guide for ES205 Xiaocang Lin & Yu-Chi Ho August 22, 2000.
Molecular Modelling - Lecture 2 Techniques for Conformational Sampling Uses CHARMM force field Written in C++
Simulated Annealing. Difficulty in Searching Global Optima starting point descend direction local minima global minima barrier to local search.
Chapter 10 Minimization or Maximization of Functions.
Role of Theory Model and understand catalytic processes at the electronic/atomistic level. This involves proposing atomic structures, suggesting reaction.
Review Session BS123A/MB223 UC-Irvine Ray Luo, MBB, BS.
Ramakrishna Lecture#2 CAD for VLSI Ramakrishna
An Introduction to Simulated Annealing Kevin Cannons November 24, 2005.
INTRO TO OPTIMIZATION MATH-415 Numerical Analysis 1.
CS-ROSETTA Yang Shen et al. Presented by Jonathan Jou.
Intro. ANN & Fuzzy Systems Lecture 37 Genetic and Random Search Algorithms (2)
Metaheuristics for the New Millennium Bruce L. Golden RH Smith School of Business University of Maryland by Presented at the University of Iowa, March.
Computational Physics (Lecture 11) PHY4061. Variation quantum Monte Carlo the approximate solution of the Hamiltonian Time Independent many-body Schrodinger’s.
Computational Physics (Lecture 10) PHY4370. Simulation Details To simulate Ising models First step is to choose a lattice. For example, we can us SC,
Simulated Annealing Chapter
Computational Physics (Lecture 10)
Department of Computer Science
Heuristic Optimization Methods
By Rohit Ray ESE 251 Simulated Annealing.
ME 521 Computer Aided Design 15-Optimization
Subject Name: Operation Research Subject Code: 10CS661 Prepared By:Mrs
Maria Okuniewski Nuclear Engineering Dept.
CSE 589 Applied Algorithms Spring 1999
Introduction to Simulated Annealing
More on Search: A* and Optimization
Boltzmann Machine (BM) (§6.4)
Xin-She Yang, Nature-Inspired Optimization Algorithms, Elsevier, 2014
More on HW 2 (due Jan 26) Again, it must be in Python 2.7.
Simulated Annealing & Boltzmann Machines
Stochastic Methods.
Presentation transcript:

Stochastic Parameter Optimization for Empirical Molecular Potentials function optimization simulated annealing tight binding parameters

Motivation simulate dynamics of atomic structures derive total energy and forces acting on atoms empirical potentials + fit parameters to experiment soft spheres: only distance dependent quantum mechanics: electrons dominate bonding millions of atoms: approximate electronic degree of freedom semi-empirical: capture QM origin of bonding tight binding: provides directional bonding fit simulated properties to experimental ones more approximations: more parameters to adjust BOP4 potential : 11 parameters [material/compound] automatic fit procedure providing one or more good parameter sets

Optimization find optimal solution to given problem such as: economy: shortest itinerary between number of cities (traveling salesman) engineering: drug design/ circuit design quantify the problem ‘goodness’ of solution depends on parameters objective function set of parameters state in vector space goal: find best local minimum on Potential Energy Surface (PES) cost function :recover exp. properties, some better than others find point in 11-D continous space

Deterministic Methods (downhill only) 1D Golden Section Search higher dimensions: Steepest Descent Conjugate Gradient Variable Metric downhill simplex (no derivative)

Monte Carlo statistical physics: access ensemble averages magnetization of Ising model higher energy states less probable trick: don’t weigh all possible states, but only representative subset simple sampling: waste time on states, that don’t contribute importance sampling: arithmetic mean ?how to judge importance without prior knowledge of energy reference?

Metropolis Algorithm judge upon relative energy-difference to previous state guarantee detailed balance of hopping between states Metropolis-function: transition probability Metropolis et al. (1953) : find optimal wiring (min. length) on chip allow for uphill climbing: move to neighboring local minima

Simulated Annealing in analogy to anneal process of metals: slower cooling: better crystalization (energetically lower state) faster cooling: freezing small crystals (higher, local minimum) Kirkpatrick et al. (1983) added T-schedule to Metropolis search search parameter space at successively lower temperature (higher ) : T controls: scale on which parameters are randomly changed: prob. at which costly uphill moves are accepted: find global minimum on PES for logarithmic annealing (single crystal) in practice: simulated quenching with exponential cooling scheme propose new state acceptreject update TopList lower T in intervals

Traveling Salesman visit all cities: combinatorial problem minimize salesman’s way different cost for crossing the river: minimize salesman’s cost equal weight: smuggler: river penalty:

Variations of the Theme: Statistic Tunneling (ST) simulated quenching is prone to freezing process is trapped in a deep local (but not global) minimum, that is surrounded by higher intermediate states -or- very good (perhaps global) minimum is surrounded by higher states (on mountain top) and might never be found transform PES: ‘tunnel’ through forbidden, higher regions preserve/amplify lower lying regions effectively raising T in higher regions

Tight Binding (TB) Parameters molecular wavefunction is linear combination of atomic wf. replace hopping integral with parameter angular dependence was given by Slater and Koster (1954) and is fitted to band structures of periodic systems dynamic modeling needs continuous distance dependence heuristic shape guided by radial solutions such as: choice of dist. dep. is the integral part of TB total energy:

Radial Dependence repulsive potential and bond integral scale with same functional form separate scaling parameter for -bonds and repulsive potential following common cut-off parameter #of parameters for s-p-bonded system: 3x2(scaling)+1(cutoff)+ 3(screening)+1(promotion)=11 strong repulsion at and strong attraction at equilibrium at

Fitting BOP4 cost-function: equilibrium values of bulk modulus rem. elastic constants lattice parameter cohesive energy lattice parameter for graphitic and  -tin phase for diamond phase

T-dependent criterion: „distance in vector space“ distinguish btw truly different sets and slight variation from same local minimum

Summary Simulated annealing invaluable to handle our multi-variable optimization drawback: may run to forbidden areas in parameters space many times, since only TopList and two current states are stored (blind search) genetic algorithm: interchange subset of parameters btw good parameterization, once annealing process is finished/frozen general strategy: locate various minima with SA at high T refine once with SA at lower T use variable metric method to find „bottom“ of local minima